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
Unknown	0	broad.mit.edu	37	1	569392	569392	+	RNA	SNP	T	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:569392T>C	uc001abc.2	+	1		c.66T>C								full-length cDNA clone CS0DL012YI10 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																		GCCATGGCCATCCCCTTATGA	0.468													61	17	---	---	---	---	PASS
ZBTB48	3104	broad.mit.edu	37	1	6648901	6648901	+	Silent	SNP	A	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6648901A>G	uc009vmc.1	+	10	1890	c.1767A>G	c.(1765-1767)CGA>CGG	p.R589R	ZBTB48_uc001anx.2_Silent_p.R589R|ZBTB48_uc009vmd.1_Silent_p.R589R|ZBTB48_uc001any.1_Silent_p.R227R	NM_005341	NP_005332	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	589	C2H2-type 11.					cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		AGTTTACCCGACAGGTAGGCC	0.622													19	76	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22163485	22163485	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22163485G>A	uc001bfj.2	-	75	10205	c.10165C>T	c.(10165-10167)CTC>TTC	p.L3389F	HSPG2_uc009vqd.2_Missense_Mutation_p.L3390F	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	3389	Ig-like C2-type 19.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	GTGGCAGGGAGAGAGCCGGGA	0.632													18	59	---	---	---	---	PASS
PTPRU	10076	broad.mit.edu	37	1	29585072	29585072	+	Silent	SNP	C	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29585072C>A	uc001bru.2	+	3	371	c.261C>A	c.(259-261)GTC>GTA	p.V87V	PTPRU_uc001brv.2_Silent_p.V87V|PTPRU_uc001brw.2_Silent_p.V87V|PTPRU_uc009vtq.2_Silent_p.V87V|PTPRU_uc009vtr.2_Silent_p.V87V	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	87	Extracellular (Potential).|MAM.				canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	7		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GAGCCCATGTCATCTTCCAGA	0.602													37	93	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144903103	144903103	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144903103C>T	uc001elw.3	-	21	3080	c.2789G>A	c.(2788-2790)AGG>AAG	p.R930K	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.R996K|PDE4DIP_uc001emc.1_Missense_Mutation_p.R930K|PDE4DIP_uc001emd.1_Missense_Mutation_p.R930K|PDE4DIP_uc001emb.1_Missense_Mutation_p.R1093K|PDE4DIP_uc001eme.1_Intron|PDE4DIP_uc001emf.1_Missense_Mutation_p.R715K	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	930	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GGTCTCCAGCCTGTTTAAGCG	0.562			T	PDGFRB	MPD								28	77	---	---	---	---	PASS
RHBG	57127	broad.mit.edu	37	1	156352506	156352506	+	Intron	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156352506C>T	uc010pho.1	+						RHBG_uc010phm.1_3'UTR|RHBG_uc010phn.1_Intron|RHBG_uc001fos.2_Intron|RHBG_uc009wrz.2_Intron|RHBG_uc001for.2_Intron	NM_020407	NP_065140	Q9H310	RHBG_HUMAN	Rhesus blood group, B glycoprotein						transepithelial ammonium transport	anchored to plasma membrane|basolateral plasma membrane|cytoplasmic vesicle membrane|integral to plasma membrane|spectrin-associated cytoskeleton	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			ovary(2)	2	Hepatocellular(266;0.158)					TCTCTCCCTACCCCTGCCTTT	0.617											OREG0013870	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	45	---	---	---	---	PASS
SEC16B	89866	broad.mit.edu	37	1	177929554	177929554	+	Intron	SNP	C	T	T	rs10913472	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177929554C>T	uc001gli.1	-						SEC16B_uc001glk.1_5'UTR|SEC16B_uc001glh.1_5'UTR|SEC16B_uc009wwz.1_Intron|SEC16B_uc001glj.1_Intron|SEC16B_uc001gll.3_Intron	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN	leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4						ATAAAACAATCAGATTTTGTG	0.468													19	197	---	---	---	---	PASS
CFHR4	10877	broad.mit.edu	37	1	196876497	196876497	+	Intron	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196876497C>T	uc001gto.2	+						CFHR4_uc009wyy.2_Missense_Mutation_p.T222M|CFHR4_uc001gtp.2_Missense_Mutation_p.T223M	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor							extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3						GGAGATACCACGTCCTTCCCG	0.398													51	143	---	---	---	---	PASS
PKP1	5317	broad.mit.edu	37	1	201285732	201285732	+	Silent	SNP	G	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201285732G>T	uc001gwd.2	+	4	1004	c.753G>T	c.(751-753)GTG>GTT	p.V251V	PKP1_uc001gwe.2_Silent_p.V251V|PKP1_uc009wzm.2_5'UTR	NM_000299	NP_000290	Q13835	PKP1_HUMAN	plakophilin 1 isoform 1b	251	ARM 1.				cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development	desmosome|intermediate filament|nucleus	intermediate filament binding|signal transducer activity|structural constituent of epidermis			ovary(2)	2						CCAAGGCTGTGCAGTACCTGA	0.567													18	70	---	---	---	---	PASS
TMEM206	55248	broad.mit.edu	37	1	212558721	212558721	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212558721G>T	uc001hjc.3	-	4	558	c.390C>A	c.(388-390)CAC>CAA	p.H130Q	TMEM206_uc010pte.1_Missense_Mutation_p.H191Q	NM_018252	NP_060722	Q9H813	TM206_HUMAN	transmembrane protein 206	130	Extracellular (Potential).					integral to membrane				breast(1)	1				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		CCTCGTAATGGTGCTTACAGC	0.542													43	156	---	---	---	---	PASS
PTPN14	5784	broad.mit.edu	37	1	214531239	214531239	+	3'UTR	SNP	C	T	T	rs2291831	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214531239C>T	uc001hkk.1	-	19						NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		AGCTGGGTCCCTCCTCCAGGA	0.552													24	239	---	---	---	---	PASS
B3GALNT2	148789	broad.mit.edu	37	1	235628908	235628908	+	Intron	SNP	G	A	A	rs1305556	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235628908G>A	uc001hxc.2	-						B3GALNT2_uc001hxd.1_3'UTR	NM_152490	NP_689703	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)			AAGATTAAGTGTAAGACATTC	0.259													19	185	---	---	---	---	PASS
CCDC115	84317	broad.mit.edu	37	2	131099730	131099730	+	5'UTR	SNP	T	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131099730T>G	uc002tqy.1	-	1					CCDC115_uc002tqw.1_5'Flank|CCDC115_uc010zaf.1_Missense_Mutation_p.K25Q|CCDC115_uc002tqx.2_Missense_Mutation_p.K25Q|CCDC115_uc002tqz.1_5'UTR|IMP4_uc002tra.1_5'Flank	NM_032357	NP_115733	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115							endosome|lysosome					0	Colorectal(110;0.1)					GCCACCTTCTTCCTTGTCACC	0.627													5	19	---	---	---	---	PASS
MMADHC	27249	broad.mit.edu	37	2	150426362	150426362	+	3'UTR	SNP	T	C	C	rs6923	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150426362T>C	uc002txb.2	-	7					MMADHC_uc002txc.2_3'UTR|MMADHC_uc010fnu.2_3'UTR	NM_015702	NP_056517	Q9H3L0	MMAD_HUMAN	methylmalonic aciduria (cobalamin deficiency)							mitochondrion				central_nervous_system(1)|skin(1)	2						GCCAATGTTGTAAATTCATAA	0.264													9	72	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168114956	168114956	+	3'UTR	SNP	G	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168114956G>T	uc002udx.2	+	10					XIRP2_uc010fpn.2_Nonsense_Mutation_p.G667*|XIRP2_uc010fpo.2_Nonsense_Mutation_p.G634*|XIRP2_uc010fpp.2_Nonsense_Mutation_p.G634*|XIRP2_uc010fpq.2_3'UTR|XIRP2_uc010fpr.2_Nonsense_Mutation_p.G412*	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						aaagaaggaaggaaggaagAA	0.323													10	45	---	---	---	---	PASS
TMEM110	375346	broad.mit.edu	37	3	52874446	52874446	+	3'UTR	SNP	C	T	T	rs6769789	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52874446C>T	uc003dge.2	-	8					MUSTN1_uc003dgb.3_Intron|TMEM110_uc003dgc.3_Intron|uc003dgd.2_5'Flank	NM_198563	NP_940965	Q86TL2	TM110_HUMAN	transmembrane protein 110							integral to membrane				large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.72e-05)|Kidney(197;0.000777)|KIRC - Kidney renal clear cell carcinoma(197;0.000915)|OV - Ovarian serous cystadenocarcinoma(275;0.0541)		AACGATGCTGCGGGATGACCT	0.592													5	19	---	---	---	---	PASS
COPG	22820	broad.mit.edu	37	3	128993749	128993749	+	Silent	SNP	C	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128993749C>G	uc003els.2	+	22	2425	c.2325C>G	c.(2323-2325)GCC>GCG	p.A775A	COPG_uc010htb.2_Silent_p.A681A	NM_016128	NP_057212	Q9Y678	COPG_HUMAN	coatomer protein complex, subunit gamma 1	775	Interaction with ZNF289/ARFGAP2.				COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(3)|breast(1)	4						TCGAAGCAGCCTGGGATGAGG	0.468													68	194	---	---	---	---	PASS
HPS3	84343	broad.mit.edu	37	3	148890142	148890142	+	3'UTR	SNP	C	T	T	rs111633351		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148890142C>T	uc003ewu.1	+	17					CP_uc011bnr.1_Intron|HPS3_uc011bnq.1_3'UTR|HPS3_uc003ewv.1_RNA	NM_032383	NP_115759	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein							cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			cacacacacacaTATATGATA	0.239									Hermansky-Pudlak_syndrome				3	9	---	---	---	---	PASS
CPN2	1370	broad.mit.edu	37	3	194062504	194062504	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194062504C>T	uc003fts.2	-	2	1018	c.928G>A	c.(928-930)GCC>ACC	p.A310T		NM_001080513	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	310	LRR 9.				protein stabilization	extracellular region	enzyme regulator activity			ovary(5)	5	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		GACAGGTGGGCAAAGGTGCCC	0.592													12	14	---	---	---	---	PASS
SRD5A3	79644	broad.mit.edu	37	4	56236328	56236328	+	3'UTR	SNP	C	T	T	rs2538	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56236328C>T	uc003hau.2	+	5					uc003hav.1_Intron|uc003haw.1_Intron	NM_024592	NP_078868	Q9H8P0	PORED_HUMAN	steroid 5 alpha-reductase 3						androgen biosynthetic process|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|polyprenol catabolic process	endoplasmic reticulum membrane|integral to membrane	3-oxo-5-alpha-steroid 4-dehydrogenase activity|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0	all_cancers(7;0.0308)|all_lung(4;0.00195)|Lung NSC(11;0.00431)|all_epithelial(27;0.0425)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.0179)			AAGTCTGGAGCCCAAAGTACA	0.408													7	33	---	---	---	---	PASS
RASSF6	166824	broad.mit.edu	37	4	74453610	74453610	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74453610C>T	uc003hhd.1	-	5	548	c.425G>A	c.(424-426)AGT>AAT	p.S142N	RASSF6_uc003hhc.1_Missense_Mutation_p.S110N|RASSF6_uc010iik.1_Missense_Mutation_p.S110N|RASSF6_uc010iil.1_Missense_Mutation_p.S98N	NM_201431	NP_958834	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family 6	142					apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			GTCCAGCTCACTAATACGATA	0.373													85	375	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79350367	79350367	+	Silent	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79350367C>T	uc003hlb.2	+	36	5270	c.4830C>T	c.(4828-4830)GGC>GGT	p.G1610G	FRAS1_uc003hkw.2_Silent_p.G1610G|FRAS1_uc010ijj.1_Silent_p.G30G	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	1609	CSPG 5.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						GCCCAGGAGGCAGCACTTCTG	0.522													44	70	---	---	---	---	PASS
MAST4	375449	broad.mit.edu	37	5	66462155	66462155	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66462155A>T	uc003jut.1	+	28	6649	c.6581A>T	c.(6580-6582)GAG>GTG	p.E2194V	MAST4_uc003juw.2_Missense_Mutation_p.E2122V|MAST4_uc003jux.2_Intron	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	2386						cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GCTCCAGCAGAGGGCGACAAG	0.572											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	44	---	---	---	---	PASS
PCDHA1	56147	broad.mit.edu	37	5	140167992	140167992	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140167992C>T	uc003lhb.2	+	1	2117	c.2117C>T	c.(2116-2118)GCG>GTG	p.A706V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lgz.2_Missense_Mutation_p.A706V	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	706	Helical; (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCATCTGCGCGGTGTCCAGC	0.682													6	15	---	---	---	---	PASS
SLIT3	6586	broad.mit.edu	37	5	168244363	168244363	+	Silent	SNP	A	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168244363A>G	uc003mab.2	-	8	1155	c.735T>C	c.(733-735)CCT>CCC	p.P245P	SLIT3_uc010jjg.2_Silent_p.P245P|SLIT3_uc010jji.2_Silent_p.P245P|SLIT3_uc003mac.1_Silent_p.P42P	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	245	LRRCT 1.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCAAATGCACAGGAGCCATGC	0.592													19	61	---	---	---	---	PASS
MED20	9477	broad.mit.edu	37	6	41888827	41888827	+	5'UTR	SNP	C	G	G	rs2274578	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41888827C>G	uc003ork.2	-	1					MED20_uc003orj.2_5'Flank|MED20_uc011duh.1_5'UTR|MED20_uc011dui.1_RNA|MED20_uc011duj.1_5'UTR|BYSL_uc003orl.2_5'Flank	NM_004275	NP_004266	Q9H944	MED20_HUMAN	Trf (TATA binding protein-related						regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	mediator complex	DNA-directed RNA polymerase activity|protein binding				0	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000367)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CACAGAAACTCCTTCAGTTCC	0.582													13	100	---	---	---	---	PASS
TJAP1	93643	broad.mit.edu	37	6	43470972	43470972	+	Intron	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43470972G>A	uc003ovd.2	+						TJAP1_uc003ovf.2_Intron|TJAP1_uc003ove.2_Intron|TJAP1_uc003ovc.2_Intron|TJAP1_uc010jyp.2_Intron|TJAP1_uc011dvh.1_Intron|TJAP1_uc003ovg.2_5'UTR|TJAP1_uc010jyq.2_3'UTR|TJAP1_uc011dvi.1_Intron|TJAP1_uc011dvj.1_Intron|TJAP1_uc003ovi.2_5'UTR	NM_001146016	NP_001139488	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 isoform a							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)			CCAGAGAGCGGGAGAGATGCC	0.597													5	4	---	---	---	---	PASS
SLC35B2	347734	broad.mit.edu	37	6	44222834	44222834	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44222834A>G	uc003oxd.2	-	4	1044	c.908T>C	c.(907-909)ATG>ACG	p.M303T	SLC35B2_uc011dvt.1_Missense_Mutation_p.M206T|SLC35B2_uc011dvu.1_Missense_Mutation_p.M170T	NM_178148	NP_835361	Q8TB61	S35B2_HUMAN	solute carrier family 35, member B2	303	Helical; (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity|signal transducer activity			ovary(1)|central_nervous_system(1)	2	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GACCCCAAACATCATCTGCAC	0.522													21	70	---	---	---	---	PASS
GPR115	221393	broad.mit.edu	37	6	47680165	47680165	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47680165C>A	uc003oza.1	+	5	631	c.373C>A	c.(373-375)CCA>ACA	p.P125T	GPR115_uc003oyz.1_Missense_Mutation_p.P182T|GPR115_uc003ozb.1_Missense_Mutation_p.P123T	NM_153838	NP_722580	Q8IZF3	GP115_HUMAN	G-protein coupled receptor 115 precursor	125	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8						CTTTCGAGCTCCAGAGACCAT	0.433													59	150	---	---	---	---	PASS
GLYATL3	389396	broad.mit.edu	37	6	49489397	49489397	+	Missense_Mutation	SNP	C	A	A	rs9369905	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49489397C>A	uc003ozi.2	+	5	466	c.353C>A	c.(352-354)GCC>GAC	p.A118D		NM_001010904	NP_001010904	Q5SZD4	GLYL3_HUMAN	glycine N-acyltransferase-like protein 3	118						mitochondrion	glycine N-acyltransferase activity				0						AAAGCGGTTGCCAATTCAAAG	0.363													42	462	---	---	---	---	PASS
TFAP2B	7021	broad.mit.edu	37	6	50786571	50786571	+	5'UTR	SNP	G	A	A	rs2272903	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50786571G>A	uc003pag.2	+	1						NM_003221	NP_003212	Q92481	AP2B_HUMAN	transcription factor AP-2 beta						nervous system development|positive regulation of transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0	Lung NSC(77;0.156)					AGACAGCGGAGTCCTGAGAAG	0.483													13	89	---	---	---	---	PASS
KHDC1L	100129128	broad.mit.edu	37	6	73935135	73935135	+	5'UTR	SNP	G	C	C	rs6927398	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73935135G>C	uc003pgm.3	-	1					KHDC1_uc011dyl.1_RNA	NM_001126063	NP_001119535	Q5JSQ8	KHDCL_HUMAN	KH homology domain containing 1-like											skin(1)	1						CGGCCATGCTGTGCTCCCACC	0.522													12	91	---	---	---	---	PASS
GRIK2	2898	broad.mit.edu	37	6	102372527	102372527	+	Silent	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102372527C>T	uc003pqp.3	+	12	2049	c.1800C>T	c.(1798-1800)GAC>GAT	p.D600D	GRIK2_uc003pqo.3_Silent_p.D600D|GRIK2_uc010kcw.2_Silent_p.D600D	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	600	Cytoplasmic (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)	CTGACTCAGACGTGGTGGAAA	0.413													98	200	---	---	---	---	PASS
MDFIC	29969	broad.mit.edu	37	7	114619733	114619733	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114619733A>T	uc003vhf.2	+	4	980	c.717A>T	c.(715-717)AAA>AAT	p.K239N		NM_199072	NP_951038	Q9P1T7	MDFIC_HUMAN	MyoD family inhibitor domain containing protein	130					activation of JUN kinase activity|interspecies interaction between organisms|negative regulation of protein import into nucleus|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|regulation of Wnt receptor signaling pathway|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleolus|nucleolus|nucleus	cyclin binding|Tat protein binding			ovary(1)	1						TTTCTCAAAAAATGCATAGAA	0.443													59	159	---	---	---	---	PASS
SLC13A1	6561	broad.mit.edu	37	7	122809377	122809377	+	Silent	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122809377C>T	uc003vkm.2	-	4	403	c.378G>A	c.(376-378)GGG>GGA	p.G126G	SLC13A1_uc010lks.2_5'UTR	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	126	Helical; (Potential).					integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)	TGCTCATGAACCCCAGCGTCA	0.488													48	126	---	---	---	---	PASS
KIAA1549	57670	broad.mit.edu	37	7	138522830	138522830	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138522830A>G	uc011kql.1	-	20	5723	c.5674T>C	c.(5674-5676)TCA>CCA	p.S1892P	KIAA1549_uc011kqi.1_Missense_Mutation_p.S660P|KIAA1549_uc003vuk.3_Missense_Mutation_p.S1826P|KIAA1549_uc011kqj.1_Missense_Mutation_p.S1876P|KIAA1549_uc011kqk.1_Missense_Mutation_p.S676P	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	1892						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						GAAGGAGCTGAGGGCTCCCTG	0.602			O	BRAF	pilocytic astrocytoma								34	111	---	---	---	---	PASS
IMPAD1	54928	broad.mit.edu	37	8	57905796	57905796	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57905796T>C	uc003xte.3	-	1	632	c.349A>G	c.(349-351)ATG>GTG	p.M117V		NM_017813	NP_060283	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	117						Golgi apparatus|integral to membrane	inositol-1(or 4)-monophosphatase activity|metal ion binding			ovary(1)	1		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				AGGTAGAACATCTTGCGGTTG	0.672													12	31	---	---	---	---	PASS
FAM49B	51571	broad.mit.edu	37	8	130864416	130864416	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130864416C>A	uc003yss.2	-	11	1174	c.625G>T	c.(625-627)GTA>TTA	p.V209L	FAM49B_uc003yst.2_Missense_Mutation_p.V209L|FAM49B_uc003ysu.2_Missense_Mutation_p.V209L|FAM49B_uc003ysv.2_Missense_Mutation_p.V63L|FAM49B_uc003ysw.2_Missense_Mutation_p.V209L|FAM49B_uc003ysx.2_Missense_Mutation_p.V209L|FAM49B_uc003ysy.1_Missense_Mutation_p.V209L	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	hypothetical protein LOC51571	209											0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			ACCTCTGATACAAATTTTGTT	0.323													65	182	---	---	---	---	PASS
HEATR7A	727957	broad.mit.edu	37	8	145234436	145234436	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145234436G>A	uc003zbk.3	+	5	484	c.247G>A	c.(247-249)GAC>AAC	p.D83N	HEATR7A_uc003zbg.2_Missense_Mutation_p.D83N|HEATR7A_uc003zbh.3_Missense_Mutation_p.D83N|HEATR7A_uc003zbi.3_Missense_Mutation_p.D83N|HEATR7A_uc011lla.1_Missense_Mutation_p.D83N|HEATR7A_uc010mft.2_Missense_Mutation_p.D83N	NM_032450	NP_115826	Q8NDA8	HTR7A_HUMAN	HEAT repeat containing 7A isoform 1	83							binding				0						GCTGGACAAGGACACAGCCAG	0.632													7	46	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66500808	66500808	+	RNA	SNP	T	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66500808T>G	uc004aed.1	+	3		c.901T>G								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						CCACCTACGGTCGGTTGTGTG	0.632													4	6	---	---	---	---	PASS
NAA35	60560	broad.mit.edu	37	9	88574730	88574730	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88574730A>C	uc004aoi.3	+	5	433	c.296A>C	c.(295-297)GAT>GCT	p.D99A	NAA35_uc004aoj.3_Missense_Mutation_p.D99A|NAA35_uc004aok.1_Missense_Mutation_p.D99A	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN	corneal wound healing-related protein	99					smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3						AAAATTAAAGATCTCACCTTG	0.308													74	431	---	---	---	---	PASS
SLC27A4	10999	broad.mit.edu	37	9	131117992	131117992	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131117992G>A	uc004but.2	+	12	1975	c.1691G>A	c.(1690-1692)CGC>CAC	p.R564H	SLC27A4_uc004buu.2_Missense_Mutation_p.R158H	NM_005094	NP_005085	Q6P1M0	S27A4_HUMAN	solute carrier family 27 (fatty acid	564					long-chain fatty acid transport|transmembrane transport	integral to membrane	fatty acid transporter activity|nucleotide binding|protein binding				0						GACCTGGAGCGCTTTGCTCAG	0.642													10	26	---	---	---	---	PASS
GLE1	2733	broad.mit.edu	37	9	131298725	131298725	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131298725A>G	uc004bvj.2	+	12	1852	c.1738A>G	c.(1738-1740)ATC>GTC	p.I580V	GLE1_uc004bvi.2_Missense_Mutation_p.I580V|GLE1_uc010myd.2_Missense_Mutation_p.I326V	NM_001003722	NP_001003722	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator homolog isoform 1	580					poly(A)+ mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear pore	protein binding				0						CTACGCTGCTATCATCCAGCT	0.473													33	87	---	---	---	---	PASS
NUP188	23511	broad.mit.edu	37	9	131744966	131744966	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131744966T>C	uc004bws.1	+	16	1677	c.1655T>C	c.(1654-1656)GTT>GCT	p.V552A	NUP188_uc004bwu.2_5'Flank	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	552					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7						TTGCTTCATGTTGTTTCAACT	0.428													28	137	---	---	---	---	PASS
AKR1C1	1645	broad.mit.edu	37	10	5009347	5009347	+	Intron	SNP	A	G	G	rs4445550	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5009347A>G	uc001iho.2	+						AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C1_uc009xhx.2_3'UTR|AKR1C1_uc001ihq.2_Intron	NM_001353	NP_001344	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1						bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)	ATTATAACATAGAAGAAGAAT	0.308													17	148	---	---	---	---	PASS
AKR1C1	1645	broad.mit.edu	37	10	5009364	5009364	+	Intron	SNP	T	C	C	rs2904802	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5009364T>C	uc001iho.2	+						AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C1_uc009xhx.2_3'UTR|AKR1C1_uc001ihq.2_Intron	NM_001353	NP_001344	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1						bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)	GAATCCTAAATCTAACTCCTA	0.338													15	107	---	---	---	---	PASS
AKR1C1	1645	broad.mit.edu	37	10	5009449	5009449	+	Intron	SNP	T	C	C	rs7076886	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5009449T>C	uc001iho.2	+						AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C1_uc009xhx.2_3'UTR|AKR1C1_uc001ihq.2_Intron	NM_001353	NP_001344	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1						bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)	AGTGCAGAACTCTCAAAGCCT	0.378													5	29	---	---	---	---	PASS
AKR1C1	1645	broad.mit.edu	37	10	5019959	5019959	+	3'UTR	SNP	G	A	A	rs8483	byFrequency	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5019959G>A	uc001iho.2	+	14					AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C1_uc001ihq.2_3'UTR	NM_001353	NP_001344	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1						bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)	CATGAGGTCTGCCAGAAGGCC	0.468													20	169	---	---	---	---	PASS
LOC387646	387646	broad.mit.edu	37	10	27538980	27538980	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27538980G>T	uc001its.2	-	1	2256	c.413C>A	c.(412-414)GCA>GAA	p.A138E		NR_003525				SubName: Full=cDNA FLJ44924 fis, clone BRAMY3014555;												0						CTGTTGAATTGCTAAAGGTCC	0.527													42	125	---	---	---	---	PASS
USP54	159195	broad.mit.edu	37	10	75276836	75276836	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75276836C>A	uc001juo.2	-	18	3365	c.3348G>T	c.(3346-3348)GAG>GAT	p.E1116D	USP54_uc010qkk.1_Missense_Mutation_p.E298D|USP54_uc001juk.2_Missense_Mutation_p.E204D|USP54_uc001jul.2_Missense_Mutation_p.E204D|USP54_uc001jum.2_RNA|USP54_uc001jun.2_RNA	NM_152586	NP_689799	Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1116					ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)					GCCTATAGGTCTCCTCACTGC	0.502													40	170	---	---	---	---	PASS
CYP2E1	1571	broad.mit.edu	37	10	135350701	135350701	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135350701C>A	uc001lnj.1	+	7	1135	c.1102C>A	c.(1102-1104)CTG>ATG	p.L368M	CYP2E1_uc001lnk.1_Missense_Mutation_p.L231M|CYP2E1_uc009ybl.1_Missense_Mutation_p.L169M|CYP2E1_uc009ybm.1_Missense_Mutation_p.L22M|CYP2E1_uc001lnl.1_Missense_Mutation_p.L169M	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,	368					drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)	GCCCTCCAACCTGCCCCATGA	0.537									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				22	111	---	---	---	---	PASS
CHID1	66005	broad.mit.edu	37	11	869837	869837	+	3'UTR	SNP	C	T	T	rs148160696	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:869837C>T	uc001lsl.2	-	13					CHID1_uc010qwu.1_Intron|CHID1_uc010qwv.1_3'UTR|CHID1_uc001lsn.2_3'UTR|CHID1_uc001lsm.2_3'UTR|CHID1_uc001lso.2_3'UTR|CHID1_uc001lsp.2_3'UTR|CHID1_uc010qww.1_3'UTR	NM_023947	NP_076436	Q9BWS9	CHID1_HUMAN	chitinase domain containing 1 isoform a						chitin catabolic process|innate immune response	extracellular region|lysosome	cation binding|chitinase activity				0		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.48e-25)|Epithelial(43;3.75e-24)|BRCA - Breast invasive adenocarcinoma(625;4.65e-05)|Lung(200;0.0624)|LUSC - Lung squamous cell carcinoma(625;0.0735)		ACACGTCCACCGCGGAGGCCG	0.612													7	50	---	---	---	---	PASS
OR52K2	119774	broad.mit.edu	37	11	4471168	4471168	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4471168A>G	uc001lyz.1	+	1	599	c.599A>G	c.(598-600)TAT>TGT	p.Y200C		NM_001005172	NP_001005172	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K,	200	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)		AACAATATCTATGGCATCGCT	0.498													142	458	---	---	---	---	PASS
PSMA1	5682	broad.mit.edu	37	11	14535561	14535561	+	Intron	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14535561C>T	uc001mlk.2	-						PSMA1_uc001mll.2_Intron|PSMA1_uc010rcp.1_Intron|PSMA1_uc001mlj.2_Intron|PSMA1_uc010rcq.1_3'UTR	NM_002786	NP_002777	P25786	PSA1_HUMAN	proteasome alpha 1 subunit isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2						AGAAATAATGCAATAGGACAC	0.318													7	21	---	---	---	---	PASS
PSMA1	5682	broad.mit.edu	37	11	14535563	14535563	+	Intron	SNP	A	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14535563A>T	uc001mlk.2	-						PSMA1_uc001mll.2_Intron|PSMA1_uc010rcp.1_Intron|PSMA1_uc001mlj.2_Intron|PSMA1_uc010rcq.1_3'UTR	NM_002786	NP_002777	P25786	PSA1_HUMAN	proteasome alpha 1 subunit isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2						AAATAATGCAATAGGACACTA	0.313													6	21	---	---	---	---	PASS
LOC440040	440040	broad.mit.edu	37	11	49598207	49598207	+	Missense_Mutation	SNP	T	C	C	rs3750925	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49598207T>C	uc010rhy.1	+	2	798	c.320T>C	c.(319-321)TTC>TCC	p.F107S	LOC440040_uc009ymb.2_Missense_Mutation_p.F107S	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0						TCCTCTTCCTTCTGCTCCAAG	0.502													7	49	---	---	---	---	PASS
OR5M9	390162	broad.mit.edu	37	11	56230205	56230205	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56230205G>A	uc010rjj.1	-	1	673	c.673C>T	c.(673-675)CGC>TGC	p.R225C		NM_001004743	NP_001004743	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M,	225	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4	Esophageal squamous(21;0.00448)					GAGCGCATGCGTAGCACAGCT	0.478													33	89	---	---	---	---	PASS
GLYATL1	92292	broad.mit.edu	37	11	58723488	58723488	+	Silent	SNP	A	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58723488A>G	uc001nnf.2	+	8	1273	c.897A>G	c.(895-897)CTA>CTG	p.L299L	uc001nng.1_Intron|GLYATL1_uc001nnh.1_Silent_p.L330L|GLYATL1_uc001nni.1_Silent_p.L299L|GLYATL1_uc001nnj.1_Silent_p.L299L			Q969I3	GLYL1_HUMAN	SubName: Full=Glycine acyltransferase family-C; SubName: Full=Glycine-N-acyltransferase-like 1, isoform CRA_a;	299						mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)	CACAGAATCTAGTTCCATTTT	0.393													27	93	---	---	---	---	PASS
SIK3	23387	broad.mit.edu	37	11	116718294	116718294	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116718294G>A	uc001ppy.2	-	22	3568	c.3532C>T	c.(3532-3534)CTC>TTC	p.L1178F	SIK3_uc001ppz.2_Missense_Mutation_p.L1017F|SIK3_uc001pqa.2_Missense_Mutation_p.L1118F|SIK3_uc001ppw.2_Missense_Mutation_p.L535F|SIK3_uc001ppx.2_Missense_Mutation_p.L556F	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK	1178						cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						CCAGCCACGAGACTCATTCCT	0.507													35	91	---	---	---	---	PASS
FAM186A	121006	broad.mit.edu	37	12	50746917	50746917	+	Missense_Mutation	SNP	A	G	G	rs10876023	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50746917A>G	uc001rwl.2	-	4	3836	c.3698T>C	c.(3697-3699)CTT>CCT	p.L1233P	FAM186A_uc010smt.1_Missense_Mutation_p.L1011P	NM_001145475	NP_001138947	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1233											0						GGCCTGCTGAAGGGTTAGAGT	0.632													8	45	---	---	---	---	PASS
HNRNPA1	3178	broad.mit.edu	37	12	54675316	54675316	+	Intron	SNP	A	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54675316A>C	uc001sfl.2	+						CBX5_uc001sfk.3_5'Flank|CBX5_uc001sfi.3_5'Flank|HNRNPA1_uc001sfm.2_Intron|HNRNPA1_uc009zng.2_Intron|HNRNPA1_uc009znh.2_Intron|HNRNPA1_uc009zni.2_Intron|HNRNPA1_uc001sfn.2_Intron|HNRNPA1_uc001sfo.3_Intron|HNRNPA1_uc001sfp.1_5'UTR|HNRNPA1_uc009znj.1_5'Flank	NM_031157	NP_112420	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1						interspecies interaction between organisms|mRNA transport|nuclear import	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|single-stranded DNA binding			skin(2)|ovary(1)	3						AAGCAGTAAAACAGCCGATTT	0.443													10	24	---	---	---	---	PASS
RPS26	6231	broad.mit.edu	37	12	56435929	56435929	+	5'UTR	SNP	C	G	G	rs1131017	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56435929C>G	uc001sjf.2	+	1						NM_001029	NP_001020	P62854	RS26_HUMAN	ribosomal protein S26						endocrine pancreas development|negative regulation of RNA splicing|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	mRNA binding|protein binding|structural constituent of ribosome			breast(1)	1			OV - Ovarian serous cystadenocarcinoma(18;0.123)			ACCGTCTCCTCTCTCCGGTCC	0.597													11	62	---	---	---	---	PASS
MDM1	56890	broad.mit.edu	37	12	68688939	68688939	+	3'UTR	SNP	C	T	T	rs7958232	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68688939C>T	uc001stz.2	-	14					MDM1_uc010stc.1_3'UTR|MDM1_uc009zqv.1_3'UTR	NM_017440	NP_059136	Q8TC05	MDM1_HUMAN	mouse Mdm1 nuclear protein homolog isoform 1							nucleus				ovary(3)|skin(2)	5			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		AAGTAGAAAACGTTAGGAAAA	0.259													14	134	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78225110	78225110	+	5'UTR	SNP	T	C	C	rs12227066	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78225110T>C	uc001syp.2	+	1					NAV3_uc001syo.2_5'UTR	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						ATTATATTATTAGCTTTTTAA	0.318										HNSCC(70;0.22)			6	37	---	---	---	---	PASS
PNP	4860	broad.mit.edu	37	14	20937596	20937596	+	5'UTR	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20937596C>T	uc001vxo.3	+	1					PNP_uc010ahm.1_5'UTR|PNP_uc010ahn.2_5'UTR|PNP_uc001vxn.3_5'UTR	NM_000270	NP_000261	P00491	PNPH_HUMAN	nucleoside phosphorylase						immune response|inosine catabolic process|interleukin-2 secretion|NAD biosynthesis via nicotinamide riboside salvage pathway|nicotinamide riboside catabolic process|positive regulation of alpha-beta T cell differentiation|positive regulation of T cell proliferation|purine base metabolic process|purine nucleotide catabolic process|purine-containing compound salvage|response to drug|urate biosynthetic process	cytoskeleton|cytosol	drug binding|nucleoside binding|phosphate binding|purine base binding|purine-nucleoside phosphorylase activity			ovary(2)	2					Aciclovir(DB00787)|Cladribine(DB00242)|Mercaptopurine(DB01033)	CAGCCTTGCTCAGTTCAGCAT	0.453													9	13	---	---	---	---	PASS
AP4E1	23431	broad.mit.edu	37	15	51237857	51237857	+	Intron	SNP	C	G	G	rs3784303	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51237857C>G	uc001zyx.1	+						AP4E1_uc010ufi.1_Intron|AP4E1_uc010ufj.1_Intron|AP4E1_uc010ufk.1_Intron|LOC100132724_uc010ufl.1_RNA	NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GTGTAAAATGCACTTCTGACA	0.363													41	411	---	---	---	---	PASS
MYO5A	4644	broad.mit.edu	37	15	52671902	52671902	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52671902A>T	uc002aby.2	-	18	2372	c.2128T>A	c.(2128-2130)TAC>AAC	p.Y710N	MYO5A_uc002abx.3_Missense_Mutation_p.Y710N|MYO5A_uc010uge.1_Missense_Mutation_p.Y579N	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1	710	Myosin head-like.				actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		AGGACACGGTAGCGGCTGAAA	0.393													42	173	---	---	---	---	PASS
CGNL1	84952	broad.mit.edu	37	15	57744412	57744412	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57744412A>G	uc002aeg.2	+	6	2055	c.1979A>G	c.(1978-1980)GAA>GGA	p.E660G	CGNL1_uc010bfw.2_Missense_Mutation_p.E660G	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1	660	Potential.					myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		CAACACAACGAAAAGGTGGAG	0.463													67	227	---	---	---	---	PASS
MAN2C1	4123	broad.mit.edu	37	15	75650917	75650917	+	Silent	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75650917G>A	uc002baf.2	-	20	2306	c.2289C>T	c.(2287-2289)ACC>ACT	p.T763T	MAN2C1_uc002bag.2_Silent_p.T763T|MAN2C1_uc002bah.2_Silent_p.T780T|MAN2C1_uc010bkk.2_Silent_p.T664T	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	763					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0						GGCCGCCCTCGGTGCCCACTG	0.647													4	16	---	---	---	---	PASS
NR2F2	7026	broad.mit.edu	37	15	96875681	96875681	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96875681G>T	uc010uri.1	+	1	1571	c.347G>T	c.(346-348)CGC>CTC	p.R116L	NR2F2_uc002btp.2_Intron|NR2F2_uc010urj.1_5'Flank|MIR1469_hsa-mir-1469|MI0007074_5'Flank|NR2F2_uc010urk.1_5'Flank	NM_021005	NP_066285	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	116	NR C4-type.|Nuclear receptor.				lipid metabolic process|negative regulation of cyclin-dependent protein kinase activity|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment	nucleus	ligand-regulated transcription factor activity|protein homodimerization activity|retinoic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(1)	3	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			TACACGTGCCGCGCCAACCGG	0.602													11	50	---	---	---	---	PASS
PDIA2	64714	broad.mit.edu	37	16	334925	334925	+	Silent	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:334925C>T	uc002cgn.1	+	9	1696	c.588C>T	c.(586-588)GAC>GAT	p.D196D	PDIA2_uc010bqt.1_Silent_p.D41D|PDIA2_uc002cgo.1_Silent_p.D196D	NM_006849	NP_006840	Q13087	PDIA2_HUMAN	protein disulfide isomerase A2 precursor	196					apoptosis|cell redox homeostasis|glycerol ether metabolic process|protein folding|protein retention in ER lumen|response to hypoxia	endoplasmic reticulum lumen	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity|steroid binding			central_nervous_system(1)|skin(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				TGGCCCAGGACGCCCTGGACA	0.637													10	26	---	---	---	---	PASS
RRN3P1	730092	broad.mit.edu	37	16	21823694	21823694	+	5'UTR	SNP	A	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21823694A>T	uc010vbl.1	-	5					uc002diq.3_Intron|RRN3P1_uc002djl.2_RNA	NR_003370				SubName: Full=Putative uncharacterized protein ENSP00000219758;												0						AAAGCCAAATACTCTTCCACT	0.378													19	71	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	74423785	74423785	+	Splice_Site	SNP	T	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74423785T>C	uc010vmt.1	+	4	424	c.423_splice	c.e4+2	p.K141_splice						RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		AAATGCAAAGTAAGGAGCTTC	0.473													5	21	---	---	---	---	PASS
PKD1L2	114780	broad.mit.edu	37	16	81241219	81241219	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81241219C>A	uc002fgh.1	-	5	782	c.782G>T	c.(781-783)AGT>ATT	p.S261I	PKD1L2_uc002fgj.2_Missense_Mutation_p.S261I	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	261	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						GAAACTCTCACTGGACACCAT	0.448													30	77	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	3144693	3144693	+	3'UTR	SNP	G	A	A	rs150972618	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3144693G>A	uc002fvf.2	+	1										SubName: Full=Olfactory receptor OR17-1;																		CTCTACCTGTGCCTCCCATTT	0.493													15	128	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8051032	8051032	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8051032G>A	uc002gkd.2	-	11	1586	c.1348C>T	c.(1348-1350)CGC>TGC	p.R450C	PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Missense_Mutation_p.R434C	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	450	PAC.				circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						GCTACCTTGCGGCTCCAGGGG	0.647			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					8	21	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11583090	11583090	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11583090G>A	uc002gne.2	+	18	3438	c.3370G>A	c.(3370-3372)GCG>ACG	p.A1124T	DNAH9_uc010coo.2_Missense_Mutation_p.A418T	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1124	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	p.A1124A(1)		skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CAACCTGGATGCGTTTATAAA	0.408													58	170	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	18344808	18344808	+	RNA	SNP	C	T	T	rs148195680	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18344808C>T	uc010vya.1	+	4		c.900C>T								Homo sapiens cDNA FLJ56791 complete cds, highly similar to Keratin, type I cytoskeletal 16.																		AACGTGGAGACGGATGCCGCA	0.607													4	12	---	---	---	---	PASS
CCT6B	10693	broad.mit.edu	37	17	33254959	33254959	+	3'UTR	SNP	C	T	T	rs75919796	byFrequency	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33254959C>T	uc002hig.2	-	14					CCT6B_uc010ctg.2_3'UTR|CCT6B_uc010wcc.1_3'UTR	NM_006584	NP_006575	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B						chaperone-mediated protein complex assembly|protein folding|spermatogenesis	cytoplasm	ATP binding|protein transporter activity|unfolded protein binding			pancreas(1)	1		Ovarian(249;0.17)				AAGACATAAACTGCATTTATT	0.279													10	69	---	---	---	---	PASS
LOC284100	284100	broad.mit.edu	37	17	36233930	36233930	+	RNA	SNP	G	A	A	rs2677184	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36233930G>A	uc002hom.1	-	1		c.2C>T			LOC284100_uc002hon.1_RNA					Homo sapiens cDNA FLJ37577 fis, clone BRCOC2003513, moderately similar to 14-3-3 protein epsilon (14-3-3E).												0						CATGGGCCCAGCCTAAAAATA	0.338													10	79	---	---	---	---	PASS
TNS4	84951	broad.mit.edu	37	17	38636043	38636043	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38636043G>T	uc010cxb.2	-	10	1957	c.1793C>A	c.(1792-1794)GCC>GAC	p.A598D	TNS4_uc002huu.3_Intron	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor	598	Phosphatase tensin-type.				apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			CACGGCCAGGGCTCCAGTCAG	0.632													28	80	---	---	---	---	PASS
KIF18B	146909	broad.mit.edu	37	17	43005445	43005445	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43005445C>T	uc010wji.1	-	13	2335	c.2234G>A	c.(2233-2235)TGG>TAG	p.W745*	KIF18B_uc002iht.2_Nonsense_Mutation_p.W754*|KIF18B_uc010wjh.1_Nonsense_Mutation_p.W742*	NM_001080443	NP_001073912			kinesin family member 18B											ovary(2)	2		Prostate(33;0.155)				TATTTTGTCCCAGCCAATGCA	0.597													22	59	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43585453	43585453	+	Intron	SNP	T	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43585453T>A	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						GCAGGAGGCCTGAGGTGGGCT	0.542													39	56	---	---	---	---	PASS
CACNA1G	8913	broad.mit.edu	37	17	48678525	48678525	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48678525C>T	uc002irk.1	+	19	4277	c.3905C>T	c.(3904-3906)CCC>CTC	p.P1302L	CACNA1G_uc002iri.1_Missense_Mutation_p.P1302L|CACNA1G_uc002irj.1_Missense_Mutation_p.P1279L|CACNA1G_uc002irl.1_Missense_Mutation_p.P1279L|CACNA1G_uc002irm.1_Missense_Mutation_p.P1279L|CACNA1G_uc002irn.1_Missense_Mutation_p.P1279L|CACNA1G_uc002iro.1_Missense_Mutation_p.P1279L|CACNA1G_uc002irp.1_Missense_Mutation_p.P1302L|CACNA1G_uc002irq.1_Missense_Mutation_p.P1279L|CACNA1G_uc002irr.1_Missense_Mutation_p.P1302L|CACNA1G_uc002irs.1_Missense_Mutation_p.P1302L|CACNA1G_uc002irt.1_Missense_Mutation_p.P1302L|CACNA1G_uc002irv.1_Missense_Mutation_p.P1302L|CACNA1G_uc002irw.1_Missense_Mutation_p.P1279L|CACNA1G_uc002iru.1_Missense_Mutation_p.P1279L|CACNA1G_uc002irx.1_Missense_Mutation_p.P1215L|CACNA1G_uc002iry.1_Missense_Mutation_p.P1215L|CACNA1G_uc002irz.1_Missense_Mutation_p.P1215L|CACNA1G_uc002isa.1_Missense_Mutation_p.P1215L|CACNA1G_uc002isb.1_Missense_Mutation_p.P1215L|CACNA1G_uc002isc.1_Missense_Mutation_p.P1215L|CACNA1G_uc002isd.1_Missense_Mutation_p.P1215L|CACNA1G_uc002ise.1_Missense_Mutation_p.P1215L|CACNA1G_uc002isf.1_Missense_Mutation_p.P1215L|CACNA1G_uc002isg.1_Missense_Mutation_p.P1215L|CACNA1G_uc002ish.1_Missense_Mutation_p.P1215L|CACNA1G_uc002isi.1_Missense_Mutation_p.P1192L|CACNA1G_uc002isj.2_Missense_Mutation_p.P26L	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	1302	Extracellular (Potential).|III.				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AAAATTGACCCCCACAGCGCT	0.587													30	89	---	---	---	---	PASS
ANKFN1	162282	broad.mit.edu	37	17	54403638	54403638	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54403638G>A	uc002iun.1	+	3	154	c.119G>A	c.(118-120)AGC>AAC	p.S40N		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	40										large_intestine(1)|ovary(1)	2						AGAAAGCAAAGCCAATGTGAT	0.423													64	217	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3071889	3071889	+	Splice_Site	SNP	T	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3071889T>A	uc002klp.2	-	37	5043	c.4709_splice	c.e37-1	p.N1570_splice	MYOM1_uc002klq.2_Splice_Site_p.N1474_splice	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						GGGCACGATCTGCAAGCATAG	0.527													29	86	---	---	---	---	PASS
SLC14A2	8170	broad.mit.edu	37	18	43207027	43207027	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43207027C>G	uc010dnj.2	+	5	757	c.436C>G	c.(436-438)CTG>GTG	p.L146V	SLC14A2_uc002lbb.2_Missense_Mutation_p.L146V|SLC14A2_uc002lbe.2_Missense_Mutation_p.L146V	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	146						apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4						CATAGGGCTGCTGATCCAGAA	0.572													38	96	---	---	---	---	PASS
C19orf24	55009	broad.mit.edu	37	19	1277275	1277275	+	Silent	SNP	G	C	C	rs757292	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1277275G>C	uc002lrw.3	+	2	404	c.375G>C	c.(373-375)GTG>GTC	p.V125V	C19orf24_uc002lrx.3_5'UTR	NM_017914	NP_060384	Q9BVV8	CS024_HUMAN	hypothetical protein LOC55009	125						cytoplasm|extracellular region part|integral to membrane					0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGAGACGGTGTTTGAGTCCC	0.647													7	48	---	---	---	---	PASS
ZNF799	90576	broad.mit.edu	37	19	12491498	12491498	+	Missense_Mutation	SNP	C	T	T	rs4804664	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12491498C>T	uc002mts.3	-	4	1044	c.578G>A	c.(577-579)CGT>CAT	p.R193H				Q96GE5	ZN799_HUMAN	Homo sapiens cDNA clone IMAGE:30340957, **** WARNING: chimeric clone ****.	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6						AGTGGTTTCACGTCTTTGAAG	0.428													13	107	---	---	---	---	PASS
ZNF799	90576	broad.mit.edu	37	19	12491654	12491654	+	Missense_Mutation	SNP	C	T	T	rs57371898	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12491654C>T	uc002mts.3	-	4	888	c.422G>A	c.(421-423)CGT>CAT	p.R141H				Q96GE5	ZN799_HUMAN	Homo sapiens cDNA clone IMAGE:30340957, **** WARNING: chimeric clone ****.	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6						CTCCCCAGTACGTGTTCTTTC	0.373													13	119	---	---	---	---	PASS
ZNF799	90576	broad.mit.edu	37	19	12491949	12491949	+	Missense_Mutation	SNP	T	C	C	rs11668955	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12491949T>C	uc002mts.3	-	4	593	c.127A>G	c.(127-129)ACC>GCC	p.T43A				Q96GE5	ZN799_HUMAN	Homo sapiens cDNA clone IMAGE:30340957, **** WARNING: chimeric clone ****.	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6						TAACTGAAGGTTTTCCAAAAT	0.403													11	85	---	---	---	---	PASS
BRD4	23476	broad.mit.edu	37	19	15378289	15378289	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15378289G>T	uc002nar.2	-	4	719	c.497C>A	c.(496-498)ACA>AAA	p.T166K	BRD4_uc002nas.2_Missense_Mutation_p.T166K|BRD4_uc002nat.3_Missense_Mutation_p.T166K|BRD4_uc002nau.3_Missense_Mutation_p.T166K	NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long	166					interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			GGTTTCTTCTGTGGGTAGCTC	0.443			T	NUT|C15orf55	lethal midline carcinoma of young people								157	477	---	---	---	---	PASS
FXYD3	5349	broad.mit.edu	37	19	35612168	35612168	+	Intron	SNP	T	A	A	rs1688016	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35612168T>A	uc010xsn.1	+						FXYD3_uc010xsj.1_Missense_Mutation_p.L39H|FXYD3_uc010xsk.1_Missense_Mutation_p.L39H|FXYD3_uc010xsl.1_Intron|FXYD3_uc010xsm.1_Intron|FXYD3_uc002nxw.2_Intron|FXYD3_uc002nxv.2_Intron|FXYD3_uc010xso.1_Intron	NM_001136011	NP_001129483	Q14802	FXYD3_HUMAN	FXYD domain containing ion transport regulator 3							chloride channel complex|integral to plasma membrane	chloride channel activity				0	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			CCGTGCCCCCTTTCCCCTCCC	0.517													22	210	---	---	---	---	PASS
KIR2DL1	3802	broad.mit.edu	37	19	55295421	55295421	+	3'UTR	SNP	C	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55295421C>T	uc002qhb.1	+	8					KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR2DL4_uc010yfl.1_5'Flank|KIR2DL3_uc010erw.1_3'UTR|KIR2DL1_uc002qgz.1_3'UTR|KIR3DP1_uc010yfi.1_Intron|KIR2DL1_uc010erz.1_3'UTR	NM_014218	NP_055033	P43626	KI2L1_HUMAN	killer cell immunoglobulin-like receptor, two						immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)		CTGAATGTGCCTCTCTCTTGC	0.463													10	13	---	---	---	---	PASS
ZSCAN22	342945	broad.mit.edu	37	19	58850251	58850251	+	Silent	SNP	T	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58850251T>C	uc002qsc.2	+	3	1182	c.1035T>C	c.(1033-1035)ATT>ATC	p.I345I	ZSCAN22_uc010yhz.1_3'UTR	NM_181846	NP_862829	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	345	C2H2-type 3.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		ACCAAAGGATTCATACTGGAG	0.587													7	30	---	---	---	---	PASS
RBM39	9584	broad.mit.edu	37	20	34302239	34302239	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34302239T>C	uc002xeb.2	-	11	1308	c.964A>G	c.(964-966)AAA>GAA	p.K322E	RBM39_uc002xdz.2_Missense_Mutation_p.K298E|RBM39_uc002xea.2_Missense_Mutation_p.K165E|RBM39_uc010gfn.2_Missense_Mutation_p.K165E|RBM39_uc010zvm.1_Missense_Mutation_p.K300E|RBM39_uc002xeg.2_Missense_Mutation_p.K300E|RBM39_uc002xec.2_Missense_Mutation_p.K322E|RBM39_uc002xed.2_Missense_Mutation_p.K40E|RBM39_uc002xee.2_Missense_Mutation_p.K165E|RBM39_uc002xef.2_Missense_Mutation_p.K165E|RBM39_uc010zvn.1_Missense_Mutation_p.K165E	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a	322	RRM 2.|Activating domain (By similarity).|Interaction with JUN (By similarity).				mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TGACCAACTTTCATTGGTCTT	0.423													52	136	---	---	---	---	PASS
CTCFL	140690	broad.mit.edu	37	20	56098186	56098186	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56098186G>A	uc010gix.1	-	2	1354	c.692C>T	c.(691-693)CCT>CTT	p.P231L	CTCFL_uc010giw.1_Missense_Mutation_p.P231L|CTCFL_uc002xym.2_Missense_Mutation_p.P231L|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Missense_Mutation_p.P231L|CTCFL_uc010gjb.1_Missense_Mutation_p.P231L|CTCFL_uc010gjc.1_Missense_Mutation_p.P231L|CTCFL_uc010gjd.1_Missense_Mutation_p.P231L|CTCFL_uc010gje.2_Missense_Mutation_p.P231L|CTCFL_uc010gjf.2_Missense_Mutation_p.P26L|CTCFL_uc010gjg.2_Intron|CTCFL_uc010gjh.1_Missense_Mutation_p.P231L|CTCFL_uc010gji.1_Missense_Mutation_p.P26L|CTCFL_uc010gjj.1_Missense_Mutation_p.P231L|CTCFL_uc010gjk.1_Missense_Mutation_p.P231L|CTCFL_uc010gjl.1_Missense_Mutation_p.P231L	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein	231					cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			ACCAGCTGTAGGTTGATCCTC	0.393													122	371	---	---	---	---	PASS
RRP1	8568	broad.mit.edu	37	21	45217342	45217342	+	Silent	SNP	C	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45217342C>A	uc002zds.2	+	6	555	c.462C>A	c.(460-462)ATC>ATA	p.I154I	RRP1_uc011aez.1_Silent_p.I154I|RRP1_uc010gpk.1_Silent_p.I4I|RRP1_uc010gpl.1_Silent_p.I52I|RRP1_uc010gpm.1_Silent_p.I21I	NM_003683	NP_003674	P56182	RRP1_HUMAN	ribosomal RNA processing 1 homolog	154					rRNA processing	nucleolus|preribosome, small subunit precursor					0				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		TGACTGAGATCCTGCACCCCA	0.592													17	85	---	---	---	---	PASS
TCN2	6948	broad.mit.edu	37	22	31010424	31010424	+	Silent	SNP	T	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31010424T>C	uc003aip.1	+	4	674	c.516T>C	c.(514-516)CAT>CAC	p.H172H	TCN2_uc003aiq.1_Silent_p.H168H|TCN2_uc003air.1_Silent_p.H145H	NM_000355	NP_000346	P20062	TCO2_HUMAN	transcobalamin II precursor	172					cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGCGGGTCCATGACAGCGTGG	0.582													16	72	---	---	---	---	PASS
SAPS2	9701	broad.mit.edu	37	22	50861936	50861936	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50861936G>T	uc003blb.1	+	11	1440	c.1018G>T	c.(1018-1020)GGG>TGG	p.G340W	SAPS2_uc003bky.1_Missense_Mutation_p.G340W|SAPS2_uc003bkz.1_Missense_Mutation_p.G340W|SAPS2_uc003blc.2_Missense_Mutation_p.G340W|SAPS2_uc003bla.1_Missense_Mutation_p.G341W|uc011arw.1_5'Flank	NM_014678	NP_055493	O75170	PP6R2_HUMAN	SAPS domain family, member 2	340						cytoplasm|intracellular membrane-bounded organelle	protein binding				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.222)		GGAGCCCCTGGGGAATGCCCG	0.602													8	45	---	---	---	---	PASS
MAGEB6	158809	broad.mit.edu	37	X	26213219	26213219	+	3'UTR	SNP	T	C	C	rs5986312	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26213219T>C	uc004dbr.2	+	2					MAGEB6_uc010ngc.1_3'UTR	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6											ovary(3)	3						TTGGCCAGGGTACCTTATGGG	0.443													11	46	---	---	---	---	PASS
GAGE1	2543	broad.mit.edu	37	X	49369711	49369711	+	3'UTR	SNP	A	G	G	rs3747318	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49369711A>G	uc004dok.1	+	5					GAGE1_uc004doj.2_3'UTR|GAGE1_uc004dol.1_Intron	NM_001468	NP_001459	Q13065	GAGE1_HUMAN	G antigen 1 isoform 1						cellular defense response						0	Ovarian(276;0.236)					ATCAAATGGCAAGAGACCGTT	0.403													20	113	---	---	---	---	PASS
CLCN5	1184	broad.mit.edu	37	X	49857048	49857048	+	3'UTR	SNP	T	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49857048T>A	uc004dos.1	+	12					CLCN5_uc004dor.1_3'UTR|CLCN5_uc004doq.1_3'UTR|CLCN5_uc004dot.1_3'UTR	NM_000084	NP_000075	P51795	CLCN5_HUMAN	chloride channel 5 isoform b						excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)					GAAATTAATTTTCTCTTTAGG	0.303													9	9	---	---	---	---	PASS
CCNB3	85417	broad.mit.edu	37	X	50090717	50090717	+	Silent	SNP	C	G	G	rs145795439	byFrequency	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50090717C>G	uc004dox.3	+	11	4201	c.3903C>G	c.(3901-3903)TCC>TCG	p.S1301S	CCNB3_uc004doy.2_Silent_p.S1301S|CCNB3_uc004doz.2_Silent_p.S197S|CCNB3_uc010njq.2_Silent_p.S193S|CCNB3_uc004dpa.2_Silent_p.S140S	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	1301					cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)					AGAAGGCTTCCAAGCTAGCTG	0.498													11	87	---	---	---	---	PASS
VSIG4	11326	broad.mit.edu	37	X	65259893	65259893	+	5'UTR	SNP	C	T	T	rs41305393	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65259893C>T	uc004dwh.2	-	1					VSIG4_uc004dwi.2_5'UTR|VSIG4_uc010nkq.1_5'UTR|VSIG4_uc004dwj.2_5'UTR|VSIG4_uc011moy.1_5'UTR|VSIG4_uc004dwk.2_5'UTR	NM_007268	NP_009199	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4						complement activation, alternative pathway	integral to membrane	protein binding				0						ACCAAAGAGGCTCAAACTTCT	0.537													9	52	---	---	---	---	PASS
GPR174	84636	broad.mit.edu	37	X	78426471	78426471	+	5'UTR	SNP	C	T	T	rs3810712	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78426471C>T	uc004edg.1	+	1						NM_032553	NP_115942	Q9BXC1	GP174_HUMAN	putative purinergic receptor FKSG79							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)|central_nervous_system(1)	2						TTTTGAACCACCATTAGGCAA	0.373										HNSCC(63;0.18)			10	64	---	---	---	---	PASS
GPR174	84636	broad.mit.edu	37	X	78426488	78426488	+	5'UTR	SNP	T	C	C	rs3810711	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78426488T>C	uc004edg.1	+	1						NM_032553	NP_115942	Q9BXC1	GP174_HUMAN	putative purinergic receptor FKSG79							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)|central_nervous_system(1)	2						GCAAAGATAGTTTCTCTAGAG	0.383										HNSCC(63;0.18)			11	90	---	---	---	---	PASS
IL13RA1	3597	broad.mit.edu	37	X	117925898	117925898	+	3'UTR	SNP	A	G	G	rs2495636	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117925898A>G	uc004eqs.2	+	11					IL13RA1_uc004eqt.1_Intron	NM_001560	NP_001551	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1 precursor							interleukin-13 receptor complex	cytokine receptor activity				0						GAACTTATTAAATGGAAACTG	0.388													9	50	---	---	---	---	PASS
RHOXF2B	727940	broad.mit.edu	37	X	119210876	119210876	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119210876A>C	uc004esj.3	-	2	647	c.457T>G	c.(457-459)TTC>GTC	p.F153V	uc004esi.1_Intron	NM_032498	NP_115887	P0C7M4	RHF2B_HUMAN	Rhox homeobox family, member 2	153	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TCGCGTTGGAAAATGCACTCC	0.667													6	10	---	---	---	---	PASS
MAGEC3	139081	broad.mit.edu	37	X	140984250	140984250	+	Intron	SNP	C	T	T	rs2205912	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140984250C>T	uc011mwp.1	+						MAGEC3_uc004fbs.2_5'UTR|MAGEC3_uc010nsj.2_Intron	NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1											skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					GGAAGACAGGCGACCTGTGAG	0.542													11	61	---	---	---	---	PASS
MAGEA5	4104	broad.mit.edu	37	X	151283336	151283336	+	3'UTR	SNP	T	C	C	rs3565	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151283336T>C	uc004ffj.2	-	3						NM_021049	NP_066387	P43359	MAGA5_HUMAN	melanoma antigen family A, 5												0	Acute lymphoblastic leukemia(192;6.56e-05)					TTCATCACACTCAGCTCCTCC	0.532													16	61	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	8843	8843	+	RNA	SNP	T	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:8843T>C	uc011mfi.1	+	1		c.181T>C			uc004cov.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		AGCCATGGCCATCCCCTTATG	0.468													32	1	---	---	---	---	PASS
SLC35E2B	728661	broad.mit.edu	37	1	1669647	1669648	+	Intron	DEL	CT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1669647_1669648delCT	uc001ahh.3	-						SLC35E2_uc009vkm.1_Intron|SLC35E2_uc001ahy.2_Intron|SLC35E2_uc001ahz.2_Intron|SLC35E2_uc001aib.1_Intron	NM_001110781	NP_001104251	P0CK96	S352B_HUMAN	similar to solute carrier family 35, member E2							integral to membrane					0						GTGGGCACCACTCTGAGTGGTC	0.673													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2393230	2393230	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2393230delA								PEX10 (49220 upstream) : PLCH2 (14524 downstream)																							TGGGGGAACCAGGAGCAGGGC	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5080067	5080068	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5080067_5080068insA								AJAP1 (236217 upstream) : NPHP4 (842802 downstream)																							GTGTCTGGGGTAAAAAAAAACA	0.347													4	2	---	---	---	---	
RERE	473	broad.mit.edu	37	1	8454125	8454125	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8454125delC	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.1_Intron|RERE_uc001apd.2_Intron	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GCTCCTGAGACCAGAAAGACA	0.418													4	2	---	---	---	---	
PRDM2	7799	broad.mit.edu	37	1	14064562	14064562	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14064562delA	uc001avi.2	+						PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Intron|PRDM2_uc001avj.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger							Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AGGAATAAAGAAAAAAAAAGA	0.308													4	2	---	---	---	---	
SPEN	23013	broad.mit.edu	37	1	16249126	16249126	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16249126delT	uc001axk.1	+						SPEN_uc010obp.1_Intron	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CTTTATGTACttttttttttg	0.204													4	2	---	---	---	---	
ZBTB17	7709	broad.mit.edu	37	1	16297522	16297522	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16297522delA	uc001axl.3	-						ZBTB17_uc010obq.1_Intron|ZBTB17_uc010obr.1_Intron|ZBTB17_uc010obs.1_Intron|ZBTB17_uc010obt.1_Intron|ZBTB17_uc010obu.1_Intron|ZBTB17_uc009vom.1_Intron|ZBTB17_uc010obv.1_Intron|ZBTB17_uc009von.1_Intron	NM_003443	NP_003434	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17						negative regulation of cell cycle	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		CAATAGAGGGAAAAAAAAAGT	0.408													4	2	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16926643	16926643	+	Intron	DEL	C	-	-	rs59187254		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16926643delC	uc009vos.1	-						NBPF1_uc001aza.3_RNA	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		taatacataacattacattTT	0.070													1	5	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16937363	16937363	+	Intron	DEL	A	-	-	rs63189863		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16937363delA	uc009vos.1	-						NBPF1_uc001aza.3_Intron|NBPF1_uc001azb.1_Intron|NBPF1_uc001azc.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		ccatctctacaaaaaatatga	0.000													4	3	---	---	---	---	
ESPNP	284729	broad.mit.edu	37	1	17043741	17043741	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17043741delT	uc001azn.1	-							NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						tttctttttcttttttttccc	0.284													4	2	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17261336	17261337	+	Intron	DEL	TC	-	-	rs148654831		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17261336_17261337delTC	uc001azt.2	+						CROCC_uc009voy.1_Intron|CROCC_uc009voz.1_Intron	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		ttcttcttcttctttttttttt	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20742898	20742898	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20742898delT	uc001bdf.1	-											Homo sapiens cDNA clone IMAGE:5269505.																		AGGAGttttctttttttcttt	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25395322	25395322	+	IGR	DEL	T	-	-	rs141140109		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25395322delT								RUNX3 (103710 upstream) : SYF2 (153445 downstream)																							agtccctaacttctctgagcc	0.219													7	4	---	---	---	---	
WDTC1	23038	broad.mit.edu	37	1	27561886	27561889	+	Intron	DEL	TGTG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27561886_27561889delTGTG	uc009vst.2	+						WDTC1_uc001bno.2_Intron	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1								protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		tctctctttctgtgtgtgtgtgtg	0.353													4	2	---	---	---	---	
PTAFR	5724	broad.mit.edu	37	1	28504249	28504249	+	5'Flank	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28504249delT	uc001bpl.2	-						PTAFR_uc001bpm.3_Intron|PTAFR_uc009vte.2_Intron	NM_000952	NP_000943	P25105	PTAFR_HUMAN	platelet-activating factor receptor						chemotaxis|inflammatory response|interferon-gamma-mediated signaling pathway|phosphatidylinositol-mediated signaling	integral to plasma membrane|nucleus	phospholipid binding|platelet activating factor receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)		TACTTTCTTCTTTTTTTTTTT	0.269													4	2	---	---	---	---	
PHACTR4	65979	broad.mit.edu	37	1	28817721	28817721	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28817721delA	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_5'Flank	NM_001048183	NP_001041648	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		tgtctacattaaaaaaaaaaa	0.040													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30230740	30230740	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30230740delG								PTPRU (577425 upstream) : MATN1 (953386 downstream)																							CGATGAGCCTGGGGACAGAAT	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36593765	36593765	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36593765delG								COL8A2 (27915 upstream) : TRAPPC3 (8410 downstream)																							TTTGCAGGGAGGGAGGGCTGC	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37210937	37210937	+	IGR	DEL	T	-	-	rs113469571		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37210937delT								CSF3R (262428 upstream) : GRIK3 (50191 downstream)																							tctttctttcttttttttttt	0.000													3	3	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42147777	42147778	+	Intron	DEL	TC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42147777_42147778delTC	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GTGGTCTCTTTCTCTCTCTCTC	0.545													6	3	---	---	---	---	
TIE1	7075	broad.mit.edu	37	1	43788752	43788752	+	3'UTR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43788752delA	uc001ciu.2	+	23					TIE1_uc010oke.1_3'UTR|TIE1_uc009vwq.2_3'UTR|TIE1_uc010okg.1_3'UTR	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and						mesoderm development	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGTCATTCAGAAAAAAATAAA	0.478													4	2	---	---	---	---	
ST3GAL3	6487	broad.mit.edu	37	1	44250785	44250786	+	Intron	INS	-	A	A	rs145108370	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44250785_44250786insA	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270	Q11203	SIAT6_HUMAN	sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				GGACTAAGACTGGGGGGGTTAG	0.446													7	4	---	---	---	---	
EIF2B3	8891	broad.mit.edu	37	1	45389487	45389487	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45389487delT	uc001cmt.1	-						EIF2B3_uc001cmu.1_Intron|EIF2B3_uc001cmv.1_Intron|EIF2B3_uc001cmw.2_Intron	NM_020365	NP_065098	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B,						negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					ctttctttcatttttttgaga	0.055													4	2	---	---	---	---	
PIK3R3	8503	broad.mit.edu	37	1	46558492	46558493	+	Intron	INS	-	C	C	rs72513292		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46558492_46558493insC	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)					tggtcttcatttctctctctct	0.000													1	7	---	---	---	---	
PIK3R3	8503	broad.mit.edu	37	1	46640602	46640603	+	Intron	INS	-	A	A	rs147870988	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46640602_46640603insA	uc010olw.1	-						TSPAN1_uc001cpd.2_5'Flank	NM_003629	NP_003620	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)					CCCCATCCCCCTCCTGACCTTC	0.525													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	46782478	46782478	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46782478delT								UQCRH (33 upstream) : NSUN4 (23912 downstream)																							taattgagaattttttttttt	0.264													5	4	---	---	---	---	
NSUN4	387338	broad.mit.edu	37	1	46810009	46810009	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46810009delT	uc001cpr.1	+						NSUN4_uc010omc.1_Intron|NSUN4_uc009vyf.1_Intron|NSUN4_uc009vyg.1_Intron|NSUN4_uc001cpt.1_Intron|NSUN4_uc001cps.1_Intron	NM_199044	NP_950245	Q96CB9	NSUN4_HUMAN	NOL1/NOP2/Sun domain family 4 protein								methyltransferase activity				0	Acute lymphoblastic leukemia(166;0.155)					atgttgttaatttttttttgt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	47092500	47092500	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47092500delA								MKNK1 (9937 upstream) : ATPAF1 (5913 downstream)																							CTATGGGGGGAAATGACTTCC	0.393													4	2	---	---	---	---	
ELAVL4	1996	broad.mit.edu	37	1	50640160	50640161	+	Intron	INS	-	T	T	rs140545221		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50640160_50640161insT	uc001csb.2	+						ELAVL4_uc001cry.3_Intron|ELAVL4_uc001crz.3_Intron|ELAVL4_uc001csa.3_Intron|ELAVL4_uc001csc.3_Intron|ELAVL4_uc009vyu.2_Intron|ELAVL4_uc010omz.1_Intron	NM_021952	NP_068771	P26378	ELAV4_HUMAN	ELAV-like 4 isoform 1						mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2						TTTTTTGTTTGTTTTTTTTTTT	0.327													2	6	---	---	---	---	
ZYG11B	79699	broad.mit.edu	37	1	53238351	53238351	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53238351delT	uc001cuj.2	+						ZYG11B_uc009vzg.2_Intron|ZYG11B_uc010onj.1_Intron	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						GAAAGGCTTGttttttttttt	0.299													11	6	---	---	---	---	
USP24	23358	broad.mit.edu	37	1	55534414	55534415	+	3'UTR	DEL	GT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55534414_55534415delGT	uc001cyg.3	-	65						NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						TTGTATGTTCGTGTAACAAAAA	0.406													3	3	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58913528	58913529	+	Intron	INS	-	C	C	rs146844714		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58913528_58913529insC	uc001cyt.1	-							NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						aatgacttaaacaaaaaaaaaa	0.069													3	5	---	---	---	---	
DOCK7	85440	broad.mit.edu	37	1	63118545	63118545	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63118545delT	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc009wah.1_Intron	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						TGTGCTTTTATTAGGTCACAC	0.358													4	2	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64642181	64642182	+	Intron	INS	-	C	C	rs149431568	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64642181_64642182insC	uc001dbj.2	+							NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						gaattgaggcaaaagttaaatg	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	64917385	64917385	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64917385delC								UBE2U (207358 upstream) : CACHD1 (19091 downstream)																							CAATTTTTCTCCCTCTGTTCC	0.388													4	2	---	---	---	---	
CACHD1	57685	broad.mit.edu	37	1	65147224	65147224	+	Intron	DEL	G	-	-	rs57993424		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65147224delG	uc001dbo.1	+						CACHD1_uc001dbp.1_Intron|CACHD1_uc001dbq.1_Intron|CACHD1_uc010opa.1_Intron	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1						calcium ion transport	integral to membrane				ovary(2)	2						ATTTTATTGTGtttttttttt	0.318													4	2	---	---	---	---	
PDE4B	5142	broad.mit.edu	37	1	66541705	66541706	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66541705_66541706insT	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)	TTCTTTCTTTCTtttttttttc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	73112110	73112110	+	IGR	DEL	A	-	-	rs71873740		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73112110delA								NEGR1 (363705 upstream) : None (None downstream)																							aggaagaaagaaaaaaaaaat	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	74283251	74283251	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74283251delA								None (None upstream) : LRRIQ3 (208453 downstream)																							ccccatctctaaaaaaaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	79145689	79145690	+	IGR	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79145689_79145690delAC								IFI44 (15928 upstream) : ELTD1 (209761 downstream)																							AATAATGCTAACACACACACAC	0.337													4	2	---	---	---	---	
PRKACB	5567	broad.mit.edu	37	1	84599560	84599560	+	Intron	DEL	C	-	-	rs75895498		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84599560delC	uc001djj.2	+						PRKACB_uc001dji.2_Intron	NM_002731	NP_002722	P22694	KAPCB_HUMAN	cAMP-dependent protein kinase catalytic subunit						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|regulation of insulin secretion|synaptic transmission|transmembrane transport|triglyceride catabolic process|water transport	cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane	ATP binding|cAMP-dependent protein kinase activity|magnesium ion binding|protein binding			lung(2)|ovary(1)	3				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)		gttcagtggaccctttgcctg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	87859619	87859620	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87859619_87859620insT								LMO4 (45016 upstream) : None (None downstream)																							CAACTGTCAGATTTTTTTTTTT	0.351													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	89139353	89139353	+	IGR	DEL	T	-	-	rs77105708		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89139353delT								None (None upstream) : PKN2 (10569 downstream)																							CACAGCTAAATTGCTTCAGAA	0.358													1	6	---	---	---	---	
PKN2	5586	broad.mit.edu	37	1	89216305	89216305	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89216305delT	uc001dmn.2	+						PKN2_uc001dmm.1_Intron|PKN2_uc010osp.1_Intron|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Intron	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2						signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		atagccacccttttggatatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	92025066	92025066	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92025066delG								CDC7 (33746 upstream) : HSP90B3P (75502 downstream)																							TACTGCATTAGGAAGCAGAAG	0.483													4	2	---	---	---	---	
ALG14	199857	broad.mit.edu	37	1	95527037	95527038	+	Intron	DEL	GA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95527037_95527038delGA	uc001dra.2	-							NM_144988	NP_659425	Q96F25	ALG14_HUMAN	asparagine-linked glycosylation 14 homolog						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity				0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		AAACAGCCTTgagagagagaga	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96827819	96827820	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96827819_96827820insA								None (None upstream) : PTBP2 (359355 downstream)																							TAAAGCAAGATAAAAAAAAATG	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98517859	98517859	+	5'Flank	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98517859delG	uc001drx.1	-											Homo sapiens cDNA FLJ37288 fis, clone BRAMY2014205.																		TATGTTTTCTGGATCCTCCAG	0.323													4	2	---	---	---	---	
LPPR5	163404	broad.mit.edu	37	1	99419271	99419271	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99419271delT	uc001dsb.2	-						LPPR5_uc001dsc.2_Intron	NM_001037317	NP_001032394	Q32ZL2	LPPR5_HUMAN	phosphatidic acid phosphatase type 2d isoform 1							integral to membrane	hydrolase activity				0						TTTTTGAAAATTTTTTTATCT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	107642365	107642366	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107642365_107642366insT								PRMT6 (40458 upstream) : NTNG1 (40263 downstream)																							ctttttctttcttttttttttc	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	108546753	108546753	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108546753delT								VAV3 (39208 upstream) : SLC25A24 (130696 downstream)																							TACCACACAGTTTCATGTAGC	0.403													4	2	---	---	---	---	
CYB561D1	284613	broad.mit.edu	37	1	110040453	110040458	+	3'UTR	DEL	ATGGGG	-	-	rs147209297	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110040453_110040458delATGGGG	uc010ovn.1	+	3					CYB561D1_uc010ovl.1_3'UTR|CYB561D1_uc010ovm.1_3'UTR|CYB561D1_uc001dxu.2_3'UTR|CYB561D1_uc001dxw.2_3'UTR|CYB561D1_uc010ovo.1_3'UTR|CYB561D1_uc009wfd.2_3'UTR|CYB561D1_uc010ovp.1_3'UTR	NM_182580	NP_872386	Q8N8Q1	C56D1_HUMAN	cytochrome b-561 domain containing 1 isoform 2						electron transport chain|transport	integral to membrane	metal ion binding				0		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0422)|Epithelial(280;0.0655)|all cancers(265;0.0685)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227)		ATTCAATAGTATGGGGACAGAATGGG	0.495													4	5	---	---	---	---	
CYB561D1	284613	broad.mit.edu	37	1	110040460	110040461	+	3'UTR	INS	-	A	A	rs11398789		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110040460_110040461insA	uc010ovn.1	+	3					CYB561D1_uc010ovl.1_3'UTR|CYB561D1_uc010ovm.1_3'UTR|CYB561D1_uc001dxu.2_3'UTR|CYB561D1_uc001dxw.2_3'UTR|CYB561D1_uc010ovo.1_3'UTR|CYB561D1_uc009wfd.2_3'UTR|CYB561D1_uc010ovp.1_3'UTR	NM_182580	NP_872386	Q8N8Q1	C56D1_HUMAN	cytochrome b-561 domain containing 1 isoform 2						electron transport chain|transport	integral to membrane	metal ion binding				0		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0422)|Epithelial(280;0.0655)|all cancers(265;0.0685)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227)		AGTATGGGGACAGAATGGGGAC	0.505													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	117770048	117770049	+	IGR	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117770048_117770049insG								VTCN1 (16499 upstream) : MAN1A2 (140036 downstream)																							AAGGATACACAGAAAACTAGCA	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120373120	120373120	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120373120delT								REG4 (18917 upstream) : NBPF7 (4269 downstream)																							atgtctcctgttttcctgcca	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142557046	142557046	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142557046delG								None (None upstream) : None (None downstream)																							TCCACCTACTGGTGGGTGAGC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142625341	142625341	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142625341delG	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		ttttttttttgagacagagtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143185152	143185152	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143185152delG	uc001eiw.1	+						uc001ejj.2_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		ACTCCTAAAAGTTGAGTGTCA	0.532													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144852792	144852793	+	Intron	DEL	TT	-	-	rs72112087		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144852792_144852793delTT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCCAAATCACTTTGTCTCAGCA	0.515			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145109259	145109260	+	Intron	INS	-	A	A	rs150048477	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145109259_145109260insA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						cactccagcccgggggcagagc	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146625037	146625037	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146625037delA								LOC728989 (110438 upstream) : PRKAB2 (1650 downstream)																							CCCACCCCTCAAAAAAAATAA	0.418													4	2	---	---	---	---	
LOC388692	388692	broad.mit.edu	37	1	149287128	149287129	+	RNA	DEL	CT	-	-	rs140343451		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149287128_149287129delCT	uc010pbf.1	+	1		c.7653_7654delCT			LOC388692_uc001esg.3_5'Flank	NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0						GGGGACTGGCCTCTCTGCACGG	0.594													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	154610934	154610935	+	IGR	INS	-	GAG	GAG	rs138134882	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154610934_154610935insGAG								ADAR (10497 upstream) : KCNN3 (68982 downstream)																							ttcttttttttgaggagtcttg	0.000													4	2	---	---	---	---	
GON4L	54856	broad.mit.edu	37	1	155822904	155822905	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155822904_155822905insA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					tccgtctcaagaaaaaaaaaaa	0.183													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	157141638	157141638	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157141638delA								ETV3 (33255 upstream) : FCRL5 (341530 downstream)																							TAAGGGCAACAAACGCTTTCC	0.343													4	2	---	---	---	---	
IFI16	3428	broad.mit.edu	37	1	158984260	158984262	+	Intron	DEL	ATT	-	-	rs10616115		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158984260_158984262delATT	uc001ftf.1	+						IFI16_uc001ftg.2_Intron|IFI16_uc010pis.1_Intron	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16						cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)					AATGGGAATAATTTCTTAGACAT	0.399													3	3	---	---	---	---	
UHMK1	127933	broad.mit.edu	37	1	162488184	162488184	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162488184delT	uc001gcc.1	+						UHMK1_uc001gcb.1_Intron|UHMK1_uc009wuu.1_Intron	NM_175866	NP_787062	Q8TAS1	UHMK1_HUMAN	kinase interacting stathmin						cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			GCACttaaaattttttttttt	0.109													5	3	---	---	---	---	
POU2F1	5451	broad.mit.edu	37	1	167368792	167368793	+	Intron	DEL	CT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167368792_167368793delCT	uc001gec.2	+						POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron|POU2F1_uc001gef.2_Intron|POU2F1_uc001geg.2_Intron|POU2F1_uc009wvg.1_Intron	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						gtctctcgtgctctctctctct	0.272													4	3	---	---	---	---	
GPR161	23432	broad.mit.edu	37	1	168076829	168076829	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168076829delC	uc001gfc.2	-						GPR161_uc001gfb.2_Intron|GPR161_uc010pll.1_Intron|GPR161_uc010plm.1_Intron|GPR161_uc009wvo.2_Intron|GPR161_uc001gfd.2_Intron|GPR161_uc010pln.1_Intron|GPR161_uc001gfe.1_5'Flank	NM_153832	NP_722561	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161 isoform 2						multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)					attttagcctccatcactgta	0.000													4	2	---	---	---	---	
KIFAP3	22920	broad.mit.edu	37	1	170036510	170036511	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170036510_170036511insA	uc001ggv.2	-						KIFAP3_uc010ply.1_Intron|KIFAP3_uc001ggw.1_Intron	NM_014970	NP_055785	Q92845	KIFA3_HUMAN	kinesin-associated protein 3						blood coagulation|plus-end-directed vesicle transport along microtubule|protein complex assembly|signal transduction	centrosome|condensed nuclear chromosome|cytosol|endoplasmic reticulum|kinesin II complex|spindle microtubule	kinesin binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					aaaaacttggcaaaaaaaacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	173354175	173354175	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173354175delT	uc001gix.1	-											Homo sapiens cDNA FLJ45305 fis, clone BRHIP3004193.																		ctagtactaatttttttaagt	0.000													4	2	---	---	---	---	
RABGAP1L	9910	broad.mit.edu	37	1	174305992	174305993	+	Intron	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174305992_174305993delTG	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						TGTTTATAAAtgtgtgtgtgtg	0.173													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	176250502	176250503	+	IGR	INS	-	A	A	rs148250710	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176250502_176250503insA								RFWD2 (74132 upstream) : PAPPA2 (181804 downstream)																							CTGGGACCGGGACTAATAAGTC	0.366													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	176337052	176337052	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176337052delA								RFWD2 (160682 upstream) : PAPPA2 (95255 downstream)																							AGGGTACATCAGGGAGATCTG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	178040944	178040944	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178040944delT								SEC16B (33802 upstream) : LOC100302401 (19699 downstream)																							CCTACAGTGATTTTTTTTTTC	0.468													3	4	---	---	---	---	
RALGPS2	55103	broad.mit.edu	37	1	178790264	178790264	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178790264delA	uc001glz.2	+						RALGPS2_uc001gly.1_Intron|RALGPS2_uc010pnb.1_Intron	NM_152663	NP_689876	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0						GAGGAAGCAGAAAATTGAGAG	0.448													4	2	---	---	---	---	
TDRD5	163589	broad.mit.edu	37	1	179586760	179586760	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179586760delT	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|TDRD5_uc001gnh.1_Intron	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						gtGACTTAACTTTTTTTTTTT	0.194													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181413465	181413466	+	IGR	DEL	AA	-	-	rs68146556		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181413465_181413466delAA								IER5 (353488 upstream) : CACNA1E (39250 downstream)																							CTGTGCTATTAAAAAAAAAAAA	0.450													4	2	---	---	---	---	
CACNA1E	777	broad.mit.edu	37	1	181465768	181465768	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181465768delT	uc001gow.2	+							NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						CTTGGGACTCTTGGAAATTTG	0.463													4	2	---	---	---	---	
CACNA1E	777	broad.mit.edu	37	1	181486281	181486282	+	Intron	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181486281_181486282insG	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						cctggggcactggggaaagctt	0.158													4	2	---	---	---	---	
C1orf21	81563	broad.mit.edu	37	1	184558466	184558466	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184558466delA	uc001gqv.1	+							NM_030806	NP_110433	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)		TCTAACTTTTAAAAACACGTG	0.408													4	2	---	---	---	---	
C1orf26	54823	broad.mit.edu	37	1	185143309	185143309	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185143309delT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823												0						AAAGTTGTAATTTTTTTTTCC	0.229													4	3	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	186008612	186008612	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186008612delT	uc001grq.1	+							NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AAAAAACTGATTTTTTTAACA	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	186565293	186565294	+	IGR	DEL	AG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186565293_186565294delAG								PDC (135054 upstream) : PTGS2 (75651 downstream)																							TAATTAATGTAGAGAGAGTTCA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	187991376	187991376	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187991376delT								None (None upstream) : None (None downstream)																							GACTTGACACTTTTTTTTTTA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	189975514	189975515	+	IGR	INS	-	C	C	rs144371154	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189975514_189975515insC								None (None upstream) : FAM5C (91282 downstream)																							tctgttagggacccgtccacac	0.040													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	190460252	190460252	+	IGR	DEL	A	-	-	rs34464477		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190460252delA								FAM5C (13493 upstream) : None (None downstream)																							TACAAGAAAGAAAAAAAAAAA	0.289													4	2	---	---	---	---	
KCNT2	343450	broad.mit.edu	37	1	196266267	196266268	+	Intron	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196266267_196266268delTG	uc001gtd.1	-						KCNT2_uc009wyt.1_Intron|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc001gth.1_Intron	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7						tttctGTAGATGTGTGTGTGTG	0.208													4	2	---	---	---	---	
KCNT2	343450	broad.mit.edu	37	1	196329407	196329407	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196329407delT	uc001gtd.1	-						KCNT2_uc009wyt.1_Intron|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7						TTGTAGTAGGTTTTTTTTTGT	0.333													4	2	---	---	---	---	
CAMSAP1L1	23271	broad.mit.edu	37	1	200784092	200784092	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200784092delT	uc001gvl.2	+						CAMSAP1L1_uc001gvk.2_Intron|CAMSAP1L1_uc001gvm.2_Intron	NM_203459	NP_982284	Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4						CCATGTAGACTTTTTTTtttt	0.134													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201144199	201144199	+	IGR	DEL	T	-	-	rs5780056		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201144199delT								TMEM9 (3497 upstream) : IGFN1 (15754 downstream)																							tgattgatagtcccccactaa	0.000													4	4	---	---	---	---	
NFASC	23114	broad.mit.edu	37	1	204805296	204805297	+	Intron	DEL	GT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204805296_204805297delGT	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			ctgtgtgtgcgtgtgtgtgtgt	0.248													4	3	---	---	---	---	
MAPKAPK2	9261	broad.mit.edu	37	1	206869115	206869117	+	Intron	DEL	CTC	-	-	rs139485827	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206869115_206869117delCTC	uc001hem.1	+						MAPKAPK2_uc001hel.1_Intron	NM_032960	NP_116584	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated						activation of MAPK activity|hormone biosynthetic process|innate immune response|leukotriene biosynthetic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|prostanoid metabolic process|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			CTCTCTCTCTCTCTTTTTTTTTT	0.433													4	2	---	---	---	---	
HHAT	55733	broad.mit.edu	37	1	210729360	210729360	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210729360delT	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron|HHAT_uc010psu.1_Intron|HHAT_uc001hia.3_Intron	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		CCTTCCCCAATTTTTTTTTAA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213588490	213588490	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213588490delT								RPS6KC1 (141683 upstream) : PROX1 (572796 downstream)																							TTTCTTCCACTTTTTTTACTG	0.398													3	3	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	216491817	216491817	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216491817delT	uc001hku.1	-						USH2A_uc001hkv.2_Intron	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ATGTCATGCCTATGAATGTTT	0.289										HNSCC(13;0.011)			4	2	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	217214919	217214919	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217214919delT	uc010puc.1	-						ESRRG_uc001hkz.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	AAGGAGTACATTTTCCATCTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	218724533	218724533	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218724533delA								TGFB2 (106574 upstream) : LYPLAL1 (622659 downstream)																							TCAGCTAGGCAAAGGGGGGAA	0.408													4	2	---	---	---	---	
TLR5	7100	broad.mit.edu	37	1	223288988	223288989	+	Intron	INS	-	AGAC	AGAC	rs141084293	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223288988_223288989insAGAC	uc001hnv.1	-						TLR5_uc001hnw.1_Intron	NM_003268	NP_003259	O60602	TLR5_HUMAN	toll-like receptor 5 precursor						cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of toll-like receptor signaling pathway	integral to membrane|plasma membrane	interleukin-1 receptor binding|transmembrane receptor activity			ovary(2)|lung(1)|skin(1)	4				GBM - Glioblastoma multiforme(131;0.0851)		gaagaggtgataacaaaaggaa	0.000													6	4	---	---	---	---	
TMEM63A	9725	broad.mit.edu	37	1	226056718	226056718	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226056718delG	uc001hpm.1	-						TMEM63A_uc010pvi.1_Intron	NM_014698	NP_055513	O94886	TM63A_HUMAN	transmembrane protein 63A							integral to membrane|lysosomal membrane	nucleotide binding			ovary(1)|breast(1)	2	Breast(184;0.197)					CTTCTAGGCTGGGAAAGCAGT	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228636802	228636803	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228636802_228636803insT								HIST3H3 (23776 upstream) : HIST3H2A (8263 downstream)																							cactttcttCCTTTTTTTTTTA	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229076129	229076129	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229076129delT								RHOU (193720 upstream) : RAB4A (330750 downstream)																							GGAGAGAAGGTTAGGAGGCCT	0.438													4	2	---	---	---	---	
ACTN2	88	broad.mit.edu	37	1	236857897	236857897	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236857897delA	uc001hyf.2	+						ACTN2_uc001hyg.2_Intron|ACTN2_uc009xgi.1_Intron	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2						focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TTTTTAAATTAAAAAAACTTT	0.234													4	2	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237220495	237220495	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237220495delT	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AGGAAACttcttttttttttg	0.239													18	9	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237886196	237886197	+	Intron	DEL	CT	-	-	rs146977948		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237886196_237886197delCT	uc001hyl.1	+						RYR2_uc010pxz.1_Intron	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ctggaatctactctcagcaaat	0.015													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238447057	238447057	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238447057delT								LOC100130331 (355440 upstream) : LOC339535 (196629 downstream)																							tttctctttctttttttttcc	0.000													4	2	---	---	---	---	
EXO1	9156	broad.mit.edu	37	1	242014735	242014735	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242014735delT	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			AAAGGTCATCTTTTTTTTCTT	0.204								Direct_reversal_of_damage|Editing_and_processing_nucleases					4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	246669136	246669136	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246669136delT	uc001ibl.2	-							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)		TTTGTCACCATTTATTCATTC	0.373													4	2	---	---	---	---	
PXDN	7837	broad.mit.edu	37	2	1678382	1678382	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1678382delC	uc002qxa.2	-						PXDN_uc002qxb.1_Intron|PXDN_uc002qxc.1_Intron	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor						extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		CCGCCTCTCACCCTCACCCCA	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5895794	5895795	+	IGR	DEL	GA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5895794_5895795delGA								SOX11 (54278 upstream) : LOC150622 (177024 downstream)																							CACAACACAGGAGAGAGAGATG	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5905134	5905134	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5905134delT								SOX11 (63618 upstream) : LOC150622 (167685 downstream)																							GTCATTTGTGTTTTTTTTTTC	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6811756	6811756	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6811756delA								LOC400940 (683392 upstream) : CMPK2 (168747 downstream)																							aGAGGTTTTGAAAAAAAATGT	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10656586	10656586	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10656586delT								ODC1 (68133 upstream) : NOL10 (54308 downstream)																							ttcttttttcttttttttgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	11018689	11018690	+	IGR	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11018689_11018690insG								PDIA6 (40586 upstream) : KCNF1 (33373 downstream)																							gagtgagagtagggggtcattc	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12517397	12517397	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12517397delA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		tatcaatattaatactaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15281929	15281929	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15281929delA								FAM84A (490996 upstream) : NBAS (25103 downstream)																							TTCCCCCAATAAAAAAGGGGC	0.438													4	2	---	---	---	---	
VSNL1	7447	broad.mit.edu	37	2	17835853	17835853	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17835853delT	uc002rcm.2	+							NM_003385	NP_003376	P62760	VISL1_HUMAN	visinin-like 1								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					tgagccaccctttctaaccac	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23645107	23645108	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23645107_23645108delTG								None (None upstream) : KLHL29 (110347 downstream)																							gtagtgtgtttgtgtgtgtgtt	0.079													4	2	---	---	---	---	
ADCY3	109	broad.mit.edu	37	2	25139257	25139257	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25139257delT	uc002rfs.3	-						ADCY3_uc010ykm.1_Intron	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3						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|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					ACCTCAGACCTTAGAACCTGG	0.303													4	2	---	---	---	---	
ZNF512	84450	broad.mit.edu	37	2	27827236	27827236	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27827236delT	uc002rla.2	+						ZNF512_uc010ylv.1_Intron|ZNF512_uc010ylw.1_Intron|ZNF512_uc002rlb.2_Intron|ZNF512_uc010ylx.1_Intron|ZNF512_uc002rlc.2_Intron|ZNF512_uc010yly.1_Intron|ZNF512_uc010ylz.1_Intron	NM_032434	NP_115810	Q96ME7	ZN512_HUMAN	zinc finger protein 512						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					CTGTGGTTTCTTTttttttag	0.194													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28561684	28561684	+	3'UTR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28561684delT	uc002rlr.2	+	13					BRE_uc002rlq.2_3'UTR|BRE_uc002rls.2_3'UTR|BRE_uc002rlt.2_3'UTR|BRE_uc002rlu.2_3'UTR|BRE_uc002rlv.2_3'UTR|BRE_uc002rlx.2_RNA	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					GCCTCAGGAATGCCCACGCCT	0.433													4	2	---	---	---	---	
PLB1	151056	broad.mit.edu	37	2	28788429	28788429	+	Intron	DEL	G	-	-	rs67312105		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28788429delG	uc002rmb.1	+						PLB1_uc010ezj.1_Intron|PLB1_uc002rmc.2_Intron|PLB1_uc002rmd.1_5'Flank	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)					CCTTGAGCCAGGAATCCAGGA	0.373													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30198885	30198885	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30198885delC								ALK (54453 upstream) : YPEL5 (170865 downstream)																							aagccgaacaccaggagtatc	0.040													4	2	---	---	---	---	
SPAST	6683	broad.mit.edu	37	2	32340026	32340027	+	Intron	INS	-	T	T	rs67016851		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32340026_32340027insT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					ATAAAGTTAAAttttttttttt	0.114													7	5	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32690982	32690983	+	Intron	INS	-	GC	GC	rs148682472	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32690982_32690983insGC	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)					CAGTATTTTCTGCCCAACTAAT	0.327													4	2	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32837756	32837756	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32837756delG	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)					gggaaagtgtgggaatataga	0.000													4	2	---	---	---	---	
TTC27	55622	broad.mit.edu	37	2	32933031	32933031	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32933031delA	uc002rom.2	+						TTC27_uc010ymx.1_Intron	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1						acttaacaacaaaaaaaaaaa	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	36430788	36430788	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36430788delA								None (None upstream) : CRIM1 (152609 downstream)																							gacatcctggaaaaaaaaagg	0.104													4	2	---	---	---	---	
ATL2	64225	broad.mit.edu	37	2	38538264	38538264	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38538264delA	uc002rqq.2	-						ATL2_uc010ynm.1_Intron|ATL2_uc010ynn.1_Intron|ATL2_uc010yno.1_Intron|ATL2_uc002rqs.2_Intron|ATL2_uc002rqr.2_Intron	NM_001135673	NP_001129145	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2 isoform 2						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			ovary(1)|kidney(1)|skin(1)	3						agaacaaaacaaaaaaaaaAG	0.244													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38704720	38704720	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38704720delT								ATL2 (100288 upstream) : HNRPLL (85608 downstream)																							ATGGTTTTTGTTTTTTTTCTG	0.308													4	2	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43768645	43768645	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43768645delT	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_Intron|THADA_uc002rta.2_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TCATGCTAAGttttttttttt	0.174													11	6	---	---	---	---	
C2orf34	79823	broad.mit.edu	37	2	44735717	44735720	+	Intron	DEL	AAAC	-	-	rs140904344		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44735717_44735720delAAAC	uc002rum.2	+							NM_024766	NP_079042	Q7Z624	CMKMT_HUMAN	hypothetical protein LOC79823							cytoplasm	calmodulin-lysine N-methyltransferase activity				0		all_hematologic(82;0.0892)|Acute lymphoblastic leukemia(82;0.17)				TACTGTGGCTAAACGTTTACCTTA	0.382													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	46919319	46919319	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46919319delC								CRIPT (66439 upstream) : SOCS5 (6780 downstream)																							gatgcattctccatatgcaga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	49024651	49024651	+	IGR	DEL	T	-	-	rs111821123		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49024651delT								LHCGR (41771 upstream) : FSHR (165002 downstream)																							CCTAGATTGATTTTTTTTTTC	0.373													4	2	---	---	---	---	
SPTBN1	6711	broad.mit.edu	37	2	54803602	54803602	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54803602delT	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron|SPTBN1_uc002rxx.2_Intron	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			GTTACTTCAATTTTTTTTTTA	0.373													4	3	---	---	---	---	
VRK2	7444	broad.mit.edu	37	2	58293867	58293867	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58293867delA	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron	NM_001130482	NP_001123954	Q86Y07	VRK2_HUMAN	vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						gcattcttttaaaaaaaatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60139597	60139597	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60139597delT								None (None upstream) : BCL11A (538706 downstream)																							TTAGCTTTTCTTTTTTAAATT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	61028528	61028528	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61028528delT								PAPOLG (2432 upstream) : REL (80224 downstream)																							TCAATAATGGTTTTTTTTTTC	0.244													4	2	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61607736	61607737	+	Intron	INS	-	C	C	rs141919220	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61607736_61607737insC	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			cacaaattcctcccatcattat	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62576034	62576034	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62576034delG								B3GNT2 (124170 upstream) : TMEM17 (151322 downstream)																							tggttttTCTGGGTTTTGTTA	0.194													4	2	---	---	---	---	
TMEM17	200728	broad.mit.edu	37	2	62753601	62753601	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62753601delG	uc002sbv.1	-									Q86X19	TMM17_HUMAN	Homo sapiens cDNA FLJ34583 fis, clone KIDNE2008666.							integral to membrane					0	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			tatttcacttgggggaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64823923	64823923	+	IGR	DEL	T	-	-	rs71393374		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64823923delT								AFTPH (3792 upstream) : SERTAD2 (34833 downstream)																							tcaaaccagattttttttctc	0.000													4	3	---	---	---	---	
MEIS1	4211	broad.mit.edu	37	2	66746423	66746423	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66746423delA	uc002sdu.2	+						MEIS1_uc002sdt.2_Intron|MEIS1_uc002sdv.2_Intron|MEIS1_uc010yqh.1_Intron|MEIS1_uc010yqi.1_Intron|MEIS1_uc002sdw.1_Intron	NM_002398	NP_002389	O00470	MEIS1_HUMAN	Meis homeobox 1								sequence-specific DNA binding transcription factor activity				0						ATGTGGTAGCAAAAAAAATAT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67441488	67441489	+	Intron	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67441488_67441489delCA	uc002sdx.2	+						uc002sdy.1_Intron					Homo sapiens, clone IMAGE:5541055, mRNA.																		atatgcacaccacacacacacC	0.134													4	3	---	---	---	---	
TGFA	7039	broad.mit.edu	37	2	70694785	70694786	+	Intron	INS	-	T	T	rs143519364	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70694785_70694786insT	uc002sgs.3	-						TGFA_uc010fdq.2_Intron|TGFA_uc010fdr.2_Intron|TGFA_uc002sgt.3_Intron|TGFA_uc002sgu.2_Intron|TGFA_uc002sgv.2_Intron|TGFA_uc002sgw.2_Intron	NM_003236	NP_003227	P01135	TGFA_HUMAN	transforming growth factor, alpha isoform 1						activation of MAPK activity|cell proliferation|positive regulation of cell division|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	cell surface|extracellular space|integral to membrane|plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity|signal transducer activity			prostate(1)	1						TGCCCACTTAGTTTTTTTGGGG	0.386													2	5	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72846309	72846312	+	Intron	DEL	AGAG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72846309_72846312delAGAG	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						ATACACAGCCagagagagagagag	0.186													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	75822946	75822946	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75822946delG								FAM176A (26098 upstream) : MRPL19 (50963 downstream)																							GAGAGAACCTGGAGGCCTCAG	0.413													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80252004	80252004	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80252004delT	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						ttgtctggtgtccaggaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	81303258	81303258	+	IGR	DEL	T	-	-	rs78410750		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81303258delT								CTNNA2 (427354 upstream) : None (None downstream)																							AAATCAGTGATTTTTTTTTCA	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	83278131	83278132	+	IGR	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83278131_83278132delAC								None (None upstream) : None (None downstream)																							ACGTGCACAGACACACACACAT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	84070570	84070570	+	IGR	DEL	T	-	-	rs78034212		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84070570delT								None (None upstream) : FUNDC2P2 (447236 downstream)																							ctatgaggggttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90403430	90403430	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90403430delG	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		tcacacccccgtgctccaaac	0.000													4	2	---	---	---	---	
LOC654342	654342	broad.mit.edu	37	2	91809968	91809968	+	Intron	DEL	A	-	-	rs113753145		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91809968delA	uc002sts.3	-						LOC654342_uc002stt.2_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0						AGACCAATATAAAAACACATT	0.269													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91902877	91902878	+	IGR	DEL	AT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91902877_91902878delAT								LOC654342 (54902 upstream) : GGT8P (60490 downstream)																							AAATGCAAACATATGGAAATTT	0.317													4	3	---	---	---	---	
ANKRD20B	729171	broad.mit.edu	37	2	95471010	95471011	+	Intron	DEL	TC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95471010_95471011delTC	uc010fhp.2	-							NR_003366				Homo sapiens ankyrin repeat domain 20B (ANKRD20B), non-coding RNA.												0						CATGTCCTTTTCATAGAAAAAG	0.351													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	97057829	97057830	+	IGR	DEL	GT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97057829_97057830delGT								NCAPH (16555 upstream) : NEURL3 (105555 downstream)																							CACCAGTtgcgtgtgtgtgtgt	0.282													4	2	---	---	---	---	
LYG2	254773	broad.mit.edu	37	2	99862076	99862076	+	Intron	DEL	A	-	-	rs144842726		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99862076delA	uc002szw.1	-						MRPL30_uc002szl.1_Intron|LYG2_uc010fip.1_Intron|LYG2_uc002szx.1_Intron	NM_175735	NP_783862	Q86SG7	LYG2_HUMAN	lysozyme G-like 2 precursor						cell wall macromolecule catabolic process|peptidoglycan catabolic process	extracellular region	lysozyme activity			ovary(1)	1						atctctaattaaaaaaaaaaa	0.104													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103502114	103502114	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103502114delA								TMEM182 (67978 upstream) : None (None downstream)																							aaggtacaagaaaaaaaaaaa	0.035													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	104920620	104920620	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104920620delT								None (None upstream) : LOC150568 (130185 downstream)																							ctcgtgaagcttacaaactca	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105044710	105044711	+	IGR	DEL	TG	-	-	rs111551260		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105044710_105044711delTG								None (None upstream) : LOC150568 (6094 downstream)																							tgggtgtgtctgtgtgtgtgtg	0.238													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106575769	106575769	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106575769delA								NCK2 (65043 upstream) : C2orf40 (106344 downstream)																							TCCACCTAATAAAAAAAAAAG	0.418													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108842592	108842593	+	IGR	INS	-	T	T	rs140688733	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108842592_108842593insT								SLC5A7 (212153 upstream) : SULT1C3 (21058 downstream)																							ATATTGCTCAGGTTTTTTTTTT	0.371													5	3	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	110262078	110262081	+	3'UTR	DEL	ACAA	-	-	rs71662090		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110262078_110262081delACAA	uc010ywt.1	+	10						NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						GTTCACACACACAAACACACACAC	0.490													4	5	---	---	---	---	
MERTK	10461	broad.mit.edu	37	2	112725119	112725119	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112725119delC	uc002thk.1	+						MERTK_uc002thl.1_Intron	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor						cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9						AGGACACACACCCCTTCCCCT	0.493													4	2	---	---	---	---	
MERTK	10461	broad.mit.edu	37	2	112731465	112731465	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112731465delC	uc002thk.1	+						MERTK_uc002thl.1_Intron	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor						cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9						TGTGGAGAGACTGGTGGAGTT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	117221696	117221696	+	IGR	DEL	T	-	-	rs34642815		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117221696delT								DPP10 (619760 upstream) : None (None downstream)																							ttcttccttctttttcactga	0.164													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119311647	119311647	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119311647delG								INSIG2 (444051 upstream) : EN1 (288101 downstream)																							CTGGTTCTGTGGATGGTGGAT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	120427489	120427492	+	IGR	DEL	AAAG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120427489_120427492delAAAG								PCDP1 (13253 upstream) : TMEM177 (9251 downstream)																							GAAAAGAAATAAAGAAGAAGAAAG	0.324													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121859411	121859411	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121859411delG								GLI2 (109183 upstream) : TFCP2L1 (114755 downstream)																							TCCAGGAGCTGGTGGAGAAGG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126435003	126435004	+	IGR	INS	-	T	T	rs141181387	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126435003_126435004insT								CNTNAP5 (762142 upstream) : GYPC (978680 downstream)																							ttttgtatgtgttttttttggt	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130067092	130067092	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130067092delA								HS6ST1 (990921 upstream) : LOC389033 (613343 downstream)																							tgttggAGATAACAGAAAAGC	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130154921	130154921	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130154921delT								None (None upstream) : LOC389033 (525514 downstream)																							TCACACTCCCTTTTCCAGGTG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130215382	130215382	+	IGR	DEL	A	-	-	rs35211702		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130215382delA								None (None upstream) : LOC389033 (465053 downstream)																							AGCAAGGCCCAGGGGAGGGAT	0.507													4	3	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	134102918	134102918	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134102918delA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002ttt.1_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						CTTTTAAATTAAAAAAAAAAG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134587404	134587404	+	IGR	DEL	T	-	-	rs67559645		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134587404delT								NCKAP5 (261373 upstream) : MGAT5 (424426 downstream)																							AAAAAAAAAATGGAGATACTT	0.294													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134832080	134832080	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134832080delA								NCKAP5 (506049 upstream) : MGAT5 (179750 downstream)																							AGCTATTACCAAAAATATACT	0.353													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137695870	137695870	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137695870delA	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		TGAGAATGCTAAGGCAGTAGG	0.408													4	2	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	138285460	138285460	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138285460delA	uc002tva.1	+						THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		gaaagcaaccaagagataaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	138991719	138991719	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138991719delT								HNMT (217786 upstream) : SPOPL (267631 downstream)																							CTGACATGGATTTTTTTTTTT	0.403													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	140017818	140017819	+	IGR	INS	-	AC	AC	rs143497585	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140017818_140017819insAC								NXPH2 (480007 upstream) : LRP1B (971177 downstream)																							GCCATTAGAGGacacacacaca	0.465													4	3	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	141740572	141740572	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141740572delA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	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)		TGTTAGCCGGAGGCAGTGGTT	0.338										TSP Lung(27;0.18)			4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142188804	142188805	+	Intron	INS	-	AGTC	AGTC	rs140560977	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142188804_142188805insAGTC	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	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)		gttcaagagaaagtcagagaga	0.005										TSP Lung(27;0.18)			3	4	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142368995	142368995	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142368995delT	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	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)		CCTCCTCACATTTTTTTTGGA	0.368										TSP Lung(27;0.18)			5	3	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142424549	142424549	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142424549delT	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	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)		TATTTCTAGATTTTTTTTTTT	0.373										TSP Lung(27;0.18)			3	3	---	---	---	---	
ARHGAP15	55843	broad.mit.edu	37	2	143889404	143889404	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143889404delG	uc002tvm.3	+						ARHGAP15_uc010zbl.1_Intron	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		GTAAATGGTTGGGGGAAGACT	0.443													4	2	---	---	---	---	
ARHGAP15	55843	broad.mit.edu	37	2	144251212	144251212	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144251212delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		CACTCCTTGCTTTTTTCCCCC	0.244													4	2	---	---	---	---	
LYPD6B	130576	broad.mit.edu	37	2	149990652	149990653	+	Intron	DEL	GA	-	-	rs11689777		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149990652_149990653delGA	uc002twv.1	+						LYPD6B_uc002tww.1_Intron|LYPD6B_uc002twx.1_Intron	NM_177964	NP_808879	Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B							anchored to membrane|plasma membrane					0						ctgaagaaaggagagagagaga	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	150339827	150339827	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150339827delA								LYPD6 (9690 upstream) : MMADHC (86323 downstream)																							TCCCTGGAGGAAAAAAAGATG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	150936301	150936302	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150936301_150936302insA								MMADHC (491971 upstream) : RND3 (388410 downstream)																							caattcaacagaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	154254049	154254049	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154254049delT								ARL6IP6 (636282 upstream) : RPRM (79803 downstream)																							CACTCACTGATTTTTAGGCTC	0.393													4	2	---	---	---	---	
GALNT13	114805	broad.mit.edu	37	2	155210283	155210283	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155210283delC	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_Intron|GALNT13_uc010fod.2_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						gaataatattccattgtgtag	0.000													4	2	---	---	---	---	
UPP2	151531	broad.mit.edu	37	2	158858175	158858175	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158858175delT	uc002tzo.2	+							NM_001135098	NP_001128570	O95045	UPP2_HUMAN	uridine phosphorylase 2 isoform b						nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0						CTTGGTCTTATTTTTTTCCCA	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162466322	162466322	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162466322delT								TBR1 (184749 upstream) : SLC4A10 (14523 downstream)																							tgccagataattttttagtag	0.000													4	2	---	---	---	---	
DPP4	1803	broad.mit.edu	37	2	162879588	162879589	+	Intron	INS	-	CC	CC			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162879588_162879589insCC	uc002ubz.2	-						DPP4_uc010fpb.2_Intron	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	cctctgtcccaccagcctgttc	0.094													8	8	---	---	---	---	
KCNH7	90134	broad.mit.edu	37	2	163292254	163292254	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163292254delT	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	AACTTGGTTCTTTTTTTTTTA	0.338													5	3	---	---	---	---	
COBLL1	22837	broad.mit.edu	37	2	165644898	165644898	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165644898delA	uc010zcw.1	-						COBLL1_uc002ucp.2_Intron|COBLL1_uc002ucq.2_Intron|COBLL1_uc010zcx.1_Intron|COBLL1_uc002ucs.1_Intron|COBLL1_uc002uct.2_Intron	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1											ovary(2)|pancreas(1)	3						CTGTACCTTTAAAAAAAAAAT	0.378													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	170433856	170433856	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170433856delA								FASTKD1 (3432 upstream) : PPIG (6994 downstream)																							GCTGGGTCTTaaaaaaaaaag	0.303													4	3	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171385963	171385964	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171385963_171385964insT	uc002ufy.2	+						MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						ttccttcttccttttttttctt	0.163													4	2	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171421753	171421753	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171421753delT	uc002ufy.2	+						MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						ggaaacagcctttttgtagag	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	172128471	172128471	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172128471delA								TLK1 (40647 upstream) : METTL8 (45444 downstream)																							CTTTTTAAGGAAAAAAAAAAA	0.378													8	4	---	---	---	---	
SCRN3	79634	broad.mit.edu	37	2	175277079	175277080	+	Intron	INS	-	T	T	rs75034236		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175277079_175277080insT	uc002uiq.2	+						SCRN3_uc010zen.1_Intron|SCRN3_uc010zeo.1_Intron|SCRN3_uc002uis.2_Intron	NM_024583	NP_078859	Q0VDG4	SCRN3_HUMAN	secernin 3						proteolysis		dipeptidase activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.229)			tctcctgggaattttttttttt	0.000													4	3	---	---	---	---	
CHRNA1	1134	broad.mit.edu	37	2	175616067	175616067	+	Intron	DEL	G	-	-	rs34092071		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175616067delG	uc002ujd.2	-						uc002uiw.2_Intron|CHRNA1_uc002uje.2_Intron	NM_001039523	NP_001034612	P02708	ACHA_HUMAN	nicotinic cholinergic receptor alpha 1 isoform a						muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(2)|central_nervous_system(1)|skin(1)	4						GACTTTCCCTGGGCTGGCCTT	0.542													3	5	---	---	---	---	
ATF2	1386	broad.mit.edu	37	2	175979807	175979807	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175979807delT	uc002ujl.2	-						ATF2_uc010fqv.2_Intron|ATF2_uc002ujv.2_Intron|ATF2_uc002ujm.2_Intron|ATF2_uc002ujn.2_Intron|ATF2_uc002ujo.2_Intron|ATF2_uc002ujp.2_Intron|ATF2_uc002ujq.2_Intron|ATF2_uc002ujr.2_Intron|ATF2_uc010fqu.2_Intron|ATF2_uc002ujs.2_Intron|ATF2_uc002ujt.2_Intron|ATF2_uc002uju.2_Intron|ATF2_uc002ujw.1_Intron|ATF2_uc002ujx.1_Intron|ATF2_uc002ujy.1_Intron	NM_001880	NP_001871	P15336	ATF2_HUMAN	activating transcription factor 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nucleoplasm	protein dimerization activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(1)|breast(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.125)			aaaaGACTCGTTTTTTTTTTT	0.249													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176591442	176591442	+	IGR	DEL	T	-	-	rs67775032		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176591442delT								ATP5G3 (544952 upstream) : KIAA1715 (198968 downstream)																							CATCAGCACCTTTGTCCATTT	0.343													3	4	---	---	---	---	
NFE2L2	4780	broad.mit.edu	37	2	178148849	178148849	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178148849delT	uc002uli.3	-						LOC100130691_uc002ulj.1_Intron	NM_001145412	NP_001138884	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 2						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			ACTACAGTTGTTACTATGCAT	0.373			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	179017601	179017601	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179017601delT								RBM45 (23221 upstream) : OSBPL6 (41773 downstream)																							Ggtttttttgtttttttttgt	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181380838	181380838	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181380838delA								CWC22 (508998 upstream) : UBE2E3 (464274 downstream)																							TGGTTGGGAGAAAAAGCCCAT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181957128	181957128	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181957128delA								UBE2E3 (28978 upstream) : ITGA4 (364491 downstream)																							aaaacccttcaaaaaatcaat	0.000													4	2	---	---	---	---	
NCKAP1	10787	broad.mit.edu	37	2	183889991	183889991	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183889991delA	uc002upc.2	-						NCKAP1_uc002upb.2_Intron	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1						apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			AAACCAACTTAAAATAATACT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	191702501	191702501	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191702501delA								NAB1 (145010 upstream) : GLS (43046 downstream)																							TTgagaaaggaaaaaaaggaa	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193937293	193937293	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193937293delG								PCGEM1 (295672 upstream) : None (None downstream)																							agttaccagtgggccgatctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	195144483	195144483	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195144483delA								None (None upstream) : None (None downstream)																							gctggaatgcaatggcgcaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	195543385	195543386	+	IGR	DEL	CA	-	-	rs140275676	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195543385_195543386delCA								None (None upstream) : SLC39A10 (978146 downstream)																							cacacacatgcacacacacaga	0.000													4	2	---	---	---	---	
PGAP1	80055	broad.mit.edu	37	2	197718317	197718318	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197718317_197718318insA	uc002utw.2	-						PGAP1_uc002utx.2_Intron|PGAP1_uc002uty.1_Intron	NM_024989	NP_079265	Q75T13	PGAP1_HUMAN	GPI deacylase						attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4						gagtttcccataaaaaaatgca	0.000													4	2	---	---	---	---	
ANKRD44	91526	broad.mit.edu	37	2	198160105	198160105	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198160105delC	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)			tgttgtagcgcccatagacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	199935397	199935397	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199935397delT								PLCL1 (920791 upstream) : SATB2 (198827 downstream)																							CTCCAATCCATTTTATTCCTT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201383658	201383658	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201383658delA								KCTD18 (8866 upstream) : SGOL2 (7207 downstream)																							actctgtttcaaaaaaaaaag	0.000													4	2	---	---	---	---	
ALS2CR12	130540	broad.mit.edu	37	2	202153880	202153881	+	Intron	INS	-	C	C	rs142645837	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202153880_202153881insC	uc010ftg.2	-						ALS2CR12_uc002uya.3_Intron|ALS2CR12_uc010fth.2_Intron	NM_139163	NP_631902	Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)						regulation of GTPase activity		protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3						GGATTTAAAAACCACCCTCAGT	0.436													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	203860886	203860886	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203860886delT								ALS2CR8 (9826 upstream) : NBEAL1 (18716 downstream)																							CTCTCTGACCTTTTTCTCTGA	0.234													4	2	---	---	---	---	
CPS1	1373	broad.mit.edu	37	2	211386892	211386892	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211386892delG	uc010fur.2	+							NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a						carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		gaatacttcagggagaccatc	0.000													4	2	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	214567898	214567898	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214567898delG	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)		aaccaataacggacatggagg	0.000													4	2	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	215146301	215146302	+	Intron	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215146301_215146302delCA	uc002veq.2	+						SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		cgggaactctcacacactcctg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	222161864	222161864	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222161864delA								None (None upstream) : EPHA4 (120885 downstream)																							ACATCTCAGGAAATGCCATGA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	224231701	224231701	+	IGR	DEL	T	-	-	rs76060077		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224231701delT								KCNE4 (311348 upstream) : SCG2 (229959 downstream)																							caacagtctattttttttttc	0.075													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	225053919	225053919	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225053919delG								SERPINE2 (149883 upstream) : FAM124B (189497 downstream)																							AAAGGGCTGTGGGGACTTATA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232467817	232467818	+	IGR	INS	-	TG	TG	rs140546038	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232467817_232467818insTG								C2orf57 (8825 upstream) : PTMA (105417 downstream)																							tccccatcacttgtcctccacc	0.000													2	6	---	---	---	---	
NGEF	25791	broad.mit.edu	37	2	233776578	233776578	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233776578delA	uc002vts.2	-						NGEF_uc010fyg.1_Intron|NGEF_uc002vtt.2_Intron	NM_019850	NP_062824	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|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	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		caaccttgctaaaaatcacta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238037872	238037875	+	IGR	DEL	TGTG	-	-	rs145995063		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238037872_238037875delTGTG								COPS8 (30385 upstream) : COL6A3 (194780 downstream)																							tgcatgtgtctgtgtgatgtgtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238866426	238866426	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238866426delG								RAMP1 (45673 upstream) : UBE2F (9274 downstream)																							ttttccagcagggaatgtgtg	0.209													4	2	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240313599	240313613	+	Intron	DEL	GAACGCAGCCCGCGT	-	-	rs139858229		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240313599_240313613delGAACGCAGCCCGCGT	uc002vyk.3	-						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)		AACTTCGTCAGAACGCAGCCCGCGTGTGCTGAAGC	0.553													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241091491	241091496	+	IGR	DEL	GCATCG	-	-	rs143522067	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241091491_241091496delGCATCG								OTOS (11418 upstream) : GPC1 (283619 downstream)																							GCGTTAGACAGCATCGGCTGAGACAG	0.340													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	995844	995844	+	IGR	DEL	G	-	-	rs35899959		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:995844delG								CHL1 (544749 upstream) : CNTN6 (138776 downstream)																							GTTAGCCTTTGGGGGTCTTTC	0.259													4	2	---	---	---	---	
SUMF1	285362	broad.mit.edu	37	3	4434517	4434517	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4434517delT	uc003bpz.1	-						SUMF1_uc003bps.1_Intron|SUMF1_uc011ass.1_Intron|SUMF1_uc010hby.1_Intron|SUMF1_uc011ast.1_Intron	NM_182760	NP_877437	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		TCTGTTCAGATTTTTTTTTTC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	6227026	6227026	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6227026delT								EDEM1 (965377 upstream) : GRM7 (675776 downstream)																							acttacagtattacacagaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	8844356	8844357	+	IGR	INS	-	C	C	rs148268337	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8844356_8844357insC								OXTR (33056 upstream) : RAD18 (77204 downstream)																							tagttactaagccagtccacac	0.025													1	5	---	---	---	---	
TATDN2	9797	broad.mit.edu	37	3	10291868	10291868	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10291868delT	uc003bvg.2	+						TATDN2_uc003bvf.2_Intron|TATDN2_uc011atr.1_Intron|TATDN2_uc011ats.1_Intron|TATDN2_uc011att.1_Intron	NM_014760	NP_055575	Q93075	TATD2_HUMAN	TatD DNase domain containing 2							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding			pancreas(2)	2						tttttttttcttttttttttG	0.373													3	3	---	---	---	---	
VGLL4	9686	broad.mit.edu	37	3	11666001	11666001	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11666001delT	uc003bwf.2	-						VGLL4_uc010hdx.1_Intron|VGLL4_uc003bwg.2_Intron	NM_014667	NP_055482	Q14135	VGLL4_HUMAN	vestigial like 4 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)		CTTTCTCTAATTTTTTTTTTA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	19861556	19861557	+	IGR	DEL	TC	-	-	rs35628134		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19861556_19861557delTC								KCNH8 (284421 upstream) : EFHB (59411 downstream)																							aaaactgctttctctctctctc	0.000													3	3	---	---	---	---	
OSBPL10	114884	broad.mit.edu	37	3	31841797	31841797	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31841797delA	uc003cev.2	-						OSBPL10_uc003ceu.1_Intron|OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)		CATGACAAGGAAGCCGCATTT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	35011514	35011514	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35011514delT								None (None upstream) : ARPP21 (669567 downstream)																							CCTAGGCTTCTTTTGCAGCCT	0.338													4	2	---	---	---	---	
ITGA9	3680	broad.mit.edu	37	3	37848007	37848008	+	Intron	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37848007_37848008delCA	uc003chd.2	+						uc003che.2_RNA	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GTCTCCTCTGCACAGCCCCTGC	0.589													4	2	---	---	---	---	
KIF15	56992	broad.mit.edu	37	3	44846300	44846300	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44846300delT	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc003cny.1_Intron	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TTTTTGCTTGTCAAACACTGA	0.239													4	2	---	---	---	---	
KIF15	56992	broad.mit.edu	37	3	44846308	44846309	+	Intron	INS	-	GA	GA			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44846308_44846309insGA	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc003cny.1_Intron	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TGTCAAACACTGAAGTTGTAAA	0.213													4	2	---	---	---	---	
USP4	7375	broad.mit.edu	37	3	49339623	49339623	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49339623delA	uc003cwq.2	-						USP4_uc003cwo.2_Intron|USP4_uc003cwp.2_Intron|USP4_uc003cwr.2_Intron	NM_003363	NP_003354	Q13107	UBP4_HUMAN	ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		gtctctatttaaaaaaaaaaa	0.209													5	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52620642	52620642	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52620642delC	uc003des.2	-	20	3198	c.3186delG	c.(3184-3186)CGGfs	p.R1062fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.R1062fs|PBRM1_uc003der.2_Frame_Shift_Del_p.R1030fs|PBRM1_uc003det.2_Frame_Shift_Del_p.R1077fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.R1077fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.R1062fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.R1037fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.R1037fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.R1061fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.R974fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.R408fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1062	BAH 1.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGGCAGAATACCGTGATTCAC	0.448			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								114	68	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54157333	54157334	+	Intron	INS	-	C	C	rs143522185	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54157333_54157334insC	uc003dhf.2	+						CACNA2D3_uc011beu.1_5'Flank|CACNA2D3_uc003dhg.1_5'Flank|CACNA2D3_uc003dhh.1_5'Flank	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		TAACTCCGCGACCCCCCTCGGG	0.525													5	3	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54168567	54168567	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54168567delG	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		CAGATCACCAGGTCCTTCACA	0.517													4	2	---	---	---	---	
C3orf63	23272	broad.mit.edu	37	3	56673439	56673439	+	Intron	DEL	A	-	-	rs113199184		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56673439delA	uc003did.3	-						C3orf63_uc003dic.3_Intron|C3orf63_uc003die.3_Intron	NM_015224	NP_056039	Q9UK61	CC063_HUMAN	retinoblastoma-associated protein 140 isoform b											ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)		GAATGCTACCAAAAAAAAAAA	0.294													4	2	---	---	---	---	
DNAH12	201625	broad.mit.edu	37	3	57400934	57400934	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57400934delA	uc003dit.2	-							NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2						TCTCAGGCTTAAAAAAAAAAC	0.299													4	3	---	---	---	---	
LOC285401	285401	broad.mit.edu	37	3	63087336	63087336	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63087336delA	uc003dlo.2	+						LOC285401_uc010hnr.1_Intron|LOC285401_uc011bfj.1_5'Flank					Homo sapiens, clone IMAGE:5557531, mRNA.												0						GGGAAAAGAGAAAAAAAAAAC	0.443													4	3	---	---	---	---	
THOC7	80145	broad.mit.edu	37	3	63843690	63843690	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63843690delA	uc003dlt.3	-						THOC7_uc003dlu.3_Intron	NM_025075	NP_079351	Q6I9Y2	THOC7_HUMAN	Ngg1 interacting factor 3 like 1 binding protein						intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	cytoplasm|THO complex part of transcription export complex	protein binding|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.000439)|Kidney(15;0.00194)|KIRC - Kidney renal clear cell carcinoma(15;0.00218)		GGCACTAATGAAAAAAAAACC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	88825288	88825288	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88825288delA								C3orf38 (618175 upstream) : EPHA3 (331386 downstream)																							atggaacgccaaaacagattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	88874465	88874465	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88874465delG								C3orf38 (667352 upstream) : EPHA3 (282209 downstream)																							TTGGACTTGTGACTGTGATGT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	89052925	89052925	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89052925delA								C3orf38 (845812 upstream) : EPHA3 (103749 downstream)																							aggaaaacctaaaaagtgtaa	0.000													4	2	---	---	---	---	
EPHA6	285220	broad.mit.edu	37	3	96738253	96738254	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96738253_96738254insT	uc010how.1	+						EPHA6_uc003drp.1_Intron	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						cacaaatgcagttttttttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	98125451	98125451	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98125451delA								OR5K3 (14977 upstream) : OR5K1 (62970 downstream)																							caagatggccaaataggaaca	0.000													4	2	---	---	---	---	
ABI3BP	25890	broad.mit.edu	37	3	100500335	100500335	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100500335delC	uc003dun.2	-						ABI3BP_uc003duj.2_Intron|ABI3BP_uc003duk.2_Intron|ABI3BP_uc003dul.2_Intron|ABI3BP_uc011bhd.1_Intron|ABI3BP_uc003dum.2_Intron	NM_015429	NP_056244	Q7Z7G0	TARSH_HUMAN	ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4						ATCTCATAGGCAGGCCACAGG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	101436945	101436945	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101436945delA								LOC285359 (4686 upstream) : CEP97 (6549 downstream)																							CTGGAAAATTAAAAAAGACAA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103699049	103699049	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103699049delA	uc003dvu.2	+											Homo sapiens cDNA clone IMAGE:6614812, partial cds.																		TGGAAGTAAGAAAAAAAAACT	0.328													4	2	---	---	---	---	
MORC1	27136	broad.mit.edu	37	3	108750374	108750374	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108750374delC	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244	Q86VD1	MORC1_HUMAN	MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8						TGAAACTGAGCCAACACTTTG	0.299													3	3	---	---	---	---	
CCDC52	152185	broad.mit.edu	37	3	113219364	113219364	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113219364delA	uc003eag.3	-						CCDC52_uc003eaf.3_Intron|CCDC52_uc011bie.1_Intron|CCDC52_uc003eai.1_Intron	NM_144718	NP_653319	Q8N0Z3	SPICE_HUMAN	coiled-coil domain containing 52						cell division|mitosis	centriole|spindle	protein binding				0						ggttatgttgaaaaaaaaaag	0.000													4	2	---	---	---	---	
SIDT1	54847	broad.mit.edu	37	3	113299128	113299128	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113299128delA	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						CCCTTAATTTAAAGGGGGCAG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115060219	115060219	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115060219delA								ZBTB20 (194092 upstream) : GAP43 (281932 downstream)																							TATGACCAAGAAAAAAAAAGC	0.403													4	2	---	---	---	---	
GAP43	2596	broad.mit.edu	37	3	115342811	115342811	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115342811delT	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		CTAGAAATAATTTTTTTTTTT	0.423													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116986406	116986406	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116986406delT								LOC285194 (550521 upstream) : None (None downstream)																							tattgatgggtgggctgctgc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	120610102	120610103	+	IGR	INS	-	TTTG	TTTG	rs147605121	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120610102_120610103insTTTG								GTF2E1 (108187 upstream) : STXBP5L (16947 downstream)																							agtcaagataatttgttttgtt	0.000													4	2	---	---	---	---	
STXBP5L	9515	broad.mit.edu	37	3	120872830	120872830	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120872830delT	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		CATGGGAATATTTAGCCAGTT	0.378													4	2	---	---	---	---	
POLQ	10721	broad.mit.edu	37	3	121168730	121168730	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121168730delA	uc003eee.3	-						POLQ_uc003eed.2_Intron	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta						DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		ACTTAACTGGAAAAAAAAATC	0.373								DNA_polymerases_(catalytic_subunits)					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	121350075	121350075	+	IGR	DEL	A	-	-	rs111509389		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121350075delA								FBXO40 (936 upstream) : HCLS1 (172 downstream)																							actccttctcaaaaaaaaaaa	0.209													4	2	---	---	---	---	
MYLK	4638	broad.mit.edu	37	3	123365361	123365362	+	Intron	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123365361_123365362delTG	uc003ego.2	-						MYLK_uc010hrr.2_Intron|MYLK_uc011bjv.1_Intron|MYLK_uc011bjw.1_Intron|MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CTTGACtgtatgtgtgtgtgtg	0.361													4	2	---	---	---	---	
ITGB5	3693	broad.mit.edu	37	3	124494235	124494236	+	Intron	DEL	GT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124494235_124494236delGT	uc003eho.2	-						ITGB5_uc010hrx.2_Intron|ITGB5_uc003ehp.1_RNA	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(2)	2				GBM - Glioblastoma multiforme(114;0.163)		gtgtgttggagtgtgtgtgtga	0.183													4	2	---	---	---	---	
ZXDC	79364	broad.mit.edu	37	3	126193347	126193347	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126193347delA	uc003eiv.2	-						ZXDC_uc010hsh.2_Intron|ZXDC_uc003eix.2_Intron	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1						positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)		TGCAAAAGGCAAAAAAAGCCA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	129350800	129350800	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129350800delT								PLXND1 (25218 upstream) : TMCC1 (15837 downstream)																							ACCTGTTCTATTTTTTTTTTC	0.532													6	4	---	---	---	---	
TMCC1	23023	broad.mit.edu	37	3	129387093	129387093	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129387093delT	uc003emz.3	-						TMCC1_uc003emy.3_Intron|TMCC1_uc011blc.1_Intron|TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1						GTTTTAAAAATTTTTTTAACT	0.189													4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140079012	140079012	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140079012delT	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						CCTGTAATCGTTCCTTTTTTC	0.244										HNSCC(16;0.037)			4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140242934	140242934	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140242934delG	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						agaaagagtaggggaattcaa	0.184										HNSCC(16;0.037)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145024365	145024365	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145024365delC								None (None upstream) : PLOD2 (762863 downstream)																							aataaaatgacccacaaatta	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145403257	145403258	+	IGR	INS	-	TT	TT	rs111771423		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145403257_145403258insTT								None (None upstream) : PLOD2 (383970 downstream)																							TCTTCTCACTCTTTTTTTTTTT	0.396													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	146426149	146426149	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146426149delG								PLSCR5 (102146 upstream) : ZIC4 (677688 downstream)																							TTTTATTTGTGGGGATCATGA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149929288	149929288	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149929288delA								PFN2 (240547 upstream) : TSC22D2 (197500 downstream)																							tcatgacaggaaagggggctc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157356814	157356815	+	IGR	INS	-	A	A	rs151061402	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157356814_157356815insA								C3orf55 (37795 upstream) : SHOX2 (456986 downstream)																							ggaatagatgcaaaaaaaaaat	0.030													4	2	---	---	---	---	
RSRC1	51319	broad.mit.edu	37	3	158150286	158150286	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158150286delT	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			TGGTGTACTATTTTTTTTCCT	0.368													4	2	---	---	---	---	
KPNA4	3840	broad.mit.edu	37	3	160220152	160220152	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160220152delT	uc003fdn.2	-							NM_002268	NP_002259	O00629	IMA4_HUMAN	karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			TTATAGAAGGttttttttttc	0.174													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163200338	163200338	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163200338delT								None (None upstream) : MIR1263 (688921 downstream)																							tctatagagcttttttttgct	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165716621	165716621	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165716621delT								BCHE (161368 upstream) : None (None downstream)																							ctgtattccctttccctttgg	0.000													4	2	---	---	---	---	
SERPINI1	5274	broad.mit.edu	37	3	167489411	167489411	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167489411delT	uc003ffa.3	+						SERPINI1_uc003ffb.3_Intron	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor						central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1						CCTGTTTAACTTTTTTTTTAG	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	169467007	169467007	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169467007delT								MECOM (85444 upstream) : TERC (15391 downstream)																							TGCTTATCTATTTTTTGCTGT	0.443													4	2	---	---	---	---	
PHC3	80012	broad.mit.edu	37	3	169867246	169867246	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169867246delT	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron|PHC3_uc011bpr.1_Intron|PHC3_uc003fgm.2_Intron|PHC3_uc003fgo.1_Intron	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			ATCAGGGCAAttttttttttt	0.209													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	170668995	170668995	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170668995delC								EIF5A2 (42569 upstream) : SLC2A2 (45142 downstream)																							ATTTGATGGTCCTAAAGGCAG	0.418													2	4	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	170950131	170950131	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170950131delA	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)			TGTATGAATGAAAAAAAAAAA	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	172314182	172314184	+	5'Flank	DEL	TCT	-	-	rs138385156		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172314182_172314184delTCT	uc003fif.1	-											Homo sapiens cDNA FLJ45650 fis, clone CTONG2009923.																		TAAACCAGGATCTTCTTCAGCCT	0.443													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178147431	178147431	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178147431delA								None (None upstream) : KCNMB2 (106793 downstream)																							ACACTAAGTTAAAAATCTCCA	0.259													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188413424	188413425	+	Intron	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188413424_188413425insG	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		aagacgctaaaggggggaacaa	0.173			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
WDR53	348793	broad.mit.edu	37	3	196288493	196288494	+	Intron	INS	-	A	A	rs140815446		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196288493_196288494insA	uc003fwt.2	-							NM_182627	NP_872433	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53											breast(1)|skin(1)	2	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		ctcaattaattaaaaaaaaaaa	0.297													6	3	---	---	---	---	
MFI2	4241	broad.mit.edu	37	3	196741706	196741706	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196741706delA	uc003fxk.3	-							NM_005929	NP_005920	P08582	TRFM_HUMAN	melanoma-associated antigen p97 isoform 1						cellular iron ion homeostasis|iron ion transport	anchored to membrane|extracellular region|integral to plasma membrane	ferric iron binding|protein binding				0	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		atggtatgttaattattatcc	0.005													4	2	---	---	---	---	
FAM193A	8603	broad.mit.edu	37	4	2678239	2678239	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2678239delT	uc010icl.2	+						FAM193A_uc010ick.2_Intron|FAM193A_uc003gfd.2_Intron|FAM193A_uc011bvm.1_Intron|FAM193A_uc011bvn.1_Intron|FAM193A_uc011bvo.1_Intron|FAM193A_uc010icm.2_Intron|FAM193A_uc003gfe.2_Intron	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603											ovary(3)	3						ttgaatcaggtttgttgttgt	0.000													4	2	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3101357	3101358	+	Intron	INS	-	TG	TG	rs10665872		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3101357_3101358insTG	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)		TGGAGGTGCTCTTGTATGGTTT	0.475													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3613084	3613085	+	IGR	INS	-	T	T	rs142256473	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3613084_3613085insT								LRPAP1 (78860 upstream) : ADRA2C (154990 downstream)																							TCACACTGTCCGCCACTCCCCT	0.530													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3621819	3621820	+	IGR	INS	-	G	G	rs141462966	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3621819_3621820insG								LRPAP1 (87595 upstream) : ADRA2C (146255 downstream)																							actaacggatagggttcaatgt	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3680482	3680496	+	5'Flank	DEL	GTGAGGAGAGAGGAG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3680482_3680496delGTGAGGAGAGAGGAG	uc003ghl.2	-											Homo sapiens cDNA clone IMAGE:5302720.																		gagatgaggagtgaggagagaggaggtgaggaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4893268	4893269	+	IGR	DEL	GT	-	-	rs141953709		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4893268_4893269delGT								MSX1 (27610 upstream) : CYTL1 (123047 downstream)																							TCTTCCTAGGgtgtgtgtgtgt	0.272													6	4	---	---	---	---	
STK32B	55351	broad.mit.edu	37	4	5127042	5127042	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5127042delT	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						agctgctgaatttttgatcat	0.134													4	2	---	---	---	---	
STK32B	55351	broad.mit.edu	37	4	5301478	5301478	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5301478delT	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						ttatccattctttttttggct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12087459	12087460	+	IGR	INS	-	T	T	rs142617370	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12087459_12087460insT								HS3ST1 (656922 upstream) : None (None downstream)																							TACAGACTAACTTTAGAAAGGA	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14069315	14069316	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14069315_14069316insA								BOD1L (439987 upstream) : CPEB2 (936206 downstream)																							GAAAGAAGGAGAAAAAAAAACA	0.317													5	3	---	---	---	---	
C1QTNF7	114905	broad.mit.edu	37	4	15373740	15373740	+	5'Flank	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15373740delA	uc011bxb.1	+						C1QTNF7_uc003gno.2_Intron	NM_001135171	NP_001128643	Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7							collagen					0						TCAGTGAGGGAAAAAAAAAGG	0.169													4	2	---	---	---	---	
PROM1	8842	broad.mit.edu	37	4	16086300	16086300	+	5'Flank	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16086300delA	uc003gop.2	-						PROM1_uc003goq.3_5'Flank	NM_001145847	NP_001139319	O43490	PROM1_HUMAN	prominin 1 isoform 2						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7						TCCGGCAGGCAAAAAAAAGAC	0.279													4	2	---	---	---	---	
NCAPG	64151	broad.mit.edu	37	4	17817588	17817588	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17817588delA	uc003gpp.2	+						NCAPG_uc011bxj.1_Intron	NM_022346	NP_071741	Q9BPX3	CND3_HUMAN	chromosome condensation protein G						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	protein binding			large_intestine(1)	1				STAD - Stomach adenocarcinoma(129;0.18)		TCTCTGACTTAAAAAAAAAAT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	19876588	19876588	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19876588delG								None (None upstream) : SLIT2 (378647 downstream)																							TTGCCATGGAGAAAGAAGAAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	22928264	22928264	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22928264delA								GBA3 (107073 upstream) : PPARGC1A (865381 downstream)																							ataatggggtaaatagttacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	23286146	23286146	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23286146delT								GBA3 (464955 upstream) : PPARGC1A (507499 downstream)																							taaatgtttatttatattatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24263422	24263422	+	IGR	DEL	T	-	-	rs141280550		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24263422delT								PPARGC1A (371722 upstream) : MIR573 (258393 downstream)																							AGCATGTCAATTTTTTTTCCT	0.368													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24407256	24407256	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24407256delG								PPARGC1A (515556 upstream) : MIR573 (114559 downstream)																							CATCACGGCTGGGGATTCTGT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26129161	26129161	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26129161delA								C4orf52 (197661 upstream) : RBPJ (192171 downstream)																							ATATACCAATAAACAATTGTA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27767465	27767465	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27767465delG								STIM2 (741657 upstream) : None (None downstream)																							gaaaaatcctgggggaagagg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	29114584	29114584	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29114584delT								None (None upstream) : None (None downstream)																							AGCCTCCTCATTTTTTTTTTC	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	31367840	31367840	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31367840delC								PCDH7 (219419 upstream) : None (None downstream)																							ACGTTGTAGTCACACCAAATG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	34833113	34833114	+	IGR	INS	-	TATC	TATC	rs10034283	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34833113_34833114insTATC								None (None upstream) : None (None downstream)																							atgtatgtatgtatctatctat	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	35925449	35925449	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35925449delT								None (None upstream) : ARAP2 (24395 downstream)																							tgcatttgggttattttataa	0.114													4	2	---	---	---	---	
ARAP2	116984	broad.mit.edu	37	4	36208475	36208475	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36208475delA	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						TCTCATGGCCAAAAAAAAAGT	0.308													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	36774173	36774173	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36774173delT								MIR1255B-1 (346123 upstream) : KIAA1239 (472517 downstream)																							AGTACTTATCTCCAAGAGTAC	0.368													4	2	---	---	---	---	
TBC1D1	23216	broad.mit.edu	37	4	38063890	38063890	+	Intron	DEL	T	-	-	rs77580901		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38063890delT	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron|TBC1D1_uc011byf.1_Intron	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1						AGTGTGCTTGTTTTTTTTTTT	0.398											OREG0016151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
FAM114A1	92689	broad.mit.edu	37	4	38871341	38871341	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38871341delT	uc003gtn.2	+						FAM114A1_uc011byh.1_Intron|FAM114A1_uc011byg.1_Intron	NM_138389	NP_612398	Q8IWE2	NXP20_HUMAN	hypothetical protein LOC92689							cytoplasm				ovary(1)	1						ACTGTTTTTGTTTTTTTTTTT	0.294													3	4	---	---	---	---	
GRXCR1	389207	broad.mit.edu	37	4	42924678	42924678	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42924678delG	uc003gwt.2	+							NM_001080476	NP_001073945	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1						cell redox homeostasis|inner ear receptor stereocilium organization|sensory perception of sound|vestibular receptor cell development	kinocilium|stereocilium	electron carrier activity|protein disulfide oxidoreductase activity			ovary(1)	1						CCAGTTCTGAGGGAGCAGTAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	44100750	44100751	+	IGR	DEL	TT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44100750_44100751delTT								None (None upstream) : KCTD8 (75171 downstream)																							tgcttttggctttttttttttt	0.000													3	4	---	---	---	---	
TEC	7006	broad.mit.edu	37	4	48178432	48178432	+	Intron	DEL	C	-	-	rs35859358		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48178432delC	uc003gxz.2	-							NM_003215	NP_003206	P42680	TEC_HUMAN	tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9						TTCTGTCCTGCCCCCCCAAAA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49228998	49228999	+	IGR	DEL	TT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49228998_49228999delTT								CWH43 (164905 upstream) : None (None downstream)																							ctgcttgtcatttttaaatata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49268345	49268346	+	IGR	INS	-	A	A	rs4694975		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49268345_49268346insA								CWH43 (204252 upstream) : None (None downstream)																							ctactaaaaataaaaaaaatta	0.000													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54347748	54347748	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54347748delT	uc003haa.2	+						LNX1_uc003haf.3_Intron|LNX1_uc003hag.3_Intron|LNX1_uc003hah.3_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	AATATGGGACTTTGGGCTTTT	0.398			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54927909	54927909	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54927909delA	uc003haa.2	+						CHIC2_uc003haj.1_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	GAGCCATGTTAAAAAAAAAAG	0.363			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			7	4	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	55073103	55073103	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55073103delA	uc003haa.2	+							NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	CAACAATGATAAAAAAAAATC	0.189			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58567958	58567958	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58567958delT								IGFBP7 (591419 upstream) : None (None downstream)																							tttttcatactttttggctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	59258021	59258021	+	IGR	DEL	A	-	-	rs142054692		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59258021delA								None (None upstream) : None (None downstream)																							gacacaaattaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	59355597	59355598	+	IGR	DEL	TT	-	-	rs56183559		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59355597_59355598delTT								None (None upstream) : None (None downstream)																							agggagactattaatataacta	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	59355600	59355603	+	IGR	DEL	ATAT	-	-	rs56036563		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59355600_59355603delATAT								None (None upstream) : None (None downstream)																							gagactattaatataactattggg	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	59679064	59679064	+	IGR	DEL	A	-	-	rs71797288		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59679064delA								None (None upstream) : None (None downstream)																							CAATCCATTTAAAAAAAAAAT	0.353													5	3	---	---	---	---	
EPHA5	2044	broad.mit.edu	37	4	66405793	66405799	+	Intron	DEL	CAGCACC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66405793_66405799delCAGCACC	uc003hcy.2	-						EPHA5_uc003hcx.2_Intron|EPHA5_uc003hcz.2_Intron|EPHA5_uc011cah.1_Intron|EPHA5_uc011cai.1_Intron|EPHA5_uc003hda.2_Intron	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor						cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						CTGACAAAGTCAGCACCATGCATGAAA	0.309										TSP Lung(17;0.13)			4	2	---	---	---	---	
EPHA5	2044	broad.mit.edu	37	4	66486112	66486112	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66486112delA	uc003hcy.2	-						EPHA5_uc003hcx.2_Intron|EPHA5_uc003hcz.2_Intron|EPHA5_uc011cah.1_Intron|EPHA5_uc011cai.1_Intron|EPHA5_uc003hda.2_Intron	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor						cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						AGATTCCTATAAAAAATGTCT	0.333										TSP Lung(17;0.13)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	66700768	66700770	+	IGR	DEL	GGT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66700768_66700770delGGT								EPHA5 (165115 upstream) : MIR1269 (441772 downstream)																							gctttgggcaggtatccattcct	0.005													4	2	---	---	---	---	
UGT2A3	79799	broad.mit.edu	37	4	69818816	69818817	+	5'Flank	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69818816_69818817insT	uc003hef.2	-						UGT2A3_uc010ihp.1_5'Flank	NM_024743	NP_079019	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family,							integral to membrane	glucuronosyltransferase activity			ovary(1)|skin(1)	2						accctcccccctttctgaattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69863502	69863503	+	IGR	INS	-	CGGA	CGGA	rs78806655	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69863502_69863503insCGGA								UGT2A3 (45993 upstream) : UGT2B7 (98690 downstream)																							aatggatgatttggatgttagc	0.045													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69863503	69863504	+	IGR	INS	-	GATTC	GATTC	rs141141985	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69863503_69863504insGATTC								UGT2A3 (45994 upstream) : UGT2B7 (98689 downstream)																							atggatgatttggatgttagct	0.045													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	70885583	70885584	+	IGR	INS	-	A	A	rs144774528	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70885583_70885584insA								STATH (17410 upstream) : HTN3 (8546 downstream)																							taaattagtagggaaaaaatac	0.104													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	72716952	72716952	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72716952delT								GC (47194 upstream) : NPFFR2 (180569 downstream)																							gttgagttcctttttggatag	0.000													4	2	---	---	---	---	
ADAMTS3	9508	broad.mit.edu	37	4	73217720	73217721	+	Intron	INS	-	A	A	rs141731622	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73217720_73217721insA	uc003hgk.1	-							NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ACAGCTCACTCAAAAAAAAATC	0.322													4	2	---	---	---	---	
ANKRD17	26057	broad.mit.edu	37	4	73963572	73963572	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73963572delA	uc003hgp.2	-						ANKRD17_uc003hgo.2_Intron|ANKRD17_uc003hgq.2_Intron|ANKRD17_uc003hgr.2_Intron	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTTAACAACCAAAAAAAAAAG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	75632211	75632212	+	IGR	INS	-	A	A	rs145561201	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75632211_75632212insA								AREG (151580 upstream) : BTC (39236 downstream)																							tatgcagccataaaaaaatggg	0.015													2	4	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77528833	77528833	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77528833delT	uc011cbx.1	+						uc011cby.1_Intron	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			GAGGGGTGCATTTTTTTTTTC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	78359891	78359892	+	IGR	INS	-	TG	TG	rs57916280		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78359891_78359892insTG								CCNG2 (268681 upstream) : CXCL13 (73015 downstream)																							acattcacacacgcactgtttc	0.000													5	3	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79176141	79176141	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79176141delG	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc003hky.1_Intron|FRAS1_uc003hkz.2_5'Flank	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						GAGTGGAGGAGCTGGTAGCTG	0.388													4	5	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79188782	79188783	+	Intron	INS	-	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79188782_79188783insC	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc003hky.1_Intron|FRAS1_uc003hkz.2_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						GCTCAGAACAGCCCCCTGGATC	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	80220993	80220993	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80220993delA	uc003hlr.1	+											Homo sapiens full length insert cDNA clone YY75G10.																		CTGCTTCCTCAAGAGATGGTA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	81129242	81129243	+	IGR	DEL	CA	-	-	rs71990062		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81129242_81129243delCA								PRDM8 (3762 upstream) : FGF5 (58499 downstream)																							acacacacaccacacacacaca	0.000													4	2	---	---	---	---	
FAM175A	84142	broad.mit.edu	37	4	84391083	84391083	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84391083delA	uc003hou.2	-						FAM175A_uc003hot.2_5'Flank|FAM175A_uc003hov.2_Intron	NM_139076	NP_620775	Q6UWZ7	F175A_HUMAN	coiled-coil domain containing 98						chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|response to ionizing radiation	BRCA1-A complex	polyubiquitin binding			kidney(1)	1						TCAATCAATTAAAAAAAAAGT	0.294													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84597836	84597837	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84597836_84597837delTG								AGPAT9 (70811 upstream) : NKX6-1 (816599 downstream)																							TGTTTGTGTTTGTGTGTGTGTG	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84812307	84812307	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84812307delA	uc010ikd.1	-											Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																		cttgtgggacaaaggtatttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84940860	84940860	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84940860delA	uc010ikd.1	-						uc003hoz.1_Intron					Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																		TGCCTGGAGCAAAAAAAAAAT	0.388													5	5	---	---	---	---	
ARHGAP24	83478	broad.mit.edu	37	4	86707802	86707803	+	Intron	INS	-	AC	AC	rs149213511	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86707802_86707803insAC	uc003hpk.2	+						ARHGAP24_uc003hpj.2_Intron|ARHGAP24_uc003hpl.2_Intron	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		ATCTCTTATGAACACACACACA	0.361													4	2	---	---	---	---	
MAPK10	5602	broad.mit.edu	37	4	87152464	87152464	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87152464delA	uc003hpq.2	-						MAPK10_uc010ikg.2_Intron|MAPK10_uc003hpr.2_Intron|MAPK10_uc003hps.2_Intron|MAPK10_uc003hpt.2_Intron|MAPK10_uc003hpu.2_Intron|MAPK10_uc003hpv.2_Intron|MAPK10_uc010ikh.1_Intron	NM_138982	NP_620448	P53779	MK10_HUMAN	mitogen-activated protein kinase 10 isoform 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		attcacctttaactgtgcatc	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90396097	90396097	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90396097delA								GPRIN3 (166936 upstream) : SNCA (249154 downstream)																							aggtcaggacaaacaccTTGT	0.149													4	2	---	---	---	---	
TMSL3	7117	broad.mit.edu	37	4	91759711	91759711	+	3'UTR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91759711delA	uc003hsy.2	-	1					FAM190A_uc003hsv.3_Intron|FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_183049	NP_898870			thymosin-like 3												0		all_cancers(2;6.48e-24)|all_epithelial(2;3.86e-25)|Colorectal(2;8.52e-12)|all_lung(2;3.73e-07)|Lung NSC(2;7.99e-07)|Renal(2;0.0243)|Hepatocellular(203;0.0411)		Epithelial(2;5.28e-11)|OV - Ovarian serous cystadenocarcinoma(123;8.9e-10)|all cancers(2;3.21e-09)|STAD - Stomach adenocarcinoma(1;0.0201)		TCATTTGAACAAAAAAAAAAT	0.264													2	4	---	---	---	---	
GRID2	2895	broad.mit.edu	37	4	94607069	94607069	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94607069delA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	ccttttctctaaaacacaggg	0.184													4	2	---	---	---	---	
EMCN	51705	broad.mit.edu	37	4	101346509	101346509	+	Intron	DEL	C	-	-	rs11304866		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101346509delC	uc003hvr.2	-						EMCN_uc011cel.1_Intron|EMCN_uc011cem.1_Intron	NM_016242	NP_057326	Q9ULC0	MUCEN_HUMAN	endomucin isoform 1							extracellular region|integral to membrane|plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		ATGCTCAGAGCCTGATGATCT	0.358													4	3	---	---	---	---	
CENPE	1062	broad.mit.edu	37	4	104056913	104056913	+	Intron	DEL	A	-	-	rs66521536		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104056913delA	uc003hxb.1	-						CENPE_uc003hxc.1_Intron	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E						blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		ccccatctACAAAAAGAACTC	0.085													3	3	---	---	---	---	
NPNT	255743	broad.mit.edu	37	4	106890536	106890536	+	3'UTR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106890536delT	uc003hya.2	+	12					NPNT_uc011cfc.1_3'UTR|NPNT_uc011cfd.1_3'UTR|NPNT_uc011cfe.1_3'UTR|NPNT_uc010ilt.1_Intron|NPNT_uc011cff.1_3'UTR|NPNT_uc010ilu.1_Intron	NM_001033047	NP_001028219	Q6UXI9	NPNT_HUMAN	nephronectin precursor						cell differentiation	membrane	calcium ion binding			skin(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		GGCTATGATGTTATGTGTTCG	0.388													4	2	---	---	---	---	
COL25A1	84570	broad.mit.edu	37	4	109953553	109953553	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109953553delA	uc003hze.1	-						COL25A1_uc003hzg.2_Intron	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		AATAAGTCCTAAACTCTTCAA	0.333													4	2	---	---	---	---	
ELOVL6	79071	broad.mit.edu	37	4	111033297	111033298	+	Intron	INS	-	TT	TT	rs143534446	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111033297_111033298insTT	uc003hzz.2	-						ELOVL6_uc003iaa.2_Intron	NM_001130721	NP_001124193	Q9H5J4	ELOV6_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, saturated fatty acid|long-chain fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process		fatty acid elongase activity|protein binding			haematopoietic_and_lymphoid_tissue(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		TACTGAAAGTCTGAGCTGGGAA	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111708360	111708360	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111708360delG								PITX2 (145243 upstream) : MIR297 (73378 downstream)																							GGGGTGATGAGGAGGAGTTAA	0.363													4	2	---	---	---	---	
C4orf21	55345	broad.mit.edu	37	4	113519249	113519250	+	Intron	INS	-	G	G	rs148084379	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113519249_113519250insG	uc003iau.2	-						C4orf21_uc003iaw.2_Intron	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like							integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		aaaggagacatggtgttcaaga	0.000													3	3	---	---	---	---	
SEC24D	9871	broad.mit.edu	37	4	119735952	119735952	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119735952delA	uc003ici.3	-						SEC24D_uc003icj.3_Intron|SEC24D_uc003icl.2_Intron|SEC24D_uc010imz.1_Intron|SEC24D_uc011cgg.1_Intron	NM_014822	NP_055637	O94855	SC24D_HUMAN	Sec24-related protein D						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0						AAAAAAAAAGAAAAAAAAAAT	0.368													6	3	---	---	---	---	
LOC285419	285419	broad.mit.edu	37	4	124758074	124758074	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124758074delT	uc011cgn.1	+						LOC285419_uc003ifd.2_Intron	NR_027105				Homo sapiens mRNA; cDNA DKFZp686P12109 (from clone DKFZp686P12109).												0						CCGGGATGGCTTTTCATTTTC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	132462957	132462957	+	IGR	DEL	A	-	-	rs71593027		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132462957delA								None (None upstream) : None (None downstream)																							AGTGAGTTAGAAAATGCCTGA	0.388													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	137706804	137706804	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137706804delT								None (None upstream) : PCDH18 (733272 downstream)																							ccttcctcccttTTATCTTCT	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	142315837	142315837	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142315837delT								ZNF330 (159989 upstream) : IL15 (241917 downstream)																							ttgctttctgttttttttttg	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	142393258	142393259	+	IGR	INS	-	AA	AA	rs145252708	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142393258_142393259insAA								ZNF330 (237410 upstream) : IL15 (164495 downstream)																							ctggatattggaaaaaaaaaac	0.000													4	2	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143109147	143109147	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143109147delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					tatatgtgggaaaaaaagact	0.050													4	2	---	---	---	---	
GAB1	2549	broad.mit.edu	37	4	144282274	144282274	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144282274delT	uc003ije.2	+						GAB1_uc003ijd.2_Intron	NM_002039	NP_002030	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1 isoform b						cell proliferation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			breast(2)|lung(1)|skin(1)	4	all_hematologic(180;0.158)					TGGGAAGGAGTTTTTTTTTTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	150177652	150177652	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150177652delA								NR3C2 (814009 upstream) : DCLK2 (822428 downstream)																							cagcatttagaaaaaaaaaag	0.070													2	4	---	---	---	---	
SH3D19	152503	broad.mit.edu	37	4	152059254	152059254	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152059254delG	uc010ipl.1	-						SH3D19_uc003imb.2_Intron|SH3D19_uc003imc.2_Intron|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)				GGAAATGGTTGAAAAAAACAC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152709545	152709546	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152709545_152709546insA								PET112L (27399 upstream) : FBXW7 (532865 downstream)																							tttcttggttcaAAAAAAAAAC	0.168													4	2	---	---	---	---	
FBXW7	55294	broad.mit.edu	37	4	153259791	153259791	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153259791delA	uc003ims.2	-						FBXW7_uc011cii.1_Intron|FBXW7_uc003imt.2_Intron|FBXW7_uc011cih.1_Intron|FBXW7_uc003imq.2_Intron|FBXW7_uc003imr.2_Intron	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform						interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				GAGTTCCTTTAAATGACATCA	0.323			Mis|N|D|F		colorectal|endometrial|T-ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154353540	154353540	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154353540delT								MND1 (17297 upstream) : KIAA0922 (33958 downstream)																							GAGGGGTGGGTTTTCAGTCCA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	156186507	156186507	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156186507delT								NPY2R (48281 upstream) : MAP9 (77307 downstream)																							CCCAATGCAGTTTTTTttttc	0.035													3	3	---	---	---	---	
RXFP1	59350	broad.mit.edu	37	4	159532461	159532461	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159532461delT	uc003ipz.2	+						RXFP1_uc010iqj.1_Intron|RXFP1_uc011cja.1_Intron|RXFP1_uc010iqo.2_Intron|RXFP1_uc011cjb.1_Intron|RXFP1_uc010iqk.2_Intron|RXFP1_uc011cjc.1_Intron|RXFP1_uc011cjd.1_Intron|RXFP1_uc010iql.2_Intron|RXFP1_uc011cje.1_Intron|RXFP1_uc010iqm.2_Intron|RXFP1_uc011cjf.1_Intron|RXFP1_uc010iqn.2_Intron	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1							integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		GAGACATGAGTGAACATGGCA	0.219													4	2	---	---	---	---	
RXFP1	59350	broad.mit.edu	37	4	159554322	159554322	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159554322delA	uc003ipz.2	+						RXFP1_uc010iqj.1_Intron|RXFP1_uc011cja.1_Intron|RXFP1_uc010iqo.2_Intron|RXFP1_uc011cjb.1_Intron|RXFP1_uc010iqk.2_Intron|RXFP1_uc011cjc.1_Intron|RXFP1_uc011cjd.1_Intron|RXFP1_uc010iql.2_Intron|RXFP1_uc011cje.1_Intron|RXFP1_uc010iqm.2_Intron|RXFP1_uc011cjf.1_Intron|RXFP1_uc010iqn.2_Intron	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1							integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		actcggtctcaaaaaaaaaaG	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	163823062	163823062	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163823062delT								FSTL5 (737876 upstream) : NAF1 (224798 downstream)																							ATTTAGTAGATTTTTTTTTAA	0.393													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164794540	164794541	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164794540_164794541insT	uc003iqs.1	-							NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				AACCTTGGCCATTTTCTCTCAT	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	168741255	168741256	+	IGR	DEL	TG	-	-	rs4040526		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168741255_168741256delTG								SPOCK3 (585514 upstream) : ANXA10 (272451 downstream)																							ttcatgtcactgtgtgtgtgtg	0.000													4	2	---	---	---	---	
CLCN3	1182	broad.mit.edu	37	4	170633491	170633491	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170633491delT	uc003isi.2	+						CLCN3_uc003ish.2_Intron|CLCN3_uc011cjz.1_Intron|CLCN3_uc011cka.1_Intron|CLCN3_uc003isj.1_Intron	NM_001829	NP_001820	P51790	CLCN3_HUMAN	chloride channel 3 isoform b						endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		TTGTCTAGCATTTTTTTTTTA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	170800583	170800584	+	IGR	DEL	TA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170800583_170800584delTA								C4orf27 (121490 upstream) : MFAP3L (107166 downstream)																							TTTTTTTTTTTAAATAACTTTT	0.317													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	171287041	171287043	+	IGR	DEL	TGG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171287041_171287043delTGG								AADAT (275669 upstream) : None (None downstream)																							acagattctttggtgaaggatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	177533920	177533921	+	IGR	INS	-	G	G	rs137964766		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177533920_177533921insG								SPCS3 (280526 upstream) : VEGFC (70770 downstream)																							GTGATAATTAATGATAGAACAT	0.351													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	178069498	178069498	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178069498delA								VEGFC (355603 upstream) : NEIL3 (161493 downstream)																							ataatacaggaaaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179844467	179844467	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179844467delA								LOC285501 (932564 upstream) : None (None downstream)																							ATCACATATCAGCGGGCCAAG	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180102898	180102898	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180102898delT								None (None upstream) : None (None downstream)																							ggaaaaatgctttttatgcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180472244	180472244	+	IGR	DEL	G	-	-	rs140175358		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180472244delG								None (None upstream) : None (None downstream)																							GAGGGCCAGAGGGGGAAACAG	0.552													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180512261	180512261	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180512261delT								None (None upstream) : None (None downstream)																							ccactacaCCTTCTCAAGCTC	0.224													4	2	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183501642	183501642	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183501642delT	uc003ivd.1	+							NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		TTCACAAAGATTTTTTTTTTC	0.318													2	4	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183712455	183712455	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183712455delC	uc003ivd.1	+							NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		TCCACATCCTCCCTGTGCCAA	0.532													4	2	---	---	---	---	
KIAA1430	57587	broad.mit.edu	37	4	186123193	186123195	+	Intron	DEL	CCC	-	-	rs66669637		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186123193_186123195delCCC	uc003ixf.3	-						KIAA1430_uc003ixg.2_Intron	NM_020827	NP_065878	Q9P2B7	K1430_HUMAN	hypothetical protein LOC57587												0		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		ttttgtttttccccccatcccct	0.054													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	186463016	186463017	+	IGR	DEL	GA	-	-	rs7694803	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186463016_186463017delGA								PDLIM3 (6304 upstream) : SORBS2 (43582 downstream)																							gtgtgtgtgtgagagagagaga	0.371													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190561493	190561493	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190561493delA								None (None upstream) : FRG1 (300481 downstream)																							ccttcttcacaaaggggtagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190568016	190568017	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190568016_190568017insA								None (None upstream) : FRG1 (293957 downstream)																							aaaagcaaatgaaaaaaaaTTA	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190593441	190593442	+	IGR	INS	-	AGAT	AGAT	rs146587550		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190593441_190593442insAGAT								None (None upstream) : FRG1 (268532 downstream)																							taaatgttgacagaattcacgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190600955	190600956	+	IGR	DEL	TT	-	-	rs138908875		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190600955_190600956delTT								None (None upstream) : FRG1 (261018 downstream)																							ATACAAATACTTTTTTGTCTTA	0.054													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	773832	773832	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:773832delG								TPPP (80322 upstream) : ZDHHC11 (21888 downstream)																							CAAACCCCACGGGAGCCCAAG	0.697													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2083128	2083129	+	IGR	DEL	TG	-	-	rs141330561		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2083128_2083129delTG								IRX4 (200248 upstream) : IRX2 (663152 downstream)																							TCTCGTTCTCTGTGTGTGTGTA	0.406													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4420509	4420510	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4420509_4420510delTG								IRX1 (818993 upstream) : LOC340094 (613962 downstream)																							tgtatatgtatgtgtgtgtgtg	0.238													4	2	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7805557	7805558	+	Intron	DEL	GT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7805557_7805558delGT	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron|ADCY2_uc010itm.1_Intron	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						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	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						AGATTTTCTCGTGTGTGTGTGT	0.332													4	2	---	---	---	---	
FASTKD3	79072	broad.mit.edu	37	5	7868313	7868314	+	Intron	INS	-	A	A	rs71591746		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7868313_7868314insA	uc003jeb.2	-						FASTKD3_uc011cmp.1_5'Flank|FASTKD3_uc003jec.2_Intron|MTRR_uc010itn.1_5'Flank|MTRR_uc003jee.3_5'Flank|MTRR_uc003jed.2_5'Flank|MTRR_uc003jef.3_5'Flank|MTRR_uc003jeg.3_5'Flank|MTRR_uc010ito.2_5'Flank	NM_024091	NP_076996	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3						apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|breast(1)|pancreas(1)	4						CGAGTATCTGGaaaaaaaaaaa	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10777415	10777416	+	IGR	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10777415_10777416delCA								DAP (16028 upstream) : CTNND2 (194536 downstream)																							taaacacaggcacacacacaca	0.134													4	2	---	---	---	---	
BASP1	10409	broad.mit.edu	37	5	17256994	17256994	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17256994delA	uc003jfx.2	+							NM_006317	NP_006308	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein						glomerular visceral epithelial cell differentiation|negative regulation of transcription, DNA-dependent	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	protein domain specific binding|transcription corepressor activity|transcription regulatory region DNA binding				0						CTGTGGGTGGAAAAAAAAATA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17806878	17806879	+	IGR	INS	-	TT	TT	rs57898485		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17806878_17806879insTT								BASP1 (529943 upstream) : None (None downstream)																							ACCAAGCCTTGTTTTTTTTTTT	0.361													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22303162	22303162	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22303162delA	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						AGCTAGAGGCAAAAAAAATGT	0.294										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27159652	27159653	+	IGR	DEL	AG	-	-	rs35238235		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27159652_27159653delAG								CDH9 (120963 upstream) : None (None downstream)																							ccaaatagaaagagtctctcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27414009	27414010	+	IGR	INS	-	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27414009_27414010insC								CDH9 (375320 upstream) : None (None downstream)																							cctcttcctttccccaaagccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30852523	30852525	+	IGR	DEL	TGT	-	-	rs142636738	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30852523_30852525delTGT								None (None upstream) : CDH6 (341271 downstream)																							tgtgtgtgtgtgttgttgttgtt	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30919191	30919192	+	IGR	INS	-	TTCTC	TTCTC	rs147622060		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30919191_30919192insTTCTC								None (None upstream) : CDH6 (274604 downstream)																							ATTCTTTTCTTCTCTGAAtcac	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31386111	31386112	+	IGR	INS	-	A	A	rs147406738	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31386111_31386112insA								CDH6 (60874 upstream) : RNASEN (14490 downstream)																							aactagtcatgaaaaaaaaagg	0.054													4	2	---	---	---	---	
GOLPH3	64083	broad.mit.edu	37	5	32135385	32135386	+	Intron	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32135385_32135386delAC	uc003jhp.1	-							NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3						cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1						ggggtttgttaccaccacagct	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	33011307	33011307	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33011307delA								C5orf23 (219488 upstream) : TARS (429495 downstream)																							AAACCAAAAGAAAAAAAAATC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34491196	34491197	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34491196_34491197delTG								C1QTNF3 (447879 upstream) : RAI14 (165236 downstream)																							TGGATTtgtatgtgtgtgtgtc	0.411													4	2	---	---	---	---	
WDR70	55100	broad.mit.edu	37	5	37396287	37396288	+	Intron	INS	-	T	T	rs146569331	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37396287_37396288insT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GCGTAAGACGGTTTTTTTTAAC	0.267													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40871291	40871291	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40871291delT								CARD6 (15837 upstream) : C7 (38308 downstream)																							cagactttagttttaggagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42251471	42251471	+	IGR	DEL	T	-	-	rs113748468		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42251471delT								FBXO4 (309808 upstream) : GHR (172555 downstream)																							TTGTCCTGTCTTTTTTTTTTT	0.328													4	2	---	---	---	---	
MGC42105	167359	broad.mit.edu	37	5	43256373	43256373	+	Intron	DEL	G	-	-	rs10941614		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43256373delG	uc003jno.2	+							NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9						ggcaagagatgaaggtggttt	0.000													2	4	---	---	---	---	
C5orf34	375444	broad.mit.edu	37	5	43494873	43494873	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43494873delT	uc003jnz.1	-							NM_198566	NP_940968	Q96MH7	CE034_HUMAN	hypothetical protein LOC375444											breast(1)	1	Lung NSC(6;2.07e-05)					CATTTTCCCATTTTTTTTTTC	0.254													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51981906	51981906	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51981906delA								None (None upstream) : ITGA1 (101868 downstream)																							tgtggcccacaaggaagagct	0.154													4	2	---	---	---	---	
ITGA1	3672	broad.mit.edu	37	5	52242517	52242517	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52242517delC	uc003jou.2	+						ITGA1_uc003jov.2_Intron|ITGA1_uc003jow.2_Intron	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TTGAGTGCCACCCTGAGAGAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56629059	56629060	+	IGR	INS	-	G	G	rs148588339	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56629059_56629060insG								GPBP1 (69649 upstream) : ACTBL2 (146784 downstream)																							GAGCTGAAGCAGGGGAGGGCTC	0.520													2	4	---	---	---	---	
KIF2A	3796	broad.mit.edu	37	5	61608839	61608839	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61608839delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron	NM_004520	NP_004511	O00139	KIF2A_HUMAN	kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		CTTATGTTTCTTTTTTTTTTA	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62502689	62502689	+	IGR	DEL	G	-	-	rs11319714		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62502689delG								ISCA1P1 (429519 upstream) : HTR1A (753590 downstream)																							taggggctgaggatgctcagc	0.144													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	64341449	64341449	+	IGR	DEL	T	-	-	rs67210336		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64341449delT								CWC27 (26859 upstream) : ADAMTS6 (103115 downstream)																							ttctactcacttttttttttg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	66598981	66598981	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66598981delA								CD180 (106364 upstream) : PIK3R1 (912623 downstream)																							TCAACAGGAGAAAAAAAGATT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67356564	67356564	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67356564delT								CD180 (863947 upstream) : PIK3R1 (155040 downstream)																							tattacagtgtttttttgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71295157	71295157	+	IGR	DEL	C	-	-	rs13187253	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71295157delC								CARTPT (278285 upstream) : MAP1B (107961 downstream)																							ttaaatttttctttttggtag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71296519	71296519	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71296519delT								CARTPT (279647 upstream) : MAP1B (106599 downstream)																							ccagttctccttttttcccct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72068029	72068031	+	IGR	DEL	TTG	-	-	rs35786889		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72068029_72068031delTTG								ZNF366 (264780 upstream) : TNPO1 (44387 downstream)																							CTTTTTCTGTttgttgttgttgt	0.286													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72454588	72454589	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72454588_72454589insT								TMEM171 (26944 upstream) : TMEM174 (14434 downstream)																							Gttttgttttgtttttttgaga	0.188													4	2	---	---	---	---	
SERINC5	256987	broad.mit.edu	37	5	79450814	79450814	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79450814delA	uc003kgj.2	-						SERINC5_uc003kgk.2_Intron|SERINC5_uc003kgl.2_Intron|SERINC5_uc003kgm.2_Intron|SERINC5_uc011ctj.1_Intron	NM_178276	NP_840060	Q86VE9	SERC5_HUMAN	developmentally regulated protein TPO1						phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)		CAGTGTCCCTAAATACTCCCG	0.398													4	2	---	---	---	---	
ATG10	83734	broad.mit.edu	37	5	81515392	81515393	+	Intron	DEL	TA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81515392_81515393delTA	uc003khs.2	+						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)		TGCTGAGGCTTATATGTTGCTT	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	87103655	87103655	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87103655delA								CCNH (394819 upstream) : TMEM161B (387369 downstream)																							tttgatggttaaaaaaaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	92428368	92428368	+	IGR	DEL	A	-	-	rs76388610		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92428368delA								None (None upstream) : FLJ42709 (316697 downstream)																							GTTCATTAGGAAAAAAAAAAA	0.383													5	6	---	---	---	---	
RHOBTB3	22836	broad.mit.edu	37	5	95069124	95069124	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95069124delA	uc003klm.2	+						RHOBTB3_uc003klk.1_Intron	NM_014899	NP_055714	O94955	RHBT3_HUMAN	rho-related BTB domain containing 3						retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		AAATGTAGGGAAAATAAAACT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96151056	96151057	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96151056_96151057insA	uc003kmo.1	-						ERAP1_uc010jbm.1_5'Flank|ERAP1_uc003kmn.2_5'Flank					Homo sapiens cDNA FLJ37666 fis, clone BRHIP2011576.																		AATGCACTGCTAAATAAAACAC	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	98722571	98722576	+	IGR	DEL	TGGGGA	-	-	rs11278923		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98722571_98722576delTGGGGA								CHD1 (460333 upstream) : LOC100133050 (992633 downstream)																							CAGAGGCCACTGGGGATGTGCTGCCA	0.466													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	103824804	103824804	+	IGR	DEL	T	-	-	rs74802446		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103824804delT								NUDT12 (926314 upstream) : RAB9BP1 (610371 downstream)																							attatttttattttttttttC	0.189													7	14	---	---	---	---	
C5orf13	9315	broad.mit.edu	37	5	111195004	111195005	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111195004_111195005insA	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947	Q16612	NP311_HUMAN	neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)		TGTAGCTAGCCAAAAAAATCTC	0.351													4	2	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112499241	112499242	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112499241_112499242insT	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		atatcctaacatttttttttgt	0.074													4	2	---	---	---	---	
KCNN2	3781	broad.mit.edu	37	5	113797428	113797428	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113797428delA	uc003kqo.2	+						KCNN2_uc003kqp.2_Intron|KCNN2_uc010jcg.2_Intron|uc003kqq.1_Intron	NM_021614	NP_067627	Q9H2S1	KCNN2_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding|small conductance calcium-activated potassium channel activity			ovary(2)	2		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)		GAGGGACAGGAAAAAAAAAAA	0.448													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115266879	115266879	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115266879delT								AP3S1 (17103 upstream) : AQPEP (31272 downstream)																							ttatggcccctttctccatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117789396	117789396	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117789396delT								None (None upstream) : DTWD2 (383175 downstream)																							CTAACGGACATTTCAAAGGAA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119477155	119477156	+	IGR	INS	-	T	T	rs142051151	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119477155_119477156insT								FAM170A (505639 upstream) : PRR16 (322863 downstream)																							GTCACATTTTCCCCTGAATGAA	0.361													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	120396723	120396723	+	IGR	DEL	A	-	-	rs73789530		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120396723delA								PRR16 (373761 upstream) : FTMT (790927 downstream)																							CATTTGGCTGAAAAAAAAAAA	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123044897	123044897	+	IGR	DEL	T	-	-	rs5871054		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123044897delT								CSNK1G3 (92435 upstream) : ZNF608 (927713 downstream)																							TGTAAATGGCTTTTTTTTAAA	0.214													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123197457	123197458	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123197457_123197458insT								CSNK1G3 (244995 upstream) : ZNF608 (775152 downstream)																							CTTGCATCTACTTTTTTTTTAA	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	135439365	135439365	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135439365delC								MIR886 (23068 upstream) : SMAD5OS (25840 downstream)																							actgctgtgtccccagcacca	0.095													4	2	---	---	---	---	
PKD2L2	27039	broad.mit.edu	37	5	137225971	137225971	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137225971delA	uc003lby.2	+						PKD2L2_uc010jep.1_Intron|PKD2L2_uc003lbw.1_Intron|PKD2L2_uc003lbx.2_Intron	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2							integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			actccgtctcaaaaaaaaaaT	0.144													4	3	---	---	---	---	
FGF1	2246	broad.mit.edu	37	5	142073790	142073790	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142073790delA	uc003lmq.2	-						FGF1_uc010jgj.2_Intron|FGF1_uc003lmr.2_Intron|FGF1_uc003lms.3_Intron	NM_001144934	NP_001138406	P05230	FGF1_HUMAN	fibroblast growth factor 1 (acidic) isoform 1						angiogenesis|cellular response to heat|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of angiogenesis|positive regulation of cell division|positive regulation of cell migration|positive regulation of cholesterol biosynthetic process|positive regulation of intracellular protein kinase cascade|positive regulation of transcription from RNA polymerase II promoter	cell cortex|cytosol|extracellular space	fibroblast growth factor receptor binding|growth factor activity|heparin binding|S100 alpha binding				0		all_neural(839;0.0416)|Ovarian(839;0.0955)|all_hematologic(541;0.1)|Prostate(461;0.157)|Lung NSC(810;0.21)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00032)	Pentosan Polysulfate(DB00686)	tttgggttctaaagacctcag	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144001568	144001568	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144001568delA								KCTD16 (144624 upstream) : None (None downstream)																							TTTCTATTCTAAAATTGACAA	0.284													4	2	---	---	---	---	
TCERG1	10915	broad.mit.edu	37	5	145889056	145889056	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145889056delT	uc003lob.2	+						TCERG1_uc003loc.2_Intron	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AATACATACCTTTTTTTTTTT	0.299													4	2	---	---	---	---	
GLRA1	2741	broad.mit.edu	37	5	151228730	151228732	+	Intron	DEL	TTC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151228730_151228732delTTC	uc003lut.2	-						GLRA1_uc003lur.2_Intron|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512	P23415	GLRA1_HUMAN	glycine receptor, alpha 1 isoform 1 precursor						muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	tttcttttctttctttctttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152729868	152729868	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152729868delA								NMUR2 (945028 upstream) : GRIA1 (139307 downstream)																							AGGCTGAAATAATGAGAATCC	0.433													4	2	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153580133	153580134	+	Intron	DEL	TG	-	-	rs111590510		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153580133_153580134delTG	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			AAAATGTGTATGTGTGTGTGTG	0.371													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154816665	154816665	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154816665delT								KIF4B (418980 upstream) : SGCD (318398 downstream)																							agagattatcttagtaatcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	155027469	155027469	+	IGR	DEL	G	-	-	rs2544750	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155027469delG								KIF4B (629784 upstream) : SGCD (107594 downstream)																							TGAGAACATTGGCTTCTTGAG	0.373													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	156127005	156127009	+	Intron	DEL	AAAAG	-	-	rs149343673		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156127005_156127009delAAAAG	uc003lwd.3	+						SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GATCAGAGACAAAAGAAGGCATGAA	0.361													4	2	---	---	---	---	
EBF1	1879	broad.mit.edu	37	5	158391686	158391690	+	Intron	DEL	CTGAG	-	-	rs72186035		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158391686_158391690delCTGAG	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGGAAATTCTCTGAGCTGAGCTTGG	0.420			T	HMGA2	lipoma								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162689187	162689187	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162689187delT								None (None upstream) : CCNG1 (175390 downstream)																							ACTGAAATGATTTTTTTTTCC	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164728253	164728253	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164728253delA								None (None upstream) : None (None downstream)																							AGTTCTTTGTAAGAAGTAATC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165759288	165759288	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165759288delT								None (None upstream) : ODZ2 (952555 downstream)																							TGCTCTAAGCTTTTTAAAGCT	0.299													4	2	---	---	---	---	
GABRP	2568	broad.mit.edu	37	5	170236370	170236370	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170236370delA	uc003mau.2	+						GABRP_uc011dev.1_Intron	NM_014211	NP_055026	O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi							cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GTGAAACATTAAAAAAAAACA	0.388											OREG0017032	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171026254	171026255	+	IGR	INS	-	G	G	rs140799115	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171026254_171026255insG								FGF18 (142092 upstream) : FBXW11 (262301 downstream)																							TTGGATGCGTTGGGGGGGCCAG	0.381													4	4	---	---	---	---	
NEURL1B	54492	broad.mit.edu	37	5	172103157	172103157	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172103157delA	uc003mbt.2	+							NM_001142651	NP_001136123	A8MQ27	NEU1B_HUMAN	neuralized homolog 1B								ligase activity|zinc ion binding				0						tcacttaaggaaaaaaaaaaa	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173638214	173638214	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173638214delA								HMP19 (102033 upstream) : MSX2 (513361 downstream)																							gtgcttaTTGAAAAAAAAAAA	0.199													5	3	---	---	---	---	
RMND5B	64777	broad.mit.edu	37	5	177571262	177571262	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177571262delC	uc003mim.2	+						RMND5B_uc003min.2_Intron|RMND5B_uc003mio.2_Intron|RMND5B_uc003mip.2_Intron|RMND5B_uc011dgf.1_Intron|RMND5B_uc003miq.2_Intron	NM_022762	NP_073599	Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog											ovary(1)|skin(1)	2	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCCTCGTGTCCAGGATGAAC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	178127158	178127158	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178127158delC								CLK4 (69542 upstream) : ZNF354A (11373 downstream)																							GGCATGGGGGCCGTCTCCATC	0.622													4	2	---	---	---	---	
ZNF354B	117608	broad.mit.edu	37	5	178288668	178288669	+	Intron	INS	-	AGAG	AGAG	rs139342631	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178288668_178288669insAGAG	uc003mjl.2	+						ZNF354B_uc003mjm.2_Intron	NM_058230	NP_478137	Q96LW1	Z354B_HUMAN	zinc finger protein 354B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCGCAGGACACAGAAGACCCCT	0.401													4	2	---	---	---	---	
ADAMTS2	9509	broad.mit.edu	37	5	178599448	178599448	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178599448delG	uc003mjw.2	-						ADAMTS2_uc011dgm.1_Intron	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		ATGAGGGGCAGGGGCCAAGGA	0.662													4	2	---	---	---	---	
ADAMTS2	9509	broad.mit.edu	37	5	178740974	178740977	+	Intron	DEL	CACT	-	-	rs72399120		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178740974_178740977delCACT	uc003mjw.2	-						ADAMTS2_uc011dgm.1_Intron	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TGCACACACACACTCACACCGAGA	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179827783	179827783	+	IGR	DEL	A	-	-	rs34982894		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179827783delA								GFPT2 (47468 upstream) : CNOT6 (93634 downstream)																							ATTAGGAGACAAATGCAAGTC	0.478													2	5	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	1746462	1746463	+	Intron	DEL	TT	-	-	rs34777755		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1746462_1746463delTT	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		GTCTTCTCTCTTTGTCTCTCAA	0.441													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2594614	2594616	+	IGR	DEL	CTT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2594614_2594616delCTT								GMDS (348768 upstream) : C6orf195 (28356 downstream)																							atttcctgtccttctgtaaaggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	5938244	5938244	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5938244delA								FARS2 (166428 upstream) : NRN1 (59991 downstream)																							TTGAACAGTTAAAAAAGGCTT	0.498													4	2	---	---	---	---	
F13A1	2162	broad.mit.edu	37	6	6271298	6271298	+	Intron	DEL	T	-	-	rs35546153		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6271298delT	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TATGGAAGCGTTATCAGGGAC	0.478													2	5	---	---	---	---	
CAGE1	285782	broad.mit.edu	37	6	7369244	7369244	+	Intron	DEL	T	-	-	rs34755964		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7369244delT	uc003mxi.2	-						CAGE1_uc003mxh.2_Intron|CAGE1_uc003mxj.2_Intron|CAGE1_uc003mxk.1_Intron	NM_205864	NP_995586	Q8TC20	CAGE1_HUMAN	cancer antigen 1												0	Ovarian(93;0.0418)					tttattttaattttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9234384	9234384	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9234384delA								HULC (580307 upstream) : None (None downstream)																							cagtgccaggaaacacattta	0.000													4	2	---	---	---	---	
GFOD1	54438	broad.mit.edu	37	6	13370944	13370945	+	Intron	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13370944_13370945delTG	uc003nat.1	-						GFOD1_uc003nas.1_Intron	NM_018988	NP_061861	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain							extracellular region	binding|oxidoreductase activity			ovary(2)	2	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			tatgtgtttatgtgtgtgtgtg	0.327													3	3	---	---	---	---	
RNF182	221687	broad.mit.edu	37	6	13929474	13929474	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13929474delA	uc003nbe.2	+						RNF182_uc003nbf.2_Intron|RNF182_uc003nbg.2_Intron	NM_152737	NP_689950	Q8N6D2	RN182_HUMAN	ring finger protein 182							cytoplasm|integral to membrane|intracellular membrane-bounded organelle	protein binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)			ACTATAAAATAAAACTGTGTG	0.323													4	2	---	---	---	---	
ATXN1	6310	broad.mit.edu	37	6	16681556	16681557	+	Intron	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16681556_16681557delAC	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.1_Intron	NM_000332	NP_000323	P54253	ATX1_HUMAN	ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				AGAGCACAGGACCAGAGCCACA	0.515													4	2	---	---	---	---	
CAP2	10486	broad.mit.edu	37	6	17556927	17556927	+	3'UTR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17556927delA	uc003ncb.2	+	13					CAP2_uc011dja.1_3'UTR|CAP2_uc011djb.1_3'UTR|CAP2_uc011djc.1_3'UTR|CAP2_uc011djd.1_3'UTR	NM_006366	NP_006357	P40123	CAP2_HUMAN	adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			GATTTAAAGGAAAAAAAAAAA	0.333													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19616689	19616689	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19616689delA								None (None upstream) : ID4 (220928 downstream)																							ccccaaggacaaaaaaaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23017186	23017186	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23017186delA								HDGFL1 (446437 upstream) : None (None downstream)																							ATGTGATGTTAAAAAGAAAAA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26006804	26006805	+	IGR	DEL	AA	-	-	rs77543654		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26006804_26006805delAA								TRIM38 (21454 upstream) : HIST1H1A (10456 downstream)																							TTTTCCaattaaaaaaaaaaaa	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28686242	28686242	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28686242delA								SCAND3 (131130 upstream) : TRIM27 (184538 downstream)																							GGAAAGCATTAAAAAATATAG	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29483088	29483088	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29483088delA								MAS1L (27409 upstream) : UBD (40302 downstream)																							gcttgggaataaacccacaca	0.070													4	2	---	---	---	---	
BAT1	7919	broad.mit.edu	37	6	31508479	31508493	+	Intron	DEL	AGCACAGCCTTCACC	-	-	rs28359838		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31508479_31508493delAGCACAGCCTTCACC	uc003ntt.2	-						BAT1_uc003nts.2_5'Flank|BAT1_uc011dnn.1_Intron|BAT1_uc003ntu.2_Intron|BAT1_uc003ntv.2_Intron|BAT1_uc003ntw.2_5'UTR|BAT1_uc003ntx.2_Intron|BAT1_uc011dno.1_Intron|BAT1_uc011dnp.1_Intron|BAT1_uc011dnq.1_Intron	NM_004640	NP_004631	Q13838	DX39B_HUMAN	HLA-B associated transcript 1						intronless viral mRNA export from host nucleus|RNA secondary structure unwinding|spliceosome assembly	nuclear speck|spliceosomal complex|transcription export complex	ATP binding|ATP-dependent protein binding|ATP-dependent RNA helicase activity|identical protein binding|U4 snRNA binding|U6 snRNA binding				0						CTTAATCACGAGCACAGCCTTCACCACCTCTTTTC	0.326													6	3	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32516494	32516494	+	Intron	DEL	G	-	-	rs112351560		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32516494delG	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						aaacctctttgctttatgaat	0.050													6	6	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34026602	34026602	+	Intron	DEL	A	-	-	rs5875483		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34026602delA	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc003oio.2_Intron|GRM4_uc003oip.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	CTCCCAGCCCAAAACCTCAGA	0.313													5	3	---	---	---	---	
FANCE	2178	broad.mit.edu	37	6	35418145	35418145	+	5'Flank	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35418145delG	uc003oko.1	+						FANCE_uc010jvw.1_5'Flank	NM_021922	NP_068741	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E						DNA repair	nucleoplasm	protein binding			ovary(1)|lung(1)|skin(1)	3						AGGGTTTGGTGGGGGGGCAAA	0.532			N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	36081041	36081041	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36081041delC								MAPK14 (2029 upstream) : MAPK13 (17221 downstream)																							atctcttgagcccaggagttc	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	36118613	36118613	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36118613delT								MAPK13 (10772 upstream) : BRPF3 (45937 downstream)																							GTTCCTATCCTTTTTTTTTTA	0.418													4	2	---	---	---	---	
BTBD9	114781	broad.mit.edu	37	6	38233983	38233983	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38233983delT	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						TGACAAACTCTTTTTTTTCTT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	41456830	41456830	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41456830delC								NCR2 (138205 upstream) : FOXP4 (57334 downstream)																							CACTTCCTTTCCCTTCTTGCC	0.512													4	2	---	---	---	---	
CLIC5	53405	broad.mit.edu	37	6	45902158	45902158	+	Intron	DEL	C	-	-	rs66790502		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45902158delC	uc003oxv.3	-						CLIC5_uc003oxu.3_Intron|CLIC5_uc003oxw.2_Intron|CLIC5_uc003oxx.2_Intron	NM_001114086	NP_001107558	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5 isoform a						female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity			ovary(1)|skin(1)	2						GAAAAGTGGACTTGAAGGGGG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	49380494	49380494	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49380494delA								None (None upstream) : MUT (18500 downstream)																							AATTAGCACCAAATGAGCACC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	54548429	54548429	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54548429delT								TINAG (293479 upstream) : FAM83B (163140 downstream)																							taaagttttattgaaatgcag	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	54572285	54572286	+	IGR	DEL	CC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54572285_54572286delCC								TINAG (317335 upstream) : FAM83B (139283 downstream)																							tgccttttttccttttgaaagt	0.000													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	56148673	56148674	+	Intron	DEL	CT	-	-	rs67475204	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56148673_56148674delCT	uc003pcu.1	-							NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			CACACACACActctctctctct	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	56301106	56301106	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56301106delC								COL21A1 (42214 upstream) : DST (21681 downstream)																							TGAACACATTCCCCACTGTAA	0.433													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57466685	57466686	+	Intron	INS	-	T	T	rs150786912		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57466685_57466686insT	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)		AGTAGAATGGGTAGATATGGGA	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58696889	58696889	+	IGR	DEL	A	-	-	rs34727436		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58696889delA								GUSBL2 (409165 upstream) : None (None downstream)																							acaataacagaaaaaaaactt	0.000													4	2	---	---	---	---	
LMBRD1	55788	broad.mit.edu	37	6	70425196	70425196	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70425196delA	uc003pfa.2	-						LMBRD1_uc003pey.2_Intron|LMBRD1_uc003pez.2_Intron|LMBRD1_uc010kal.2_Intron|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838	Q9NUN5	LMBD1_HUMAN	liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1						ACTATTTTAGAAAAAAAAATA	0.333													4	2	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70748183	70748183	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70748183delC	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						tggggctccacccccagaaat	0.050													4	2	---	---	---	---	
KCNQ5	56479	broad.mit.edu	37	6	73339131	73339132	+	Intron	DEL	CA	-	-	rs139360108		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73339131_73339132delCA	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		CTCTTCTAATCAGTCTTTAGAA	0.292													2	4	---	---	---	---	
KCNQ5	56479	broad.mit.edu	37	6	73442220	73442221	+	Intron	DEL	AG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73442220_73442221delAG	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		AGCAAGTGAAAGAGAGTGCGGT	0.351													3	6	---	---	---	---	
CD109	135228	broad.mit.edu	37	6	74420970	74420970	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74420970delT	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4						TTTGACCTGCTTTTTTTTTTA	0.269													3	3	---	---	---	---	
CD109	135228	broad.mit.edu	37	6	74490730	74490731	+	Intron	INS	-	TA	TA	rs145114558		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74490730_74490731insTA	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4						atgtgtatgcgtgtgtgtgtgt	0.139													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	79225014	79225014	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79225014delC								None (None upstream) : IRAK1BP1 (352175 downstream)																							aggttgtaaacctTTAATAGA	0.139													4	2	---	---	---	---	
BCKDHB	594	broad.mit.edu	37	6	80878277	80878278	+	Intron	INS	-	GAAC	GAAC			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80878277_80878278insGAAC	uc003pjd.2	+						BCKDHB_uc003pje.2_Intron	NM_000056	NP_000047	P21953	ODBB_HUMAN	branched chain keto acid dehydrogenase E1 beta						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|carboxy-lyase activity|protein binding				0		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)		ggagggaggaaggaaggaaggg	0.198													4	2	---	---	---	---	
SNAP91	9892	broad.mit.edu	37	6	84269419	84269420	+	Intron	DEL	TT	-	-	rs145988652		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84269419_84269420delTT	uc011dze.1	-						SNAP91_uc011dzd.1_Intron|SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		TTTGGCAAACTTATTGCAGTTA	0.327													3	4	---	---	---	---	
CYB5R4	51167	broad.mit.edu	37	6	84638707	84638707	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84638707delA	uc003pkf.2	+							NM_016230	NP_057314	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4						cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		AAACACCATTAAAAAAGAAAG	0.323													4	2	---	---	---	---	
ZNF292	23036	broad.mit.edu	37	6	87944586	87944586	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87944586delT	uc003plm.3	+							NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GATTGTGTGATTTTTTTTTTC	0.398													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	88971229	88971229	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88971229delC								CNR1 (95462 upstream) : RNGTT (348760 downstream)																							CAAGGATTCACCATAAGCCAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100209655	100209656	+	IGR	INS	-	T	T	rs145670309	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100209655_100209656insT								PRDM13 (146201 upstream) : MCHR2 (158130 downstream)																							TTTCCCTTGACTTTTTTTTTCT	0.401													4	2	---	---	---	---	
DSE	29940	broad.mit.edu	37	6	116633391	116633391	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116633391delT	uc003pws.2	+						DSE_uc011ebf.1_Intron|DSE_uc003pwq.1_Intron|DSE_uc003pwr.2_Intron	NM_001080976	NP_001074445	Q9UL01	DSE_HUMAN	dermatan sulfate epimerase precursor						dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		CTTTTTATGCTTTTTGAGCTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	120128779	120128779	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120128779delA								MAN1A1 (457853 upstream) : None (None downstream)																							ttataaatgcaaaaataattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	120370886	120370886	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120370886delG								MAN1A1 (699960 upstream) : None (None downstream)																							tcccctttaaggactgagccc	0.000													4	2	---	---	---	---	
C6orf170	221322	broad.mit.edu	37	6	121625284	121625284	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121625284delT	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)		TAATGCTACATTTTTTTTACC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	135108173	135108173	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135108173delA								SGK1 (468977 upstream) : ALDH8A1 (130356 downstream)																							ACAAGTGGCCAAAAAAGCAAG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147370208	147370208	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147370208delG	uc003qlt.1	-						uc003qlu.1_Intron|uc003qlv.2_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																		tagatccaaagctgaactcct	0.000													4	2	---	---	---	---	
RGS17	26575	broad.mit.edu	37	6	153360625	153360625	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153360625delA	uc003qpm.2	-							NM_012419	NP_036551	Q9UGC6	RGS17_HUMAN	regulator of G-protein signalling 17						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			pancreas(1)	1		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		AGGGCAACGTAAACATTTTGG	0.423									Lung_Cancer_Familial_Clustering_of				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	153665194	153665195	+	IGR	INS	-	A	A	rs150581755	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153665194_153665195insA								RGS17 (212805 upstream) : OPRM1 (666441 downstream)																							gaaatatgcataaacccataat	0.035													4	2	---	---	---	---	
IPCEF1	26034	broad.mit.edu	37	6	154478046	154478046	+	3'UTR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154478046delT	uc003qpx.2	-	12					OPRM1_uc003qpt.1_Intron|IPCEF1_uc003qpv.2_3'UTR|IPCEF1_uc003qpw.2_3'UTR|IPCEF1_uc010kjh.2_3'UTR	NM_015553	NP_056368	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0						AATCCTAATCTTTAGCAGGTG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	155992225	155992225	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155992225delA								NOX3 (215188 upstream) : MIR1202 (275706 downstream)																							ATGAAATCATAAAAAAAATGT	0.423													4	2	---	---	---	---	
TAGAP	117289	broad.mit.edu	37	6	159458987	159458987	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159458987delT	uc003qrz.2	-						TAGAP_uc011eft.1_Intron|TAGAP_uc003qsa.2_Intron	NM_054114	NP_473455	Q8N103	TAGAP_HUMAN	T-cell activation Rho GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CGGAGCAGGGTTTTCATGTTT	0.463													4	2	---	---	---	---	
PNLDC1	154197	broad.mit.edu	37	6	160223520	160223520	+	Intron	DEL	T	-	-	rs74710112		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160223520delT	uc003qsx.1	+						PNLDC1_uc003qsy.1_Intron	NM_173516	NP_775787	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain							integral to membrane|nucleus	nucleic acid binding				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TCTGTTATGGTTTTTTTTTTG	0.299													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164349588	164349588	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164349588delA								QKI (354696 upstream) : None (None downstream)																							TTAAATTGACAAAAAGTCAAT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164993401	164993401	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164993401delT								QKI (998509 upstream) : C6orf118 (699754 downstream)																							tgatactgagtttttttttta	0.000													4	2	---	---	---	---	
MLLT4	4301	broad.mit.edu	37	6	168290259	168290260	+	Intron	INS	-	C	C	rs141987779		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168290259_168290260insC	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron|MLLT4_uc003qwf.2_Intron	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		gattacaggctccgcccccatg	0.099			T	MLL	AL								4	2	---	---	---	---	
THBS2	7058	broad.mit.edu	37	6	169636632	169636632	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169636632delC	uc003qwt.2	-							NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor						cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		cacactcattccccatccaca	0.075													4	2	---	---	---	---	
WDR27	253769	broad.mit.edu	37	6	170073125	170073126	+	Intron	INS	-	AC	AC			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170073125_170073126insAC	uc003qwx.2	-						WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron|WDR27_uc011egw.1_Intron|WDR27_uc010kkx.2_Intron			A2RRH5	WDR27_HUMAN	RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		GAATGCATGAAACACTCAAGGG	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170530538	170530538	+	IGR	DEL	C	-	-	rs67985666		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170530538delC								C6orf208 (327569 upstream) : LOC154449 (32884 downstream)																							AGACTCCACACCGGGAGTCAG	0.602													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945211	945211	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945211delA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						aggagaaaggagaaaggagaa	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4658233	4658233	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4658233delA								SDK1 (349604 upstream) : FOXK1 (25155 downstream)																							ctgagtgaggaaaaaaaagcc	0.000													4	2	---	---	---	---	
MMD2	221938	broad.mit.edu	37	7	4964942	4964942	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4964942delC	uc003sno.3	-						MMD2_uc003snl.1_Intron|MMD2_uc003snn.3_Intron|MMD2_uc010ksq.2_Intron	NM_001100600	NP_001094070	Q8IY49	PAQRA_HUMAN	monocyte to macrophage							integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		CCTCGAGACGCCACAGTGGCC	0.537													14	12	---	---	---	---	
MMD2	221938	broad.mit.edu	37	7	4964946	4964947	+	Intron	DEL	AG	-	-	rs58035576		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4964946_4964947delAG	uc003sno.3	-						MMD2_uc003snl.1_Intron|MMD2_uc003snn.3_Intron|MMD2_uc010ksq.2_Intron	NM_001100600	NP_001094070	Q8IY49	PAQRA_HUMAN	monocyte to macrophage							integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		GAGACGCCACAGTGGCCTTCCC	0.554													12	12	---	---	---	---	
MMD2	221938	broad.mit.edu	37	7	4964951	4964952	+	Intron	INS	-	T	T	rs59417947		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4964951_4964952insT	uc003sno.3	-						MMD2_uc003snl.1_Intron|MMD2_uc003snn.3_Intron|MMD2_uc010ksq.2_Intron	NM_001100600	NP_001094070	Q8IY49	PAQRA_HUMAN	monocyte to macrophage							integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		GCCACAGTGGCCTTCCCTGAGG	0.564													14	11	---	---	---	---	
MMD2	221938	broad.mit.edu	37	7	4964955	4964956	+	Intron	DEL	CC	-	-	rs61045910		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4964955_4964956delCC	uc003sno.3	-						MMD2_uc003snl.1_Intron|MMD2_uc003snn.3_Intron|MMD2_uc010ksq.2_Intron	NM_001100600	NP_001094070	Q8IY49	PAQRA_HUMAN	monocyte to macrophage							integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		CAGTGGCCTTCCCTGAGGGCCA	0.579													14	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	7075453	7075453	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7075453delA								C7orf28B (209592 upstream) : C1GALT1 (146793 downstream)																							ctgatccatcaagttaatttt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	9370404	9370405	+	IGR	DEL	TC	-	-	rs35007601		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9370404_9370405delTC								NXPH1 (577812 upstream) : PER4 (303495 downstream)																							GATTCATGGGtctctctctctc	0.342													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12570725	12570725	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12570725delA								VWDE (126873 upstream) : SCIN (25462 downstream)																							GCAGGTGGGCAAAAAAATTAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12988208	12988209	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12988208_12988209insA								ARL4A (257652 upstream) : ETV1 (942649 downstream)																							GTATAGTTTGGAAAAATGTTTG	0.332													4	2	---	---	---	---	
TMEM195	392636	broad.mit.edu	37	7	15302075	15302075	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15302075delT	uc003stb.1	-							NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						caagaaaaactacaagacact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	15924008	15924011	+	IGR	DEL	ACAC	-	-	rs148540541		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15924008_15924011delACAC								MEOX2 (197700 upstream) : ISPD (203141 downstream)																							ATGTAGGTATacacacacacacac	0.034													3	3	---	---	---	---	
ITGB8	3696	broad.mit.edu	37	7	20450032	20450032	+	3'UTR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20450032delA	uc003suu.2	+	14					ITGB8_uc011jyh.1_3'UTR	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(3)	3						ACATGTGAGGAAAAAAATAAT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24357406	24357407	+	IGR	INS	-	T	T	rs11419567		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24357406_24357407insT								NPY (25929 upstream) : MPP6 (255678 downstream)																							ATTTTGTTTTGTTTTTTTTTTT	0.376													7	5	---	---	---	---	
SKAP2	8935	broad.mit.edu	37	7	27003357	27003357	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27003357delA	uc011jzj.1	-							NM_003930	NP_003921	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1						actgctctttaaaaaaaaaag	0.139													4	2	---	---	---	---	
TAX1BP1	8887	broad.mit.edu	37	7	27861539	27861539	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27861539delA	uc003szl.2	+						TAX1BP1_uc011jzo.1_Intron|TAX1BP1_uc003szk.2_Intron|TAX1BP1_uc011jzp.1_Intron	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)						anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)			gtcaaatcataaaattgttat	0.040													4	2	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28435420	28435421	+	Intron	INS	-	T	T	rs71555740		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28435420_28435421insT	uc003szo.2	+							NM_182899	NP_878902	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						ttctttctttcttttttttttc	0.381													3	3	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28445537	28445537	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28445537delG	uc003szo.2	+							NM_182899	NP_878902	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						gcagaatcctggacccaatgc	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	28899130	28899130	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28899130delT								CREB5 (33621 upstream) : TRIL (93846 downstream)																							CCTCCTTAGCTTCTGTTCCTC	0.468													4	2	---	---	---	---	
WIPF3	644150	broad.mit.edu	37	7	29884647	29884647	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29884647delT	uc003taj.1	+							NM_001080529	NP_001073998	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3											ovary(1)	1						TTTTCTTTCCTTTTTTTTTTT	0.398													4	2	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33507443	33507443	+	Intron	DEL	G	-	-	rs77233759		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33507443delG	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc003tdr.1_Intron|BBS9_uc003tds.1_Intron|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			CTGGTGAGGAGAAAATGTGAC	0.373									Bardet-Biedl_syndrome				5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35453587	35453588	+	IGR	DEL	AC	-	-	rs68101334		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35453587_35453588delAC								TBX20 (160345 upstream) : HERPUD2 (218684 downstream)																							ACCTacacatacacacacacac	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	39634732	39634732	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39634732delC								C7orf36 (22262 upstream) : LOC646999 (14354 downstream)																							AACCTCTTCTCCAGAACCTCC	0.388													4	2	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40193914	40193915	+	Intron	INS	-	AATGT	AATGT	rs144141131	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40193914_40193915insAATGT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						CAAAAGATGTGAATGTAATGTA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46076725	46076727	+	IGR	DEL	GCA	-	-	rs78685192	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46076725_46076727delGCA								IGFBP3 (115854 upstream) : None (None downstream)																							TGAATTGGAGGcagcagcagcag	0.276													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46390531	46390532	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46390531_46390532insT								IGFBP3 (429660 upstream) : TNS3 (924221 downstream)																							CTTGTCCAGCATTTTTTTTAAC	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	48695029	48695030	+	IGR	INS	-	A	A	rs142976960	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48695029_48695030insA								ABCA13 (7938 upstream) : CDC14C (269127 downstream)																							CCCAAATCCACAAAATCCCACT	0.446													1	5	---	---	---	---	
VWC2	375567	broad.mit.edu	37	7	49888865	49888866	+	Intron	INS	-	GA	GA			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49888865_49888866insGA	uc003tot.1	+							NM_198570	NP_940972	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2						negative regulation of BMP signaling pathway|positive regulation of neuron differentiation	basement membrane|extracellular space					0						ATTTCCCCGAGGAGAGAGAGAG	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52779915	52779915	+	IGR	DEL	A	-	-	rs1623443	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52779915delA								None (None upstream) : POM121L12 (323434 downstream)																							gggatttcccatttttttttc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57730266	57730267	+	IGR	INS	-	A	A	rs146222690		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57730266_57730267insA								ZNF716 (197001 upstream) : None (None downstream)																							ATGTCTGCTCTAAAAGATAGTA	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61889810	61889810	+	IGR	DEL	T	-	-	rs112965445		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61889810delT								None (None upstream) : LOC643955 (861862 downstream)																							gagaaactggttttgtgatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63834723	63834723	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63834723delG								ZNF679 (107423 upstream) : ZNF680 (145532 downstream)																							ctgcaggtaagggccattgtg	0.000													4	2	---	---	---	---	
ZNF680	340252	broad.mit.edu	37	7	64002610	64002610	+	Intron	DEL	A	-	-	rs112615249		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64002610delA	uc003tta.2	-						ZNF680_uc010kzr.2_Intron|ZNF680_uc003ttb.2_Intron	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.118)|all_lung(88;0.243)				agaacccaacaaaaaaaatct	0.000													6	6	---	---	---	---	
ZNF273	10793	broad.mit.edu	37	7	64389512	64389513	+	3'UTR	INS	-	AATTAATTCTCATA	AATTAATTCTCATA	rs113287383		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64389512_64389513insAATTAATTCTCATA	uc003tto.2	+	4					ZNF273_uc003ttl.2_3'UTR|ZNF273_uc003ttn.2_3'UTR	NM_021148	NP_066971	Q14593	ZN273_HUMAN	zinc finger protein 273						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGTGGAGTTTTCCTTATTGCAC	0.337													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65056885	65056886	+	IGR	DEL	CC	-	-	rs78263008		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65056885_65056886delCC								ZNF92 (190888 upstream) : INTS4L2 (55891 downstream)																							CACACACACACCCACACACAAG	0.322													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65637972	65637972	+	IGR	DEL	T	-	-	rs112031658		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65637972delT								CRCP (18421 upstream) : TPST1 (32287 downstream)																							tctttggatcttttttttttc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67913939	67913940	+	IGR	INS	-	TCTC	TCTC	rs145934851	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67913939_67913940insTCTC								None (None upstream) : None (None downstream)																							TGGACCATTGGtctctctctcc	0.228													2	4	---	---	---	---	
PMS2L5	5383	broad.mit.edu	37	7	74312039	74312039	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74312039delA	uc003ubl.2	+						PMS2L5_uc003ubk.2_Intron|PMS2L5_uc010lbw.2_Intron|PMS2L5_uc003ubm.3_Intron	NR_027775				SubName: Full=Postmeiotic segregation increased 2-like 5;												0						tagTGTAAGGAAAAAAAAAAA	0.139													4	3	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76626356	76626357	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76626356_76626357insT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						ggtgtatggaggtgtggagtgt	0.000													4	2	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76659015	76659016	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76659015_76659016insT	uc011kgn.1	+											Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						CTGAGTCCCtcttttttttttt	0.287													9	4	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	77684370	77684370	+	Intron	DEL	T	-	-	rs7791207	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77684370delT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				caggcgtgtgttttttttaaa	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	80977689	80977690	+	IGR	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80977689_80977690delCA								SEMA3C (426014 upstream) : HGF (353755 downstream)																							cactcacaggcacacacacaca	0.178													4	2	---	---	---	---	
CACNA2D1	781	broad.mit.edu	37	7	81675755	81675755	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81675755delA	uc003uhr.1	-							NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	TCCATTGTATAAAAAAAGAAA	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	82196971	82196971	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82196971delC								CACNA2D1 (123940 upstream) : PCLO (186350 downstream)																							GCCTTTGTTTCCATGACATCA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	82341396	82341397	+	IGR	INS	-	G	G	rs145705824	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82341396_82341397insG								CACNA2D1 (268365 upstream) : PCLO (41924 downstream)																							taatagtagctgggggggttca	0.000													4	2	---	---	---	---	
PCLO	27445	broad.mit.edu	37	7	82457498	82457499	+	Intron	INS	-	T	T	rs146095985	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82457498_82457499insT	uc003uhx.2	-						PCLO_uc003uhv.2_Intron|PCLO_uc003uht.1_Intron|PCLO_uc003uhu.1_Intron	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1						cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TGCCCTTATGATTTTTTTTTAA	0.287													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84338386	84338386	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84338386delG								SEMA3A (514169 upstream) : SEMA3D (286488 downstream)																							CCTAAAGAGTGGAATATTCCA	0.234													4	2	---	---	---	---	
RUNDC3B	154661	broad.mit.edu	37	7	87364104	87364109	+	Intron	DEL	CTCCAT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87364104_87364109delCTCCAT	uc003ujb.2	+						RUNDC3B_uc011khd.1_Intron|RUNDC3B_uc011khe.1_Intron|RUNDC3B_uc003ujc.2_Intron|RUNDC3B_uc003ujd.2_Intron	NM_138290	NP_612147	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B isoform a											skin(1)	1	Esophageal squamous(14;0.00164)					ccatactgtactccatctcccagcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89581351	89581351	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89581351delT								ZNF804B (615007 upstream) : DPY19L2P4 (167363 downstream)																							tctcTGTGCCTTTTTTTCCCT	0.214													4	2	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90463699	90463699	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90463699delA	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						AAGACAAGTGAAAAGCAAGTA	0.239													4	2	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90732762	90732762	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90732762delT	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						TCAGGAAGTCTTAGAAACTTA	0.428													4	2	---	---	---	---	
BET1	10282	broad.mit.edu	37	7	93606931	93606932	+	Intron	DEL	TC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93606931_93606932delTC	uc003une.3	-									O15155	BET1_HUMAN	Homo sapiens Bet1p homolog (hbet1) mRNA, complete cds.						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding				0	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)			GCTCTCCGTTTCTCTCTCTCTA	0.431													4	2	---	---	---	---	
SMURF1	57154	broad.mit.edu	37	7	98666281	98666283	+	Intron	DEL	AAC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98666281_98666283delAAC	uc003upu.1	-						SMURF1_uc003upv.1_Intron|SMURF1_uc003upt.2_Intron	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			aacaacaacaaacaacaacaaca	0.217													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	99690268	99690269	+	IGR	DEL	TA	-	-	rs140427823		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99690268_99690269delTA								COPS6 (448 upstream) : MCM7 (135 downstream)																							ccccagtgtctatactgggggc	0.203													3	5	---	---	---	---	
PILRA	29992	broad.mit.edu	37	7	99991218	99991218	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99991218delA	uc003uuo.1	+						PILRA_uc011kjo.1_Intron|PILRA_uc003uup.1_Intron|PILRA_uc003uuq.1_Intron	NM_013439	NP_038467	Q9UKJ1	PILRA_HUMAN	paired immunoglobulin-like type 2 receptor alpha						interspecies interaction between organisms	extracellular region|integral to membrane|plasma membrane	protein binding|receptor activity			skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					gaccagaagtaaaagtagctt	0.100													4	2	---	---	---	---	
EMID2	136227	broad.mit.edu	37	7	101039752	101039752	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101039752delT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)					TAAGCAtttcttttttttttg	0.269													4	2	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101631491	101631491	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101631491delA	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						aatctgtttcaaaaaaaaaaa	0.229													4	2	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101896944	101896945	+	Intron	INS	-	G	G	rs140922376	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101896944_101896945insG	uc003uyt.2	+						CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron|uc003uyy.2_5'Flank	NM_001913	NP_001904	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform b						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						TTTTGAACTGAGGGGCGACAGC	0.470													1	5	---	---	---	---	
COG5	10466	broad.mit.edu	37	7	106861141	106861141	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106861141delG	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						AGCTATTGCAGGGAAAAAGTG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	108596026	108596026	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108596026delT								C7orf66 (71389 upstream) : None (None downstream)																							TACATGTTGGTTTTTGATTCA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	112204420	112204421	+	IGR	DEL	GA	-	-	rs145191710		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112204420_112204421delGA								C7orf53 (73485 upstream) : TMEM168 (201368 downstream)																							agCCCTGATGGAGAGTGCTTAC	0.134													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117582997	117582998	+	IGR	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117582997_117582998delAC								CTTNBP2 (69436 upstream) : NAA38 (241088 downstream)																							tatggaagagacacacacaatg	0.040													4	2	---	---	---	---	
C7orf58	79974	broad.mit.edu	37	7	120769948	120769949	+	Intron	INS	-	A	A	rs67558562		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120769948_120769949insA	uc003vjq.3	+						C7orf58_uc003vjr.1_Intron|C7orf58_uc003vjs.3_Intron|C7orf58_uc003vjt.3_Intron|C7orf58_uc010lkk.1_Intron	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					TCAATGAAAAGAAAAAAAAAAA	0.327													2	4	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126568927	126568928	+	Intron	DEL	AA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126568927_126568928delAA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	ACTTTTAGGGAAAAAAAAATAC	0.366										HNSCC(24;0.065)			4	2	---	---	---	---	
AHCYL2	23382	broad.mit.edu	37	7	129053965	129053965	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129053965delG	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						TCTATGGGCTGGGATGATTAT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	130108441	130108441	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130108441delA								TSGA14 (27587 upstream) : MEST (17605 downstream)																							atatacatgtaaagcaatttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	130528302	130528303	+	IGR	DEL	AG	-	-	rs59949488		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130528302_130528303delAG								KLF14 (109442 upstream) : MIR29A (33203 downstream)																							aaaaaaaaaaagaaTTGTGGAA	0.257													7	5	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132195101	132195101	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132195101delC	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron|PLXNA4_uc003vrb.2_Intron	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						GCATTGTCAGCCAGCATCCTA	0.458													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133664551	133664551	+	Intron	DEL	A	-	-	rs28736340		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133664551delA	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron|EXOC4_uc011kpq.1_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				aaaaaaaaagaaaaaaaaaCC	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150624752	150624753	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150624752_150624753insA								ABP1 (66373 upstream) : KCNH2 (17297 downstream)																							gccttggcaggaaaaaaactgc	0.000													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151986074	151986074	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151986074delA	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		aatgagaactaaaaattagtc	0.000			N		medulloblastoma								11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	154881467	154881467	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154881467delG								HTR5A (4008 upstream) : INSIG1 (208019 downstream)																							AATAGGCTGAGGGGGAATGGG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156285576	156285576	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156285576delT								SHH (680609 upstream) : C7orf4 (47609 downstream)																							GAGCTTTTCCTTCCTTTCCAT	0.488													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157897768	157897768	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157897768delC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		caaactccatcccagctccat	0.000													4	2	---	---	---	---	
FBXO25	26260	broad.mit.edu	37	8	363407	363407	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:363407delT	uc003wox.2	+						FBXO25_uc003woy.2_Intron|FBXO25_uc003woz.2_Intron	NM_183421	NP_904357	Q8TCJ0	FBX25_HUMAN	F-box only protein 25 isoform 1							nucleus|SCF ubiquitin ligase complex	actin binding|ubiquitin-protein ligase activity			lung(1)	1		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		TGCTTTCGTCTTTTTTTTTTT	0.100													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2227373	2227374	+	IGR	INS	-	TG	TG	rs144758496		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2227373_2227374insTG								MYOM2 (133994 upstream) : CSMD1 (565502 downstream)																							TGGGAAGGAACGGGAAATTTCT	0.490													6	6	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3683837	3683837	+	Intron	DEL	G	-	-	rs112583361		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3683837delG	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)		TGTCTTAACTGGGGGCTTGAA	0.453													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	4695645	4695645	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4695645delT	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)		ACAGTAAAACTTTTTTTTAAA	0.413													4	2	---	---	---	---	
MCPH1	79648	broad.mit.edu	37	8	6388520	6388521	+	Intron	INS	-	T	T	rs138438159	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6388520_6388521insT	uc003wqi.2	+						ANGPT2_uc003wqj.3_Intron|ANGPT2_uc003wqk.3_Intron|ANGPT2_uc010lri.2_Intron|ANGPT2_uc003wql.3_Intron	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		TAAATCTGCTCTTTTTTTAAAA	0.441													2	4	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	14354581	14354581	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14354581delA	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		TCACTTCTGTAAATAGCCTCC	0.199													4	2	---	---	---	---	
EFHA2	286097	broad.mit.edu	37	8	16909714	16909714	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16909714delT	uc003wxd.2	+							NM_181723	NP_859074	Q86XE3	EFHA2_HUMAN	EF-hand domain family, member A2							integral to membrane	calcium ion binding			skin(1)	1				Colorectal(111;0.0686)|COAD - Colon adenocarcinoma(73;0.239)		GAGACTTAAATTTTTttttgt	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	18119478	18119478	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18119478delT								NAT1 (38281 upstream) : NAT2 (129277 downstream)																							acatgccaaattttaagcagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20253489	20253489	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20253489delC								LZTS1 (140686 upstream) : None (None downstream)																							TCCTTAGAAGCCTTTGAGCAA	0.463													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21112214	21112214	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21112214delT								LZTS1 (999411 upstream) : GFRA2 (437316 downstream)																							gcaatctacatttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21316406	21316406	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21316406delG								None (None upstream) : GFRA2 (233124 downstream)																							ctggaagggtggtacacccta	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23887975	23887975	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23887975delA								STC1 (175655 upstream) : ADAM28 (263605 downstream)																							atacccatataaaaaacctgc	0.005													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	25455226	25455227	+	Intron	INS	-	T	T	rs139356577	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25455226_25455227insT	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		AGCTGCTTTGCTTTTGAAAGTA	0.416													3	4	---	---	---	---	
DPYSL2	1808	broad.mit.edu	37	8	26488188	26488188	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26488188delC	uc003xfb.1	+						DPYSL2_uc003xfa.2_Intron|DPYSL2_uc011lag.1_Intron|DPYSL2_uc010luk.1_Intron|DPYSL2_uc011lah.1_Intron	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		cattctactgcccatgagtgg	0.144													4	2	---	---	---	---	
ADRA1A	148	broad.mit.edu	37	8	26662480	26662481	+	Intron	DEL	TC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26662480_26662481delTC	uc003xfh.1	-						ADRA1A_uc003xfc.1_Intron|ADRA1A_uc010lul.1_Intron|ADRA1A_uc003xfd.1_Intron|ADRA1A_uc003xfe.1_Intron|ADRA1A_uc010lum.1_Intron|ADRA1A_uc003xff.1_Intron|ADRA1A_uc003xfg.1_Intron	NM_000680	NP_000671	P35348	ADA1A_HUMAN	alpha-1A-adrenergic receptor isoform 1						activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)	TCGGAGTCAGTCTCTCTCTCTC	0.267													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32212975	32212976	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32212975_32212976insA	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)		actcccgtctcaaaaaaacaaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	35028119	35028119	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35028119delA								None (None upstream) : UNC5D (64856 downstream)																							acctcaagggaaaaaaaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	36381038	36381038	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36381038delC								UNC5D (728858 upstream) : KCNU1 (260804 downstream)																							AGTTGGGGCACTGCTGAGATG	0.463													4	2	---	---	---	---	
KCNU1	157855	broad.mit.edu	37	8	36765638	36765638	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36765638delC	uc010lvw.2	+						KCNU1_uc003xjw.2_Intron	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1							voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		tctgttacatcccagtgcTGT	0.159													4	2	---	---	---	---	
WHSC1L1	54904	broad.mit.edu	37	8	38139365	38139366	+	Intron	INS	-	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38139365_38139366insC	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron|WHSC1L1_uc003xlh.2_5'Flank	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			GCATTGCTGGGATCTGGGGATA	0.421			T	NUP98	AML								4	4	---	---	---	---	
PRKDC	5591	broad.mit.edu	37	8	48848624	48848624	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48848624delA	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				TGATTGCCTTAAAAAAAAAAC	0.303								NHEJ					4	2	---	---	---	---	
RP1	6101	broad.mit.edu	37	8	55621648	55621648	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55621648delT	uc011ldy.1	+									P56715	RP1_HUMAN	SubName: Full=cDNA, FLJ79410, moderately similar to Oxygen-regulated protein 1;						axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			tttgtccaggtttgcccactt	0.194													4	2	---	---	---	---	
YTHDF3	253943	broad.mit.edu	37	8	64116742	64116742	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64116742delT	uc003xuy.2	+						YTHDF3_uc010lys.2_Intron|YTHDF3_uc003xuz.2_Intron|YTHDF3_uc003xva.2_Intron|YTHDF3_uc011len.1_Intron	NM_152758	NP_689971	Q7Z739	YTHD3_HUMAN	YTH domain family, member 3												0	Breast(64;0.0716)	all_cancers(86;0.169)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.146)	BRCA - Breast invasive adenocarcinoma(89;0.161)			TATCCTCTCATTTTTTTTTCT	0.294													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	68888630	68888631	+	Intron	DEL	AG	-	-	rs145646130		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68888630_68888631delAG	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						ggagagagacagagagagagag	0.015													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	69799052	69799052	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69799052delA								C8orf34 (67796 upstream) : SULF1 (579807 downstream)																							ctagcaacataattgataatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70249183	70249184	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70249183_70249184delTG								C8orf34 (517927 upstream) : SULF1 (129675 downstream)																							TTAAACTGCTTGGTGAGGCTCC	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72476452	72476453	+	IGR	INS	-	GTGC	GTGC			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72476452_72476453insGTGC								EYA1 (201985 upstream) : MSC (277324 downstream)																							tgtgtgtgtgtgtatgtgtatg	0.287													4	2	---	---	---	---	
STAU2	27067	broad.mit.edu	37	8	74538310	74538311	+	Intron	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74538310_74538311delAC	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|STAU2_uc003xzo.2_Intron|STAU2_uc003xzp.2_Intron|STAU2_uc011lfi.1_Intron|STAU2_uc003xzq.2_Intron|STAU2_uc010lzk.2_Intron|STAU2_uc010lzl.1_Intron	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			AAGTacacatacacacacacac	0.089													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76255549	76255549	+	IGR	DEL	A	-	-	rs11388768		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76255549delA								CRISPLD1 (308758 upstream) : HNF4G (64634 downstream)																							TCTCACAATCAAAAAAAAATT	0.299													4	2	---	---	---	---	
HNF4G	3174	broad.mit.edu	37	8	76428527	76428527	+	Intron	DEL	T	-	-	rs75042844		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76428527delT	uc003yaq.2	+						HNF4G_uc003yap.1_Intron	NM_004133	NP_004124	Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma						endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			agttcaaatatttttttttaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81379665	81379665	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81379665delC								TPD52 (295829 upstream) : ZBTB10 (18189 downstream)																							tctcaattctccctcctaaat	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88395145	88395146	+	IGR	INS	-	AAAC	AAAC	rs10635788		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88395145_88395146insAAAC								CNBD1 (190 upstream) : DCAF4L2 (487827 downstream)																							AAAGTAGTTGTAAAAAATTAAA	0.307													4	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88952040	88952040	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88952040delT								DCAF4L2 (65744 upstream) : MMP16 (97422 downstream)																							ccctaaagactttttttttta	0.000													3	3	---	---	---	---	
ESRP1	54845	broad.mit.edu	37	8	95705620	95705620	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95705620delT	uc003ygq.3	+						ESRP1_uc003ygr.3_Intron|ESRP1_uc003ygs.3_Intron|ESRP1_uc003ygt.3_Intron|ESRP1_uc003ygu.3_Intron|ESRP1_uc003ygv.2_Intron|ESRP1_uc003ygw.2_Intron	NM_017697	NP_060167	Q6NXG1	ESRP1_HUMAN	RNA binding motif protein 35A isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4						CTCTTGGCAGTTTTTTTCTAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	97482198	97482198	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97482198delG								PTDSS1 (135424 upstream) : SDC2 (23684 downstream)																							ACTGAATTGTGGGACCTGCCT	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101355696	101355696	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101355696delC								RNF19A (33369 upstream) : ANKRD46 (166291 downstream)																							TTTTTACTTGCAGCCAAATAC	0.333													4	2	---	---	---	---	
YWHAZ	7534	broad.mit.edu	37	8	101936665	101936665	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101936665delT	uc011lhe.1	-						YWHAZ_uc003yjv.2_Intron|YWHAZ_uc011lhf.1_Intron|YWHAZ_uc003yjw.2_Intron|YWHAZ_uc010mbq.2_Intron|YWHAZ_uc011lhg.1_Intron|YWHAZ_uc010mbr.2_Intron|YWHAZ_uc003yjx.2_Intron|YWHAZ_uc003yjy.2_Intron	NM_001135702	NP_001129174	P63104	1433Z_HUMAN	tyrosine 3/tryptophan 5 -monooxygenase						anti-apoptosis|mRNA metabolic process|platelet activation|signal transduction	cytosol|melanosome	transcription factor binding				0	all_cancers(14;7.43e-06)|all_epithelial(15;2.77e-08)|Lung NSC(17;6.08e-05)|all_lung(17;0.000197)		Epithelial(11;2.79e-11)|all cancers(13;5.45e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.75e-05)		Ginkgo biloba(DB01381)	AACAAGGTCCTTTTTTTTTTT	0.299													4	2	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102884821	102884821	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102884821delT	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			GGAATTCAGATTTTCTAAAAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103530585	103530585	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103530585delT								UBR5 (106090 upstream) : ODF1 (33263 downstream)																							acgcattaacttattatcaca	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103530588	103530589	+	IGR	DEL	TT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103530588_103530589delTT								UBR5 (106093 upstream) : ODF1 (33259 downstream)																							cattaacttattatcacatcaa	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	106989932	106989932	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106989932delC								ZFPM2 (173167 upstream) : OXR1 (292541 downstream)																							cccagtaaaacccagtaccaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	107085028	107085028	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107085028delT								ZFPM2 (268263 upstream) : OXR1 (197445 downstream)																							TATGTTATTCTTTTCTTTTTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	108163941	108163941	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108163941delC								ABRA (381469 upstream) : ANGPT1 (97770 downstream)																							CCTTTCTTTTCTGGCCTTCCT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	111496827	111496827	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111496827delA								KCNV1 (508751 upstream) : None (None downstream)																							AATAGTTTGCAAATGCACACA	0.299													4	2	---	---	---	---	
TRPS1	7227	broad.mit.edu	37	8	116453212	116453213	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116453212_116453213insA	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TTTGCTTTGCTAAAAAAAAACC	0.322									Langer-Giedion_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	122397343	122397343	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122397343delT								SNTB1 (573034 upstream) : HAS2 (227928 downstream)																							AACCAAGGTCTTTTTTTTTCT	0.448													4	2	---	---	---	---	
ATAD2	29028	broad.mit.edu	37	8	124368112	124368112	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124368112delA	uc003yqh.3	-						ATAD2_uc011lii.1_Intron|ATAD2_uc003yqi.3_Intron|ATAD2_uc003yqj.2_Intron	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AATCTTCTGTAACCAAGATTT	0.333													4	2	---	---	---	---	
NSMCE2	286053	broad.mit.edu	37	8	126115700	126115700	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126115700delT	uc003yrw.2	+						NSMCE2_uc003yrv.2_Intron	NM_173685	NP_775956	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			cgtggtgtgattttttttgtc	0.090													4	2	---	---	---	---	
LOC727677	727677	broad.mit.edu	37	8	128460153	128460153	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128460153delT	uc003yse.1	-						LOC727677_uc011liv.1_Intron					Homo sapiens isolate DGPc1_8_exons1-2-3-4-5 unknown mRNA, alternatively spliced.												0						TACCTTTGCCTTTTTTTCCAA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	128564030	128564030	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128564030delT								LOC727677 (69646 upstream) : MYC (183735 downstream)																							ctcagcggggttttccctgaa	0.000													4	2	---	---	---	---	
PVT1	5820	broad.mit.edu	37	8	128911185	128911186	+	Intron	INS	-	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128911185_128911186insC	uc010mdq.2	+						PVT1_uc003ysl.2_Intron|PVT1_uc010mdp.1_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0						GGACACCCCCACCCCCCGTTGA	0.545													4	2	---	---	---	---	
FAM49B	51571	broad.mit.edu	37	8	130896418	130896418	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130896418delT	uc003yss.2	-						FAM49B_uc003yst.2_Intron|FAM49B_uc003ysu.2_Intron|FAM49B_uc003ysv.2_Intron|FAM49B_uc003ysw.2_Intron|FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			GATACCCTAGTTTTTTTAAAC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	132104661	132104661	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132104661delG								ADCY8 (51826 upstream) : EFR3A (811698 downstream)																							cagagaccctggatgacatat	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	132766152	132766153	+	IGR	INS	-	CAC	CAC	rs142054936	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132766152_132766153insCAC								ADCY8 (713317 upstream) : EFR3A (150206 downstream)																							accatcaccatcatcatcatca	0.391													4	2	---	---	---	---	
KCNQ3	3786	broad.mit.edu	37	8	133411100	133411100	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133411100delG	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			AGGTGATACTGGCATCTGCCC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	133507571	133507571	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133507571delT								KCNQ3 (14567 upstream) : HPYR1 (65174 downstream)																							acagtttggattttttttttt	0.045													4	3	---	---	---	---	
TG	7038	broad.mit.edu	37	8	133916988	133916988	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133916988delA	uc003ytw.2	+						TG_uc010mdw.2_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AAGGGAGGGTAAAaaaaacaa	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134676758	134676758	+	IGR	DEL	T	-	-	rs35254543		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134676758delT								ST3GAL1 (92575 upstream) : ZFAT (813275 downstream)																							TGGTTCTCAGTTCTGTTGCCA	0.458													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138870628	138870629	+	IGR	DEL	AG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138870628_138870629delAG								None (None upstream) : FAM135B (271639 downstream)																							agcaaaagcaagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139062015	139062016	+	IGR	INS	-	CT	CT	rs144931407	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139062015_139062016insCT								None (None upstream) : FAM135B (80252 downstream)																							gaagTTCTAGACTATTTCCTTT	0.223													4	2	---	---	---	---	
KCNK9	51305	broad.mit.edu	37	8	140671719	140671720	+	Intron	INS	-	C	C	rs141690905	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140671719_140671720insC	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron	NM_016601	NP_057685	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)			CTTGGACCCTACCCCtgtattg	0.272													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	145705510	145705510	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145705510delC								FOXH1 (3792 upstream) : PPP1R16A (9907 downstream)																							tgatccgagtcccacaaagga	0.159													4	2	---	---	---	---	
AK3	50808	broad.mit.edu	37	9	4722393	4722394	+	Intron	DEL	CC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4722393_4722394delCC	uc003ziq.1	-						AK3_uc003zip.1_Intron|AK3_uc011lma.1_Intron|AK3_uc003zir.1_Intron	NM_016282	NP_057366	Q9UIJ7	KAD3_HUMAN	adenylate kinase 3						blood coagulation	mitochondrial matrix	ATP binding|GTP binding|nucleoside triphosphate adenylate kinase activity			ovary(2)	2	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0302)		GTCCCAAGCACCCCTCTCCCCA	0.292													9	7	---	---	---	---	
MPDZ	8777	broad.mit.edu	37	9	13146749	13146749	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13146749delT	uc010mia.1	-						MPDZ_uc010mhx.2_Intron|MPDZ_uc011lmm.1_Intron|MPDZ_uc003zkz.3_Intron|MPDZ_uc010mhy.2_Intron|MPDZ_uc010mhz.2_Intron|MPDZ_uc011lmn.1_Intron|MPDZ_uc003zlb.3_Intron	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)		TGCATGTGAATTTTTTTTTTC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26753461	26753462	+	IGR	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26753461_26753462delAC								None (None upstream) : C9orf82 (87222 downstream)																							AGAAATACTAACACACACACAG	0.337													4	2	---	---	---	---	
ARID3C	138715	broad.mit.edu	37	9	34623641	34623642	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34623641_34623642insG	uc011lon.1	-	4	645_646	c.645_646insC	c.(643-648)GCCGCCfs	p.A215fs		NM_001017363	NP_001017363	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT- like)	215_216					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		CTGTCTATGGCGGCCTGGAGCT	0.678													4	2	---	---	---	---	
CD72	971	broad.mit.edu	37	9	35611425	35611425	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35611425delC	uc003zxb.2	-						CD72_uc003zxc.1_Intron|CD72_uc010mkt.1_Intron	NM_001782	NP_001773	P21854	CD72_HUMAN	CD72 molecule						axon guidance|cell adhesion	integral to plasma membrane	receptor binding|sugar binding|transmembrane receptor activity				0			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			AGCTCTAGTGCCCCAAGTGGC	0.532											OREG0019172	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SHB	6461	broad.mit.edu	37	9	38052896	38052896	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38052896delT	uc004aax.2	-							NM_003028	NP_003019	Q15464	SHB_HUMAN	Src homology 2 domain containing adaptor protein						angiogenesis|apoptosis|cell differentiation|signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity			central_nervous_system(2)|skin(1)	3		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)		cagatcctccttatgcatgaa	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66708770	66708770	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66708770delC								LOC442421 (205743 upstream) : AQP7P1 (545497 downstream)																							atgaaattctcctacctcagc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67907806	67907808	+	IGR	DEL	GTT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67907806_67907808delGTT								FAM27B (113617 upstream) : None (None downstream)																							AAAGAAACTAGTTGTTTAATTAA	0.227													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68382363	68382364	+	IGR	INS	-	T	T	rs140126949	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68382363_68382364insT								FAM27B (588174 upstream) : MIR1299 (619875 downstream)																							tggatcttttctttttttcatt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68428346	68428348	+	IGR	DEL	GTT	-	-	rs76003680	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68428346_68428348delGTT								FAM27B (634157 upstream) : MIR1299 (573891 downstream)																							AATTCTTAACGTTATTTACTGAC	0.310													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69804754	69804754	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69804754delT								LOC100133920 (139805 upstream) : FOXD4L5 (370955 downstream)																							tcacataaccttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	72991364	72991365	+	IGR	INS	-	A	A	rs147373667	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72991364_72991365insA								SMC5 (21575 upstream) : KLF9 (8150 downstream)																							TTGTGTACTTTAAAAAAAAATG	0.218													4	2	---	---	---	---	
TLE1	7088	broad.mit.edu	37	9	84231237	84231237	+	Intron	DEL	A	-	-	rs113282087	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84231237delA	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2						AACATGCCATAAAAAAAAAAC	0.463													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93316857	93316857	+	Intron	DEL	C	-	-	rs35234644		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93316857delC	uc004aqt.1	-											Homo sapiens cDNA FLJ46333 fis, clone TESTI4045701.																		TTTCTAGTAACCCACTTCCTC	0.428													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	97223213	97223214	+	IGR	INS	-	T	T	rs143269476	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97223213_97223214insT								HIATL1 (12 upstream) : FBP2 (97791 downstream)																							TGTCTTGTGTCTTTTTTTTAAA	0.307													4	3	---	---	---	---	
FANCC	2176	broad.mit.edu	37	9	97951474	97951474	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97951474delT	uc004avh.2	-						FANCC_uc004avi.3_Intron|FANCC_uc010mrm.1_Intron|FANCC_uc011lul.1_Intron	NM_000136	NP_000127	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C						protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)				GCCTTCAATGTTTTTTTTTTC	0.328			D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				4	4	---	---	---	---	
PTCH1	5727	broad.mit.edu	37	9	98234651	98234651	+	Intron	DEL	T	-	-	rs78470848		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98234651delT	uc004avk.3	-						PTCH1_uc010mro.2_Intron|PTCH1_uc010mrp.2_Intron|PTCH1_uc010mrq.2_Intron|PTCH1_uc004avl.3_Intron|PTCH1_uc010mrr.2_Intron|PTCH1_uc004avm.3_Intron|PTCH1_uc010mrs.1_Intron	NM_000264	NP_000255	Q13635	PTC1_HUMAN	patched isoform L						embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GAACCGGGAGTTTTGTGAGAT	0.537									Basal_Cell_Nevus_syndrome				3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98338108	98338109	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98338108_98338109insT								PTCH1 (58861 upstream) : C9orf130 (230263 downstream)																							agtgcaagtgattttttttctg	0.119													4	2	---	---	---	---	
TDRD7	23424	broad.mit.edu	37	9	100226431	100226431	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100226431delT	uc004axj.2	+						TDRD7_uc011lux.1_Intron	NM_014290	NP_055105	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7						lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)				TTCTCTGGCCTCCAGGCCTCC	0.488													4	2	---	---	---	---	
NCBP1	4686	broad.mit.edu	37	9	100421638	100421638	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100421638delT	uc004axq.2	+							NM_002486	NP_002477	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa						gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)				GATCCTTCCATTTTGTGTTGT	0.408													4	2	---	---	---	---	
GABBR2	9568	broad.mit.edu	37	9	101254392	101254392	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101254392delC	uc004ays.2	-							NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	tttttcctggcctagatattt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102056120	102056120	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102056120delC								SEC61B (63220 upstream) : NR4A3 (528017 downstream)																							AGAACCAGTTCCTGGAGGTTT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	105353560	105353561	+	IGR	DEL	AG	-	-	rs146861281		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105353560_105353561delAG								GRIN3A (852698 upstream) : CYLC2 (404032 downstream)																							ATAATAAAACAGAGAAATACGA	0.322													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	109148571	109148572	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109148571_109148572insT	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																		CCTTCATTAAATTTTTTTTCTG	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110866015	110866015	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110866015delT								KLF4 (613968 upstream) : ACTL7B (750856 downstream)																							TTTAGCTGCATTTTTTTGTTA	0.388													4	2	---	---	---	---	
EPB41L4B	54566	broad.mit.edu	37	9	112071681	112071681	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112071681delC	uc004bdz.1	-						EPB41L4B_uc004bea.2_Intron	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3						GAAAGACCTGCCAGGGAAGCT	0.478													4	2	---	---	---	---	
SVEP1	79987	broad.mit.edu	37	9	113282807	113282807	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113282807delG	uc010mtz.2	-						SVEP1_uc010mua.1_Intron|SVEP1_uc004beu.2_Intron|SVEP1_uc004bev.2_Intron	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						GAATTCTTGAGGTTATCACGT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115697170	115697170	+	IGR	DEL	G	-	-	rs68024831		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115697170delG								SLC46A2 (43977 upstream) : ZNF883 (62232 downstream)																							GTCCCAGGAAGGAAGTAACAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	124860604	124860604	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124860604delG								TTLL11 (4719 upstream) : NDUFA8 (45736 downstream)																							aaccagctctgggatgggtcc	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126734420	126734421	+	IGR	DEL	GT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126734420_126734421delGT								DENND1A (42003 upstream) : LHX2 (39468 downstream)																							gaatgtgagagtgtgtgagtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	129329655	129329656	+	IGR	DEL	CA	-	-	rs71377947		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129329655_129329656delCA								FAM125B (55956 upstream) : LMX1B (47092 downstream)																							ctctctctctcacacacacaca	0.000													4	2	---	---	---	---	
GOLGA2	2801	broad.mit.edu	37	9	131024603	131024607	+	Intron	DEL	AAAAC	-	-	rs111944122		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131024603_131024607delAAAAC	uc011maw.1	-						GOLGA2_uc010mxw.2_Intron|GOLGA2_uc004buh.2_5'Flank|GOLGA2_uc004bul.1_Intron|uc004bun.2_5'Flank	NM_004486	NP_004477	Q08379	GOGA2_HUMAN	Golgi autoantigen, golgin subfamily a, 2							Golgi cisterna membrane	protein binding			ovary(1)	1						ATGATGCTTTaaaacaaaacaaaac	0.332													4	2	---	---	---	---	
TBC1D13	54662	broad.mit.edu	37	9	131560530	131560530	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131560530delA	uc010myj.2	+						TBC1D13_uc010myk.2_Intron|TBC1D13_uc010myl.2_Intron	NM_018201	NP_060671	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13							intracellular	Rab GTPase activator activity				0						agaccctgtcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
ABL1	25	broad.mit.edu	37	9	133659477	133659477	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133659477delA	uc004bzv.2	+							NM_007313	NP_009297	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase						actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)	aattgattctaaaatgtacat	0.179			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	136484018	136484018	+	IGR	DEL	T	-	-	rs74638208		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136484018delT								FAM163B (38673 upstream) : DBH (17467 downstream)																							tgtttttgtcttttttttttt	0.149													3	4	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1737815	1737816	+	Intron	DEL	GA	-	-	rs5782591		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1737815_1737816delGA	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)		gcatgtttgtgagagtgtgtgc	0.198													4	3	---	---	---	---	
TAF3	83860	broad.mit.edu	37	10	7889676	7889676	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7889676delG	uc010qbd.1	+							NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						ccaaagtgctgggattacaga	0.000													4	2	---	---	---	---	
TAF3	83860	broad.mit.edu	37	10	7960916	7960917	+	Intron	DEL	TA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7960916_7960917delTA	uc010qbd.1	+							NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						tgctgcgtggtatacagaagaa	0.000													4	2	---	---	---	---	
TAF3	83860	broad.mit.edu	37	10	8019488	8019488	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8019488delT	uc010qbd.1	+							NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						ACGTAAAGGATTTTTTTTTTC	0.303													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10371704	10371704	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10371704delA								None (None upstream) : SFTA1P (454698 downstream)																							CCCTGATGAGAAAAAAAAGTC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	12302567	12302567	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12302567delT								CDC123 (9980 upstream) : CAMK1D (89016 downstream)																							GGGttttttgtttttttgttt	0.164													4	2	---	---	---	---	
FAM107B	83641	broad.mit.edu	37	10	14638245	14638246	+	Intron	INS	-	C	C	rs139831213	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14638245_14638246insC	uc001ina.1	-						FAM107B_uc010qbu.1_Intron|FAM107B_uc001imy.1_Intron|FAM107B_uc001imz.1_Intron	NM_031453	NP_113641	Q9H098	F107B_HUMAN	hypothetical protein LOC83641											breast(4)	4						caacctgctctcccaccagact	0.000													2	6	---	---	---	---	
VIM	7431	broad.mit.edu	37	10	17279529	17279529	+	3'UTR	DEL	T	-	-	rs71724273		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17279529delT	uc001iou.2	+	10					VIM_uc001iov.1_3'UTR|VIM_uc001iow.1_RNA|VIM_uc001iox.1_3'UTR|VIM_uc001ioy.1_3'UTR|VIM_uc001ioz.1_RNA|VIM_uc001ipb.1_RNA|VIM_uc009xjv.1_3'UTR|VIM_uc001ipc.1_3'UTR	NM_003380	NP_003371	P08670	VIME_HUMAN	vimentin						cellular component disassembly involved in apoptosis|cellular component movement|interspecies interaction between organisms|muscle filament sliding	cytosol|intermediate filament	protein C-terminus binding|structural constituent of cytoskeleton			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4						TTAAAACTGCTTTTTTTTTTC	0.264													3	3	---	---	---	---	
MRC1	4360	broad.mit.edu	37	10	17871264	17871264	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17871264delA	uc001ipk.2	+							NM_002438	NP_002429	P22897	MRC1_HUMAN	mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0						AGAACAACTTAAAAAATACCT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	26603499	26603502	+	IGR	DEL	GTGG	-	-	rs60023298		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26603499_26603502delGTGG								GAD2 (10008 upstream) : APBB1IP (123764 downstream)																							AGAAAGAGTCGTGGGTGGGTTTGA	0.436													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	26677464	26677465	+	IGR	INS	-	TG	TG	rs138702058	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26677464_26677465insTG								GAD2 (83973 upstream) : APBB1IP (49801 downstream)																							CCATGAGTGGTtgtgtgtgtgt	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	26870718	26870718	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26870718delG								APBB1IP (13988 upstream) : C10orf50 (8076 downstream)																							CAGAGATTACGGGGGGAAGAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29111179	29111179	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29111179delA								BAMBI (139311 upstream) : LYZL1 (466811 downstream)																							TAAACTCAGTAATAGTTTCTA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31897208	31897209	+	IGR	DEL	AG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31897208_31897209delAG								ZEB1 (79081 upstream) : ARHGAP12 (198016 downstream)																							agagagagacagagagagagag	0.371													3	4	---	---	---	---	
ARHGAP12	94134	broad.mit.edu	37	10	32097148	32097148	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32097148delA	uc001ivz.1	-						ARHGAP12_uc001ivy.1_Intron|ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001ivw.1_Intron|ARHGAP12_uc001ivx.1_Intron	NM_018287	NP_060757	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)				TAATTTCTTTAAAAAAAAAAA	0.303													4	2	---	---	---	---	
ARHGAP12	94134	broad.mit.edu	37	10	32135494	32135494	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32135494delA	uc001ivz.1	-						ARHGAP12_uc001ivy.1_Intron|ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001iwd.1_Intron|ARHGAP12_uc009xlr.1_Intron	NM_018287	NP_060757	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)				ggcttctgataaggcactcac	0.000													4	2	---	---	---	---	
C10orf68	79741	broad.mit.edu	37	10	32906316	32906316	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32906316delA	uc001iwn.3	+						C10orf68_uc001iwl.1_Intron|C10orf68_uc001iwm.1_Intron	NM_024688	NP_078964	Q9H943	CJ068_HUMAN	chromosome 10 open reading frame 68											skin(2)|ovary(1)	3						ttaagttgttaatttgtggtc	0.000													4	2	---	---	---	---	
NRP1	8829	broad.mit.edu	37	10	33499615	33499615	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33499615delA	uc001iwx.3	-						NRP1_uc001iwv.3_Intron|NRP1_uc009xlz.2_Intron|NRP1_uc001iww.3_Intron|NRP1_uc001iwy.3_Intron|NRP1_uc001iwz.2_Intron|NRP1_uc001ixa.2_Intron|NRP1_uc001ixb.1_Intron	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a						axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)	CTTGCCCATTACCCACTATTT	0.358													4	2	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	34612376	34612376	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34612376delA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixo.1_Intron|PARD3_uc001ixp.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron|PARD3_uc001ixs.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				GTGAggaggtaaaaaagctat	0.179													4	2	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	34650760	34650761	+	Intron	INS	-	A	A	rs143237762	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34650760_34650761insA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixo.1_Intron|PARD3_uc001ixp.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron|PARD3_uc001ixs.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				GCTAATGGGttaaaaaaaaaat	0.257													4	2	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	35060822	35060822	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35060822delG	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				CAGCTCGCCAGGATAAGCCAA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37792112	37792112	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37792112delT								ANKRD30A (270617 upstream) : ZNF248 (298335 downstream)																							gattccatgctttttttttct	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42654253	42654255	+	IGR	DEL	TAT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42654253_42654255delTAT								None (None upstream) : LOC441666 (173060 downstream)																							caaatttgcatattattactaat	0.034													8	4	---	---	---	---	
ZNF37B	100129482	broad.mit.edu	37	10	43013001	43013001	+	RNA	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43013001delC	uc001jab.3	-	5		c.6199delG			ZNF37B_uc001jac.3_RNA|ZNF37B_uc001jaa.3_RNA					Homo sapiens cDNA: FLJ23327 fis, clone HEP12630, highly similar to HSZNF37 Homo sapiens ZNF37A mRNA for zinc finger protein.												0						cttcccctgacccccagggta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	43256701	43256701	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43256701delG								ZNF33B (122709 upstream) : BMS1 (21253 downstream)																							TGGAGAAACTGGGGGCAATTC	0.463													4	2	---	---	---	---	
GPRIN2	9721	broad.mit.edu	37	10	47004506	47004509	+	3'UTR	DEL	TCTG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47004506_47004509delTCTG	uc010qfq.1	+	1						NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth												0						catgcattgctctgtctcagtttt	0.039													7	6	---	---	---	---	
ARHGAP22	58504	broad.mit.edu	37	10	49847424	49847424	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49847424delA	uc010qgm.1	-						ARHGAP22_uc001jgv.2_Intron	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 2						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1						TGCCAACTCTAAGACTGAGGG	0.318													4	2	---	---	---	---	
WDFY4	57705	broad.mit.edu	37	10	50169876	50169877	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50169876_50169877insT	uc001jha.3	+						WDFY4_uc009xob.2_Intron|WDFY4_uc010qgn.1_Intron	NM_020945	NP_065996	Q6ZS81	WDFY4_HUMAN	WDFY family member 4							integral to membrane	binding				0						atcttttgtgatttttttttta	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	50536329	50536329	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50536329delG								C10orf71 (792 upstream) : DRGX (37833 downstream)																							tccgtttggtgggggtctggg	0.000													4	2	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51040619	51040619	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51040619delA	uc001jif.2	-						PARG_uc001jih.2_Intron|PARG_uc001jig.2_Intron|PARG_uc010qgv.1_Intron|PARG_uc009xoi.2_Intron|PARG_uc010qgw.1_Intron|PARG_uc009xoj.2_Intron|PARG_uc010qgx.1_Intron	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		AATACTCAACAAAATACTGTG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	58501814	58501815	+	IGR	INS	-	G	G	rs140996249	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58501814_58501815insG								ZWINT (380780 upstream) : None (None downstream)																							tggtgacaagaaaagagagtaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63342563	63342563	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63342563delT								TMEM26 (129355 upstream) : C10orf107 (80156 downstream)																							tgtcaaatgcttgctggtggc	0.040													4	2	---	---	---	---	
RTKN2	219790	broad.mit.edu	37	10	63944226	63944226	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63944226delA	uc009xpf.1	-							NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2						signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)					TCAGAATCAcaaaaggcagtc	0.164													3	3	---	---	---	---	
ZNF365	22891	broad.mit.edu	37	10	64324752	64324752	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64324752delG	uc001jmd.1	+						ZNF365_uc001jmc.2_Intron	NM_199452	NP_955524	Q70YC4	TALAN_HUMAN	zinc finger protein 365 isoform D											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					cctgaattatggaagttcttg	0.239													4	2	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68175087	68175087	+	Intron	DEL	A	-	-	rs34074288		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68175087delA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						ctacccacacagcagctacta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	70835586	70835586	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70835586delT								KIAA1279 (58852 upstream) : SRGN (12242 downstream)																							gttaattttgttttttttcag	0.035													3	3	---	---	---	---	
DNAJC9	23234	broad.mit.edu	37	10	75007794	75007794	+	5'Flank	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75007794delG	uc001jtr.2	-						DNAJC9_uc010qkg.1_5'UTR|MRPS16_uc010qkh.1_Intron	NM_015190	NP_056005	Q8WXX5	DNJC9_HUMAN	DnaJ homolog, subfamily C, member 9						protein folding		heat shock protein binding|unfolded protein binding				0	Prostate(51;0.0119)					GGTTGAGGCTGGGGATAAAAC	0.453													4	2	---	---	---	---	
ANXA7	310	broad.mit.edu	37	10	75172668	75172668	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75172668delG	uc001jtz.2	-						ANXA7_uc001jua.2_Intron|ANXA7_uc001jub.2_Intron|ANXA7_uc010qki.1_Intron|ANXA7_uc009xre.2_Intron|ANXA7_uc009xrf.1_Intron	NM_004034	NP_004025	P20073	ANXA7_HUMAN	annexin VII isoform 2								calcium ion binding|calcium-dependent phospholipid binding|calcium-dependent protein binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)					TAAAAGGGCTGGGTCTCACCG	0.418													4	2	---	---	---	---	
AP3M1	26985	broad.mit.edu	37	10	75884746	75884746	+	Intron	DEL	T	-	-	rs79136387		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75884746delT	uc001jwf.2	-						AP3M1_uc001jwg.2_Intron|AP3M1_uc001jwh.2_Intron|AP3M1_uc010qla.1_Intron	NM_207012	NP_996895	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit						protein targeting to lysosome|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus|lysosome	protein binding				0	Prostate(51;0.0112)					tttctttttcttttttttttg	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80524175	80524175	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80524175delA								RPS24 (707605 upstream) : LOC283050 (178909 downstream)																							tcagtgatgtaaggacacatg	0.269													4	2	---	---	---	---	
CDHR1	92211	broad.mit.edu	37	10	85966087	85966087	+	Intron	DEL	T	-	-	rs5786647		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85966087delT	uc001kcv.2	+						CDHR1_uc001kcw.2_Intron|CDHR1_uc009xst.2_Intron	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor						homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1						GGAGGAAACGTTGGACTCCCA	0.478													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	90379378	90379378	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90379378delT								LIPJ (12646 upstream) : LIPF (44716 downstream)																							TTTTATTGGGTTTTTTTTTCT	0.333													4	2	---	---	---	---	
BTAF1	9044	broad.mit.edu	37	10	93716747	93716747	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93716747delA	uc001khr.2	+						BTAF1_uc009xua.1_Intron|BTAF1_uc001khs.1_Intron	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				tctctgtctcaaaaaaaaaaa	0.075													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	94845982	94845983	+	IGR	DEL	CA	-	-	rs79789758		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94845982_94845983delCA								CYP26A1 (8341 upstream) : MYOF (220204 downstream)																							GGTGATCATTCACACTTTCTGA	0.441													3	3	---	---	---	---	
ALDH18A1	5832	broad.mit.edu	37	10	97417884	97417884	+	5'Flank	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97417884delG	uc001kkz.2	-						ALDH18A1_uc001kky.2_5'Flank|ALDH18A1_uc010qog.1_5'Flank|ALDH18A1_uc010qoh.1_5'Flank	NM_002860	NP_002851	P54886	P5CS_HUMAN	pyrroline-5-carboxylate synthetase isoform 1						proline biosynthetic process	mitochondrial inner membrane	ATP binding|glutamate 5-kinase activity|glutamate-5-semialdehyde dehydrogenase activity			pancreas(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)	L-Glutamic Acid(DB00142)	acagccttatggaagagagag	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	97718936	97718937	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97718936_97718937insT	uc001klg.1	-						uc001klj.1_Intron					Homo sapiens cDNA FLJ34077 fis, clone FCBBF3003481, weakly similar to ZINC FINGER PROTEIN 195.																		aaatcaaaccattaatttgaaa	0.000													4	2	---	---	---	---	
C10orf28	27291	broad.mit.edu	37	10	99984019	99984019	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99984019delT	uc001kow.3	+						C10orf28_uc001kox.3_Intron|C10orf28_uc001koy.3_Intron|C10orf28_uc009xvx.2_Intron|C10orf28_uc009xvy.2_Intron|C10orf28_uc001koz.3_Intron	NM_014472	NP_055287	Q4KMY3	Q4KMY3_HUMAN	growth inhibition and differentiation related								nucleotide binding			large_intestine(1)|skin(1)	2		Colorectal(252;0.234)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)		ATGTGGCATATTTTTTTTTTG	0.154													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	100077376	100077377	+	IGR	INS	-	TT	TT	rs111412431		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100077376_100077377insTT								LOXL4 (49369 upstream) : PYROXD2 (65946 downstream)																							CTTTAAAGAGATTTTTTTTTTT	0.342													4	2	---	---	---	---	
KCNIP2	30819	broad.mit.edu	37	10	103591404	103591405	+	Intron	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103591404_103591405delCA	uc001kub.2	-						KCNIP2_uc010qqg.1_5'Flank|KCNIP2_uc001ktx.2_5'Flank|KCNIP2_uc001kty.2_5'Flank|KCNIP2_uc001ktz.2_Intron|KCNIP2_uc009xwu.2_Intron|KCNIP2_uc009xwv.2_Intron|KCNIP2_uc001kuc.2_Intron|KCNIP2_uc001kue.2_Intron|KCNIP2_uc001kud.2_Intron|KCNIP2_uc001kuf.2_Intron|KCNIP2_uc001kua.2_Intron|KCNIP2_uc009xww.2_Intron|KCNIP2_uc010qqh.1_Intron|KCNIP2_uc010qqi.1_Intron	NM_173191	NP_775283	Q9NS61	KCIP2_HUMAN	Kv channel interacting protein 2 isoform 2						clustering of voltage-gated potassium channels|detection of calcium ion|muscle contraction|regulation of heart contraction|signal transduction|synaptic transmission	cytoplasm|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|calcium ion binding|ER retention sequence binding|identical protein binding|protein N-terminus binding				0		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)		TATGCATGCTCACACACACACA	0.431													5	3	---	---	---	---	
ARL3	403	broad.mit.edu	37	10	104462311	104462311	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104462311delT	uc001kwa.2	-							NM_004311	NP_004302	P36405	ARL3_HUMAN	ADP-ribosylation factor-like 3						cell cycle|cytokinesis|small GTPase mediated signal transduction	centrosome|cytoplasmic microtubule|Golgi membrane|midbody|nucleus|photoreceptor connecting cilium|spindle microtubule	GDP binding|GTP binding|metal ion binding|microtubule binding				0		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)		TTTGGGTTCCTAACTTTGAGT	0.303													4	2	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106547375	106547375	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106547375delT	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GCAAGTGGGATTTTTTTTCCA	0.438													3	3	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106693065	106693065	+	Intron	DEL	T	-	-	rs78674721		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106693065delT	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		cctctggctattttttttttt	0.000													3	4	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106940835	106940835	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106940835delG	uc001kyi.1	+						SORCS3_uc010qqz.1_Intron	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GTTCCCATGAGGGAGGATCTT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109148876	109148876	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109148876delT								SORCS1 (224584 upstream) : None (None downstream)																							TTAAAACCTATTTACAAATGG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109811482	109811483	+	IGR	INS	-	TG	TG	rs146833242	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109811482_109811483insTG								SORCS1 (887190 upstream) : None (None downstream)																							taattagcatatgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111037234	111037235	+	IGR	DEL	CT	-	-	rs144476604		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111037234_111037235delCT								None (None upstream) : XPNPEP1 (587289 downstream)																							CATGGTAATGCTCTCTCTCTCT	0.366													6	3	---	---	---	---	
SMC3	9126	broad.mit.edu	37	10	112334451	112334452	+	Intron	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112334451_112334452delCA	uc001kze.2	+							NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		CCACCACCTCCACACACACACA	0.540													4	2	---	---	---	---	
SMC3	9126	broad.mit.edu	37	10	112340975	112340975	+	Intron	DEL	T	-	-	rs67616631		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112340975delT	uc001kze.2	+							NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		GCACACTGACttttttttttt	0.149													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113183627	113183627	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113183627delG								ADRA2A (342967 upstream) : GPAM (725995 downstream)																							cctacattttggtcacattaa	0.070													4	2	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114258296	114258296	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114258296delA	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		CTTCTTTCttaaaaaaaaaat	0.303													3	4	---	---	---	---	
VAX1	11023	broad.mit.edu	37	10	118893338	118893338	+	3'UTR	DEL	A	-	-	rs141466557	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118893338delA	uc009xyx.2	-	3					VAX1_uc001ldb.1_Intron	NM_001112704	NP_001106175	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1 isoform a							nucleus	sequence-specific DNA binding			ovary(2)	2				all cancers(201;0.0108)		AAGGTAGTAGAAAAAAAAAAT	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	119349795	119349795	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119349795delG								EMX2 (40739 upstream) : RAB11FIP2 (414634 downstream)																							ACTGGCTAATGGGGGGTGGGG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	120317121	120317121	+	IGR	DEL	A	-	-	rs33967689		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120317121delA								C10orf84 (215282 upstream) : PRLHR (35795 downstream)																							attgtgaatcaaaaaaatgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	121965222	121965222	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121965222delA								SEC23IP (263977 upstream) : PPAPDC1A (251244 downstream)																							AACTTGCAAGAAATGGCACAT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122069519	122069519	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122069519delG								SEC23IP (368274 upstream) : PPAPDC1A (146947 downstream)																							ACTGTTTTTTGCTCTTGAAGC	0.249													4	2	---	---	---	---	
HTRA1	5654	broad.mit.edu	37	10	124244300	124244300	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124244300delG	uc001lgj.2	+							NM_002775	NP_002766	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1 precursor						proteolysis|regulation of cell growth	extracellular space	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				gtcacactctggtccatctga	0.214													4	2	---	---	---	---	
HTRA1	5654	broad.mit.edu	37	10	124245316	124245316	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124245316delC	uc001lgj.2	+							NM_002775	NP_002766	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1 precursor						proteolysis|regulation of cell growth	extracellular space	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				AGTTAATGATCCTTAGTGGGA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	124481752	124481752	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124481752delT								C10orf120 (22414 upstream) : FLJ46361 (34458 downstream)																							GCTCAAACTCTTTTTTTTTGT	0.264													4	2	---	---	---	---	
CPXM2	119587	broad.mit.edu	37	10	125484315	125484315	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125484315delT	uc001lhj.2	-									Q8N436	CPXM2_HUMAN	Homo sapiens cDNA FLJ56000 complete cds, highly similar to Carboxypeptidase-like protein X2 precursor.						cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TTGCTGCCCCTATCCGTAGTC	0.517													5	7	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126799705	126799705	+	Intron	DEL	T	-	-	rs111354041		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126799705delT	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		GAAGTAGAGATTTTTTTTTTT	0.338													3	3	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	129230936	129230936	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129230936delT	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|DOCK1_uc009yaq.2_Intron	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						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)		TCTAGAGATCTTTTTTTTGTT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	129613727	129613727	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129613727delA								FOXI2 (74277 upstream) : CLRN3 (62387 downstream)																							ACACGGTGACAAAAATATTGA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130980481	130980481	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130980481delA								None (None upstream) : MGMT (284973 downstream)																							TCTGTCTTGGAAGCTCCTCTT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132005205	132005206	+	IGR	INS	-	CA	CA			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132005205_132005206insCA								GLRX3 (22421 upstream) : TCERG1L (885450 downstream)																							ACTGAAAGCTGCACACTCTGTC	0.327													4	2	---	---	---	---	
TCERG1L	256536	broad.mit.edu	37	10	132974877	132974878	+	Intron	INS	-	CA	CA	rs143998824		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132974877_132974878insCA	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		agagacacgtgcacacaccatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134766558	134766559	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134766558_134766559insT								C10orf93 (10494 upstream) : GPR123 (117874 downstream)																							CGTTGTGGTCATTTTTTTTCTT	0.396													4	2	---	---	---	---	
NUP98	4928	broad.mit.edu	37	11	3807972	3807972	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3807972delG	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyj.1_Intron|NUP98_uc001lyk.1_Intron|NUP98_uc010qxv.1_Intron	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1						carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TGGGTACAATGACAAAACTTA	0.353			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								4	2	---	---	---	---	
RRM1	6240	broad.mit.edu	37	11	4165373	4165373	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4165373delA	uc009yej.2	+							NM_001033		P23921	RIR1_HUMAN	ribonucleoside-diphosphate reductase M1 chain						deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	ggttaaggataaattgttgca	0.000													4	2	---	---	---	---	
HPX	3263	broad.mit.edu	37	11	6462506	6462506	+	5'Flank	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6462506delA	uc001mdg.2	-						HPX_uc009yfc.2_5'Flank|HPX_uc010rai.1_5'Flank	NM_000613	NP_000604	P02790	HEMO_HUMAN	hemopexin precursor						cellular iron ion homeostasis|interspecies interaction between organisms	extracellular space	heme transporter activity|metal ion binding|protein binding				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)		TAAGTCAGGGAAGTGAGTAGA	0.483													4	2	---	---	---	---	
SBF2	81846	broad.mit.edu	37	11	10014370	10014371	+	Intron	INS	-	TG	TG	rs142364187	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10014370_10014371insTG	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		CTAAGATATTATGAGTTCCATA	0.238													13	6	---	---	---	---	
GALNTL4	374378	broad.mit.edu	37	11	11490088	11490089	+	Intron	INS	-	A	A	rs138270411	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11490088_11490089insA	uc001mjo.2	-							NM_198516	NP_940918	Q6P9A2	GLTL4_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)		GAAACAGATGGAAAAAAAAAAG	0.495													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15563808	15563808	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15563808delA								INSC (295056 upstream) : SOX6 (424188 downstream)																							TCTGACTTTTAAAAAAATCCA	0.358													4	2	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16500356	16500356	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16500356delT	uc001mmi.3	-						SOX6_uc001mmg.2_5'Flank|SOX6_uc001mmh.1_Intron|SOX6_uc001mmj.2_Intron			P35712	SOX6_HUMAN	Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						TAAAAAGACATTTCCAAAAAC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	17658297	17658297	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17658297delG	uc001mnh.1	+											SubName: Full=Putative uncharacterized protein OTOG;																		CATGTTTCTCggggggcagcc	0.224													4	2	---	---	---	---	
HPS5	11234	broad.mit.edu	37	11	18306690	18306690	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18306690delA	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3						AAGGCTATTTaaaaaaaaaaa	0.303									Hermansky-Pudlak_syndrome				5	4	---	---	---	---	
NAV2	89797	broad.mit.edu	37	11	19799288	19799289	+	Intron	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19799288_19799289insG	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						GAGTCATTGAAGGGGGGTGGGA	0.495													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	30881963	30881964	+	Intron	INS	-	TTGTTT	TTGTTT	rs143609604	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30881963_30881964insTTGTTT	uc001mss.1	-											Homo sapiens mRNA for KIAA1493 protein, partial cds.																		TATTTTGGGGATTGTTTTTGTT	0.361													7	6	---	---	---	---	
CD44	960	broad.mit.edu	37	11	35218082	35218082	+	Intron	DEL	T	-	-	rs56325384		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35218082delT	uc001mvu.2	+						CD44_uc001mvv.2_Intron|CD44_uc001mvw.2_Intron|CD44_uc001mvx.2_Intron|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Intron|CD44_uc010rer.1_Intron|CD44_uc009ykh.2_Intron|CD44_uc010res.1_Intron|CD44_uc010ret.1_Intron|CD44_uc010reu.1_Intron	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor						cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)	ccagatgacatttaagatcct	0.109													5	5	---	---	---	---	
SLC1A2	6506	broad.mit.edu	37	11	35389784	35389784	+	Intron	DEL	T	-	-	rs75878668	byFrequency	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35389784delT	uc001mwd.2	-						SLC1A2_uc001mwe.2_Intron|SLC1A2_uc010rev.1_Intron	NM_004171	NP_004162	P43004	EAA2_HUMAN	excitatory amino acid transporter 2						D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)	AGCTATATGATTTCCCTGGAT	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39945763	39945763	+	IGR	DEL	A	-	-	rs11296365		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39945763delA								None (None upstream) : LRRC4C (189990 downstream)																							tcccccacccaaaaaaaaaga	0.000													4	2	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40584081	40584082	+	Intron	INS	-	AG	AG	rs72508032		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40584081_40584082insAG	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)				catgaggaaacactcccataaa	0.000													4	2	---	---	---	---	
CKAP5	9793	broad.mit.edu	37	11	46778305	46778305	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46778305delT	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Intron	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2						ggaccttgaattttttttttt	0.000													4	2	---	---	---	---	
MTCH2	23788	broad.mit.edu	37	11	47652983	47652983	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47652983delA	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0						acaaacaaacaaaaaaaaaCT	0.144													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48360602	48360603	+	IGR	INS	-	A	A	rs147819328	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48360602_48360603insA								OR4C3 (13122 upstream) : OR4C45 (6299 downstream)																							cttgcttacagaaaacacactg	0.000													3	3	---	---	---	---	
STX3	6809	broad.mit.edu	37	11	59544333	59544333	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59544333delT	uc001nog.2	+						STX3_uc010rkx.1_Intron|STX3_uc010rky.1_Intron	NM_004177	NP_004168	Q13277	STX3_HUMAN	syntaxin 3						cellular response to oxidative stress|intracellular protein transport|neuron projection development|neurotransmitter transport	apical plasma membrane|azurophil granule|cell-cell junction|growth cone|integral to membrane|plasma membrane enriched fraction|SNARE complex|specific granule	arachidonic acid binding|SNAP receptor activity			ovary(2)	2						AAACGCCACATTTTTGTCTAA	0.413													4	2	---	---	---	---	
PACS1	55690	broad.mit.edu	37	11	65936876	65936877	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65936876_65936877insT	uc001oha.1	+						PACS1_uc001ogz.1_Intron	NM_018026	NP_060496	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1						interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6						tggttcattacttttttttttt	0.000													4	2	---	---	---	---	
CHKA	1119	broad.mit.edu	37	11	67845915	67845915	+	Intron	DEL	A	-	-	rs35053057		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67845915delA	uc001onj.2	-						CHKA_uc001onk.2_Intron	NM_001277	NP_001268	P35790	CHKA_HUMAN	choline kinase alpha isoform a						lipid transport|phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|choline kinase activity|drug binding|ethanolamine kinase activity|signal transducer activity			ovary(1)|central_nervous_system(1)	2					Choline(DB00122)	tgttggtgacaaaaaaaagaa	0.199													4	2	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	70012657	70012657	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70012657delT	uc001opj.2	+						ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						CATTCCCACCTCCCCAGTGGC	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	70036032	70036033	+	IGR	DEL	TA	-	-	rs11235501		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70036032_70036033delTA								ANO1 (383 upstream) : FADD (13236 downstream)																							tgtatatgtctatgtgtgcatg	0.119													5	3	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70386479	70386480	+	Intron	INS	-	C	C	rs140779547	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70386479_70386480insC	uc001oqc.2	-						SHANK2_uc010rqn.1_Intron|SHANK2_uc001opz.2_Intron|uc009ysn.1_Intron|SHANK2_uc010rqp.1_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			GCAGGCTGGGGCCCCTCCCTCC	0.639													4	2	---	---	---	---	
PDE2A	5138	broad.mit.edu	37	11	72369721	72369721	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72369721delT	uc010rrc.1	-						PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_Intron|PDE2A_uc001osq.2_Intron	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	GAAAATGAACTTTTTTTTGGA	0.159													4	2	---	---	---	---	
GDPD5	81544	broad.mit.edu	37	11	75156849	75156849	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75156849delC	uc001owo.3	-						GDPD5_uc001owp.3_Intron|GDPD5_uc001own.3_Intron|GDPD5_uc009yuc.2_Intron|GDPD5_uc009yud.2_Intron|GDPD5_uc009yue.1_Intron	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1						AATTTCACTTCCCAGACACAG	0.318											OREG0021238	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
MAP6	4135	broad.mit.edu	37	11	75327123	75327124	+	Intron	DEL	TA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75327123_75327124delTA	uc001owu.2	-						MAP6_uc001owv.2_Intron	NM_033063	NP_149052	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6 isoform 1							Golgi apparatus|microtubule|perinuclear region of cytoplasm	calmodulin binding				0	Ovarian(111;0.11)					GAAATAGAATTATATAAGGAAC	0.366													4	2	---	---	---	---	
INTS4	92105	broad.mit.edu	37	11	77600897	77600897	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77600897delA	uc001oys.2	-						C11orf67_uc001oyp.2_Intron|C11orf67_uc001oyr.1_Intron|INTS4_uc001oyt.2_Intron	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4						snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			AGGTGCTATGAAGGGGGTTTT	0.468													4	2	---	---	---	---	
INTS4	92105	broad.mit.edu	37	11	77670974	77670974	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77670974delT	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4						snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			TGcatgtgactttttttttat	0.065													4	2	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	78489372	78489373	+	Intron	INS	-	G	G	rs141572581	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78489372_78489373insG	uc001ozl.3	-							NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						GTATGTGGGGCGGGGGGAGGGA	0.495													4	2	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	78976720	78976721	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78976720_78976721insT	uc001ozl.3	-						ODZ4_uc009yvc.2_Intron	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						CTTGTGTGTGATTTTTTTTTAA	0.317													6	3	---	---	---	---	
TMEM135	65084	broad.mit.edu	37	11	86822257	86822257	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86822257delT	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Intron|TMEM135_uc001pcg.1_Intron	NM_022918	NP_075069	Q86UB9	TM135_HUMAN	transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TGATGGCCTATTTTTTTGGTC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	87481419	87481419	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87481419delT								TMEM135 (446851 upstream) : RAB38 (365012 downstream)																							TACACCATGCttttttttttt	0.179													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	89356746	89356749	+	IGR	DEL	AGAG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89356746_89356749delAGAG								NOX4 (33967 upstream) : FOLH1B (35716 downstream)																							ACACTAAGATagagagagacagag	0.309													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95857794	95857796	+	Intron	DEL	ATC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95857794_95857796delATC	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)				CCTTCtccttatcatcatcatca	0.217			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	97852393	97852393	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97852393delT								None (None upstream) : None (None downstream)																							tgattttcCCTTTTTTATTCT	0.149													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	100030219	100030220	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100030219_100030220insA	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TGTTGAGCTTTAAAAAAAAATG	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	103710499	103710499	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103710499delT								DYNC2H1 (359908 upstream) : PDGFD (67416 downstream)																							agcaatgttgtttttttttgg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	105148490	105148490	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105148490delT								CARD18 (138684 upstream) : GRIA4 (332310 downstream)																							GGGGAGTTACTTTTTGTGGCT	0.418													4	2	---	---	---	---	
ZBTB16	7704	broad.mit.edu	37	11	113974537	113974537	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113974537delT	uc001pop.2	+						ZBTB16_uc001poo.1_Intron|ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		GGGCCTTCTATTTCAAACAGA	0.527													4	2	---	---	---	---	
SIK3	23387	broad.mit.edu	37	11	116906447	116906447	+	Intron	DEL	T	-	-	rs113834558		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116906447delT	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12						attgttttaatttttTTTTTT	0.184													4	2	---	---	---	---	
CEP164	22897	broad.mit.edu	37	11	117278967	117278968	+	Intron	INS	-	A	A	rs139225595	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117278967_117278968insA	uc001prc.2	+						CEP164_uc001prb.2_Intron|CEP164_uc001prf.2_Intron|CEP164_uc009yzp.1_Intron|CEP164_uc001prg.1_Intron	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa						cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		GAATGGTCCGGAATATACCTGG	0.530													2	7	---	---	---	---	
PKNOX2	63876	broad.mit.edu	37	11	125113189	125113189	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125113189delG	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		TTCAGGGCCTGGAGGCTCAGC	0.532													4	2	---	---	---	---	
DDX25	29118	broad.mit.edu	37	11	125789535	125789535	+	Intron	DEL	T	-	-	rs72526224		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125789535delT	uc001qcz.3	+						DDX25_uc010sbk.1_Intron	NM_013264	NP_037396	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25						mRNA export from nucleus|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|nucleus	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(1)	1	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		TCATACCACATTTCCTAGTTC	0.413													1	6	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133110276	133110276	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133110276delC	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		CTTTCTTCTTCCCACACATGG	0.423													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133161533	133161533	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133161533delT	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		CTGCTTCTTATTTTTTTGGCA	0.517													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2219219	2219219	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2219219delA	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	TGGATTAAAGAAAAAAAAATT	0.458													4	2	---	---	---	---	
CLEC9A	283420	broad.mit.edu	37	12	10195712	10195712	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10195712delT	uc001qxa.2	+							NM_207345	NP_997228	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A						positive regulation of cytokine secretion|receptor-mediated endocytosis	cell surface|integral to membrane	receptor activity|sugar binding			ovary(1)	1						GTAATCCAACTTTTTTTTTTG	0.308													7	4	---	---	---	---	
LRP6	4040	broad.mit.edu	37	12	12352308	12352308	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12352308delA	uc001rah.3	-						BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Intron	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				CTTTGAAGTGAAAAAAAAGGT	0.338													4	3	---	---	---	---	
ABCC9	10060	broad.mit.edu	37	12	22041045	22041056	+	Intron	DEL	GACAGAGGGGTT	-	-	rs145112683		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22041045_22041056delGACAGAGGGGTT	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	aattgctgaggacagaggggtttccaggacat	0.175													5	4	---	---	---	---	
RASSF8	11228	broad.mit.edu	37	12	26110479	26110479	+	5'Flank	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26110479delA	uc001rgx.2	+						RASSF8_uc001rgy.2_5'Flank|RASSF8_uc001rgz.2_5'Flank|uc001rgu.1_Intron|uc001rgv.3_RNA|RASSF8_uc001rgw.1_5'Flank	NM_007211	NP_009142	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family						signal transduction						0	Colorectal(261;0.0847)					ACAAAGGGCCAAAAAACCCCA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	27855781	27855781	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27855781delA								REP15 (5215 upstream) : MRPS35 (7948 downstream)																							GCCAAGGCTGAaaaaaaaaga	0.308													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31069191	31069191	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31069191delA								CAPRIN2 (161743 upstream) : TSPAN11 (10171 downstream)																							ATTGGAACATAAAAAAATGTA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34113454	34113454	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34113454delA								SYT10 (520700 upstream) : ALG10 (61762 downstream)																							GCAAAACATTAAAAAAAAAAA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	37920753	37920754	+	IGR	DEL	CT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37920753_37920754delCT								None (None upstream) : ALG10B (789803 downstream)																							ccttcatagactctacaaagag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38593971	38593971	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38593971delG								None (None upstream) : ALG10B (116586 downstream)																							agttgggaaaggatttaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38808696	38808696	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38808696delT								ALG10B (85169 upstream) : CPNE8 (237306 downstream)																							AAGATCATCATTTTCACTCAG	0.358													4	2	---	---	---	---	
SLC2A13	114134	broad.mit.edu	37	12	40189658	40189658	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40189658delT	uc010skm.1	-						C12orf40_uc009zjv.1_Intron	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)				cattggggcatttttttcttt	0.000										HNSCC(50;0.14)			4	2	---	---	---	---	
ADAMTS20	80070	broad.mit.edu	37	12	43860813	43860813	+	Intron	DEL	G	-	-	rs35870813		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43860813delG	uc010skx.1	-							NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TCTGGCATCTGAATCTACACA	0.388													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	46794987	46794988	+	IGR	DEL	AT	-	-	rs113820783		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46794987_46794988delAT								SLC38A2 (28342 upstream) : SLC38A4 (363556 downstream)																							ttttggtaacatagcattgcat	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47428667	47428667	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47428667delA								SLC38A4 (208887 upstream) : AMIGO2 (40824 downstream)																							ttgtggttgtaaggtggctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47815710	47815710	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47815710delA								FAM113B (185269 upstream) : RPAP3 (240006 downstream)																							agcaaaaATcaggcatacctc	0.000													4	2	---	---	---	---	
SPATS2	65244	broad.mit.edu	37	12	49907165	49907165	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49907165delT	uc001rud.2	+						SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron|SPATS2_uc001rug.2_Intron	NM_023071	NP_075559	Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1						ACATTCTAGATTTTTTTTTCT	0.338													4	2	---	---	---	---	
CBX5	23468	broad.mit.edu	37	12	54646179	54646179	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54646179delA	uc001sfh.3	-						CBX5_uc001sfk.3_Intron|CBX5_uc001sfi.3_Intron|CBX5_uc001sfj.3_Intron	NM_001127322	NP_001120794	P45973	CBX5_HUMAN	heterochromatin protein 1-alpha						blood coagulation|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|nuclear centromeric heterochromatin|nuclear envelope|nucleolus|transcriptional repressor complex	methylated histone residue binding|protein binding, bridging|repressing transcription factor binding				0						aggaaaaatgaaaaaaaaaaa	0.129													5	4	---	---	---	---	
SLC16A7	9194	broad.mit.edu	37	12	60069274	60069274	+	Intron	DEL	A	-	-	rs11344830		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60069274delA	uc001sqs.2	+						SLC16A7_uc001sqt.2_Intron	NM_004731	NP_004722	O60669	MOT2_HUMAN	solute carrier family 16, member 7							integral to plasma membrane|membrane fraction	pyruvate secondary active transmembrane transporter activity|secondary active monocarboxylate transmembrane transporter activity|symporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(3;0.0303)	Pyruvic acid(DB00119)	cggaactgtgaaaaaaacaaa	0.080													4	2	---	---	---	---	
FAM19A2	338811	broad.mit.edu	37	12	62274149	62274149	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62274149delC	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		ATTAAGGATGCCAACACCAAG	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	63791526	63791526	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63791526delT								AVPR1A (244936 upstream) : DPY19L2 (161167 downstream)																							aaaagaaacatttggggtgac	0.010													4	2	---	---	---	---	
TMEM5	10329	broad.mit.edu	37	12	64180890	64180890	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64180890delA	uc001srq.1	+						TMEM5_uc001srr.1_Intron|TMEM5_uc001srs.1_Intron	NM_014254	NP_055069	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5							integral to plasma membrane					0		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		tgagtcaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SRGAP1	57522	broad.mit.edu	37	12	64347084	64347084	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64347084delT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TTCTATTTTATTTTTTTCATC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69577440	69577440	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69577440delT								CPM (220420 upstream) : CPSF6 (55877 downstream)																							ATCAACATGCTTTTTTTTTTC	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70353358	70353359	+	IGR	DEL	TT	-	-	rs34064387		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70353358_70353359delTT								RAB3IP (136376 upstream) : CNOT2 (283418 downstream)																							AGAAATTTGATTTTTTTTTTAG	0.381													4	3	---	---	---	---	
NAP1L1	4673	broad.mit.edu	37	12	76450179	76450179	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76450179delA	uc001sxw.2	-						NAP1L1_uc001sxv.2_Intron|NAP1L1_uc001sxz.2_Intron|NAP1L1_uc001sxx.2_Intron|NAP1L1_uc001sxy.2_Intron|NAP1L1_uc010sty.1_Intron|NAP1L1_uc010stz.1_Intron|NAP1L1_uc010sua.1_Intron|NAP1L1_uc001syb.2_Intron|NAP1L1_uc001sya.2_Intron|NAP1L1_uc001syc.2_Intron	NM_139207	NP_631946	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1						DNA replication|nucleosome assembly|positive regulation of cell proliferation	chromatin assembly complex|melanosome	protein binding			ovary(1)|skin(1)	2		Colorectal(145;0.09)				CCATTTTAGTAAAAAAAAAAT	0.348													6	4	---	---	---	---	
NAP1L1	4673	broad.mit.edu	37	12	76479910	76479911	+	5'Flank	INS	-	T	T	rs145405072	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76479910_76479911insT	uc001sxw.2	-						NAP1L1_uc001sxz.2_5'Flank|NAP1L1_uc001sxx.2_5'Flank|NAP1L1_uc001sxy.2_5'Flank|NAP1L1_uc010sty.1_5'Flank|NAP1L1_uc010stz.1_5'Flank|NAP1L1_uc010sua.1_5'Flank|NAP1L1_uc001syb.2_5'Flank|NAP1L1_uc001sya.2_5'Flank|NAP1L1_uc001syc.2_5'Flank	NM_139207	NP_631946	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1						DNA replication|nucleosome assembly|positive regulation of cell proliferation	chromatin assembly complex|melanosome	protein binding			ovary(1)|skin(1)	2		Colorectal(145;0.09)				AATTATTTGCCTTCCCACTCTA	0.376													2	4	---	---	---	---	
OSBPL8	114882	broad.mit.edu	37	12	76761494	76761494	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76761494delT	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1						tttgtgtgtatttttttagat	0.000													4	2	---	---	---	---	
OSBPL8	114882	broad.mit.edu	37	12	76881522	76881522	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76881522delA	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1						TTCAATAATTAAAAAAAAAAT	0.289													6	3	---	---	---	---	
ZDHHC17	23390	broad.mit.edu	37	12	77206097	77206097	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77206097delT	uc001syk.1	+						ZDHHC17_uc001syi.1_Intron|ZDHHC17_uc001syj.2_Intron	NM_015336	NP_056151	Q8IUH5	ZDH17_HUMAN	huntingtin interacting protein 14						lipoprotein transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|protein binding|protein-cysteine S-palmitoleyltransferase activity|signal transducer activity|zinc ion binding				0						actgcactagtttttttttgc	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80827965	80827965	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80827965delC								PPP1R12A (498730 upstream) : PTPRQ (10161 downstream)																							acaaattgctccacagcaaca	0.000													4	2	---	---	---	---	
ACSS3	79611	broad.mit.edu	37	12	81575033	81575041	+	Intron	DEL	CTAAGGCAT	-	-	rs11277540		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81575033_81575041delCTAAGGCAT	uc001szl.1	+						ACSS3_uc001szm.1_Intron|ACSS3_uc001szn.1_Intron	NM_024560	NP_078836	Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3							mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4						agccaggtcactaaggcatctgcagtcat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89229242	89229242	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89229242delA								KITLG (255004 upstream) : DUSP6 (512597 downstream)																							agttctctggaaaagtcccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91909233	91909234	+	IGR	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91909233_91909234insG								DCN (332427 upstream) : BTG1 (469632 downstream)																							agagaagaggagagagagagag	0.233													4	2	---	---	---	---	
FGD6	55785	broad.mit.edu	37	12	95553785	95553785	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95553785delA	uc001tdp.3	-						FGD6_uc009zsx.2_Intron	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3						cctgtctcttaaaaaaaaaaa	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96001449	96001450	+	IGR	INS	-	G	G	rs150955992	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96001449_96001450insG								USP44 (56186 upstream) : NTN4 (50134 downstream)																							GTCTTATAAAACTCTTTTGATA	0.391													3	3	---	---	---	---	
SCYL2	55681	broad.mit.edu	37	12	100705212	100705212	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100705212delT	uc001thn.2	+						SCYL2_uc009ztw.1_Intron|SCYL2_uc001thm.1_Intron	NM_017988	NP_060458	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 protein						endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization	clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|protein kinase activity|receptor binding			lung(3)|ovary(2)|skin(1)	6						TTAAATAGGGTTTTTTTTTTT	0.318													6	4	---	---	---	---	
ANO4	121601	broad.mit.edu	37	12	101501892	101501892	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101501892delA	uc010svm.1	+						ANO4_uc001thw.2_Intron|ANO4_uc001thx.2_Intron|ANO4_uc001thy.2_Intron	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						AAATTCCCTGAAAAGAGTCAG	0.408										HNSCC(74;0.22)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102738299	102738299	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102738299delT								PMCH (146685 upstream) : IGF1 (51346 downstream)																							GTTTGGTATGTTTTTTTTTCT	0.169													4	2	---	---	---	---	
STAB2	55576	broad.mit.edu	37	12	104077967	104077967	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104077967delC	uc001tjw.2	+							NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						GTAAACGGTTCCCCCACCATC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	105190044	105190059	+	IGR	DEL	GTGTGTGTGTGTGTGT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105190044_105190059delGTGTGTGTGTGTGTGT								CHST11 (38161 upstream) : SLC41A2 (7217 downstream)																							gtAGGTGAACgtgtgtgtgtgtgtgtgtgtgtgtgt	0.023													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108389421	108389422	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108389421_108389422insT								ASCL4 (219001 upstream) : WSCD2 (134089 downstream)																							cagttttctagttttttttttt	0.000													3	5	---	---	---	---	
ANKRD13A	88455	broad.mit.edu	37	12	110462353	110462353	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110462353delT	uc001tpx.2	+						ANKRD13A_uc009zvl.1_Intron|ANKRD13A_uc010sxw.1_Intron|ANKRD13A_uc001tpy.2_5'Flank	NM_033121	NP_149112	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13												0						CATCAGTGCATTTAAAACATA	0.264													4	2	---	---	---	---	
DDX54	79039	broad.mit.edu	37	12	113619098	113619098	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113619098delT	uc001tup.2	-						DDX54_uc001tuq.3_Intron	NM_024072	NP_076977	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54						estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nucleolus	ATP binding|ATP-dependent RNA helicase activity|estrogen receptor binding|RNA binding|transcription corepressor activity			skin(2)|central_nervous_system(1)	3						AGTAAGTACAttttttttttt	0.229													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114025700	114025700	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114025700delA								LHX5 (115823 upstream) : RBM19 (228843 downstream)																							GCTCTTCCCTAATCCTCCAAC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114791703	114791704	+	IGR	INS	-	A	A	rs59746696		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114791703_114791704insA								RBM19 (387527 upstream) : TBX5 (32 downstream)																							GAAAGAACAGGAAAAAAAAAAA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115604160	115604160	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115604160delA								TBX3 (482191 upstream) : MED13L (792223 downstream)																							acaaaagtttaaatttgaggc	0.070													4	2	---	---	---	---	
FBXO21	23014	broad.mit.edu	37	12	117585978	117585979	+	Intron	INS	-	C	C	rs144274588	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117585978_117585979insC	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_Intron	NM_033624	NP_296373	O94952	FBX21_HUMAN	F-box only protein 21 isoform 1						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)		TTCTTTTTAAACATAAAACAGG	0.327													5	3	---	---	---	---	
TAOK3	51347	broad.mit.edu	37	12	118604653	118604654	+	Intron	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118604653_118604654delAC	uc001twx.2	-						TAOK3_uc001twv.2_Intron|TAOK3_uc001tww.2_Intron|TAOK3_uc001twy.3_Intron	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					acacacacatacacacacacac	0.317													4	2	---	---	---	---	
SUDS3	64426	broad.mit.edu	37	12	118854540	118854540	+	3'UTR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118854540delG	uc001twz.2	+	12						NM_022491	NP_071936	Q9H7L9	SDS3_HUMAN	suppressor of defective silencing 3						chromatin modification|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	Sin3 complex	histone deacetylase binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GTTAGTAGATGGGGGTACTTC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119983081	119983081	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119983081delA	uc001txf.2	-											Homo sapiens full length insert cDNA clone ZD48A05.																		CTTTCCTGCCAAAAAAAAATG	0.418											OREG0022181	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	123388702	123388702	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123388702delA								VPS37B (7990 upstream) : ABCB9 (24838 downstream)																							tatttttgttaaaaaatatgg	0.025													4	2	---	---	---	---	
SCARB1	949	broad.mit.edu	37	12	125268663	125268663	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125268663delC	uc001ugo.3	-						SCARB1_uc001ugn.3_Intron|SCARB1_uc001ugm.3_Intron|SCARB1_uc010tbd.1_Intron	NM_005505	NP_005496	Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1 isoform 1						adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|reverse cholesterol transport|triglyceride homeostasis|wound healing	caveola	1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity			kidney(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	AGTCCCTCAGCCAGTCCCCAG	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128607392	128607406	+	IGR	DEL	GTCTGCACTGGACTC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128607392_128607406delGTCTGCACTGGACTC								None (None upstream) : TMEM132C (291885 downstream)																							tcgaatacctgtctgcactggactcgtctttctgc	0.200													5	3	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	128930893	128930893	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128930893delA	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						TTTTGGTGGCATGAGCCACAG	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130708857	130708858	+	IGR	INS	-	GT	GT	rs142902508	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130708857_130708858insGT								FZD10 (58573 upstream) : PIWIL1 (113756 downstream)																							tgagtgtatgcgtgtgtgtgca	0.045													2	4	---	---	---	---	
MMP17	4326	broad.mit.edu	37	12	132310260	132310261	+	5'Flank	DEL	TC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132310260_132310261delTC	uc001ujc.1	+							NM_016155	NP_057239	Q9ULZ9	MMP17_HUMAN	matrix metalloproteinase 17 preproprotein						proteolysis	anchored to membrane|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)		tctctttctttctctctctctc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132374981	132374981	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132374981delT								MMP17 (38665 upstream) : ULK1 (4298 downstream)																							tatacaacaattttttttttt	0.000													4	3	---	---	---	---	
ULK1	8408	broad.mit.edu	37	12	132398255	132398256	+	Intron	DEL	AC	-	-	rs68126752		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132398255_132398256delAC	uc001uje.2	+							NM_003565	NP_003556	O75385	ULK1_HUMAN	Unc-51-like kinase 1						autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		cccaaaaaaaacaaaaaaaTGC	0.317													5	3	---	---	---	---	
PSPC1	55269	broad.mit.edu	37	13	20325235	20325236	+	Intron	INS	-	T	T	rs77021164		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20325235_20325236insT	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879	Q8WXF1	PSPC1_HUMAN	paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		AGTAAGTTGTGTTCTTTTTTTT	0.213													7	4	---	---	---	---	
RNF17	56163	broad.mit.edu	37	13	25451475	25451476	+	Intron	INS	-	AC	AC	rs140599228	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25451475_25451476insAC	uc001upr.2	+						RNF17_uc010aab.2_Intron|RNF17_uc010tde.1_Intron|RNF17_uc001ups.2_Intron|RNF17_uc010aac.2_Intron|RNF17_uc010aad.2_Intron	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17						multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		GCTTTATATATACATATAAAGC	0.272													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27473401	27473402	+	IGR	DEL	AG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27473401_27473402delAG								GPR12 (138479 upstream) : USP12 (169036 downstream)																							TTCTCTTTTCAGAGAGAGAGAG	0.431													4	3	---	---	---	---	
FLT3	2322	broad.mit.edu	37	13	28631814	28631814	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28631814delG	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)	CCTTGAGGGTGGGAGAGCTCC	0.483			Mis|O		AML|ALL								6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30304565	30304566	+	IGR	INS	-	GAAT	GAAT	rs143745482	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30304565_30304566insGAAT								SLC7A1 (134740 upstream) : UBL3 (33980 downstream)																							TGGTCTTTAGCGAATGAATGAA	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	32064007	32064008	+	IGR	INS	-	TCTA	TCTA	rs9547755	byFrequency	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32064007_32064008insTCTA								B3GALTL (157598 upstream) : RXFP2 (249671 downstream)																							atttgtatctgtctatctatct	0.000													4	2	---	---	---	---	
BRCA2	675	broad.mit.edu	37	13	32909712	32909712	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32909712delA	uc001uub.1	+							NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset						cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TTACTTTTCTAATTCCTTTTC	0.264			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			4	2	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33315050	33315050	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33315050delT	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		CCTTTCAACCTTTTTTTTTTT	0.358													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	44869003	44869005	+	IGR	DEL	GTT	-	-	rs145285416	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44869003_44869005delGTT								LOC121838 (264405 upstream) : SERP2 (78973 downstream)																							GTCATCAGAAGTTGCCCATTGCC	0.340													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	44869008	44869011	+	IGR	DEL	CCAT	-	-	rs10580769		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44869008_44869011delCCAT								LOC121838 (264410 upstream) : SERP2 (78967 downstream)																							CAGAAGTTGCCCATTGCCCATTAG	0.343													5	3	---	---	---	---	
LRCH1	23143	broad.mit.edu	37	13	47249486	47249487	+	Intron	INS	-	T	T	rs146391029	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47249486_47249487insT	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		GTCCAGAGATGTTTTTTTTTCA	0.376													4	2	---	---	---	---	
RCBTB1	55213	broad.mit.edu	37	13	50134443	50134446	+	Intron	DEL	AGAA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50134443_50134446delAGAA	uc001vde.1	-							NM_018191	NP_060661	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and						cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(1)	1		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		GTAATAACATAGAAAGATCAGTTT	0.348													4	2	---	---	---	---	
VPS36	51028	broad.mit.edu	37	13	52992422	52992423	+	Intron	INS	-	A	A	rs137939288	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52992422_52992423insA	uc001vgs.2	-						VPS36_uc001vgq.2_Intron	NM_016075	NP_057159	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36						cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|late endosome|membrane|nucleus	lipid binding			skin(1)	1		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		attaaaaaaataaaaagaggcc	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	54255985	54255985	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54255985delA								OLFM4 (629799 upstream) : MIR1297 (630122 downstream)																							CAAACCACTGAAAAAAAGTGT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	55982021	55982021	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55982021delC								None (None upstream) : None (None downstream)																							CACACATAATCCCCTTTCTAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59497347	59497347	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59497347delT								None (None upstream) : DIAPH3 (742378 downstream)																							TTATTCCCCATAAACATTCAG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59688658	59688658	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59688658delC								None (None upstream) : DIAPH3 (551067 downstream)																							AATCAGAGGACCACAGGTGCT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59771341	59771341	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59771341delG								None (None upstream) : DIAPH3 (468384 downstream)																							GAAGACCAGAGGGGGAAAAAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64071919	64071919	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64071919delA								None (None upstream) : OR7E156P (239649 downstream)																							aatccactggaaaaaaaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64124425	64124426	+	IGR	INS	-	TG	TG	rs141777091	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64124425_64124426insTG								None (None upstream) : OR7E156P (187142 downstream)																							TGATCTACTAAtgtgtgtgtgt	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64134282	64134282	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64134282delC								None (None upstream) : OR7E156P (177286 downstream)																							acctcactctccccagcctcg	0.000													4	2	---	---	---	---	
PCDH9	5101	broad.mit.edu	37	13	67701649	67701650	+	Intron	INS	-	GG	GG			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67701649_67701650insGG	uc001vik.2	-						PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		TGCAGGGTGCTAGTGTGTGTGT	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	67840882	67840882	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67840882delT								PCDH9 (36414 upstream) : None (None downstream)																							tcaacatTTCTTTTTTTTTTG	0.169													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71049031	71049032	+	IGR	INS	-	T	T	rs80079246		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71049031_71049032insT								ATXN8OS (335146 upstream) : DACH1 (963066 downstream)																							GACAAAAAATATTTTTTTTTaa	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	72940317	72940318	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72940317_72940318insA								DACH1 (498987 upstream) : C13orf37 (342177 downstream)																							ACTTTGGTAGTAAAAAACACAA	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73065411	73065411	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73065411delA								DACH1 (624081 upstream) : C13orf37 (217084 downstream)																							TCAGAGGCAGAAAAAAAAAAA	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75540287	75540288	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75540287_75540288insA								KLF12 (831893 upstream) : LOC647288 (271602 downstream)																							CTCTTATGGTGAAAAAAAAAGA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78910281	78910281	+	Intron	DEL	A	-	-	rs75219003		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78910281delA	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																		CAGTGAAAAGAAAAAAAAAAT	0.373													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81947601	81947602	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81947601_81947602delTG								None (None upstream) : None (None downstream)																							gtgtgtgtgttgtgtgtgtgtg	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82091607	82091607	+	IGR	DEL	T	-	-	rs36033168		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82091607delT								None (None upstream) : None (None downstream)																							ttacccatccttttttttttt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83018054	83018055	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83018054_83018055delTG								None (None upstream) : None (None downstream)																							gggttgtgtttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83524030	83524030	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83524030delA								None (None upstream) : SLITRK1 (927314 downstream)																							TATTCCAGGGAAAAAAATAAG	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	84444236	84444236	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84444236delA								None (None upstream) : SLITRK1 (7108 downstream)																							ttggttgattaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90705746	90705746	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90705746delC								None (None upstream) : MIR622 (177690 downstream)																							ATGGACACTACCTAATTCCAC	0.254													4	2	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	92523961	92523961	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92523961delC	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)				TTTTTTTTTTCAGCCACTTTG	0.294													4	2	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	93502190	93502190	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93502190delT	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)				GACACTGACATGAACTACACC	0.403													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	95004540	95004540	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95004540delC	uc001vlt.2	+							NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				CCCAGGCTCACCCCACCTTAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	98488371	98488371	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98488371delG								RAP2A (368120 upstream) : IPO5 (117558 downstream)																							tttacaaaaagtctgaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	99280354	99280354	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99280354delT								STK24 (50958 upstream) : SLC15A1 (55703 downstream)																							TGATTGTGGGttttttttttc	0.184													4	2	---	---	---	---	
TM9SF2	9375	broad.mit.edu	37	13	100188554	100188554	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100188554delT	uc001voj.1	+						TM9SF2_uc010afz.1_Intron	NM_004800	NP_004791	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2 precursor						transport	endosome membrane|integral to plasma membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					Gttttttttgttttttttttt	0.119													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102427874	102427875	+	Intron	DEL	GT	-	-	rs34273365		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102427874_102427875delGT	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1A						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TCTGGGGTGAGTGTGTGTGTGT	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106468297	106468297	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106468297delT								DAOA (324915 upstream) : EFNB2 (673801 downstream)																							CCCCCTCTGATCTTGAAGCCT	0.433													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106967438	106967438	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106967438delG								DAOA (824056 upstream) : EFNB2 (174660 downstream)																							CAGGGATCCTGGGGTTTTGCT	0.493													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108007633	108007633	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108007633delA	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						AGCAAAAGGGAAAAAAAGAAG	0.393													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108490268	108490269	+	Intron	INS	-	A	A	rs140562926	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108490268_108490269insA	uc001vql.2	-						uc001vqm.2_5'Flank	NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						GTATACAGATTAAAAAAAAACA	0.337													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	109113941	109113941	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109113941delT								TNFSF13B (154577 upstream) : MYO16 (134559 downstream)																							AACTGAACAAttttttttttt	0.174													3	4	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109333843	109333843	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109333843delG	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			TGTTCTGTGTGGGAGGTTGTA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	110658985	110658985	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110658985delT								IRS2 (220071 upstream) : COL4A1 (142326 downstream)																							CACCTTGCCCTTGGCCTCCTA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111643531	111643531	+	IGR	DEL	T	-	-	rs142151649	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111643531delT								ANKRD10 (76115 upstream) : ARHGEF7 (124093 downstream)																							TTAATCATAATTAGAAACCAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19010563	19010566	+	IGR	DEL	GCAA	-	-	rs145483626	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19010563_19010566delGCAA								None (None upstream) : OR11H12 (367028 downstream)																							tgcaaacatcgcaaagaagtttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20211546	20211548	+	IGR	DEL	GCC	-	-	rs68122128		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20211546_20211548delGCC								P704P (191274 upstream) : OR4Q3 (4039 downstream)																							AACAGCAGCAGCCTAGGGAATCC	0.433													2	4	---	---	---	---	
STXBP6	29091	broad.mit.edu	37	14	25454326	25454326	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25454326delT	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)		TGGATATCTGTTCATCTTGTG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35390294	35390295	+	IGR	INS	-	ATT	ATT	rs113610910		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35390294_35390295insATT								BAZ1A (45441 upstream) : C14orf19 (18833 downstream)																							ACACATATTGCAtttttttttt	0.188													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	39974397	39974397	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39974397delC								FBXO33 (72693 upstream) : None (None downstream)																							agtggtgtatccacgaaagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	50500833	50500833	+	IGR	DEL	A	-	-	rs10533335		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50500833delA								C14orf182 (26595 upstream) : C14orf183 (49537 downstream)																							gatgatagatagatagataga	0.194													3	3	---	---	---	---	
GNG2	54331	broad.mit.edu	37	14	52424362	52424362	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52424362delA	uc001wzi.2	+						GNG2_uc001wzh.2_Intron|GNG2_uc010aoc.1_Intron|GNG2_uc001wzj.2_Intron|GNG2_uc001wzk.2_Intron	NM_053064	NP_444292	P59768	GBG2_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|platelet activation|synaptic transmission	heterotrimeric G-protein complex	protein binding|signal transducer activity				0	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)	ctgacccattactaccttcta	0.000													4	2	---	---	---	---	
NID2	22795	broad.mit.edu	37	14	52481240	52481244	+	Intron	DEL	TTACT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52481240_52481244delTTACT	uc001wzo.2	-						NID2_uc010tqs.1_Intron|NID2_uc010tqt.1_Intron|NID2_uc001wzp.2_Intron	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor							basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					GGAAGAAAAGTTACTTTACCACATA	0.498											OREG0022678	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	39	17	---	---	---	---	
TXNDC16	57544	broad.mit.edu	37	14	52910703	52910703	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52910703delA	uc001wzs.2	-						TXNDC16_uc010tqu.1_Intron|TXNDC16_uc010aoe.2_Intron	NM_020784	NP_065835	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16 isoform 1						cell redox homeostasis	extracellular region					0	Breast(41;0.0716)					AAGACATAGCAAAAGAAGAAA	0.353													4	2	---	---	---	---	
SYT16	83851	broad.mit.edu	37	14	62539103	62539104	+	Intron	DEL	GT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62539103_62539104delGT	uc001xfu.1	+						SYT16_uc010tsd.1_Intron	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		ACATGCAGGGGTGTGTGTGTGT	0.441													4	2	---	---	---	---	
RBM25	58517	broad.mit.edu	37	14	73582699	73582699	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73582699delG	uc001xno.2	+						RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		TCATTTAAGTGGGGGGAAAGA	0.433													4	2	---	---	---	---	
C14orf179	112752	broad.mit.edu	37	14	76474737	76474737	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76474737delA	uc010asm.1	+						C14orf179_uc001xsf.2_Intron|C14orf179_uc010asl.1_Intron|C14orf179_uc001xsg.2_Intron|C14orf179_uc010tve.1_Intron|C14orf179_uc001xse.2_Intron	NM_001102564	NP_001096034	Q96FT9	IFT43_HUMAN	hypothetical protein LOC112752 isoform 2						cilium morphogenesis|intraflagellar retrograde transport						0				BRCA - Breast invasive adenocarcinoma(234;0.0199)		AAAATAATATAATAGCCACTG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	86337053	86337054	+	IGR	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86337053_86337054delCA								FLRT2 (242784 upstream) : None (None downstream)																							cacacacatgcacacacacaca	0.114													4	2	---	---	---	---	
ATXN3	4287	broad.mit.edu	37	14	92548977	92548977	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92548977delT	uc001yac.3	-						ATXN3_uc010aug.2_Intron|ATXN3_uc001yad.3_Intron|ATXN3_uc010auh.2_Intron|ATXN3_uc001yae.3_Intron|ATXN3_uc010twl.1_Intron	NM_004993	NP_004984	P54252	ATX3_HUMAN	ataxin 3 reference isoform						cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		TCCAACTAAGTtttttttttc	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98677837	98677837	+	IGR	DEL	A	-	-	rs145605375		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98677837delA								C14orf64 (233376 upstream) : C14orf177 (500113 downstream)																							TTGGAGGAAGAAAAAAAAAAT	0.234													4	2	---	---	---	---	
DYNC1H1	1778	broad.mit.edu	37	14	102486578	102486578	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102486578delA	uc001yks.2	+						DYNC1H1_uc001ykt.1_Intron	NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						GCCCCAGGGTAACAAAGTCAC	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20422184	20422185	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20422184_20422185insA								None (None upstream) : GOLGA6L6 (314909 downstream)																							taactctcactaaaaaatgact	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20514042	20514043	+	IGR	INS	-	GAG	GAG	rs147472139	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20514042_20514043insGAG								None (None upstream) : GOLGA6L6 (223051 downstream)																							tgaaatgagatgagatgatata	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20593342	20593342	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20593342delT	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		CACATAGGCATTTTACAGATA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20594769	20594770	+	Intron	DEL	AT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20594769_20594770delAT	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		ATAAATACACATGATTTCAAGA	0.396													4	2	---	---	---	---	
LOC646214	646214	broad.mit.edu	37	15	21935593	21935593	+	RNA	DEL	A	-	-	rs111463627		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21935593delA	uc010tzj.1	-	1		c.5147delT				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						AATGAAAAACAAAAAGAACAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22152284	22152285	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22152284_22152285delTG								CXADRP2 (135406 upstream) : LOC727924 (125747 downstream)																							TGCAATAAACtgtgtgtgtgtg	0.292													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22554752	22554752	+	IGR	DEL	G	-	-	rs60676008		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22554752delG								MIR1268 (41472 upstream) : GOLGA8DP (147533 downstream)																							ctggtgtggtgtagttttatc	0.000													2	4	---	---	---	---	
NIPA1	123606	broad.mit.edu	37	15	23052358	23052363	+	Intron	DEL	GGCCAC	-	-	rs72277823		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23052358_23052363delGGCCAC	uc001yvc.2	-						NIPA1_uc001yvd.2_Intron|NIPA1_uc001yve.2_Intron	NM_144599	NP_653200	Q7RTP0	NIPA1_HUMAN	non-imprinted in Prader-Willi/Angelman syndrome						cell death	early endosome|integral to membrane|plasma membrane					0		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		AGGAATACCAGGCCACGGAGGCTCCC	0.650													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23685749	23685751	+	IGR	DEL	CTC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23685749_23685751delCTC								GOLGA8E (237326 upstream) : MKRN3 (124703 downstream)																							ctcgcatcttctcctcctggtcc	0.000													7	6	---	---	---	---	
MKRN3	7681	broad.mit.edu	37	15	23839979	23839979	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23839979delT	uc001ywi.2	+									Q13064	MKRN3_HUMAN	SubName: Full=MKRN3 protein;							ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			lung(6)|large_intestine(2)|ovary(2)	10		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		agaaaaaggcttttttaattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	28701620	28701621	+	IGR	INS	-	G	G	rs71287560		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28701620_28701621insG								GOLGA8G (64449 upstream) : WHAMML2 (281108 downstream)																							TCCAGGCAGGACCCCCAGCTGC	0.644													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	35423887	35423887	+	IGR	DEL	A	-	-	rs79341832		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35423887delA								ZNF770 (143433 upstream) : LOC723972 (105640 downstream)																							aCAACTATACAAAAAAAAAAC	0.209													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39712095	39712096	+	IGR	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39712095_39712096insG								C15orf54 (165047 upstream) : THBS1 (161184 downstream)																							GGTGACAGCAAGGGCAAATCAT	0.480													4	2	---	---	---	---	
PLA2G4E	123745	broad.mit.edu	37	15	42304895	42304895	+	5'Flank	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42304895delG	uc001zow.1	-							NM_001080490	NP_001073959	Q3MJ16	PA24E_HUMAN	phospholipase A2, group 4E						phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity				0		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		GTGACAAGATGGGAACGTTGT	0.507													4	2	---	---	---	---	
VPS39	23339	broad.mit.edu	37	15	42453256	42453256	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42453256delT	uc001zpd.2	-						VPS39_uc001zpc.2_Intron|VPS39_uc001zpb.2_Intron	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39						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)		GCATGGGGTATTTTTTTATTA	0.463													4	2	---	---	---	---	
VPS39	23339	broad.mit.edu	37	15	42495970	42495970	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42495970delA	uc001zpd.2	-						VPS39_uc001zpc.2_Intron	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39						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)		TAGCCAGAGGACCTGTCCCAT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	42953150	42953150	+	Intron	DEL	T	-	-	rs147143825		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42953150delT	uc001zqg.2	+						uc001zqh.2_Intron					Homo sapiens cDNA FLJ16106 fis, clone THYMU1000496, moderately similar to KINESIN-LIKE PROTEIN KIF1C.																		TTTTGTTTTGTTTTTTTTTTT	0.353													1	6	---	---	---	---	
CKMT1A	548596	broad.mit.edu	37	15	43988365	43988365	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43988365delA	uc001zsn.2	+						CKMT1A_uc010uea.1_Intron|CKMT1A_uc010ueb.1_Intron|CKMT1A_uc010bdo.2_Intron|CKMT1A_uc001zso.3_Intron	NM_001015001	NP_001015001	P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1A precursor						creatine metabolic process	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)	Creatine(DB00148)	ATGCCCTCATAAATGCTTTTT	0.502													33	15	---	---	---	---	
C15orf33	196951	broad.mit.edu	37	15	49719836	49719836	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49719836delT	uc001zxl.2	-						C15orf33_uc001zxm.2_Intron|FGF7_uc001zxn.2_Intron	NM_152647	NP_689860	Q96M60	CO033_HUMAN	hypothetical protein LOC196951											ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)		TTCTCATGACTTTTTTTTGAA	0.353													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	55402873	55402873	+	IGR	DEL	G	-	-	rs11344353		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55402873delG								UNC13C (482068 upstream) : RSL24D1 (70648 downstream)																							CCCTTCCtgtggggcagaggc	0.333													4	2	---	---	---	---	
CCPG1	9236	broad.mit.edu	37	15	55653371	55653371	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55653371delT	uc002acv.1	-						CCPG1_uc002acy.2_Intron|CCPG1_uc002acu.1_Intron|CCPG1_uc002acw.1_Intron|CCPG1_uc002acx.2_Intron|CCPG1_uc010bfk.1_Intron|CCPG1_uc002acz.1_Intron	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)		GGTGTAAGAAttttttttttt	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	56324578	56324579	+	IGR	INS	-	T	T	rs113161754		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56324578_56324579insT								NEDD4 (38743 upstream) : RFX7 (54900 downstream)																							caaaagcttgattttttttttc	0.173													5	3	---	---	---	---	
FAM81A	145773	broad.mit.edu	37	15	59771837	59771837	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59771837delA	uc002agc.2	+							NM_152450	NP_689663	Q8TBF8	FA81A_HUMAN	hypothetical protein LOC145773											ovary(1)	1						ggagacacccagggggatcac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60279526	60279526	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60279526delA								BNIP2 (297884 upstream) : FOXB1 (16895 downstream)																							agagagagagagagagagaAt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60279528	60279528	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60279528delA								BNIP2 (297886 upstream) : FOXB1 (16893 downstream)																							agagagagagagagagaAtaa	0.010													4	2	---	---	---	---	
RORA	6095	broad.mit.edu	37	15	60989764	60989765	+	Intron	DEL	TT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60989764_60989765delTT	uc002agx.2	-							NM_134261	NP_599023	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						TCAAGTCTACTTTTTTTTTTTT	0.376													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	61978609	61978609	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61978609delT								RORA (457107 upstream) : VPS13C (165983 downstream)																							taccaggacattttgaagata	0.095													4	2	---	---	---	---	
RAB8B	51762	broad.mit.edu	37	15	63532803	63532803	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63532803delT	uc002alz.2	+						RAB8B_uc010uih.1_Intron	NM_016530	NP_057614	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)|kidney(1)	2						CCCCACTTGCTTTTTTTTTTC	0.328													4	3	---	---	---	---	
CORO2B	10391	broad.mit.edu	37	15	68901276	68901277	+	Intron	DEL	AG	-	-	rs72398422		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68901276_68901277delAG	uc002arj.3	+							NM_006091	NP_006082	Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6						GGTACTAGGAAGAGAGAGAGAG	0.460													4	6	---	---	---	---	
CORO2B	10391	broad.mit.edu	37	15	68933006	68933006	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68933006delG	uc002arj.3	+						CORO2B_uc010bic.2_Intron	NM_006091	NP_006082	Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6						aacacgggctgggcattacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	69968072	69968075	+	IGR	DEL	TGAG	-	-	rs147496849		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69968072_69968075delTGAG								LOC145837 (104293 upstream) : C15orf50 (159498 downstream)																							TGCACCAGGCTGAGTGAGGGAGTG	0.569													3	3	---	---	---	---	
TLE3	7090	broad.mit.edu	37	15	70366401	70366401	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70366401delC	uc002asm.2	-						TLE3_uc002ask.2_Intron|TLE3_uc002asl.2_Intron|TLE3_uc010ukd.1_Intron|TLE3_uc010bik.1_Intron|TLE3_uc010bil.1_Intron|TLE3_uc002asn.2_Intron|TLE3_uc002asp.2_Intron|TLE3_uc002aso.2_Intron|TLE3_uc010bim.1_Intron	NM_005078	NP_005069	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform a						organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2						AAGACGTAAACCCAAATTCCA	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	72902933	72902933	+	5'Flank	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72902933delC	uc010ukq.1	-											DQ578838																		AGGCATGGAGCCCCCAATCAT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	77859825	77859825	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77859825delG								HMG20A (81882 upstream) : LINGO1 (45544 downstream)																							TGAGAGACCTGGGGGCAGGTG	0.617													4	2	---	---	---	---	
ACSBG1	23205	broad.mit.edu	37	15	78527039	78527039	+	5'Flank	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78527039delC	uc002bdh.2	-						ACSBG1_uc010umw.1_5'Flank|ACSBG1_uc010umx.1_5'Flank|ACSBG1_uc010umy.1_5'Flank	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin						long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1						CTTTCCTTTTCTTTGTGGTTT	0.403													4	2	---	---	---	---	
DNAJA4	55466	broad.mit.edu	37	15	78574450	78574450	+	3'UTR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78574450delA	uc002bdj.1	+	7					DNAJA4_uc002bdi.2_3'UTR|DNAJA4_uc002bdk.2_3'UTR|DNAJA4_uc002bdm.1_3'UTR	NM_001130182	NP_001123654	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4						protein folding|response to heat	membrane	ATP binding|heat shock protein binding|metal ion binding|unfolded protein binding			skin(1)	1						CTTGTCATATAAAAGGAATTT	0.348													4	2	---	---	---	---	
STARD5	80765	broad.mit.edu	37	15	81611436	81611436	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81611436delA	uc002bgm.2	-						STARD5_uc002bgn.2_Intron	NM_181900	NP_871629	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer protein 5						C21-steroid hormone biosynthetic process|lipid transport	cytosol	lipid binding			ovary(1)	1						CTTCCGCAGGAAAAAAAAAAA	0.488													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82407631	82407631	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82407631delC								MEX3B (69270 upstream) : EFTUD1 (14930 downstream)																							CACCTGGCTGCCTCGACCATG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87734935	87734935	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87734935delA								AGBL1 (162652 upstream) : NCRNA00052 (385225 downstream)																							CTGCCACAATAAAAAAAAAAT	0.383													4	4	---	---	---	---	
C15orf42	90381	broad.mit.edu	37	15	90139154	90139154	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90139154delT	uc002boe.2	+							NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	leucine-rich repeat kinase 1						cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|mitotic cell cycle DNA replication checkpoint|regulation of DNA-dependent DNA replication initiation|response to ionizing radiation	nucleus	chromatin binding|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			GCTTTACAGATTTTTTTTTTT	0.249													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98782338	98782338	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98782338delT								ARRDC4 (265271 upstream) : FAM169B (198053 downstream)																							AGAAGCTCTATTTCTGTTAAG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	900236	900236	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:900236delG								PRR25 (36376 upstream) : LMF1 (3399 downstream)																							GGCTGCGTGTGGGACGATTTC	0.507													4	2	---	---	---	---	
ADCY9	115	broad.mit.edu	37	16	4142838	4142838	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4142838delT	uc002cvx.2	-							NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9						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 plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6						GTTGGTTTGGTTTTTTAATGT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5571660	5571661	+	Intron	INS	-	T	T	rs144322516	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5571660_5571661insT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																		TTGCCTCTAGGTTTGTAAGCAA	0.505													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5915903	5915904	+	IGR	DEL	GA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5915903_5915904delGA								FAM86A (768114 upstream) : A2BP1 (153228 downstream)																							tgtgcaggaggagagagagaga	0.000													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6256990	6256991	+	Intron	INS	-	C	C	rs35769347		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6256990_6256991insC	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		AAAGCTACTTTTTTTTTTTTTC	0.347													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7208699	7208702	+	Intron	DEL	TGTG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7208699_7208702delTGTG	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		tctgtgtgtttgtgtggtgcatat	0.000													4	2	---	---	---	---	
ABAT	18	broad.mit.edu	37	16	8805349	8805349	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8805349delG	uc002czc.3	+						ABAT_uc002czd.3_5'Flank|ABAT_uc010buh.2_5'Flank	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor						behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	AGTAGGCAGTGGGTCTGTTAA	0.453													4	2	---	---	---	---	
GRIN2A	2903	broad.mit.edu	37	16	10005993	10005995	+	Intron	DEL	GAT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10005993_10005995delGAT	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc010uyn.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	tggtaatgacgatgacgatAaag	0.010													3	3	---	---	---	---	
CLEC16A	23274	broad.mit.edu	37	16	11154578	11154578	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11154578delT	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041	Q2KHT3	CL16A_HUMAN	C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2						CCCCCTTTGATTTTTTTTTTT	0.423													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17954478	17954478	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17954478delA								XYLT1 (389740 upstream) : NOMO2 (556705 downstream)																							GTCACTCCGGAATGTTAACCG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	19371600	19371601	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19371600_19371601insT								LOC728276 (55884 upstream) : TMC5 (50260 downstream)																							CTGTGCTTGACTTtttttttta	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20136931	20136931	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20136931delA								GPR139 (51831 upstream) : GP2 (184881 downstream)																							tttctccaccaaaaaaaatga	0.000													4	2	---	---	---	---	
GP2	2813	broad.mit.edu	37	16	20340336	20340336	+	5'Flank	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20340336delC	uc002dgv.2	-						GP2_uc002dgw.2_5'Flank|GP2_uc002dgx.2_5'Flank|GP2_uc002dgy.2_5'Flank	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform							anchored to membrane|extracellular region|plasma membrane				ovary(3)|skin(1)	4						TTCCTTGACTCCGCATGTTCA	0.418													4	2	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	20955471	20955472	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20955471_20955472insA	uc010vbe.1	-						DNAH3_uc010vbd.1_Intron	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		tcttttaaattaaaaaaaaaag	0.005													4	2	---	---	---	---	
VWA3A	146177	broad.mit.edu	37	16	22134675	22134675	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22134675delA	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron|VWA3A_uc010bxc.2_Intron	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		CAATGCCTTTAAAAAAAAAAA	0.478													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22732957	22732958	+	IGR	DEL	CC	-	-	rs10557533		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22732957_22732958delCC								LOC653786 (144771 upstream) : HS3ST2 (92902 downstream)																							ccacacacctcccccccaccgc	0.000													5	3	---	---	---	---	
PRKCB	5579	broad.mit.edu	37	16	24163337	24163338	+	Intron	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24163337_24163338insG	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	TCGTTTTGGTTGGGGGAATGGG	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27471140	27471140	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27471140delA								IL21R (9025 upstream) : GTF3C1 (795 downstream)																							CTTTAAAGGGAAAAAAAATAG	0.428													3	3	---	---	---	---	
ITGAM	3684	broad.mit.edu	37	16	31343181	31343182	+	3'UTR	INS	-	GTGTGTGCGA	GTGTGTGCGA	rs142861575	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31343181_31343182insGTGTGTGCGA	uc002ebq.2	+	30					ITGAM_uc002ebr.2_3'UTR|ITGAM_uc010can.2_3'UTR	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						tgtgtatgtgcgtgtgtgcaag	0.267													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32452341	32452341	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32452341delA								HERC2P4 (288467 upstream) : TP53TG3B (232500 downstream)																							CTTTATAATCAATAGATTTGT	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32819286	32819286	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32819286delT								TP53TG3B (130408 upstream) : SLC6A10P (69511 downstream)																							tcatttcatatcatttcctca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33370073	33370074	+	IGR	DEL	TC	-	-	rs113975885		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33370073_33370074delTC								SLC6A10P (473610 upstream) : MIR1826 (595434 downstream)																							TTTTTGTTGTTCTCAACCTGAG	0.436													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33451081	33451081	+	IGR	DEL	C	-	-	rs34538164		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33451081delC								SLC6A10P (554618 upstream) : MIR1826 (514427 downstream)																							tctgagggtgctgtatagtaa	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33537029	33537030	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33537029_33537030insT								SLC6A10P (640566 upstream) : MIR1826 (428478 downstream)																							TTTTCCAACAATTTTTTTTCAG	0.292													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33918733	33918733	+	IGR	DEL	A	-	-	rs76673674		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33918733delA								None (None upstream) : MIR1826 (46775 downstream)																							atcttcacataaaaagtagaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46688498	46688498	+	IGR	DEL	A	-	-	rs75307232		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46688498delA								SHCBP1 (33187 upstream) : VPS35 (5093 downstream)																							Ctgttaatggaaaaaaaaaac	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	48751242	48751242	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48751242delA								N4BP1 (107122 upstream) : CBLN1 (560969 downstream)																							tccatcttggaagacattcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	48903359	48903359	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48903359delC								N4BP1 (259239 upstream) : CBLN1 (408852 downstream)																							ggcctcctcaccccgccttcc	0.000													4	2	---	---	---	---	
CYLD	1540	broad.mit.edu	37	16	50794708	50794711	+	Intron	DEL	ATAT	-	-	rs139067203		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50794708_50794711delATAT	uc002egp.1	+						CYLD_uc002egn.1_Intron|CYLD_uc002ego.2_Intron|CYLD_uc010cbs.1_Intron|CYLD_uc002egq.1_Intron|CYLD_uc002egr.1_Intron|CYLD_uc002egs.1_Intron	NM_015247	NP_056062	Q9NQC7	CYLD_HUMAN	ubiquitin carboxyl-terminal hydrolase CYLD						cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3)	28		all_cancers(37;0.0156)				tatctggaggatatatatattccc	0.000			Mis|N|F|S		cylindroma	cylindroma			Familial_Cylindromatosis|Multiple_Trichoepithelioma_Familial				1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52245008	52245008	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52245008delT								None (None upstream) : TOX3 (226910 downstream)																							cctcatcttcttgatagcacc	0.169													4	2	---	---	---	---	
CCDC135	84229	broad.mit.edu	37	16	57738289	57738290	+	Intron	DEL	AC	-	-	rs71383261		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57738289_57738290delAC	uc002emi.2	+						CCDC135_uc002emj.2_Intron|CCDC135_uc002emk.2_Intron	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135							cytoplasm				central_nervous_system(1)	1						ACGCAAGCGTacacacacacac	0.421													6	3	---	---	---	---	
KATNB1	10300	broad.mit.edu	37	16	57773136	57773138	+	Intron	DEL	CTG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57773136_57773138delCTG	uc002eml.1	+							NM_005886	NP_005877	Q9BVA0	KTNB1_HUMAN	katanin p80 subunit B 1						cell division|mitosis|negative regulation of microtubule depolymerization|positive regulation of microtubule depolymerization|protein targeting	katanin complex|microtubule|spindle pole	microtubule binding|protein heterodimerization activity				0		all_neural(199;0.223)				TATTGGGCATCTGCTGCTGCTGC	0.581													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58268141	58268141	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58268141delG								CSNK2A2 (36359 upstream) : CCDC113 (15699 downstream)																							AAAAGGTGGAGGGACTGAGTG	0.488													4	2	---	---	---	---	
CDH8	1006	broad.mit.edu	37	16	61891973	61891974	+	Intron	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61891973_61891974delAC	uc002eog.1	-						CDH8_uc002eoh.2_5'Flank	NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		AAATAATCAAacacacacacac	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62602942	62602942	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62602942delA								CDH8 (532906 upstream) : None (None downstream)																							tgtGAGTAATAAAAAAAATGT	0.174													4	2	---	---	---	---	
LOC283867	283867	broad.mit.edu	37	16	65558108	65558108	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65558108delT	uc010cdp.1	-						LOC283867_uc002eol.1_Intron					Homo sapiens cDNA clone IMAGE:5276218.												0				OV - Ovarian serous cystadenocarcinoma(108;0.17)		GGAAAACTTGTTTTTTTCTGG	0.418													4	2	---	---	---	---	
ZNF23	7571	broad.mit.edu	37	16	71498014	71498016	+	5'Flank	DEL	ATA	-	-	rs67540871		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71498014_71498016delATA	uc002faf.2	-						ZNF23_uc010vmf.1_5'Flank|ZNF23_uc002fag.2_5'Flank|ZNF23_uc002fah.2_5'Flank|ZNF23_uc002fai.2_Intron|uc002faj.1_RNA	NM_145911	NP_666016	P17027	ZNF23_HUMAN	zinc finger protein 23						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		GAAAAATGAGATAATAATGCACA	0.296													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73481634	73481635	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73481634_73481635insA								HTA (353964 upstream) : PSMD7 (849046 downstream)																							ggaagttggtcaagaagaattt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73576266	73576266	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73576266delT								HTA (448596 upstream) : PSMD7 (754415 downstream)																							ACATGCAGAATTTTTTTTTTC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73907877	73907877	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73907877delA								HTA (780207 upstream) : PSMD7 (422804 downstream)																							AAGTAAGAAGAAAAAAAAAAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74299544	74299545	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74299544_74299545insT								None (None upstream) : PSMD7 (31136 downstream)																							GAGTTCTGTTGTTTTTTTTAAA	0.297													4	2	---	---	---	---	
VAT1L	57687	broad.mit.edu	37	16	77927025	77927025	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77927025delA	uc002ffg.1	+							NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1						TAACAACAACAAAAAAAGCCT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79387398	79387398	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79387398delA								WWOX (140835 upstream) : MAF (240348 downstream)																							TGATGGCATGAAGTGTGCTAC	0.383													4	2	---	---	---	---	
GAN	8139	broad.mit.edu	37	16	81397079	81397080	+	Intron	INS	-	A	A	rs143165204	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81397079_81397080insA	uc002fgo.2	+							NM_022041	NP_071324	Q9H2C0	GAN_HUMAN	gigaxonin						cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)				GGAACACTGGGAAAAAAGATTT	0.257													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84282058	84282061	+	IGR	DEL	TGTG	-	-	rs149898360		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84282058_84282061delTGTG								KCNG4 (8702 upstream) : WFDC1 (46340 downstream)																							caaaaggttttgtgtgtgtgtgtg	0.137													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86168723	86168723	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86168723delG								IRF8 (212514 upstream) : LOC732275 (196733 downstream)																							CTATTAAAGAGGAATGATCAA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86833596	86833596	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86833596delC								FOXL1 (218293 upstream) : FBXO31 (529348 downstream)																							CATCCTGTTGCCCCTTTGTGA	0.423													4	2	---	---	---	---	
TUSC5	286753	broad.mit.edu	37	17	1182046	1182047	+	5'Flank	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1182046_1182047delCA	uc002fsi.1	+							NM_172367	NP_758955	Q8IXB3	TUSC5_HUMAN	LOST1						response to biotic stimulus	integral to membrane				skin(2)	2				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ACTTTCAAACCACACACACACA	0.312													4	2	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2845346	2845346	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2845346delT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						agagttcctgttttggcctct	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7858598	7858598	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7858598delA								CNTROB (5703 upstream) : GUCY2D (47390 downstream)																							aaaaaaaaagaaaaaaaaaGA	0.199													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	12247090	12247090	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12247090delT								MAP2K4 (200040 upstream) : MYOCD (322117 downstream)																							ATTTTTAAACTTTTTTTTTTT	0.393													4	3	---	---	---	---	
TBC1D26	353149	broad.mit.edu	37	17	15639050	15639051	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15639050_15639051insT	uc010cov.2	+						TBC1D26_uc010cou.1_Intron|TBC1D26_uc002gpb.3_Intron	NM_178571	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26							intracellular	Rab GTPase activator activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		GATGGGTTTTGTTTTTAGAAAG	0.554													16	8	---	---	---	---	
RAI1	10743	broad.mit.edu	37	17	17672440	17672443	+	Intron	DEL	AGAA	-	-	rs138675889		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17672440_17672443delAGAA	uc002grm.2	+							NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1							cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)		AAAGGAAATTAGAAAGAAGAAATG	0.544													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	19548141	19548141	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19548141delT								SLC47A1 (65795 upstream) : ALDH3A2 (3923 downstream)																							AATTAAACACTTTGTATATGT	0.368													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21228580	21228581	+	IGR	INS	-	A	A	rs148228062		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21228580_21228581insA								MAP2K3 (10031 upstream) : KCNJ12 (51118 downstream)																							caagtagggataaaaaaataag	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21229525	21229526	+	IGR	INS	-	T	T	rs138391409		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21229525_21229526insT								MAP2K3 (10976 upstream) : KCNJ12 (50173 downstream)																							gtttaaaatgattttttctttt	0.000													8	6	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21306688	21306690	+	Intron	DEL	ACA	-	-	rs144651249	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21306688_21306690delACA	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)	attggttttgacaacatcataca	0.039										Prostate(3;0.18)			0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	22010669	22010669	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22010669delT								FLJ36000 (97599 upstream) : None (None downstream)																							ACAGGGTGTGTTTTTTTTTCA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25770971	25770974	+	IGR	DEL	TTTG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25770971_25770974delTTTG								WSB1 (130326 upstream) : KSR1 (28062 downstream)																							GATATGCAtttttgtttgtttgtt	0.255													6	4	---	---	---	---	
RAB11FIP4	84440	broad.mit.edu	37	17	29729208	29729215	+	Intron	DEL	CATCCATC	-	-	rs72052824		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29729208_29729215delCATCCATC	uc002hgn.1	+							NM_032932	NP_116321	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)						cytokinesis|interspecies interaction between organisms|protein transport	cleavage furrow|endocytic vesicle|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding			skin(1)	1		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				tctgtccatgcatccatccatccatcca	0.317													4	3	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31614804	31614804	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31614804delC	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	CTCTAGAACTCCATCTCTCAC	0.537													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31775400	31775400	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31775400delG	uc002hhu.2	-							NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	tactttatatgggaaagattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32639398	32639398	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32639398delA								CCL11 (24199 upstream) : CCL8 (6668 downstream)																							ggccatcttgaaaaccgacaa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35097668	35097669	+	IGR	DEL	AG	-	-	rs66718564		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35097668_35097669delAG								MRM1 (132262 upstream) : LHX1 (196830 downstream)																							catgtgtgtaagagagtgctgg	0.064													2	5	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35651048	35651048	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35651048delA	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron|ACACA_uc002hnq.2_Intron|ACACA_uc002hnp.1_Intron	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	tcattcgttgaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36403151	36403151	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36403151delT	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																		TTGCTACTAATTTTTTTTTTC	0.348													4	2	---	---	---	---	
MSL1	339287	broad.mit.edu	37	17	38279568	38279570	+	In_Frame_Del	DEL	CAG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38279568_38279570delCAG	uc002hub.2	+	1	119_121	c.100_102delCAG	c.(100-102)CAGdel	p.Q38del	MSL1_uc002hua.3_5'UTR|MSL1_uc002huc.2_5'Flank	NM_001012241	NP_001012241	Q68DK7	MSL1_HUMAN	hampin	239	Potential.				histone H4-K16 acetylation	MSL complex					0						CCTCATCGAACAGCAGCAGCAGC	0.601													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39607506	39607507	+	IGR	DEL	AA	-	-	rs140267265	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39607506_39607507delAA								KRT38 (9910 upstream) : KRT32 (8259 downstream)																							atgtcagcataaacagaaatat	0.000													4	2	---	---	---	---	
JUP	3728	broad.mit.edu	37	17	39808306	39808308	+	Intron	DEL	ACC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39808306_39808308delACC	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)		cacacacactaccaccaaccaac	0.000													4	5	---	---	---	---	
DBF4B	80174	broad.mit.edu	37	17	42825051	42825051	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42825051delA	uc002ihf.2	+						DBF4B_uc002ihe.2_Intron|DBF4B_uc010wjc.1_Intron	NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1						cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)				GGGGCTGGCCAAAAAAAATAA	0.483													4	2	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43912267	43912268	+	3'UTR	INS	-	G	G	rs140399885	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43912267_43912268insG	uc010dap.2	+	14					CRHR1_uc010wjx.1_3'UTR|CRHR1_uc002ijp.2_3'UTR|CRHR1_uc002ijm.2_3'UTR|CRHR1_uc002ijn.2_3'UTR|CRHR1_uc010dar.2_3'UTR|CRHR1_uc010dao.2_3'UTR|CRHR1_uc010daq.2_3'UTR	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		ACTGACAGCCTGGGGGGGCCGC	0.678													3	3	---	---	---	---	
MAPT	4137	broad.mit.edu	37	17	44001012	44001013	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44001012_44001013insT	uc002ijr.3	+						MAPT_uc010dau.2_Intron|MAPT_uc002ijs.3_Intron|MAPT_uc002ijx.3_Intron|MAPT_uc002ijt.3_Intron|MAPT_uc002iju.3_Intron|MAPT_uc002ijv.3_Intron	NM_016835	NP_058519	P10636	TAU_HUMAN	microtubule-associated protein tau isoform 1						cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)				GGCCTACCCACTTTAGCTTTTA	0.421													3	4	---	---	---	---	
MAPT	4137	broad.mit.edu	37	17	44102682	44102683	+	Splice_Site	INS	-	T	T	rs79400568		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44102682_44102683insT	uc002ijr.3	+	14	3742	c.3422_splice	c.e14+1		MAPT_uc010dau.2_Splice_Site|MAPT_uc002ijs.3_Splice_Site|MAPT_uc002ijx.3_Splice_Site|MAPT_uc002ijt.3_Splice_Site|MAPT_uc002iju.3_Splice_Site|MAPT_uc002ijv.3_3'UTR	NM_016835	NP_058519	P10636	TAU_HUMAN	microtubule-associated protein tau isoform 1						cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)				GCAGTCACCCCGTCTGCGCCGC	0.634													4	3	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44246690	44246693	+	Intron	DEL	AACT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44246690_44246693delAACT	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				GAGCACAGTGAACTAACAAATGAT	0.319													4	3	---	---	---	---	
NPEPPS	9520	broad.mit.edu	37	17	45663680	45663681	+	Intron	INS	-	TA	TA			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45663680_45663681insTA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_5'Flank	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						TGATGCAAGAGtatatatatat	0.282													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51903786	51903786	+	5'Flank	DEL	A	-	-	rs140333986	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51903786delA	uc010wna.1	-											Homo sapiens cDNA FLJ53902 complete cds, highly similar to Homo sapiens kinesin family member 2B (KIF2B), mRNA.																		TCTTTCTTTTAAAAAAAAGCT	0.249													4	2	---	---	---	---	
TOM1L1	10040	broad.mit.edu	37	17	52998317	52998318	+	Intron	INS	-	AC	AC	rs147785496	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52998317_52998318insAC	uc002iud.2	+						TOM1L1_uc002iuc.2_Intron|TOM1L1_uc010dca.1_Intron|TOM1L1_uc010wnb.1_Intron|TOM1L1_uc010wnc.1_Intron|TOM1L1_uc010dbz.2_Intron|TOM1L1_uc010wnd.1_Intron|TOM1L1_uc010dcb.1_Intron	NM_005486	NP_005477	O75674	TM1L1_HUMAN	target of myb1-like 1						intracellular protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	cytosol|endosome membrane|Golgi stack|lysosome	SH3 domain binding|ubiquitin binding			ovary(1)	1						aaccgacgctgacatgatttgg	0.168													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54802547	54802547	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54802547delT								NOG (129596 upstream) : C17orf67 (66728 downstream)																							AAATAAGGACTTTTTTTTTTA	0.378													5	4	---	---	---	---	
SEPT4	5414	broad.mit.edu	37	17	56603934	56603935	+	Intron	INS	-	AC	AC	rs9891939		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56603934_56603935insAC	uc002iwm.1	-						SEPT4_uc002iwk.1_Intron|SEPT4_uc010wnw.1_Intron|SEPT4_uc002iwl.1_5'UTR|SEPT4_uc002iwn.1_Intron|SEPT4_uc002iwo.1_Intron|SEPT4_uc002iwp.1_Intron|SEPT4_uc010wnx.1_Intron|SEPT4_uc010wny.1_Intron|SEPT4_uc010dcy.1_Intron	NM_004574	NP_004565	O43236	SEPT4_HUMAN	septin 4 isoform 1						apoptosis|cell cycle|cytokinesis|regulation of apoptosis	cytoskeleton|mitochondrion|nucleus	GTP binding|GTPase activity|protein binding|structural molecule activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)					cacacacacaaacacacacaca	0.421													9	4	---	---	---	---	
TANC2	26115	broad.mit.edu	37	17	61448094	61448095	+	Intron	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61448094_61448095delCA	uc002jal.3	+						TANC2_uc010wpe.1_Intron|TANC2_uc002jam.1_Intron	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2						tgccatctttcacacactgctt	0.000													4	2	---	---	---	---	
CCDC47	57003	broad.mit.edu	37	17	61841220	61841220	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61841220delA	uc002jbs.3	-						CCDC47_uc010ddx.2_Intron|CCDC47_uc002jbt.2_Intron	NM_020198	NP_064583	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47 precursor							integral to membrane	protein binding				0						aaattaaattaaaaaaaaaaa	0.199													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	67785381	67785382	+	IGR	DEL	GA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67785381_67785382delGA								MAP2K6 (246919 upstream) : KCNJ16 (286044 downstream)																							taagtatcctgagagagagaga	0.000													4	2	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71601683	71601683	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71601683delA	uc010dfm.2	-							NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						GAGAGATGGTAATAATGACCC	0.333													4	2	---	---	---	---	
ICT1	3396	broad.mit.edu	37	17	73011739	73011740	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73011739_73011740insA	uc002jmm.2	+							NM_001545	NP_001536	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1 precursor						mitochondrial translational termination	mitochondrial large ribosomal subunit	aminoacyl-tRNA hydrolase activity|translation release factor activity, codon nonspecific			ovary(1)|central_nervous_system(1)	2	all_lung(278;0.226)					aaggtaagaggaaaatttcaga	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	73426440	73426441	+	IGR	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73426440_73426441insG								GRB2 (24650 upstream) : KIAA0195 (26223 downstream)																							TCCAGCAGCCAGGGGGAGAATG	0.446													4	2	---	---	---	---	
SLC26A11	284129	broad.mit.edu	37	17	78197681	78197681	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78197681delT	uc002jyb.1	+						SLC26A11_uc002jyc.1_Intron|SLC26A11_uc002jyd.1_Intron|SLC26A11_uc010dhv.1_Intron	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			ATTTATtctgtttttgctggg	0.109													4	2	---	---	---	---	
CCDC57	284001	broad.mit.edu	37	17	80114791	80114791	+	3'UTR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80114791delC	uc002kdz.1	-	15					CCDC57_uc002kdx.1_Intron|CCDC57_uc010dik.1_3'UTR	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)			CCCTGGGGATCCACGCTGTCT	0.542													4	2	---	---	---	---	
WDR45L	56270	broad.mit.edu	37	17	80593303	80593304	+	Intron	DEL	TT	-	-	rs72249995		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80593303_80593304delTT	uc002kfq.2	-						WDR45L_uc002kfr.2_Intron	NM_019613	NP_062559	Q5MNZ6	WIPI3_HUMAN	WDR45-like						autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1	Breast(20;0.00106)|all_neural(118;0.0952)	all_cancers(8;0.101)|all_epithelial(8;0.198)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.0835)			TCTTTTCAGGtttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5660494	5660495	+	IGR	INS	-	CT	CT	rs147864410	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5660494_5660495insCT								EPB41L3 (29852 upstream) : TMEM200C (229689 downstream)																							tacctccagccctatacccatt	0.000													4	5	---	---	---	---	
L3MBTL4	91133	broad.mit.edu	37	18	5971070	5971070	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5971070delT	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				AACACTGACCTTTTTAGTATG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10201835	10201835	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10201835delT								VAPA (241818 upstream) : APCDD1 (252790 downstream)																							GTGAATGTAGTTTTGGCAGGT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11091746	11091746	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11091746delT								FAM38B (389767 upstream) : GNAL (597390 downstream)																							AGTGTTGTTGTTTTTATTGGA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11120603	11120603	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11120603delT								FAM38B (418624 upstream) : GNAL (568533 downstream)																							CTGAACAGCCTCTGATATGAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11570734	11570734	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11570734delT								FAM38B (868755 upstream) : GNAL (118402 downstream)																							ATATAATACCTTGTCAAAGAA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11591386	11591386	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11591386delC								FAM38B (889407 upstream) : GNAL (97750 downstream)																							GATACTGTGACCAGCACTGTG	0.348													4	2	---	---	---	---	
MPPE1	65258	broad.mit.edu	37	18	11885429	11885429	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11885429delA	uc002kqf.2	-						MPPE1_uc002kqn.2_Intron|MPPE1_uc002kqg.2_Intron|MPPE1_uc002kqh.2_Intron|MPPE1_uc002kqi.2_Intron|MPPE1_uc002kqj.2_Intron|MPPE1_uc002kqk.2_Intron|MPPE1_uc002kql.2_Intron|MPPE1_uc002kqm.2_Intron	NM_023075	NP_075563	Q53F39	MPPE1_HUMAN	metallophosphoesterase 1 precursor						ER to Golgi vesicle-mediated transport|GPI anchor biosynthetic process	cis-Golgi network|endoplasmic reticulum exit site|ER-Golgi intermediate compartment membrane|integral to membrane	GPI anchor binding|manganese ion binding|phosphoric diester hydrolase activity				0						GCCCTCCCTGAAGGATAAAGT	0.473													4	2	---	---	---	---	
CEP192	55125	broad.mit.edu	37	18	13006149	13006149	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13006149delT	uc010xac.1	+						CEP192_uc002krs.1_Intron	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa											ovary(4)|pancreas(1)	5						CTATATCTACTTTTTTTTTCC	0.299													3	4	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13567304	13567304	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13567304delG	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		AACAGTGTCTGGATTGCTTCA	0.493													4	2	---	---	---	---	
OSBPL1A	114876	broad.mit.edu	37	18	21752741	21752741	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21752741delA	uc002kve.2	-						OSBPL1A_uc002kvd.2_Intron|OSBPL1A_uc010xbc.1_Intron	NM_080597	NP_542164	Q9BXW6	OSBL1_HUMAN	oxysterol-binding protein-like 1A isoform B						cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					ATGAAACATTAAAAAAAGCTA	0.313													4	2	---	---	---	---	
OSBPL1A	114876	broad.mit.edu	37	18	21764380	21764380	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21764380delC	uc002kve.2	-						OSBPL1A_uc002kvd.2_Intron|OSBPL1A_uc010xbc.1_Intron	NM_080597	NP_542164	Q9BXW6	OSBL1_HUMAN	oxysterol-binding protein-like 1A isoform B						cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					gcagtaaaagcCCCATTACAA	0.109													4	2	---	---	---	---	
CHST9	83539	broad.mit.edu	37	18	24524596	24524596	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24524596delC	uc002kwd.2	-						C18orf16_uc010xbm.1_Intron|CHST9_uc002kwc.2_Intron|CHST9_uc002kwe.2_Intron	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)					ATTAAACTTTCACAGATAAAT	0.328													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27507321	27507321	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27507321delT								None (None upstream) : MIR302F (371555 downstream)																							AAGTGATGGATATTTCACATT	0.323													4	2	---	---	---	---	
FAM59A	64762	broad.mit.edu	37	18	29981415	29981415	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29981415delA	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A											ovary(1)|skin(1)	2						TCTTAAAAAGAAAAAAAAAGA	0.313													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	31087322	31087323	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31087322_31087323insT								C18orf34 (66637 upstream) : ASXL3 (71218 downstream)																							TCATACTCTGGTTTCTGACCCA	0.243													4	2	---	---	---	---	
RPRD1A	55197	broad.mit.edu	37	18	33609588	33609588	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33609588delA	uc002kzf.1	-						RPRD1A_uc002kze.1_Intron|RPRD1A_uc002kzg.2_Intron|RPRD1A_uc010dmw.2_Intron|RPRD1A_uc010dmx.2_Intron	NM_018170	NP_060640	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing											ovary(1)|breast(1)	2						ATGCCCACTTaaaaaaaaaaa	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38050376	38050377	+	IGR	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38050376_38050377delTG								LOC647946 (670094 upstream) : None (None downstream)																							gtgtgtgttttgtgtgtgtgtg	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38699564	38699564	+	IGR	DEL	T	-	-	rs78763565		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38699564delT								None (None upstream) : KC6 (360674 downstream)																							CAGCATAAGCTTTTTTTTTTC	0.338													4	2	---	---	---	---	
PIK3C3	5289	broad.mit.edu	37	18	39567469	39567470	+	Intron	DEL	CA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39567469_39567470delCA	uc002lap.2	+						PIK3C3_uc010xcl.1_Intron	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3						cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(8)|ovary(1)|breast(1)	10						ATTATAATTTCATCTCTTTGTA	0.277										TSP Lung(28;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41206840	41206840	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41206840delA								SYT4 (349225 upstream) : None (None downstream)																							ctggcaatataactgagagta	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41813601	41813601	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41813601delT								SYT4 (955986 upstream) : SETBP1 (446537 downstream)																							TTTTTAATTGTAGTAAAGAAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	42106773	42106774	+	Intron	INS	-	G	G			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42106773_42106774insG	uc002lax.3	-											Homo sapiens cDNA clone IMAGE:5265929.																		CCTGTAGCATTGGGGAAATAAG	0.446													4	2	---	---	---	---	
KATNAL2	83473	broad.mit.edu	37	18	44530329	44530330	+	Intron	INS	-	AG	AG	rs111413183	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44530329_44530330insAG	uc002lco.2	+						KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593	Q8IYT4	KATL2_HUMAN	katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4						GGATGTGATCCAGTGTGTTAGA	0.416													4	2	---	---	---	---	
MYO5B	4645	broad.mit.edu	37	18	47708172	47708172	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47708172delA	uc002leb.2	-							NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		AATGGCAATTAAAAGGGCAAG	0.373													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50749168	50749168	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50749168delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TTAACTCAGCTTTTTTACCAA	0.294													4	2	---	---	---	---	
POLI	11201	broad.mit.edu	37	18	51823662	51823662	+	3'UTR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51823662delT	uc002lfj.3	+	10					POLI_uc010xds.1_3'UTR|POLI_uc002lfk.3_3'UTR|POLI_uc010dpg.2_3'UTR	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	DNA polymerase iota						DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		tttgttgttgttttttttttt	0.254								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	56107658	56107658	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56107658delT								NEDD4L (38886 upstream) : MIR122 (10648 downstream)																							ATAGAACACCTGGGGAAAGAA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	56758936	56758936	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56758936delG								LOC390858 (38490 upstream) : SEC11C (48189 downstream)																							AGCATATCATGGGGACTATGA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57429205	57429206	+	IGR	DEL	AA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57429205_57429206delAA								CCBE1 (64561 upstream) : PMAIP1 (137986 downstream)																							AATTGTACTTAAAAAAAAAAAA	0.272													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57462295	57462295	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57462295delT								CCBE1 (97651 upstream) : PMAIP1 (104897 downstream)																							TATGTGATGCTTTAAGAAACC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57803391	57803391	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57803391delC								PMAIP1 (231853 upstream) : MC4R (235173 downstream)																							GTTCACCATTCCCAGCTATAT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58715899	58715899	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58715899delA								MC4R (675898 upstream) : CDH20 (285089 downstream)																							ACTCACTGATAAAAAGCCCTC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58864390	58864390	+	IGR	DEL	A	-	-	rs3862710		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58864390delA								MC4R (824389 upstream) : CDH20 (136598 downstream)																							TTGAAGATTTAAAAAAAAAAT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58869841	58869841	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58869841delT								MC4R (829840 upstream) : CDH20 (131147 downstream)																							TTTTTCTTTGTTTTTTTTTTT	0.214													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	60102913	60102913	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60102913delC								TNFRSF11A (49411 upstream) : ZCCHC2 (87745 downstream)																							aaattaacttccatgtggaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63645962	63645962	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63645962delA								CDH7 (97788 upstream) : CDH19 (525359 downstream)																							agattaacataaaacttcacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68836077	68836077	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68836077delG								SOCS6 (838643 upstream) : None (None downstream)																							acattgtcgtgggaaatagaa	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71312698	71312698	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71312698delA								NETO1 (777888 upstream) : FBXO15 (427890 downstream)																							CTCTTCCACCAAAAAAAAAAG	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71713177	71713177	+	IGR	DEL	G	-	-	rs74178962		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71713177delG								None (None upstream) : FBXO15 (27411 downstream)																							ACAAAAAGTAGAAAAGTGTTA	0.353													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	72893471	72893471	+	IGR	DEL	T	-	-	rs35964127		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72893471delT								ZNF407 (115843 upstream) : ZADH2 (15808 downstream)																							ttttcgtttgtctgaaaatat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75227534	75227534	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75227534delG								GALR1 (245440 upstream) : None (None downstream)																							CAGATCACCAGGCACCAATTC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76576943	76576944	+	IGR	INS	-	ACTG	ACTG	rs146216741	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76576943_76576944insACTG								None (None upstream) : SALL3 (163331 downstream)																							TCCATCCTCACACTGCATCCCT	0.594													0	6	---	---	---	---	
TLE2	7089	broad.mit.edu	37	19	3009883	3009884	+	Intron	INS	-	T	T	rs144892530	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3009883_3009884insT	uc002lww.2	-						TLE2_uc010xhb.1_Intron|TLE2_uc010dth.2_Intron|TLE2_uc010xhc.1_Intron|TLE2_uc010dti.2_Intron|TLE2_uc010xhd.1_Intron	NM_003260	NP_003251	Q04725	TLE2_HUMAN	transducin-like enhancer protein 2 isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		Ctttctctctctctttttttct	0.238													4	5	---	---	---	---	
PTPRS	5802	broad.mit.edu	37	19	5278194	5278195	+	Intron	INS	-	A	A	rs111490914		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5278194_5278195insA	uc002mbv.2	-						PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.1_Intron|PTPRS_uc002mbw.2_Intron|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron|PTPRS_uc002mbz.1_Intron	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,						cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		TAGAAACTGCCAAAAAAAAAAA	0.332													4	2	---	---	---	---	
STXBP2	6813	broad.mit.edu	37	19	7699180	7699180	+	5'Flank	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7699180delC	uc002mha.3	+						PCP2_uc002mgz.2_5'Flank|STXBP2_uc002mhb.3_5'Flank|STXBP2_uc010dvj.2_5'Flank|STXBP2_uc010xjr.1_5'Flank|STXBP2_uc010dvk.2_5'Flank	NM_006949	NP_008880	Q15833	STXB2_HUMAN	syntaxin binding protein 2 isoform a						leukocyte mediated cytotoxicity|neutrophil degranulation|protein transport|regulation of mast cell degranulation|vesicle docking involved in exocytosis	azurophil granule|cytolytic granule|cytosol|specific granule|tertiary granule	syntaxin-3 binding			central_nervous_system(1)	1						AGGTCCCCATCCCCTTCCCTT	0.607													4	2	---	---	---	---	
ZNF558	148156	broad.mit.edu	37	19	8939936	8939936	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8939936delA	uc010dwg.1	-							NM_144693	NP_653294	Q96NG5	ZN558_HUMAN	zinc finger protein 558						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			central_nervous_system(1)	1						actccatctcaaaaaaaaaaa	0.000													0	6	---	---	---	---	
ZNF844	284391	broad.mit.edu	37	19	12184372	12184372	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12184372delT	uc002mtb.2	+						ZNF844_uc010dym.1_Intron	NM_001136501	NP_001129973	Q08AG5	ZN844_HUMAN	zinc finger protein 844						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CAAAATCCAGTTTTTTTTTTT	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14431801	14431801	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14431801delT								LPHN1 (114804 upstream) : CD97 (60412 downstream)																							TTGCTGCCtctttttttttga	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15059216	15059217	+	IGR	INS	-	T	T	rs146822753	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15059216_15059217insT								OR7C2 (5957 upstream) : SLC1A6 (1774 downstream)																							Atttatttatctttttttttga	0.045													4	2	---	---	---	---	
LSM4	25804	broad.mit.edu	37	19	18424055	18424055	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18424055delA	uc002niq.2	-							NM_012321	NP_036453	Q9Y4Z0	LSM4_HUMAN	U6 snRNA-associated Sm-like protein 4						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|mRNA processing|RNA splicing	cytosol|U6 snRNP	protein binding|RNA binding				0						acttggtcttaaaaaaacaaa	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	28474503	28474503	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28474503delG								LOC148189 (189655 upstream) : LOC148145 (981537 downstream)																							AAGTCACTAAGGGGGGTTTTC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29359987	29359988	+	IGR	DEL	CA	-	-	rs72261991		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29359987_29359988delCA								None (None upstream) : LOC148145 (96052 downstream)																							aatgcacaagcacacacacacg	0.213													1	6	---	---	---	---	
GPATCH1	55094	broad.mit.edu	37	19	33591687	33591687	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33591687delT	uc002nug.1	+							NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					TAGAAGGGGCTTTTTTTTTTT	0.448													1	6	---	---	---	---	
PEPD	5184	broad.mit.edu	37	19	33999856	33999858	+	Intron	DEL	CAT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33999856_33999858delCAT	uc002nur.3	-						PEPD_uc010xrr.1_Intron|PEPD_uc010xrs.1_Intron	NM_000285	NP_000276	P12955	PEPD_HUMAN	prolidase isoform 1						cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)					TCCAGAGCAGCATCACAGAGAAG	0.542													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	46981673	46981674	+	IGR	DEL	GT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46981673_46981674delGT								PNMAL1 (6853 upstream) : PNMAL2 (12774 downstream)																							gtgtgtgtgcgtgtgtgtgtgA	0.233													4	2	---	---	---	---	
SLC8A2	6543	broad.mit.edu	37	19	47972376	47972377	+	Intron	INS	-	GT	GT	rs73940853		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47972376_47972377insGT	uc002pgx.2	-						SLC8A2_uc010xyq.1_Intron|SLC8A2_uc010xyr.1_Intron	NM_015063	NP_055878	Q9UPR5	NAC2_HUMAN	solute carrier family 8 member 2 precursor						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		TGCCtgtgtgcgtgtgtgtgtg	0.490													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	52093368	52093369	+	5'Flank	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52093368_52093369insA	uc002pxc.1	+											Homo sapiens cDNA FLJ36480 fis, clone THYMU2017449.																		CATTTTTTGCTAAAAAACGGAG	0.287													4	2	---	---	---	---	
ZNF534	147658	broad.mit.edu	37	19	52953704	52953705	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52953704_52953705insA	uc002pzj.1	+						ZNF534_uc010epo.1_Intron			Q76KX8	ZN534_HUMAN	SubName: Full=Putative uncharacterized protein;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						tattctttgtcaaaaatcagct	0.000													4	2	---	---	---	---	
ZNF83	55769	broad.mit.edu	37	19	53165491	53165491	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53165491delT	uc010epz.2	-						ZNF83_uc010eqb.1_Intron	NM_001105554	NP_001099024	P51522	ZNF83_HUMAN	zinc finger protein 83 isoform b							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		TGCTGTCAAGtttggctaagt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57162130	57162130	+	Intron	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57162130delC	uc002qnn.1	+											Homo sapiens cDNA FLJ37880 fis, clone BRSTN2000220.																		CAGGGACAAGCCCAGGGGCAA	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57814039	57814039	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57814039delC								ZNF460 (8603 upstream) : ZNF543 (17838 downstream)																							gcactgttttcccaggatgcc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	58731838	58731838	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58731838delA								ZNF274 (6911 upstream) : ZNF544 (8232 downstream)																							aaaaaaaaacaaaaaaaaaaT	0.104													4	2	---	---	---	---	
C20orf96	140680	broad.mit.edu	37	20	264335	264336	+	Intron	INS	-	A	A	rs141598893	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:264335_264336insA	uc002wde.1	-						C20orf96_uc002wdc.2_Intron|C20orf96_uc002wdd.2_Intron|C20orf96_uc010zpi.1_Intron|C20orf96_uc010zpj.1_Intron|C20orf96_uc010zpk.1_Intron	NM_153269	NP_695001	Q9NUD7	CT096_HUMAN	hypothetical protein LOC140680												0		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			TCTTGAGTCTTAAACAGAACAG	0.183													3	3	---	---	---	---	
SNPH	9751	broad.mit.edu	37	20	1272814	1272815	+	Intron	INS	-	CATA	CATA	rs145671625	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1272814_1272815insCATA	uc002wes.2	+						SNPH_uc002wet.2_Intron	NM_014723	NP_055538	O15079	SNPH_HUMAN	syntaphilin						synaptic vesicle docking involved in exocytosis	cell junction|integral to membrane|synapse|synaptosome	syntaxin-1 binding			ovary(2)	2						TTAGTCTAAGGCATAGCATCCT	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6271645	6271645	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6271645delA								FERMT1 (167454 upstream) : BMP2 (477100 downstream)																							TCTGTTGGTTAAAAACAAAAG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7684858	7684858	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7684858delA								BMP2 (923948 upstream) : HAO1 (178773 downstream)																							CAACACACACAAAGTCGAGAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	9865041	9865042	+	IGR	DEL	CT	-	-	rs80002065		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9865041_9865042delCT								PAK7 (45354 upstream) : ANKRD5 (150655 downstream)																							GTAGCTATTACTTGGGAGCTGT	0.460													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	10612255	10612255	+	IGR	DEL	T	-	-	rs112175375		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10612255delT								C20orf94 (8230 upstream) : JAG1 (6077 downstream)																							TAGACTTCAATTAGGCACCAA	0.418													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	14294738	14294739	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14294738_14294739insA	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TCTTATTTAACAAAAAAATGTA	0.297													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	14762506	14762506	+	Intron	DEL	T	-	-	rs79602396		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14762506delT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002wox.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TTCATGTATCTTTTTTTAAAA	0.154													4	2	---	---	---	---	
BFSP1	631	broad.mit.edu	37	20	17479888	17479889	+	Intron	DEL	TT	-	-	rs138887018		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17479888_17479889delTT	uc002wpo.2	-						BFSP1_uc002wpp.2_Intron|BFSP1_uc010zrn.1_Intron|BFSP1_uc010zro.1_Intron	NM_001195	NP_001186	Q12934	BFSP1_HUMAN	filensin isoform 1							cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1						CCTTACACAAtttttttttttt	0.188													5	3	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19319935	19319935	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19319935delT	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						AGGTATCTAGTTTTTTTTTTC	0.413													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22424844	22424844	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22424844delT								LOC284788 (23563 upstream) : C20orf56 (116350 downstream)																							catttctttattttttttaat	0.080													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24727988	24727988	+	IGR	DEL	A	-	-	rs73903525		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24727988delA								TMEM90B (80821 upstream) : CST7 (201878 downstream)																							GAATATGACCAACCTGATCCC	0.353													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25910992	25910992	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25910992delC								FAM182B (62206 upstream) : LOC100134868 (79443 downstream)																							ATTTAAAAAACAACTTGTAGT	0.274													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25910993	25910994	+	IGR	INS	-	GT	GT			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25910993_25910994insGT								FAM182B (62207 upstream) : LOC100134868 (79441 downstream)																							TTTAAAAAACAACTTGTAGTTG	0.272													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26107573	26107574	+	IGR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26107573_26107574insT								C20orf191 (12896 upstream) : MIR663 (81248 downstream)																							tcagaatcacattttttcagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26202672	26202679	+	IGR	DEL	TTATTGAC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26202672_26202679delTTATTGAC								MIR663 (13758 upstream) : None (None downstream)																							AAATATCCATTTATTGACTTATTGACTA	0.380													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26212113	26212114	+	IGR	DEL	AA	-	-	rs72151337		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26212113_26212114delAA								MIR663 (23199 upstream) : None (None downstream)																							taatatggataagtgtcaaaaa	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26232389	26232390	+	IGR	INS	-	C	C	rs145433999		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26232389_26232390insC								MIR663 (43475 upstream) : None (None downstream)																							gtgcagggggaccccgcttcaa	0.000													4	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29624433	29624433	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29624433delA	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						CAGGAAGACTAAAAAAAGGGA	0.289													4	2	---	---	---	---	
ZNF341	84905	broad.mit.edu	37	20	32355190	32355191	+	Intron	INS	-	T	T	rs113861453		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32355190_32355191insT	uc002wzy.2	+						ZNF341_uc002wzx.2_Intron|ZNF341_uc010geq.2_Intron|ZNF341_uc010ger.2_Intron	NM_032819	NP_116208	Q9BYN7	ZN341_HUMAN	zinc finger protein 341						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						GTGATCACttcttttttttttt	0.267													4	2	---	---	---	---	
ACTR5	79913	broad.mit.edu	37	20	37384245	37384245	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37384245delA	uc002xjd.2	+							NM_024855	NP_079131	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog						DNA recombination|double-strand break repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent|UV-damage excision repair	cytoplasm|Ino80 complex	ATP binding|protein binding				0		Myeloproliferative disorder(115;0.00878)				CCGCCCCACCAAAAAAAAAAA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38202710	38202710	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38202710delT								LOC339568 (349319 upstream) : None (None downstream)																							AAATCCATTATTTTTTTCTTC	0.388													4	2	---	---	---	---	
CHD6	84181	broad.mit.edu	37	20	40212037	40212038	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40212037_40212038insA	uc002xka.1	-						CHD6_uc002xkd.2_Intron|CHD6_uc002xkc.2_Intron	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				agtaatgaaggaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42929056	42929057	+	IGR	INS	-	C	C	rs146966254	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42929056_42929057insC								GDAP1L1 (20045 upstream) : FITM2 (6140 downstream)																							ccagcttacctcccttctccta	0.144													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	43065449	43065449	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43065449delG								HNF4A (5420 upstream) : TTPAL (39098 downstream)																							GCAAGTGGGAGGAGGCAGCGG	0.582													11	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44055970	44055971	+	IGR	DEL	AC	-	-	rs34799055		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44055970_44055971delAC								PIGT (1086 upstream) : WFDC2 (42423 downstream)																							tctgtctcaaacacacacacac	0.233													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49925436	49925437	+	IGR	DEL	AC	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49925436_49925437delAC								KCNG1 (285761 upstream) : NFATC2 (82329 downstream)																							TAACTCTCATAcacacacacaa	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49992650	49992651	+	IGR	DEL	GA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49992650_49992651delGA								KCNG1 (352975 upstream) : NFATC2 (15115 downstream)																							agaaatacctgaacctgggtaa	0.213													4	2	---	---	---	---	
ATP9A	10079	broad.mit.edu	37	20	50233480	50233481	+	Intron	DEL	TT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50233480_50233481delTT	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4						atagagaaACtttttttttttt	0.005													6	3	---	---	---	---	
ATP9A	10079	broad.mit.edu	37	20	50292427	50292427	+	Intron	DEL	A	-	-	rs10539699		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50292427delA	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4						tcaaaaaaagaaaaaaaaaaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53643473	53643473	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53643473delT								DOK5 (375764 upstream) : CBLN4 (929024 downstream)																							ttgttggaggtttttttttta	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54772900	54772900	+	IGR	DEL	G	-	-	rs5842101		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54772900delG								CBLN4 (192888 upstream) : MC3R (50888 downstream)																							ATTTCCATCTGTTGCATTTAG	0.383													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55303770	55303771	+	IGR	INS	-	ACAT	ACAT	rs141837724	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55303770_55303771insACAT								TFAP2C (89434 upstream) : BMP7 (440038 downstream)																							TTCTCTGGGGGACAAAGTGTGC	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56300063	56300063	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56300063delA								PMEPA1 (13522 upstream) : C20orf85 (425920 downstream)																							AGACAGAAACAAAAAATGCCC	0.398													4	2	---	---	---	---	
PHACTR3	116154	broad.mit.edu	37	20	58381551	58381551	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58381551delG	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_Intron|PHACTR3_uc002yax.2_Intron	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			ttgctccACTGGCCTGTAGCA	0.040													4	2	---	---	---	---	
ZBTB46	140685	broad.mit.edu	37	20	62439418	62439419	+	5'Flank	DEL	GG	-	-	rs10577517		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62439418_62439419delGG	uc002ygv.1	-						ZBTB46_uc002ygu.2_Intron|uc002ygw.2_5'Flank	NM_025224	NP_079500	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CCTTCCCACAGGGGACACTCAC	0.639													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9735165	9735166	+	Intron	DEL	AG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9735165_9735166delAG	uc011abu.1	+											Homo sapiens, clone IMAGE:4720764, mRNA.																		CTATTCTGGAAGAAAAAAGAAC	0.431													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9851327	9851327	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9851327delG								None (None upstream) : None (None downstream)																							gtggcaaaaagaaaaatcacc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10598662	10598663	+	5'Flank	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10598662_10598663insA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		accaggggcagaaaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10866338	10866338	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10866338delT								None (None upstream) : TPTE (40405 downstream)																							GTAGCTGTTGTTAGGGATAGG	0.453													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10984603	10984605	+	Intron	DEL	CTC	-	-	rs71277400		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10984603_10984605delCTC	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ATCTTTGCTTCTCCTCAAATAGG	0.458													4	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11069159	11069160	+	Intron	DEL	TA	-	-	rs58532396		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11069159_11069160delTA	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)		aataatatattaaaaaaaactt	0.000													3	7	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11081636	11081646	+	Intron	DEL	GAAAATGGGAA	-	-	rs57380297		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11081636_11081646delGAAAATGGGAA	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)		TTACAGACTGGAAAATGGGAAAAAGATGAGA	0.275													5	3	---	---	---	---	
NRIP1	8204	broad.mit.edu	37	21	16342207	16342207	+	Intron	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16342207delG	uc002yjx.2	-							NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1						androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		GTAAGGAGTAGGATGAGAAGA	0.308													4	2	---	---	---	---	
CHODL	140578	broad.mit.edu	37	21	19560426	19560427	+	Intron	INS	-	T	T	rs145506210	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19560426_19560427insT	uc002ykt.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002yku.2_Intron			Q9H9P2	CHODL_HUMAN	RecName: Full=Chondrolectin; AltName: Full=Transmembrane protein MT75; Flags: Precursor;						muscle organ development	integral to membrane|perinuclear region of cytoplasm	sugar binding			upper_aerodigestive_tract(1)	1		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)		aaaattgatcattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20319573	20319573	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20319573delC								TMPRSS15 (543603 upstream) : None (None downstream)																							actccacccacccccccacca	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	22037226	22037226	+	IGR	DEL	A	-	-	rs77886081		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22037226delA								None (None upstream) : C21orf131 (77688 downstream)																							AGCATACATTAAAAAAAAAAG	0.333													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	24091443	24091444	+	IGR	INS	-	C	C			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24091443_24091444insC								None (None upstream) : None (None downstream)																							acaacatttttccctctgggac	0.000													4	2	---	---	---	---	
GRIK1	2897	broad.mit.edu	37	21	30979114	30979118	+	Intron	DEL	TCTTG	-	-	rs72042869		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30979114_30979118delTCTTG	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron|uc002ynp.1_Intron	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)	CTCTGTTGTTtcttgtcttgtcttg	0.312													6	3	---	---	---	---	
GRIK1	2897	broad.mit.edu	37	21	31216516	31216517	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31216516_31216517insA	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)	GAATATGATTTAAAAAAAAAAC	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35318325	35318326	+	Intron	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35318325_35318326delTG	uc002ytn.2	+											Homo sapiens cDNA, FLJ18587.																		aacactccaatgtgtgtgtgtt	0.000													4	2	---	---	---	---	
KCNJ15	3772	broad.mit.edu	37	21	39663117	39663117	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39663117delT	uc002ywv.2	+						KCNJ15_uc002yww.2_Intron|KCNJ15_uc002ywx.2_Intron	NM_002243	NP_002234	Q99712	IRK15_HUMAN	potassium inwardly-rectifying channel J15						synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6						CACAAATTCCTTTATGTGTAT	0.418													4	2	---	---	---	---	
ERG	2078	broad.mit.edu	37	21	39981380	39981380	+	Intron	DEL	A	-	-	rs142679958		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39981380delA	uc010gnw.2	-						ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				AAGGTATCTCAAAAAAAAAGA	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44250096	44250097	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44250096_44250097insA								PDE9A (54480 upstream) : WDR4 (13109 downstream)																							aattggttgagaaaaaaaaCAA	0.188													4	2	---	---	---	---	
RRP1B	23076	broad.mit.edu	37	21	45094046	45094046	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45094046delT	uc002zdk.2	+							NM_015056	NP_055871	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1 homolog B						rRNA processing	cytosol|nucleolus|preribosome, small subunit precursor	protein binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.178)		ACGTTGGGTAttttttgagac	0.204													4	2	---	---	---	---	
KRTAP10-1	386677	broad.mit.edu	37	21	45959206	45959206	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45959206delC	uc002zfh.1	-	1	873	c.828delG	c.(826-828)GCGfs	p.A276fs	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198691	NP_941964	P60331	KR101_HUMAN	keratin associated protein 10-1	276						keratin filament				skin(1)	1						GGCGGGAGCACGCGGGGCGGC	0.716													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	46821275	46821275	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46821275delT								LOC642852 (104007 upstream) : COL18A1 (3822 downstream)																							gtttctgtgctttttttttgt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16948332	16948332	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16948332delC								OR11H1 (498528 upstream) : CCT8L2 (123316 downstream)																							aaggagcatacctcaaaataa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17351804	17351804	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17351804delG								HSFYL1 (41579 upstream) : GAB4 (91025 downstream)																							CATTATCCCTGGTATAGGGCA	0.453													4	2	---	---	---	---	
DGCR2	9993	broad.mit.edu	37	22	19111995	19111995	+	5'Flank	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19111995delC	uc002zoq.1	-						DGCR2_uc002zor.1_5'Flank|DGCR2_uc011agr.1_5'Flank	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2 precursor						cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)					GGGGGAAGGGCCACGGCAGGT	0.592													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22425992	22425992	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22425992delT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						ACAGATGTCATTTTGAGTGAC	0.498													4	2	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23141588	23141589	+	Intron	INS	-	A	A	rs146526170	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23141588_23141589insA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						agtttgtaaagaaaaaaaaggg	0.119													4	2	---	---	---	---	
CYTSA	23384	broad.mit.edu	37	22	24767079	24767079	+	Intron	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24767079delA	uc002zzw.2	+						CYTSA_uc002zzv.3_Intron|CYTSA_uc011ajq.1_Intron	NM_015330	NP_056145	Q69YQ0	CYTSA_HUMAN	cytospin A						cell cycle|cell division						0						CTGCAAAAAGAAAAAAAAGAA	0.060													4	2	---	---	---	---	
GGT1	2678	broad.mit.edu	37	22	25016169	25016170	+	Intron	INS	-	T	T	rs28418841	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25016169_25016170insT	uc003aan.1	+						GGT1_uc003aas.1_Intron|GGT1_uc003aat.1_Intron|GGT1_uc003aau.1_Intron|GGT1_uc003aav.1_Intron|GGT1_uc003aaw.1_Intron|GGT1_uc003aax.1_Intron	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)	aaaaaaaaaaaaTCTTTCCTCC	0.277													4	4	---	---	---	---	
KIAA1671	85379	broad.mit.edu	37	22	25481604	25481605	+	Intron	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25481604_25481605delTG	uc003abn.2	+						KIAA1671_uc003abl.2_Intron	NM_001145206	NP_001138678	Q9BY89	K1671_HUMAN	hypothetical protein LOC85379											lung(1)	1						ATGCTCACCCTGTGTGTGTGAG	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	28130890	28130891	+	IGR	DEL	TT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28130890_28130891delTT								None (None upstream) : MN1 (13375 downstream)																							tttttttttctttttttttttt	0.238													4	2	---	---	---	---	
AP1B1	162	broad.mit.edu	37	22	29745509	29745510	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29745509_29745510insT	uc003afj.2	-						AP1B1_uc003afi.2_Intron|AP1B1_uc003afk.2_Intron|AP1B1_uc003afl.2_Intron|AP1B1_uc011ako.1_Intron	NM_001127	NP_001118	Q10567	AP1B1_HUMAN	adaptor-related protein complex 1 beta 1 subunit						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding|protein transporter activity			ovary(1)|skin(1)	2						TCTGAGttttgttttttttttt	0.292													3	3	---	---	---	---	
ASCC2	84164	broad.mit.edu	37	22	30215049	30215049	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30215049delT	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580	Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			TCCAAGCTCCTGGAGGCTCCG	0.438													4	2	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	32932418	32932420	+	Intron	DEL	TAC	-	-	rs149033849		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32932418_32932420delTAC	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						acttgggtattactactgctttc	0.182													8	5	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33833452	33833452	+	Intron	DEL	A	-	-	rs62225295		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33833452delA	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				taacatacctaatTTTTTTTT	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36528298	36528298	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36528298delA								RBM9 (103713 upstream) : APOL3 (8074 downstream)																							AAGAAGGAAGAAAAAAAGATA	0.507													4	2	---	---	---	---	
BAIAP2L2	80115	broad.mit.edu	37	22	38481013	38481014	+	3'UTR	INS	-	G	G	rs142449191	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38481013_38481014insG	uc003auw.2	-	14					SLC16A8_uc003auu.2_5'Flank|BAIAP2L2_uc003auv.2_RNA	NM_025045	NP_079321	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2						filopodium assembly|signal transduction		cytoskeletal adaptor activity|SH3 domain binding			pancreas(1)	1	Melanoma(58;0.045)					GGGGCAGAAAAGGGGGAAAGAG	0.574													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41995222	41995224	+	RNA	DEL	AAG	-	-	rs147313112		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41995222_41995224delAAG	uc003bam.1	-	1		c.436_438delCTT								Homo sapiens cDNA FLJ33406 fis, clone BRACE2010477.																		GTGAAGTGGCAAGAAGTTGTGGC	0.512													2	4	---	---	---	---	
ARFGAP3	26286	broad.mit.edu	37	22	43216376	43216377	+	Intron	DEL	TA	-	-	rs10585135		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43216376_43216377delTA	uc003bdd.2	-						ARFGAP3_uc010gzf.2_Intron|ARFGAP3_uc011apu.1_Intron	NM_014570	NP_055385	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating						intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1						TGCTGCCCCCTATGTTCTGTGA	0.347											OREG0026610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45468670	45468671	+	IGR	INS	-	T	T	rs145803051	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45468670_45468671insT								PHF21B (62861 upstream) : NUP50 (91055 downstream)																							CTACACATGGGttttttttgtt	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45490019	45490019	+	IGR	DEL	C	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45490019delC								PHF21B (84210 upstream) : NUP50 (69707 downstream)																							ACGCCGCACACCCCCAACTCC	0.338													4	2	---	---	---	---	
UPK3A	7380	broad.mit.edu	37	22	45687491	45687492	+	Intron	DEL	TG	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45687491_45687492delTG	uc003bfy.2	+						UPK3A_uc010gzy.2_Intron	NM_006953	NP_008884	O75631	UPK3A_HUMAN	uroplakin 3A precursor						epithelial cell differentiation	endoplasmic reticulum membrane|integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		tgagtgtgactgtgtgtgtgtg	0.000													4	2	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47390014	47390015	+	Intron	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47390014_47390015insT	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		AGGTGTCATTCTTTTTTTTTAA	0.238													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49620841	49620841	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49620841delA								FAM19A5 (473099 upstream) : C22orf34 (187335 downstream)																							attaggtggtaaatttatgtt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49688606	49688607	+	IGR	INS	-	AC	AC	rs140379801	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49688606_49688607insAC								FAM19A5 (540864 upstream) : C22orf34 (119569 downstream)																							TTAATAAAATAACACCAACATG	0.465													5	4	---	---	---	---	
MOV10L1	54456	broad.mit.edu	37	22	50529105	50529106	+	Intron	INS	-	TG	TG	rs150705221	by1000genomes	TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50529105_50529106insTG	uc003bjj.2	+						MOV10L1_uc003bjk.3_Intron|MOV10L1_uc011arp.1_Intron|MOV10L1_uc010han.2_Intron	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1						germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CCTGAGGTGTTTGTGTGTGTGT	0.322													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	221992	221992	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:221992delT	uc004cpd.1	-						uc004cpe.1_Intron	NM_012227	NP_036359			pseudoautosomal GTP-binding protein-like																		tttccttttgttttttttttt	0.169													16	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	904242	904243	+	IGR	INS	-	CA	CA			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:904242_904243insCA								SHOX (284097 upstream) : CRLF2 (410644 downstream)																							ATTTGCTGGTCCACACACAAGC	0.322													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	36229987	36229987	+	IGR	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36229987delT								CXorf59 (66800 upstream) : CXorf30 (24064 downstream)																							GTACAGTGTCTTTTTTTTTGT	0.343													6	3	---	---	---	---	
PABPC1L2A	340529	broad.mit.edu	37	X	72297406	72297407	+	3'UTR	INS	-	T	T			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72297406_72297407insT	uc004ebg.2	-	1						NM_001012977	NP_001012995	Q5JQF8	PAP1M_HUMAN	poly(A) binding protein, cytoplasmic 1-like 2A								nucleotide binding|RNA binding				0	Renal(35;0.156)					CTGCTTTGTGATTTTTTTTTCT	0.396													4	2	---	---	---	---	
MAGT1	84061	broad.mit.edu	37	X	77111274	77111274	+	Intron	DEL	T	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77111274delT	uc004fof.2	-						MAGT1_uc004fog.3_Intron	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1						protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				upper_aerodigestive_tract(1)	1						GAAAACACTAttttttttttt	0.134													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	113699405	113699406	+	IGR	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113699405_113699406insA								None (None upstream) : HTR2C (119145 downstream)																							gtgacagctggaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	117411936	117411936	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117411936delA								KLHL13 (161148 upstream) : WDR44 (68106 downstream)																							ttcctgcatTAaaaaaatatt	0.015													4	2	---	---	---	---	
CUL4B	8450	broad.mit.edu	37	X	119674392	119674393	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119674392_119674393delTT	uc004esw.2	-	13	1959_1960	c.1522_1523delAA	c.(1522-1524)AATfs	p.N508fs	CUL4B_uc010nqq.2_Frame_Shift_Del_p.N207fs|CUL4B_uc004esv.2_Frame_Shift_Del_p.N490fs	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1	508					cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3						TTTTTCAGGATTAATTACAATA	0.292													99	79	---	---	---	---	
ZDHHC9	51114	broad.mit.edu	37	X	128976076	128976077	+	Intron	INS	-	A	A			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128976076_128976077insA	uc004euv.2	-						ZDHHC9_uc004euw.2_Intron|ZDHHC9_uc004eux.1_Intron|ZDHHC9_uc004euy.1_Intron	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9							endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1						AGCAGAAAAAGAAAAAAAAATG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	139551653	139551653	+	IGR	DEL	A	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139551653delA								CXorf66 (503976 upstream) : SOX3 (33499 downstream)																							CACCCGGCTCAAAAAAAAAAG	0.284													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	155014931	155014934	+	IGR	DEL	GCCA	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155014931_155014934delGCCA								SPRY3 (2814 upstream) : VAMP7 (96013 downstream)																							gaagatgaaggccagccagatctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	10033142	10033142	+	IGR	DEL	G	-	-			TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10033142delG								TTTY22 (382288 upstream) : None (None downstream)																							CGGCCGCCGAGGGGGCTACCG	0.706													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58977476	58977477	+	IGR	INS	-	CT	CT	rs112503231		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58977476_58977477insCT								None (None upstream) : None (None downstream)																							acaggatctccctctcacacag	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59029846	59029847	+	IGR	INS	-	CAG	CAG	rs141550993		TCGA-CW-5584-01A-01D-1534-10	TCGA-CW-5584-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59029846_59029847insCAG								None (None upstream) : None (None downstream)																							agtggaataaacagatctgctg	0.000													3	5	---	---	---	---	
