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
AHDC1	27245	broad.mit.edu	37	1	27874970	27874970	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27874970C>T	uc009vsy.2	-	6	4626	c.3657G>A	c.(3655-3657)TGG>TGA	p.W1219*	AHDC1_uc009vsz.1_Nonsense_Mutation_p.W1219*	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1219							DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CACTCTGGTTCCAGTTGTAGC	0.602													4	21	---	---	---	---	PASS
FNDC7	163479	broad.mit.edu	37	1	109276125	109276125	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109276125T>C	uc001dvx.2	+	10	2111	c.2111T>C	c.(2110-2112)CTT>CCT	p.L704P	FNDC7_uc010ova.1_Missense_Mutation_p.L471P	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	705	Fibronectin type-III 8.					extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		GGATTGAAGCTTACTTTCTGT	0.393													5	143	---	---	---	---	PASS
LOC388692	388692	broad.mit.edu	37	1	149282131	149282131	+	RNA	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149282131G>A	uc010pbf.1	+	1		c.2656G>A				NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0						GTCTTCAAACGAATTCAGTGC	0.448													6	435	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152281560	152281560	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152281560C>T	uc001ezu.1	-	3	5838	c.5802G>A	c.(5800-5802)TGG>TGA	p.W1934*		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1934	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGACCCAGACCACCTCTCAG	0.572									Ichthyosis				4	164	---	---	---	---	PASS
PAQR6	79957	broad.mit.edu	37	1	156216471	156216471	+	Splice_Site	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156216471C>T	uc001fnu.1	-	2	121	c.51_splice	c.e2+1	p.R17_splice	PAQR6_uc010phf.1_Intron|PAQR6_uc001fny.1_Intron|PAQR6_uc001fnv.1_Intron|PAQR6_uc010phg.1_Intron|PAQR6_uc001fnx.1_Splice_Site|PAQR6_uc001fnw.1_Splice_Site|PAQR6_uc001fnz.1_Splice_Site|PAQR6_uc010phh.1_Splice_Site_p.R17_splice|PAQR6_uc001foa.1_Splice_Site|PAQR6_uc001fob.1_Splice_Site	NM_198406	NP_940798	Q6TCH4	PAQR6_HUMAN	progestin and adipoQ receptor family member VI							integral to membrane	receptor activity				0	Hepatocellular(266;0.158)					GAGCCCCTCACCCGGGGGACC	0.597													4	101	---	---	---	---	PASS
DNAH14	127602	broad.mit.edu	37	1	225495996	225495996	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225495996A>G	uc001how.2	+	58	9060	c.8845A>G	c.(8845-8847)ACT>GCT	p.T2949A	DNAH14_uc001hox.2_RNA	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform	2296					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						GGAAACAGAAACTCTAATGGA	0.318													6	400	---	---	---	---	PASS
DNAH14	127602	broad.mit.edu	37	1	225512473	225512473	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225512473C>A	uc001how.2	+	62	9598	c.9383C>A	c.(9382-9384)GCT>GAT	p.A3128D	DNAH14_uc001hox.2_RNA	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform	2475					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						GTAGCTGAAGCTCAAAACGTC	0.368													6	353	---	---	---	---	PASS
ITPKB	3707	broad.mit.edu	37	1	226827344	226827344	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226827344C>T	uc010pvo.1	-	6	2807	c.2467G>A	c.(2467-2469)GTG>ATG	p.V823M		NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	823							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)				TCCCGGTTCACGGTGCCGTCT	0.562													8	244	---	---	---	---	PASS
SIPA1L2	57568	broad.mit.edu	37	1	232649742	232649742	+	Silent	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232649742A>G	uc001hvg.2	-	1	1502	c.1344T>C	c.(1342-1344)TCT>TCC	p.S448S		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	448					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TTGTGCAGTGAGAGCTGAGTG	0.522													5	152	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240492641	240492641	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240492641T>C	uc010pyd.1	+	10	4535	c.4310T>C	c.(4309-4311)TTC>TCC	p.F1437S	FMN2_uc010pye.1_Missense_Mutation_p.F1441S|FMN2_uc010pyf.1_Missense_Mutation_p.F83S|FMN2_uc010pyg.1_Missense_Mutation_p.F33S	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1437	FH2.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TTCCTTAGGTTCCTTTATGAA	0.378													8	631	---	---	---	---	PASS
GREB1	9687	broad.mit.edu	37	2	11752468	11752468	+	Intron	SNP	T	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11752468T>G	uc002rbk.1	+						GREB1_uc002rbp.1_5'UTR	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		AAGTGGATGGTGTGCTTATTT	0.463													6	33	---	---	---	---	PASS
ANAPC1	64682	broad.mit.edu	37	2	112583404	112583404	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112583404T>C	uc002thi.2	-	22	2901	c.2654A>G	c.(2653-2655)GAG>GGG	p.E885G		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	885					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						AACCAAGCTCTCATCACCAAG	0.269													6	300	---	---	---	---	PASS
GPR148	344561	broad.mit.edu	37	2	131486857	131486857	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131486857C>T	uc002trv.1	+	1	135	c.133C>T	c.(133-135)CCC>TCC	p.P45S		NM_207364	NP_997247	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	45	Extracellular (Potential).			CMPQAASNTSLGLGDLRVPSSMLYWLFLPSSLLAAA -> S S (in Ref. 2; AAP34196).		integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1	Colorectal(110;0.1)					CCTCAGGGTGCCCAGCTCCAT	0.627													5	44	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179477756	179477756	+	Silent	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179477756G>A	uc010zfg.1	-	214	42212	c.41988C>T	c.(41986-41988)GGC>GGT	p.G13996G	uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.G7691G|TTN_uc010zfi.1_Silent_p.G7624G|TTN_uc010zfj.1_Silent_p.G7499G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	14923							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGATGTTTTGCCTACATCTT	0.398													10	172	---	---	---	---	PASS
CERKL	375298	broad.mit.edu	37	2	182409489	182409489	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182409489G>A	uc002unx.2	-	12	1482	c.1381C>T	c.(1381-1383)CGA>TGA	p.R461*	CERKL_uc002uny.2_Nonsense_Mutation_p.R435*|CERKL_uc010zfm.1_Nonsense_Mutation_p.R417*|CERKL_uc002unz.2_Nonsense_Mutation_p.R183*|CERKL_uc002uoa.2_Nonsense_Mutation_p.R366*|CERKL_uc002uob.2_Nonsense_Mutation_p.R183*|CERKL_uc002uoc.2_Nonsense_Mutation_p.R322*|CERKL_uc010frk.2_RNA|CERKL_uc002uod.1_Nonsense_Mutation_p.R230*|CERKL_uc002unw.2_Nonsense_Mutation_p.R31*	NM_001030311	NP_001025482	Q49MI3	CERKL_HUMAN	ceramide kinase-like isoform b	461					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis	endoplasmic reticulum|endoplasmic reticulum|Golgi apparatus|Golgi apparatus|nucleolus|nucleolus	diacylglycerol kinase activity			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.088)			GAAGTGTTTCGGGCAATTATA	0.279													5	439	---	---	---	---	PASS
ANKRD44	91526	broad.mit.edu	37	2	197866491	197866491	+	Silent	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197866491T>C	uc002uua.1	-	22	2423	c.2346A>G	c.(2344-2346)CCA>CCG	p.P782P	ANKRD44_uc002utz.3_Silent_p.P514P	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	807	ANK 24.						protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CACAGTGCAGTGGAGTAAAGG	0.328													12	515	---	---	---	---	PASS
SUMO1	7341	broad.mit.edu	37	2	203071957	203071957	+	Intron	SNP	A	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203071957A>C	uc002uyz.1	-						SUMO1_uc002uza.1_3'UTR	NM_001005781	NP_001005781	P63165	SUMO1_HUMAN	SMT3 suppressor of mif two 3 homolog 1 isoform a						DNA repair|interferon-gamma-mediated signaling pathway|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|palate development|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein complex assembly|protein sumoylation|regulation of interferon-gamma-mediated signaling pathway|regulation of protein localization	cytoplasm|nuclear membrane|nuclear pore|nuclear speck	ubiquitin protein ligase binding				0						AGGGAAAAGAAAAAAAATAAA	0.338													17	140	---	---	---	---	PASS
RAPH1	65059	broad.mit.edu	37	2	204360043	204360043	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204360043C>A	uc002vad.2	-	2	259	c.34G>T	c.(34-36)GGT>TGT	p.G12C	RAPH1_uc002vae.2_Missense_Mutation_p.G12C|RAPH1_uc002vaf.2_Missense_Mutation_p.G12C	NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains	12					cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						TCTTCAGCACCATGATCAATT	0.398													6	550	---	---	---	---	PASS
RBM44	375316	broad.mit.edu	37	2	238742986	238742986	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238742986C>G	uc002vxi.3	+	15	3233	c.3101C>G	c.(3100-3102)TCT>TGT	p.S1034C		NM_001080504	NP_001073973	Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	1033							nucleotide binding|RNA binding			ovary(4)	4		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		AATGGCTTATCTATTACTACT	0.308													12	189	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188197	10188197	+	Splice_Site	SNP	G	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188197G>T	uc003bvc.2	+	2	554	c.341_splice	c.e2-1	p.G114_splice	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(7)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGTCCCGATAGGTCACCTTTG	0.333		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				15	164	---	---	---	---	PASS
ITGA9	3680	broad.mit.edu	37	3	37544743	37544743	+	Silent	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37544743C>T	uc003chd.2	+	6	740	c.687C>T	c.(685-687)AAC>AAT	p.N229N	ITGA9_uc003chc.2_Silent_p.N229N	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor	229	Extracellular (Potential).|FG-GAP 3.				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)		TTACGGACAACACCTATTTAA	0.478													7	328	---	---	---	---	PASS
SACM1L	22908	broad.mit.edu	37	3	45748396	45748396	+	Silent	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45748396T>C	uc003cos.2	+	4	534	c.330T>C	c.(328-330)ATT>ATC	p.I110I	SACM1L_uc011bag.1_Silent_p.I7I|SACM1L_uc011bah.1_Intron	NM_014016	NP_054735	Q9NTJ5	SAC1_HUMAN	suppressor of actin 1	110						Golgi apparatus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		TAACTGATATTCAGGTAAGAA	0.388													6	267	---	---	---	---	PASS
DOCK3	1795	broad.mit.edu	37	3	51184039	51184039	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51184039A>G	uc011bds.1	+	10	829	c.806A>G	c.(805-807)GAA>GGA	p.E269G		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	269						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		GAGAAGATAGAACGAATGTGT	0.428													6	378	---	---	---	---	PASS
KIAA1524	57650	broad.mit.edu	37	3	108285344	108285344	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108285344C>T	uc003dxb.3	-	11	1684	c.1415G>A	c.(1414-1416)TGC>TAC	p.C472Y	KIAA1524_uc010hpv.1_Missense_Mutation_p.C39Y	NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen	472						cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						ATATACTCACCATAATTCAGA	0.363													8	566	---	---	---	---	PASS
STAG1	10274	broad.mit.edu	37	3	136062774	136062774	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136062774G>A	uc003era.1	-	30	3638	c.3346C>T	c.(3346-3348)CAA>TAA	p.Q1116*	STAG1_uc003erb.1_Nonsense_Mutation_p.Q1116*	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1116					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						GATGTGAGTTGTGGTGCTGGC	0.488													22	224	---	---	---	---	PASS
OSTN	344901	broad.mit.edu	37	3	190936537	190936537	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190936537C>A	uc011bsn.1	+	2	104	c.104C>A	c.(103-105)GCC>GAC	p.A35D		NM_198184	NP_937827	P61366	OSTN_HUMAN	osteocrin precursor	35					cell differentiation|multicellular organismal development|ossification		hormone activity			pancreas(1)|skin(1)	2	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)		GCCTTATAGGCCTTTGATTCT	0.428													27	375	---	---	---	---	PASS
ANAPC4	29945	broad.mit.edu	37	4	25408451	25408451	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25408451A>G	uc003gro.2	+	19	1447	c.1318A>G	c.(1318-1320)ATG>GTG	p.M440V	ANAPC4_uc003grp.2_Missense_Mutation_p.M326V	NM_013367	NP_037499	Q9UJX5	APC4_HUMAN	anaphase-promoting complex subunit 4	440					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)				TTGTTGATAGATGACTCAGAA	0.264													8	787	---	---	---	---	PASS
RG9MTD2	93587	broad.mit.edu	37	4	100470320	100470320	+	Silent	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100470320T>C	uc003huy.2	-	8	1258	c.945A>G	c.(943-945)GAA>GAG	p.E315E	RG9MTD2_uc003huz.3_Silent_p.E315E|RG9MTD2_uc003hva.3_Silent_p.E315E	NM_152292	NP_689505	Q8TBZ6	RG9D2_HUMAN	RNA (guanine-9-) methyltransferase domain	315							methyltransferase activity			ovary(2)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;1.7e-08)		GTGAATCTAGTTCATTTCTGC	0.418													7	593	---	---	---	---	PASS
NHEDC2	133308	broad.mit.edu	37	4	103966100	103966100	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103966100C>T	uc003hwx.3	-	8	1815	c.943G>A	c.(943-945)GCA>ACA	p.A315T	NHEDC2_uc010iln.1_Missense_Mutation_p.A167T|NHEDC2_uc003hwy.2_Missense_Mutation_p.A315T|NHEDC2_uc011cew.1_Missense_Mutation_p.A258T|NHEDC2_uc011cex.1_Missense_Mutation_p.A258T	NM_178833	NP_849155	Q86UD5	NHDC2_HUMAN	Na+/H+ exchanger domain containing 2	315	Helical; (Potential).				sodium ion transport	integral to membrane|mitochondrial membrane	solute:hydrogen antiporter activity				0				OV - Ovarian serous cystadenocarcinoma(123;2.3e-08)		GATCCAGTTGCCACACCAATT	0.373													6	482	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123246391	123246391	+	Silent	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123246391A>G	uc003ieh.2	+	63	10956	c.10911A>G	c.(10909-10911)CGA>CGG	p.R3637R	KIAA1109_uc003iel.1_Silent_p.R1572R|KIAA1109_uc003iem.2_Silent_p.R7R	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	3637					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						GCAGTTCTCGAGTAGGAGAAA	0.333													6	317	---	---	---	---	PASS
TTC29	83894	broad.mit.edu	37	4	147628655	147628655	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147628655C>T	uc003ikw.3	-	12	1606	c.1379G>A	c.(1378-1380)CGT>CAT	p.R460H	TTC29_uc010ipc.2_RNA|TTC29_uc003ikx.3_Missense_Mutation_p.R486H|TTC29_uc010ipd.1_Missense_Mutation_p.R459H	NM_031956	NP_114162	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	460							binding				0	all_hematologic(180;0.151)					TTCTTCCAAACGTTCTGAGTT	0.318													10	624	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14477072	14477072	+	Silent	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14477072C>T	uc003jff.2	+	41	6159	c.6153C>T	c.(6151-6153)CAC>CAT	p.H2051H	TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Silent_p.H1700H	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2051	DH 2.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					TTGTTAAACACGTAAGCACAA	0.353													6	428	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16675008	16675008	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16675008G>T	uc003jft.3	-	35	5386	c.4918C>A	c.(4918-4920)CTG>ATG	p.L1640M	MYO10_uc011cnb.1_Missense_Mutation_p.L269M|MYO10_uc011cnc.1_Missense_Mutation_p.L519M|MYO10_uc011cnd.1_Missense_Mutation_p.L997M|MYO10_uc011cne.1_Missense_Mutation_p.L997M|MYO10_uc010itx.2_Missense_Mutation_p.L1262M	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1640	MyTH4.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						CGACTCGGCAGGAAGGTGCAG	0.557													3	34	---	---	---	---	PASS
NIPBL	25836	broad.mit.edu	37	5	37007468	37007468	+	Silent	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37007468C>A	uc003jkl.3	+	18	4630	c.4131C>A	c.(4129-4131)ACC>ACA	p.T1377T	NIPBL_uc003jkk.3_Silent_p.T1377T	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1377					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AATGTTCTACCCATAAGCAGA	0.299													5	462	---	---	---	---	PASS
PPAP2A	8611	broad.mit.edu	37	5	54826082	54826082	+	Intron	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54826082T>C	uc003jqa.2	-						PPAP2A_uc003jpz.2_Intron|PPAP2A_uc003jqb.2_Intron|RNF138P1_uc003jqc.1_RNA	NM_003711	NP_003702	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|androgen receptor signaling pathway|germ cell migration|negative regulation of cell proliferation|phospholipid dephosphorylation|regulation of lipid metabolic process|sphingolipid metabolic process	integral to plasma membrane|membrane fraction	phosphatidate phosphatase activity|sphingosine-1-phosphate phosphatase activity			ovary(2)	2		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				AACTGATGTCTCTGATTTAGA	0.363													7	489	---	---	---	---	PASS
ARSB	411	broad.mit.edu	37	5	78135248	78135248	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78135248C>T	uc003kfq.2	-	6	2430	c.1144G>A	c.(1144-1146)GAA>AAA	p.E382K	ARSB_uc003kfr.3_Missense_Mutation_p.E382K	NM_000046	NP_000037	P15848	ARSB_HUMAN	arylsulfatase B isoform 1 precursor	382					lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		GGGCTTCCTTCACTGGAAAAC	0.393													5	292	---	---	---	---	PASS
AQPEP	206338	broad.mit.edu	37	5	115329447	115329447	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115329447A>G	uc003kro.2	+	6	1434	c.1270A>G	c.(1270-1272)AAC>GAC	p.N424D	AQPEP_uc003krp.2_RNA|AQPEP_uc003krq.2_5'Flank|AQPEP_uc003krr.2_5'Flank|AQPEP_uc003krs.2_5'Flank	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	424	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						GTGGTTTGGAAACTTGGTTAC	0.308													6	394	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127674649	127674649	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127674649A>G	uc003kuu.2	-	26	3887	c.3448T>C	c.(3448-3450)TTC>CTC	p.F1150L	FBN2_uc003kuv.2_Missense_Mutation_p.F1117L	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	1150	EGF-like 16; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ATCATCATGAAGCCACTTTCA	0.517													4	63	---	---	---	---	PASS
NEUROG1	4762	broad.mit.edu	37	5	134870643	134870643	+	3'UTR	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134870643A>G	uc003lax.2	-	1						NM_006161	NP_006152	Q92886	NGN1_HUMAN	neurogenin 1						positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter	nucleus	chromatin binding|E-box binding|sequence-specific DNA binding transcription factor activity|transcription factor binding transcription factor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGGGAGGGGGAAAGTAACAGT	0.592													9	126	---	---	---	---	PASS
FAM153A	285596	broad.mit.edu	37	5	177166139	177166139	+	Splice_Site	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177166139C>A	uc010jkp.1	-	11	728	c.307_splice	c.e11-1	p.A103_splice	FAM153A_uc011dgd.1_Intron|FAM153A_uc003mib.1_Splice_Site|FAM153A_uc003mic.2_Splice_Site_p.A103_splice	NM_173663	NP_775934	Q9UHL3	F153A_HUMAN	hypothetical protein LOC285596											skin(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	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)			CTGCGTCTGCCTGCGTTTAGA	0.438													29	351	---	---	---	---	PASS
TAAR5	9038	broad.mit.edu	37	6	132910004	132910004	+	Silent	SNP	G	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132910004G>T	uc003qdk.2	-	1	874	c.822C>A	c.(820-822)GTC>GTA	p.V274V		NM_003967	NP_003958	O14804	TAAR5_HUMAN	trace amine associated receptor 5	274	Helical; Name=6; (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			skin(1)	1	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		GGAGGCTGTCGACCATCGTGT	0.507													12	85	---	---	---	---	PASS
BBS9	27241	broad.mit.edu	37	7	33296941	33296941	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33296941T>C	uc003tdn.1	+	6	1049	c.536T>C	c.(535-537)CTT>CCT	p.L179P	BBS9_uc003tdo.1_Missense_Mutation_p.L179P|BBS9_uc003tdp.1_Missense_Mutation_p.L179P|BBS9_uc003tdq.1_Missense_Mutation_p.L179P|BBS9_uc010kwn.1_RNA|BBS9_uc011kan.1_Missense_Mutation_p.L179P|BBS9_uc011kao.1_Missense_Mutation_p.L57P	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	179					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)			CCTGGCTTTCTTCTGCCTGGT	0.433									Bardet-Biedl_syndrome				7	631	---	---	---	---	PASS
VPS41	27072	broad.mit.edu	37	7	38768162	38768162	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38768162A>G	uc003tgy.2	-	27	2410	c.2384T>C	c.(2383-2385)CTT>CCT	p.L795P	VPS41_uc003tgz.2_Missense_Mutation_p.L770P|VPS41_uc010kxn.2_Missense_Mutation_p.L706P|VPS41_uc003tgx.2_RNA	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1	795	RING-type; atypical.				Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4						AATAGGGGAAAGGCACGACTC	0.403													7	423	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48319495	48319495	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48319495C>T	uc003toq.2	+	18	8729	c.8704C>T	c.(8704-8706)CAA>TAA	p.Q2902*	ABCA13_uc010kys.1_5'Flank	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	2902					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						ATACTGGCAACAAATCCCACT	0.333													5	129	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48563959	48563959	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48563959C>A	uc003toq.2	+	54	14192	c.14167C>A	c.(14167-14169)CTT>ATT	p.L4723I	ABCA13_uc010kys.1_Missense_Mutation_p.L1798I|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Missense_Mutation_p.L453I	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4723	ABC transporter 2.				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						GTTATACAACCTTAGTAAACA	0.358													5	477	---	---	---	---	PASS
TYW1B	441250	broad.mit.edu	37	7	72093945	72093945	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72093945G>A	uc011kej.1	-	15	1703	c.1544C>T	c.(1543-1545)GCA>GTA	p.A515V	TYW1B_uc011keh.1_Missense_Mutation_p.A353V|TYW1B_uc011kei.1_Missense_Mutation_p.A141V	NM_001145440	NP_001138912	Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B isoform	515					tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0						CACGTTCCATGCTTTCACGAG	0.522													4	70	---	---	---	---	PASS
POLR2J3	548644	broad.mit.edu	37	7	102213039	102213039	+	5'UTR	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102213039T>C	uc011kkw.1	-	1					UPK3BL_uc003uzy.2_Intron|POLR2J3_uc003uzw.2_5'UTR	NM_001097615	NP_001091084	Q9GZM3	RPB1B_HUMAN	polymerase (RNA) II (DNA directed) polypeptide							nucleus	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0						ATAAGAGGCCTCTTCCGGATT	0.662													4	6	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103175830	103175830	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103175830G>A	uc003vca.2	-	46	7442	c.7282C>T	c.(7282-7284)CGG>TGG	p.R2428W	RELN_uc010liz.2_Missense_Mutation_p.R2428W	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2428					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ACCAGGATCCGTTGCAGATGA	0.458													5	207	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116339341	116339341	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116339341A>G	uc003vij.2	+	2	390	c.203A>G	c.(202-204)AAC>AGC	p.N68S	MET_uc010lkh.2_Missense_Mutation_p.N68S|MET_uc011knc.1_Missense_Mutation_p.N68S|MET_uc011knd.1_Missense_Mutation_p.N68S|MET_uc011kne.1_Missense_Mutation_p.N68S|MET_uc011knf.1_Missense_Mutation_p.N68S|MET_uc011kng.1_Missense_Mutation_p.N68S|MET_uc011knh.1_Missense_Mutation_p.N68S|MET_uc011kni.1_Missense_Mutation_p.N68S|MET_uc003vii.1_Missense_Mutation_p.N87S|MET_uc010lkg.2_Missense_Mutation_p.N68S|MET_uc011kmz.1_Missense_Mutation_p.N68S|MET_uc011kna.1_Missense_Mutation_p.N68S|MET_uc011knb.1_Missense_Mutation_p.N68S	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	68	Extracellular (Potential).|Sema.				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding	p.982_1028del47(8)		upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GGTGCCACTAACTACATTTAT	0.443			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				5	193	---	---	---	---	PASS
TAS2R3	50831	broad.mit.edu	37	7	141464108	141464108	+	Silent	SNP	C	A	A	rs111759960		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141464108C>A	uc003vwp.1	+	1	212	c.150C>A	c.(148-150)ACC>ACA	p.T50T		NM_016943	NP_058639	Q9NYW6	TA2R3_HUMAN	taste receptor T2R3	50	Helical; Name=2; (Potential).				sensory perception of taste		taste receptor activity			central_nervous_system(1)	1	Melanoma(164;0.0171)					TCATCACCACCCTGGCACTCT	0.398													5	426	---	---	---	---	PASS
OR2F2	135948	broad.mit.edu	37	7	143633180	143633180	+	Silent	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143633180G>A	uc011ktv.1	+	1	855	c.855G>A	c.(853-855)CTG>CTA	p.L285L		NM_001004685	NP_001004685	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F,	285	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	Melanoma(164;0.0903)					TGCCTCTGCTGAACCCTGTGA	0.458													19	183	---	---	---	---	PASS
MMP16	4325	broad.mit.edu	37	8	89059004	89059004	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89059004C>T	uc003yeb.3	-	9	1664	c.1382G>A	c.(1381-1383)AGA>AAA	p.R461K		NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1	461	Extracellular (Potential).|Hemopexin-like 3.				collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8						TTCACTATATCTCCAATATCT	0.338													9	365	---	---	---	---	PASS
ANGPT1	284	broad.mit.edu	37	8	108359177	108359177	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108359177T>C	uc003ymn.2	-	2	914	c.446A>G	c.(445-447)GAG>GGG	p.E149G	ANGPT1_uc003ymo.2_Missense_Mutation_p.E149G	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor	149					activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			TACCTGGGTCTCAACATCTGT	0.483													6	253	---	---	---	---	PASS
FREM1	158326	broad.mit.edu	37	9	14776040	14776040	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14776040G>A	uc003zlm.2	-	25	5194	c.4604C>T	c.(4603-4605)CCT>CTT	p.P1535L	FREM1_uc010mic.2_Intron|FREM1_uc003zlk.2_5'Flank|FREM1_uc003zll.2_Missense_Mutation_p.P71L	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	1535	CSPG 11.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)		AGGTGTATCAGGGTCGGTCAG	0.602													5	110	---	---	---	---	PASS
UNC13B	10497	broad.mit.edu	37	9	35403789	35403789	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35403789T>C	uc003zwq.2	+	39	4827	c.4535T>C	c.(4534-4536)ATA>ACA	p.I1512T	UNC13B_uc003zwr.2_Missense_Mutation_p.I1531T|ATP8B5P_uc010mkn.1_5'Flank|ATP8B5P_uc010mko.2_5'Flank|ATP8B5P_uc010mkp.2_5'Flank|ATP8B5P_uc003zwu.2_5'Flank	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like	1512	C2 3.				excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GAGTTGCAGATATGCGTGAAG	0.552													4	110	---	---	---	---	PASS
KIF27	55582	broad.mit.edu	37	9	86495277	86495277	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86495277G>A	uc004ana.2	-	11	2722	c.2578C>T	c.(2578-2580)CGA>TGA	p.R860*	KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Nonsense_Mutation_p.R860*	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27	860	Potential.				cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5						TTTTCTTCTCGTAGTTTTCTT	0.353													10	751	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	88464393	88464393	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88464393C>T	uc004aoh.1	+	10	1683	c.580C>T	c.(580-582)CAA>TAA	p.Q194*						RecName: Full=Kinesin-like protein KIF27;																		AAGAAAACTACAAGAAGAAAA	0.343													5	382	---	---	---	---	PASS
OR13C8	138802	broad.mit.edu	37	9	107332250	107332250	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107332250G>T	uc011lvo.1	+	1	802	c.802G>T	c.(802-804)GTT>TTT	p.V268F		NM_001004483	NP_001004483	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C,	268	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						TAAAGCCTCTGTTGATTCAGG	0.448													22	122	---	---	---	---	PASS
FCN1	2219	broad.mit.edu	37	9	137802991	137802991	+	Missense_Mutation	SNP	C	T	T	rs149439264	byFrequency	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137802991C>T	uc004cfi.2	-	8	813	c.721G>A	c.(721-723)GGG>AGG	p.G241R		NM_002003	NP_001994	O00602	FCN1_HUMAN	ficolin 1 precursor	241	Fibrinogen C-terminal.				opsonization|signal transduction	collagen|extracellular space	antigen binding|calcium ion binding|receptor binding|sugar binding			large_intestine(1)|ovary(1)	2		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		GCACTGCCCCCGACAAAGGCT	0.468													4	146	---	---	---	---	PASS
OR51L1	119682	broad.mit.edu	37	11	5020987	5020987	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5020987G>A	uc010qyu.1	+	1	775	c.775G>A	c.(775-777)GGG>AGG	p.G259R		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	259	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		GCCAGTTATTGGGGTGTCAAT	0.473													48	408	---	---	---	---	PASS
OR52E8	390079	broad.mit.edu	37	11	5878479	5878479	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5878479C>T	uc010qzr.1	-	1	454	c.454G>A	c.(454-456)GGC>AGC	p.G152S	TRIM5_uc001mbq.1_Intron	NM_001005168	NP_001005168	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E,	152	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACAGCAATGCCTGCAATGAGG	0.502													14	95	---	---	---	---	PASS
TCN1	6947	broad.mit.edu	37	11	59634006	59634006	+	5'UTR	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59634006A>G	uc001noj.2	-	1						NM_001062	NP_001053	P20061	TCO1_HUMAN	transcobalamin I precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular region	cobalamin binding			ovary(2)	2		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GATGGGCAGAAGGTAATGAGA	0.468													5	147	---	---	---	---	PASS
AQP11	282679	broad.mit.edu	37	11	77320379	77320379	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77320379T>C	uc001oyj.2	+	3	1131	c.773T>C	c.(772-774)CTT>CCT	p.L258P	AQP11_uc009yuu.2_RNA	NM_173039	NP_766627	Q8NBQ7	AQP11_HUMAN	aquaporin 11	258						cell surface|integral to membrane	transporter activity				0	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			AGCTTTTTCCTTCCATGGCTG	0.333													8	690	---	---	---	---	PASS
WNT5B	81029	broad.mit.edu	37	12	1755046	1755046	+	Silent	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1755046C>T	uc009zdq.2	+	5	950	c.708C>T	c.(706-708)GCC>GCT	p.A236A	WNT5B_uc001qjj.2_Silent_p.A236A|WNT5B_uc001qjk.2_Silent_p.A236A|WNT5B_uc001qjl.2_Silent_p.A236A	NM_032642	NP_116031	Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family,	236					angiogenesis|anterior/posterior pattern formation|cell migration involved in gastrulation|cellular response to retinoic acid|chondrocyte differentiation|convergent extension involved in axis elongation|convergent extension involved in gastrulation|dorsal/ventral axis specification|endocrine pancreas development|fat cell differentiation|lens fiber cell development|negative regulation of canonical Wnt receptor signaling pathway|neuron differentiation|positive regulation of cell migration|positive regulation of fat cell differentiation|respiratory system development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			TGCAGCTGGCCGAGTTCCGCA	0.647													3	0	---	---	---	---	PASS
STRAP	11171	broad.mit.edu	37	12	16052865	16052865	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16052865T>C	uc001rdc.3	+	8	1157	c.803T>C	c.(802-804)ATT>ACT	p.I268T	STRAP_uc010shw.1_Missense_Mutation_p.I281T|STRAP_uc001rdd.3_Missense_Mutation_p.I174T	NM_007178	NP_009109	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated	268	WD 7.				mRNA processing|RNA splicing	cell junction|mitochondrion|spliceosomal complex	identical protein binding			skin(1)	1		Hepatocellular(102;0.121)				TTTGGTCCTATTCACTGTGTG	0.358													6	354	---	---	---	---	PASS
BICD1	636	broad.mit.edu	37	12	32490734	32490734	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32490734G>A	uc001rku.2	+	7	2635	c.2554G>A	c.(2554-2556)GGC>AGC	p.G852S	BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron|BICD1_uc001rkw.1_Missense_Mutation_p.G134S	NM_001714	NP_001705	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 isoform 1	852					anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GGTCAGCAGTGGCACTCAGAG	0.502													9	78	---	---	---	---	PASS
RACGAP1P	83956	broad.mit.edu	37	12	45457920	45457920	+	RNA	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45457920C>T	uc001rol.2	-	1		c.1275G>A				NR_026583				Homo sapiens FKSG42 (FKSG42) mRNA, complete cds.												0						ACTTTGCTGACGAGGGGTACA	0.438													8	295	---	---	---	---	PASS
ZFC3H1	196441	broad.mit.edu	37	12	72037976	72037976	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72037976T>C	uc001swo.2	-	5	1761	c.1402A>G	c.(1402-1404)AGA>GGA	p.R468G		NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2	468	Potential.				RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5						tcttcctctcttttccttctc	0.219													9	806	---	---	---	---	PASS
PXN	5829	broad.mit.edu	37	12	120660800	120660800	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120660800A>G	uc001txt.2	-	4	490	c.359T>C	c.(358-360)TTC>TCC	p.F120S	PXN_uc001txv.2_5'UTR|PXN_uc001txx.2_5'UTR|PXN_uc001txy.2_Missense_Mutation_p.F120S|PXN_uc001txz.2_RNA|uc001tya.2_5'Flank	NM_001080855	NP_001074324	P49023	PAXI_HUMAN	paxillin isoform 1	120					cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTTGTTGGGGAAGCTTTGAGA	0.527													7	213	---	---	---	---	PASS
NME2P1	283458	broad.mit.edu	37	12	120720306	120720306	+	RNA	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120720306C>T	uc001tyb.1	+	1		c.367C>T				NR_001577				Homo sapiens non-metastatic cells 2, protein (NM23B) expressed in, pseudogene 1 (NME2P1), non-coding RNA.												0						AGGGGCTGAACGTCGTGAAGA	0.567													12	83	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23985433	23985433	+	5'UTR	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23985433T>C	uc001uon.2	-	2						NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin						cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CGCTTCTTTCTTCTGTTTAAG	0.403													7	501	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39264232	39264232	+	Silent	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39264232A>G	uc001uwv.2	+	1	3060	c.2751A>G	c.(2749-2751)GAA>GAG	p.E917E		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	917	CSPG 5.|Extracellular (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GCTCCTTGGAAGTCAGTGACA	0.522													4	60	---	---	---	---	PASS
ZC3H14	79882	broad.mit.edu	37	14	89038503	89038503	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89038503C>A	uc001xww.2	+	5	590	c.365C>A	c.(364-366)GCG>GAG	p.A122E	ZC3H14_uc010twd.1_Missense_Mutation_p.A122E|ZC3H14_uc010twe.1_Missense_Mutation_p.A122E|ZC3H14_uc001xwx.2_Missense_Mutation_p.A122E|ZC3H14_uc010twf.1_5'UTR|ZC3H14_uc001xwy.2_Missense_Mutation_p.A88E|ZC3H14_uc010twg.1_5'Flank	NM_024824	NP_079100	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14 isoform 1	122						cytoplasm|cytoplasm|nuclear speck	protein binding|RNA binding|zinc ion binding			ovary(2)|skin(1)	3						ATTCCTAGCGCGAGACCTGAA	0.478													11	212	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106667750	106667750	+	RNA	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106667750C>T	uc010tyt.1	-	877		c.22115G>A								Parts of antibodies, mostly variable regions.												0						CAGCCCCTTCCCTGGAGCTTG	0.567													8	87	---	---	---	---	PASS
ADAM10	102	broad.mit.edu	37	15	58938323	58938323	+	Silent	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58938323A>G	uc002afd.1	-	6	1110	c.666T>C	c.(664-666)TGT>TGC	p.C222C	ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor	222	Peptidase M12B.|Extracellular (Potential).				cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)		TATAAAGCTGACAAGTATTTT	0.343													8	626	---	---	---	---	PASS
C15orf26	161502	broad.mit.edu	37	15	81440257	81440257	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81440257G>A	uc002bgb.2	+	6	722	c.695G>A	c.(694-696)CGG>CAG	p.R232Q		NM_173528	NP_775799	Q6P656	CO026_HUMAN	hypothetical protein LOC161502	232											0						GCAGCCCACCGGCATCTTTTC	0.388													12	199	---	---	---	---	PASS
C16orf91	283951	broad.mit.edu	37	16	1476300	1476300	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1476300G>A	uc010uvd.1	-	3	323	c.323C>T	c.(322-324)CCC>CTC	p.P108L		NM_001010878	NP_001010878	Q4G0I0	CSMT1_HUMAN	hypothetical protein LOC283951	Error:Variant_position_missing_in_Q4G0I0_after_alignment						integral to membrane					0						GGAGCCTTTGGGTTGGGCTGG	0.607													5	157	---	---	---	---	PASS
IL4R	3566	broad.mit.edu	37	16	27367167	27367167	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27367167G>A	uc002don.2	+	8	951	c.709G>A	c.(709-711)GTC>ATC	p.V237I	IL4R_uc002dop.3_Missense_Mutation_p.V222I|IL4R_uc010bxy.2_Missense_Mutation_p.V237I|IL4R_uc002doo.2_Missense_Mutation_p.V77I	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a	237	Helical; (Potential).				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2						CCTGCTGGGCGTCAGCGTTTC	0.617													5	60	---	---	---	---	PASS
SULT1A2	6799	broad.mit.edu	37	16	28607132	28607132	+	Silent	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28607132G>A	uc002dqg.1	-	2	471	c.120C>T	c.(118-120)GAC>GAT	p.D40D	uc010vct.1_Intron|SULT1A2_uc002dqh.1_Silent_p.D40D	NM_177528	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A,	40					3'-phosphoadenosine 5'-phosphosulfate metabolic process|amine biosynthetic process|catecholamine metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0						TGATGAGCAGGTCATCAGGCC	0.647													6	44	---	---	---	---	PASS
SPATA22	84690	broad.mit.edu	37	17	3352323	3352323	+	Silent	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3352323C>T	uc002fvm.2	-	6	687	c.450G>A	c.(448-450)TCG>TCA	p.S150S	SPATA22_uc010vrg.1_Silent_p.S134S|SPATA22_uc010vrf.1_Silent_p.S150S|SPATA22_uc002fvn.2_Silent_p.S150S|SPATA22_uc002fvo.2_Silent_p.S150S|SPATA22_uc002fvp.2_Silent_p.S150S|SPATA22_uc010ckf.2_Silent_p.S107S	NM_032598	NP_115987	Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	150											0						GTTGAGCTCCCGAACTCACTG	0.348													7	761	---	---	---	---	PASS
MYH10	4628	broad.mit.edu	37	17	8409786	8409786	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8409786T>C	uc002gll.2	-	25	3239	c.3143A>G	c.(3142-3144)AAG>AGG	p.K1048R	MYH10_uc002glm.2_Missense_Mutation_p.K1079R|MYH10_uc010cnx.2_Missense_Mutation_p.K1057R	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle	1048	Potential.				actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2						CTGACGAGTCTTTTCTTCCTT	0.473													6	256	---	---	---	---	PASS
KRT31	3881	broad.mit.edu	37	17	39551296	39551296	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39551296T>C	uc002hwn.2	-	6	954	c.901A>G	c.(901-903)ACA>GCA	p.T301A	KRT31_uc010cxn.2_Missense_Mutation_p.T301A	NM_002277	NP_002268	Q15323	K1H1_HUMAN	keratin 31	301	Coil 2.|Rod.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000496)				TCACTCTCTGTCAGCGTGTTT	0.567													5	80	---	---	---	---	PASS
USP32	84669	broad.mit.edu	37	17	58378995	58378995	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58378995A>G	uc002iyo.1	-	3	543	c.257T>C	c.(256-258)CTC>CCC	p.L86P	USP32_uc010wov.1_Missense_Mutation_p.L86P	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	86					protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			TCTTGTAAGGAGGACAAGTCC	0.333													7	507	---	---	---	---	PASS
TBC1D3P2	440452	broad.mit.edu	37	17	60347011	60347011	+	Silent	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60347011A>G	uc002izq.2	-	8	625	c.513T>C	c.(511-513)CTT>CTC	p.L171L	TBC1D3P2_uc010woz.1_RNA|uc010wpa.1_5'Flank					SubName: Full=Putative uncharacterized protein TBC1D3E;												0						GGAGGATGTAAAGTAGTTCCC	0.483													3	13	---	---	---	---	PASS
TBC1D3P2	440452	broad.mit.edu	37	17	60347013	60347013	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60347013G>A	uc002izq.2	-	8	623	c.511C>T	c.(511-513)CTT>TTT	p.L171F	TBC1D3P2_uc010woz.1_RNA|uc010wpa.1_5'Flank					SubName: Full=Putative uncharacterized protein TBC1D3E;												0						AGGATGTAAAGTAGTTCCCGC	0.478													3	12	---	---	---	---	PASS
ZNF519	162655	broad.mit.edu	37	18	14105315	14105315	+	Silent	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14105315T>C	uc002kst.1	-	3	1377	c.1224A>G	c.(1222-1224)GAA>GAG	p.E408E	ZNF519_uc002ksq.1_Intron|ZNF519_uc002ksr.1_Intron|ZNF519_uc010dlm.1_Intron	NM_145287	NP_660330	Q8TB69	ZN519_HUMAN	zinc finger protein 519	408	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CTTTGCCACATTCCTTACACT	0.393													5	178	---	---	---	---	PASS
MIB1	57534	broad.mit.edu	37	18	19423173	19423173	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19423173G>C	uc002ktq.2	+	14	2044	c.2044G>C	c.(2044-2046)GTT>CTT	p.V682L	MIB1_uc002ktp.2_Missense_Mutation_p.V321L	NM_020774	NP_065825	Q86YT6	MIB1_HUMAN	mindbomb homolog 1	682	ANK 8.				Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)			TACCCAGATTGTTAGGGTAAA	0.353													9	298	---	---	---	---	PASS
C18orf10	25941	broad.mit.edu	37	18	34376942	34376942	+	Silent	SNP	C	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34376942C>G	uc002kzw.1	-	7	1157	c.729G>C	c.(727-729)GTG>GTC	p.V243V	C18orf10_uc002kzv.1_Intron|C18orf10_uc010xci.1_Silent_p.V208V|C18orf10_uc002kzx.1_Silent_p.V200V	NM_015476	NP_056291	Q68CL5	TPGS2_HUMAN	tubulin polyglutamylase complex subunit 2	243						cytoplasm|microtubule				skin(1)	1						CTAGCTTATTCACAAAGGAGT	0.463													22	497	---	---	---	---	PASS
ZNF136	7695	broad.mit.edu	37	19	12296984	12296984	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12296984T>G	uc002mti.2	+	3	286	c.186T>G	c.(184-186)AAT>AAG	p.N62K	ZNF136_uc010xmh.1_5'UTR	NM_003437	NP_003428	P52737	ZN136_HUMAN	zinc finger protein 136	62	KRAB.				negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|transcription corepressor activity|zinc ion binding			ovary(1)|pancreas(1)	2						GAGGGAGAAATCTAAGGTAAT	0.338													21	299	---	---	---	---	PASS
CNOT3	4849	broad.mit.edu	37	19	54646868	54646868	+	Silent	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54646868C>T	uc002qdj.1	+	3	350	c.39C>T	c.(37-39)CGC>CGT	p.R13R	CNOT3_uc010yel.1_Silent_p.R13R|CNOT3_uc002qdi.2_5'UTR|CNOT3_uc002qdk.1_Silent_p.R13R|CNOT3_uc010ere.1_5'Flank	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	13					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					AGATTGATCGCTGCCTCAAGA	0.542													4	223	---	---	---	---	PASS
ZNF549	256051	broad.mit.edu	37	19	58049193	58049193	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58049193C>A	uc002qpb.1	+	4	1070	c.821C>A	c.(820-822)CCT>CAT	p.P274H	ZNF547_uc002qpm.3_Intron|ZNF549_uc010eud.1_Intron|ZNF549_uc002qpa.1_Missense_Mutation_p.P261H	NM_153263	NP_694995	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	274					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GCAGAAAAGCCTTATGTGTGC	0.398													4	125	---	---	---	---	PASS
C20orf30	29058	broad.mit.edu	37	20	5081347	5081347	+	3'UTR	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5081347G>A	uc002wll.2	-	5					C20orf30_uc010gbi.2_Intron|C20orf30_uc002wlk.2_3'UTR|C20orf30_uc002wlm.2_3'UTR|C20orf30_uc002wln.2_3'UTR|C20orf30_uc002wlo.2_RNA	NM_001009924	NP_001009924	Q96A57	CT030_HUMAN	hypothetical protein LOC29058 isoform 2							integral to membrane					0						GCAAGCTGCAGAATTCCTTAG	0.423											OREG0025754	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	41	---	---	---	---	PASS
TRPC4AP	26133	broad.mit.edu	37	20	33596526	33596526	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33596526C>G	uc002xbk.2	-	13	1570	c.1536G>C	c.(1534-1536)AGG>AGC	p.R512S	TRPC4AP_uc002xbj.2_5'Flank|TRPC4AP_uc010zuq.1_Missense_Mutation_p.R103S|TRPC4AP_uc002xbl.2_Missense_Mutation_p.R504S|TRPC4AP_uc010zur.1_Missense_Mutation_p.R473S|TRPC4AP_uc002xbm.1_Missense_Mutation_p.R512S	NM_015638	NP_056453	Q8TEL6	TP4AP_HUMAN	TRPC4-associated protein isoform a	512					protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TTAATAAGCCCCTCTTCCCAT	0.537													18	250	---	---	---	---	PASS
MOCS3	27304	broad.mit.edu	37	20	49576093	49576093	+	Silent	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49576093C>T	uc002xvy.1	+	1	731	c.714C>T	c.(712-714)AAC>AAT	p.N238N	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	238					enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			skin(2)|ovary(1)	3						CAGTGACCAACTGCGCGGACG	0.622													5	21	---	---	---	---	PASS
ZNF217	7764	broad.mit.edu	37	20	52193398	52193398	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52193398C>A	uc002xwq.3	-	3	2176	c.1905G>T	c.(1903-1905)CAG>CAT	p.Q635H	ZNF217_uc010gij.1_Missense_Mutation_p.Q627H	NM_006526	NP_006517	O75362	ZN217_HUMAN	zinc finger protein 217	635					negative regulation of transcription, DNA-dependent	histone deacetylase complex	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|lung(1)|breast(1)	6	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GGTTATTTGCCTGAGTTTCAA	0.453													6	503	---	---	---	---	PASS
RAB22A	57403	broad.mit.edu	37	20	56886167	56886167	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56886167C>A	uc002xyz.2	+	2	367	c.105C>A	c.(103-105)AAC>AAA	p.N35K		NM_020673	NP_065724	Q9UL26	RB22A_HUMAN	RAS-related protein RAB-22A	35	Effector region (By similarity).				endocytosis|endosome organization|protein transport|small GTPase mediated signal transduction	early endosome|endosome membrane|plasma membrane	GTP binding|GTPase activity|protein binding				0	all_epithelial(3;5.09e-14)|Lung NSC(12;0.000122)|all_lung(29;0.00042)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;4.73e-08)|all cancers(14;4.83e-07)			CAAACATCAACCCAACAATAG	0.408													49	486	---	---	---	---	PASS
CDH26	60437	broad.mit.edu	37	20	58571010	58571010	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58571010T>C	uc002ybe.2	+	12	2089	c.1789T>C	c.(1789-1791)TGT>CGT	p.C597R	CDH26_uc002ybf.1_Missense_Mutation_p.C177R|CDH26_uc010zzy.1_RNA|CDH26_uc002ybg.2_Missense_Mutation_p.C111R|CDH26_uc002ybh.2_5'Flank|CDH26_uc002ybi.2_5'Flank	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a	597	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			GATCTGCCCCTGTGCCAGTGG	0.547													6	251	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11038734	11038734	+	3'UTR	SNP	G	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11038734G>C	uc002yit.1	-	6					TPTE_uc002yis.1_RNA	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)		CTACCTGTTTGGACCGAGGTC	0.373													6	247	---	---	---	---	PASS
RRP1B	23076	broad.mit.edu	37	21	45096164	45096164	+	Silent	SNP	T	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45096164T>C	uc002zdk.2	+	7	675	c.561T>C	c.(559-561)GAT>GAC	p.D187D		NM_015056	NP_055871	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1 homolog B	187					rRNA processing	cytosol|nucleolus|preribosome, small subunit precursor	protein binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.178)		TTTTAGCAGATCAGAATCTCA	0.413													5	215	---	---	---	---	PASS
DDX17	10521	broad.mit.edu	37	22	38881836	38881836	+	3'UTR	SNP	G	A	A	rs34004602		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38881836G>A	uc003avy.3	-	13					DDX17_uc003avw.3_3'UTR|DDX17_uc010gxp.2_3'UTR|DDX17_uc003avx.3_3'UTR	NM_001098504	NP_001091974	Q92841	DDX17_HUMAN	DEAD box polypeptide 17 isoform 3						RNA processing	nucleus	ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity			skin(3)|upper_aerodigestive_tract(1)	4	Melanoma(58;0.0286)					aaaaaaaaaagaaaaaaggaa	0.284													4	16	---	---	---	---	PASS
RAI2	10742	broad.mit.edu	37	X	17818567	17818567	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17818567G>A	uc004cyf.2	-	3	2134	c.1564C>T	c.(1564-1566)CGG>TGG	p.R522W	RAI2_uc004cyg.2_Missense_Mutation_p.R522W|RAI2_uc010nfa.2_Missense_Mutation_p.R522W|RAI2_uc004cyh.3_Missense_Mutation_p.R522W|RAI2_uc011miy.1_Missense_Mutation_p.R472W	NM_021785	NP_068557	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	522					embryo development					ovary(1)|breast(1)	2	Hepatocellular(33;0.183)					GTGGCCAGCCGTTGTTTTTTG	0.373													17	396	---	---	---	---	PASS
CXorf22	170063	broad.mit.edu	37	X	35974094	35974094	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35974094A>T	uc004ddj.2	+	8	1250	c.1191A>T	c.(1189-1191)AAA>AAT	p.K397N	CXorf22_uc010ngv.2_RNA	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	397										large_intestine(1)|lung(1)|ovary(1)	3						GATTTCAGAAAGTGGAATTAG	0.368													5	123	---	---	---	---	PASS
CACNA1F	778	broad.mit.edu	37	X	49072841	49072841	+	Splice_Site	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49072841C>T	uc004dnb.2	-	27	3331	c.3269_splice	c.e27+1	p.A1090_splice	CACNA1F_uc010nip.2_Splice_Site_p.A1079_splice	NM_005183	NP_005174	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)	CTGTCCCTCACGCAGGCCAGC	0.572													7	40	---	---	---	---	PASS
AKAP4	8852	broad.mit.edu	37	X	49958758	49958758	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49958758C>G	uc004dow.1	-	5	730	c.606G>C	c.(604-606)CAG>CAC	p.Q202H	AKAP4_uc004dov.1_Intron|AKAP4_uc010njp.1_Missense_Mutation_p.Q24H|AKAP4_uc004dou.1_Missense_Mutation_p.Q193H	NM_003886	NP_003877	Q5JQC9	AKAP4_HUMAN	A-kinase anchor protein 4 isoform 1	202					cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	8	Ovarian(276;0.236)					TGACTGCTCTCTGAGTGCTAG	0.443													21	302	---	---	---	---	PASS
ARHGEF9	23229	broad.mit.edu	37	X	62898302	62898302	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62898302A>G	uc004dvl.2	-	5	1551	c.712T>C	c.(712-714)TTC>CTC	p.F238L	ARHGEF9_uc004dvj.1_Missense_Mutation_p.F127L|ARHGEF9_uc004dvk.1_Missense_Mutation_p.F100L|ARHGEF9_uc011mos.1_Missense_Mutation_p.F217L|ARHGEF9_uc004dvm.1_Missense_Mutation_p.F217L|ARHGEF9_uc011mot.1_Missense_Mutation_p.F185L|ARHGEF9_uc004dvn.2_Missense_Mutation_p.F245L	NM_015185	NP_056000	O43307	ARHG9_HUMAN	Cdc42 guanine exchange factor 9	238	DH.				apoptosis|induction of apoptosis by extracellular signals|ion transmembrane transport|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(5)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	8						GTCAAAAGGAAACCATCGATA	0.498													4	86	---	---	---	---	PASS
BRWD3	254065	broad.mit.edu	37	X	79978092	79978092	+	Silent	SNP	C	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79978092C>T	uc004edt.2	-	17	2108	c.1845G>A	c.(1843-1845)CAG>CAA	p.Q615Q	BRWD3_uc010nmi.1_5'Flank|BRWD3_uc004edo.2_Silent_p.Q211Q|BRWD3_uc004edp.2_Silent_p.Q444Q|BRWD3_uc004edq.2_Silent_p.Q211Q|BRWD3_uc010nmj.1_Silent_p.Q211Q|BRWD3_uc004edr.2_Silent_p.Q285Q|BRWD3_uc004eds.2_Silent_p.Q211Q|BRWD3_uc004edu.2_Silent_p.Q285Q|BRWD3_uc004edv.2_Silent_p.Q211Q|BRWD3_uc004edw.2_Silent_p.Q211Q|BRWD3_uc004edx.2_Silent_p.Q211Q|BRWD3_uc004edy.2_Silent_p.Q211Q|BRWD3_uc004edz.2_Silent_p.Q285Q|BRWD3_uc004eea.2_Silent_p.Q285Q|BRWD3_uc004eeb.2_Silent_p.Q211Q	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	615										ovary(4)	4						GTGGTATAAGCTGTTCATCTT	0.388													4	233	---	---	---	---	PASS
LONRF3	79836	broad.mit.edu	37	X	118124435	118124435	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118124435C>A	uc004eqw.2	+	5	1358	c.1327C>A	c.(1327-1329)CCT>ACT	p.P443T	LONRF3_uc004eqx.2_Missense_Mutation_p.P402T|LONRF3_uc004eqy.2_RNA|LONRF3_uc004eqz.2_Missense_Mutation_p.P187T	NM_001031855	NP_001027026	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger	443					proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2						AATCGCAGATCCTCCCACTGA	0.478													7	126	---	---	---	---	PASS
STAG2	10735	broad.mit.edu	37	X	123191777	123191777	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123191777C>G	uc004etz.3	+	14	1705	c.1366C>G	c.(1366-1368)CCA>GCA	p.P456A	STAG2_uc004eua.2_Missense_Mutation_p.P456A|STAG2_uc004eub.2_Missense_Mutation_p.P456A|STAG2_uc004euc.2_Missense_Mutation_p.P456A|STAG2_uc004eud.2_Missense_Mutation_p.P456A|STAG2_uc004eue.2_Missense_Mutation_p.P456A	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	456					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						AAGACAAGGTCCAAATGCCAA	0.328													8	277	---	---	---	---	PASS
SLC25A14	9016	broad.mit.edu	37	X	129507022	129507022	+	3'UTR	SNP	C	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129507022C>A	uc004evn.1	+	11					SLC25A14_uc004evo.1_3'UTR|SLC25A14_uc004evp.1_3'UTR|SLC25A14_uc004evq.1_3'UTR|SLC25A14_uc004evr.1_3'UTR	NM_003951	NP_003942	O95258	UCP5_HUMAN	solute carrier family 25, member 14 isoform						aerobic respiration|mitochondrial transport	integral to plasma membrane|mitochondrial inner membrane	binding			ovary(1)	1						AAGTGTTTACCAAGCCGTTGG	0.433													7	44	---	---	---	---	PASS
FMR1	2332	broad.mit.edu	37	X	147014114	147014114	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147014114G>T	uc010nst.2	+	8	990	c.801G>T	c.(799-801)GAG>GAT	p.E267D	FMR1_uc011mwz.1_Missense_Mutation_p.E267D|FMR1_uc004fcj.2_Missense_Mutation_p.E267D|FMR1_uc004fck.3_Missense_Mutation_p.E267D|FMR1_uc004fcl.3_Missense_Mutation_p.E128D|FMR1_uc011mxa.1_Translation_Start_Site	NM_002024	NP_002015	Q06787	FMR1_HUMAN	fragile X mental retardation 1	267					mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					TTTATGGAGAGGTAAATATTT	0.358									Fragile_X_syndrome				47	297	---	---	---	---	PASS
MECP2	4204	broad.mit.edu	37	X	153296886	153296886	+	Silent	SNP	G	C	C	rs61748385		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153296886G>C	uc004fjv.2	-	4	619	c.393C>G	c.(391-393)GCC>GCG	p.A131A	MECP2_uc004fjw.2_Silent_p.A143A	NM_004992	NP_004983	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 1	131	MBD.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TAGAGCGAAAGGCTTTTCCCT	0.502													10	49	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	155252868	155252868	+	Silent	SNP	T	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155252868T>A	uc004fnw.1	+	6	1571	c.912T>A	c.(910-912)CCT>CCA	p.P304P	uc004fnx.3_Silent_p.P90P	NM_182905	NP_878908			WAS protein family homolog 1																		TAGCCGAGCCTCTCAAGGCAG	0.632													3	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14760	14760	+	5'Flank	SNP	G	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14760G>A	uc004coy.2	+						uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		GACCCCAATACGCAAAATTAA	0.423													91	211	---	---	---	---	PASS
PRDM16	63976	broad.mit.edu	37	1	3308671	3308672	+	Intron	DEL	CT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3308671_3308672delCT	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GCCCAACATCCTCTCTCTCTCC	0.540			T	EVI1	MDS|AML								4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7036308	7036309	+	Intron	DEL	GT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7036308_7036309delGT	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AGCCGGAGAAGTGTGACTGCAT	0.559													4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7100220	7100221	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7100220_7100221insT	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GCTAACTGTGATTTTTTTTTTT	0.356													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	9095604	9095604	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9095604delC								SLC2A7 (9200 upstream) : SLC2A5 (1403 downstream)																							CTCCCGGCCACCAGCCTCTGC	0.493													4	2	---	---	---	---	
PRDM2	7799	broad.mit.edu	37	1	14086829	14086829	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14086829delA	uc001avi.2	+						PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Intron|PRDM2_uc001avj.2_Intron|PRDM2_uc009vod.1_Intron|PRDM2_uc001avk.2_Intron|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.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)		TAAGCACATTAAAAAAAAAAC	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	14854947	14854949	+	IGR	DEL	CTC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14854947_14854949delCTC								PRDM2 (703375 upstream) : KAZ (70264 downstream)																							acaaagaacactcctcctaccta	0.025													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	22733948	22733948	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22733948delA								WNT4 (263563 upstream) : ZBTB40 (44396 downstream)																							CAGAGAAAAGAAAAAATGCTG	0.403													4	2	---	---	---	---	
CLIC4	25932	broad.mit.edu	37	1	25117815	25117815	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25117815delT	uc001bjo.2	+						CLIC4_uc001bjn.2_Intron|CLIC4_uc001bjp.1_Intron	NM_013943	NP_039234	Q9Y696	CLIC4_HUMAN	chloride intracellular channel 4						cellular response to calcium ion|establishment or maintenance of apical/basal cell polarity|keratinocyte differentiation|negative regulation of cell migration|regulation of cytoskeleton organization	actin cytoskeleton|apical part of cell|cell surface|cell-cell junction|centrosome|chloride channel complex|cytoplasmic vesicle membrane|cytosol|microvillus|midbody|mitochondrion|nuclear matrix|perinuclear region of cytoplasm|soluble fraction	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)		GCTGTAGCAATAGACTGTATT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	34935526	34935526	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34935526delT								C1orf94 (250797 upstream) : MIR552 (199674 downstream)																							GGGTGCCTTCTTTGGTAGTGA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35117750	35117750	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35117750delA								C1orf94 (433021 upstream) : MIR552 (17450 downstream)																							TTCAAACCGCACCCTCTTGGC	0.468													4	2	---	---	---	---	
EIF2C4	192670	broad.mit.edu	37	1	36304187	36304187	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36304187delT	uc001bzj.1	+							NM_017629	NP_060099	Q9HCK5	AGO4_HUMAN	eukaryotic translation initiation factor 2C, 4						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CCTTCATAGGTTTTTTTTGTT	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	40965960	40965960	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40965960delT								ZNF642 (3946 upstream) : DEM1 (8473 downstream)																							acccaaatcgttttttcctct	0.000													4	2	---	---	---	---	
ZCCHC11	23318	broad.mit.edu	37	1	52890675	52890675	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52890675delA	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						atctctaggcaaaaaaaaaat	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56038662	56038662	+	IGR	DEL	C	-	-	rs113422342		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56038662delC								USP24 (357900 upstream) : PPAP2B (921771 downstream)																							GGCAATAGGGCAGGGTGTAGG	0.577													3	3	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58243061	58243062	+	Intron	INS	-	TC	TC	rs78316380		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58243061_58243062insTC	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						caaataatttttgttttctttc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	60788290	60788290	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60788290delT								C1orf87 (248864 upstream) : NFIA (754656 downstream)																							TTAATTTAAGTTTTTTTttta	0.154													4	2	---	---	---	---	
ST6GALNAC5	81849	broad.mit.edu	37	1	77498128	77498128	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77498128delA	uc001dhi.2	+						ST6GALNAC5_uc010ori.1_Intron|ST6GALNAC5_uc009wbw.2_Intron	NM_030965	NP_112227	Q9BVH7	SIA7E_HUMAN	sialyltransferase 7E						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)|skin(1)	2						aggaagatagaaatgattaac	0.065													4	2	---	---	---	---	
AK5	26289	broad.mit.edu	37	1	77930568	77930569	+	Intron	DEL	GA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77930568_77930569delGA	uc001dhn.2	+						AK5_uc001dho.2_Intron	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1						ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1						ataatgagaggagagagagatt	0.124													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	85836292	85836293	+	Intron	INS	-	A	A	rs148336620	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85836292_85836293insA	uc001dlb.2	-						DDAH1_uc001dlc.2_Intron|uc001dla.1_Intron|DDAH1_uc010osb.1_Intron|DDAH1_uc009wco.2_Intron	NM_012137	NP_036269	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	ccaggtgaaagaaatggtggtg	0.000													4	5	---	---	---	---	
LOC339524	339524	broad.mit.edu	37	1	87578113	87578113	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87578113delT	uc001dme.1	+							NM_001134492	NP_001127964			heparan sulfate 2-O-sulfotransferase 1 isoform												0						CTTTTGTGGGTTTTTTTTTCT	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88066114	88066115	+	IGR	INS	-	A	A	rs139603172	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88066114_88066115insA								LMO4 (251511 upstream) : None (None downstream)																							AAAAAAACAACAAAAAAAACTT	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88631957	88631958	+	IGR	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88631957_88631958insA								LMO4 (817354 upstream) : PKN2 (517964 downstream)																							AAGAAAATGAGAAAAAAATTCT	0.317													4	2	---	---	---	---	
PKN2	5586	broad.mit.edu	37	1	89216848	89216849	+	Intron	DEL	TT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89216848_89216849delTT	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)		tttacctctctttttacctctc	0.119													4	2	---	---	---	---	
LRRC8C	84230	broad.mit.edu	37	1	90102186	90102203	+	Intron	DEL	CACCCTTGACCAAGCCTC	-	-	rs67153129		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90102186_90102203delCACCCTTGACCAAGCCTC	uc001dnl.3	+							NM_032270	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member							endoplasmic reticulum membrane|integral to membrane				ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CCACACACCTCACCCTTGACCAAGcctccaccagctga	0.280													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	104624212	104624212	+	IGR	DEL	C	-	-	rs35133439		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104624212delC								AMY1A (417040 upstream) : None (None downstream)																							GGTGTTTTAACCCTCATAGCA	0.388													2	4	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120530023	120530023	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120530023delA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAAGGGTTCTAAAAAAACAGG	0.318			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	2	---	---	---	---	
LOC647121	647121	broad.mit.edu	37	1	121294554	121294554	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121294554delA	uc001eiu.1	+							NR_003955				Homo sapiens cDNA FLJ46881 fis, clone UTERU3015647, moderately similar to Embigin precursor.												0						gctgtaaaataaaaaaaaaag	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142784487	142784488	+	Intron	INS	-	C	C	rs142084929		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142784487_142784488insC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		atcctcactctcccccccaccc	0.000													5	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145018621	145018621	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145018621delA	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GCTGAAATGTAAGATCATATG	0.303			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145076977	145076980	+	Intron	DEL	ATAG	-	-	rs68189964		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145076977_145076980delATAG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_5'Flank|PDE4DIP_uc001emh.2_5'Flank|PDE4DIP_uc001emk.2_5'Flank			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						ctctctctctatagatagatagat	0.010													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145192617	145192617	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145192617delC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TCTGCTGTGTCCTGAATCAGT	0.299													2	5	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145194931	145194934	+	Intron	DEL	CAAA	-	-	rs139628584		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145194931_145194934delCAAA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TATATTTTGTCAAACAAAAAGAAG	0.368													6	3	---	---	---	---	
NBPF15	284565	broad.mit.edu	37	1	148556867	148556868	+	5'Flank	INS	-	TGTC	TGTC	rs111615504		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148556867_148556868insTGTC	uc001esb.1	+							NM_001102663	NP_001096133	Q8N660	NBPFF_HUMAN	hypothetical protein LOC728936							cytoplasm					0	all_hematologic(923;0.032)					TGATTTCCCTGTATCTGTCTTT	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152369375	152369375	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152369375delT								FLG2 (36893 upstream) : CRNN (12344 downstream)																							aaaaggactgttagacaaaaa	0.000													4	2	---	---	---	---	
LENEP	55891	broad.mit.edu	37	1	154965798	154965798	+	5'Flank	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154965798delA	uc001fgi.2	+							NM_018655	NP_061125	Q9Y5L5	LENEP_HUMAN	lens epithelial protein						multicellular organismal development		DNA binding				0	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			AACCACTGGGAAAAGGGCAAT	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	155863594	155863594	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155863594delA								SYT11 (8605 upstream) : RIT1 (4007 downstream)																							GCTTTTGTTCAAAAAACTGAG	0.403													4	2	---	---	---	---	
GPR161	23432	broad.mit.edu	37	1	168082893	168082893	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168082893delA	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	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)					atgtacacataaaaaagaacg	0.000													4	2	---	---	---	---	
TBX19	9095	broad.mit.edu	37	1	168269389	168269389	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168269389delC	uc001gfl.2	+						TBX19_uc001gfj.3_Intron|TBX19_uc001gfm.2_Intron	NM_005149	NP_005140	O60806	TBX19_HUMAN	T-box 19						anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)					GGAGCAATATCCCCAAATTAT	0.333													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	172231106	172231106	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172231106delG	uc001gie.2	+						DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						ctcaggtaaagggggaaggag	0.000													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	172356907	172356907	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172356907delG	uc001gie.2	+						DNM3_uc001gif.2_Intron|DNM3_uc001gih.1_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						TACAGAAAAAGGGGAAAAGAT	0.413													4	2	---	---	---	---	
RC3H1	149041	broad.mit.edu	37	1	173933820	173933821	+	Intron	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173933820_173933821insA	uc001gju.3	-						RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Intron	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin						cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						AATTGTTTCTTAAAAAACACTA	0.139													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175516482	175516483	+	Intron	INS	-	TCA	TCA	rs144624193	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175516482_175516483insTCA	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					AGTCTATAACTTCAACCCCTTC	0.485													5	5	---	---	---	---	
PAPPA2	60676	broad.mit.edu	37	1	176451302	176451302	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176451302delG	uc001gkz.2	+						PAPPA2_uc001gky.1_Intron|PAPPA2_uc009www.2_Intron	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						AGGTAAAAGAGGACAGCCATT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208140044	208140045	+	IGR	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208140044_208140045delTG								CD34 (55361 upstream) : PLXNA2 (55545 downstream)																							TAAgtgtgtatgtgtgtgtgtg	0.396													4	2	---	---	---	---	
PLXNA2	5362	broad.mit.edu	37	1	208224174	208224174	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208224174delA	uc001hgz.2	-							NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		gccatgtcttaaaaaaaaaaa	0.194													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208545950	208545950	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208545950delT								PLXNA2 (128285 upstream) : None (None downstream)																							tcttctccacttttttttata	0.209													3	3	---	---	---	---	
BATF3	55509	broad.mit.edu	37	1	212865736	212865736	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212865736delA	uc001hjl.1	-							NM_018664	NP_061134	Q9NR55	BATF3_HUMAN	basic leucine zipper transcription factor,						transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0046)|all cancers(67;0.00785)|GBM - Glioblastoma multiforme(131;0.0731)|Epithelial(68;0.0781)		ACGAAAGAGCAAAAAAAACCC	0.209													4	2	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	216380382	216380383	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216380382_216380383insT	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)		tgatggggtcatttttttttca	0.005										HNSCC(13;0.011)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223260519	223260519	+	IGR	DEL	T	-	-	rs78885551		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223260519delT								DISP1 (81184 upstream) : TLR5 (23065 downstream)																							TTTCTGTTTCTTTTTTTTTTT	0.398													5	4	---	---	---	---	
DNAH14	127602	broad.mit.edu	37	1	225579271	225579272	+	Intron	INS	-	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225579271_225579272insG	uc001how.2	+						DNAH14_uc001hox.2_Intron	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						agcagggagtagggggcattta	0.035													4	2	---	---	---	---	
OBSCN	84033	broad.mit.edu	37	1	228534127	228534127	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228534127delT	uc009xez.1	+						OBSCN_uc001hsn.2_Intron|OBSCN_uc001hsr.1_Intron	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				tggagtcctatttttaggctt	0.000													4	2	---	---	---	---	
EDARADD	128178	broad.mit.edu	37	1	236621654	236621655	+	Intron	INS	-	AA	AA	rs141613581	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236621654_236621655insAA	uc001hxu.1	+						EDARADD_uc001hxv.1_Intron	NM_145861	NP_665860	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain isoform A						cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			gtcctggccttaaaaaacttat	0.079													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	237068829	237068829	+	IGR	DEL	A	-	-	rs145496222		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237068829delA								MTR (1549 upstream) : RYR2 (136873 downstream)																							CCCTGTGTCGAAAGAGCCAAG	0.254													2	4	---	---	---	---	
CHRM3	1131	broad.mit.edu	37	1	239648438	239648438	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239648438delA	uc001hyo.1	+									P20309	ACM3_HUMAN	Homo sapiens clone N10 NTera2D1 teratocarcinoma, m3 muscarinic acetylcholine receptor mRNA, partial cds.						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)	ATTCCAGCTCAATGATAAATT	0.418													4	2	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241266260	241266260	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241266260delC	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			ggtctgttttcccactattag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	241526079	241526080	+	IGR	INS	-	CTC	CTC	rs151152958	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241526079_241526080insCTC								RGS7 (5601 upstream) : FH (134826 downstream)																							ttgatgtctgtctcctagaaaa	0.000													2	4	---	---	---	---	
AKT3	10000	broad.mit.edu	37	1	243950226	243950226	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243950226delA	uc001iab.1	-						AKT3_uc001hzz.1_Intron	NM_005465	NP_005456	Q9Y243	AKT3_HUMAN	AKT3 kinase isoform 1						signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)			TAAAGAAGGCAAAAAAAAGAA	0.383													4	2	---	---	---	---	
PXDN	7837	broad.mit.edu	37	2	1696511	1696512	+	Intron	DEL	AC	-	-	rs145611427		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1696511_1696512delAC	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)		AGGTGCAGGAACACACAGAGGT	0.550													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4803007	4803007	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4803007delT								None (None upstream) : None (None downstream)																							ctcctagttctttttttttta	0.000													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5501141	5501142	+	IGR	INS	-	AGA	AGA	rs111330381		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5501141_5501142insAGA								None (None upstream) : SOX11 (331657 downstream)																							ACTGTAGCTCCAGGAGTCAGAA	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6843635	6843635	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6843635delA								LOC400940 (715271 upstream) : CMPK2 (136868 downstream)																							acaaacaagtaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	9158510	9158510	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9158510delT								MBOAT2 (14634 upstream) : ASAP2 (188384 downstream)																							GTGATGACTCTTTTTTTTCCT	0.259													4	2	---	---	---	---	
LPIN1	23175	broad.mit.edu	37	2	11920008	11920008	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11920008delT	uc010yjn.1	+						LPIN1_uc010yjm.1_Intron|LPIN1_uc002rbt.2_Intron|LPIN1_uc002rbs.2_Intron	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1						fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TAGGATTTACttttttttttt	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12683259	12683260	+	Intron	INS	-	CA	CA	rs146272927	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12683259_12683260insCA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		GATTGGTAATTcacacacacac	0.312													3	3	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15444133	15444133	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15444133delG	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						CCAAGGCTCAGAAGCAGGGTG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16168608	16168609	+	IGR	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16168608_16168609delAC								MYCN (81480 upstream) : FAM49A (565292 downstream)																							AGATACATTAACACACACACAC	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	22907847	22907848	+	IGR	DEL	GT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22907847_22907848delGT								None (None upstream) : KLHL29 (847607 downstream)																							AGTTAtgtgcgtgtgtgtgtgt	0.292													2	4	---	---	---	---	
ASXL2	55252	broad.mit.edu	37	2	26038266	26038266	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26038266delT	uc002rgs.2	-							NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					cctcacctccttttctcctag	0.129													4	2	---	---	---	---	
CAPN13	92291	broad.mit.edu	37	2	30969607	30969607	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30969607delA	uc002rnn.2	-							NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					GCACACCTAGAGGTGAACTGG	0.448													4	2	---	---	---	---	
GALNT14	79623	broad.mit.edu	37	2	31193270	31193270	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31193270delT	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					taaatacacatttttgttgtg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35648251	35648251	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35648251delA								None (None upstream) : CRIM1 (935146 downstream)																							ACAAGTGTCTAAAACAGGAAG	0.448													4	2	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42905917	42905918	+	Intron	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42905917_42905918delTG	uc002rso.1	+						MTA3_uc002rsp.1_Intron|MTA3_uc002rsq.2_Intron|MTA3_uc002rsr.2_Intron	NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						AATGCATCACTGTGTGTGTGTG	0.307													4	2	---	---	---	---	
EML6	400954	broad.mit.edu	37	2	55062850	55062850	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55062850delT	uc002ryb.3	+							NM_001039753	NP_001034842	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like							cytoplasm|microtubule					0						ccaggagtgattttttggaca	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65858788	65858788	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65858788delT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																		TCCCTCAAGCTTTATCTCCAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	69219952	69219952	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69219952delT								GKN1 (11841 upstream) : ANTXR1 (20324 downstream)																							TCAGGTACTGTTTTTTTTTTA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	75162383	75162384	+	IGR	INS	-	TC	TC	rs146467516	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75162383_75162384insTC								HK2 (41909 upstream) : POLE4 (23391 downstream)																							agctcctgctttctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89378904	89378905	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89378904_89378905insT	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		tattataattgtttttttttcc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	104877913	104877913	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104877913delC								None (None upstream) : LOC150568 (172892 downstream)																							CTGTAAGCCACCCCCATGCCA	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105625021	105625022	+	IGR	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105625021_105625022insA								POU3F3 (151551 upstream) : MRPS9 (29461 downstream)																							cgtaagtaaagaaaaaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106574593	106574593	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106574593delT								NCK2 (63867 upstream) : C2orf40 (107520 downstream)																							AAGACTGCTCTTTTTTTTGCC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108275223	108275223	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108275223delG								ST6GAL2 (771660 upstream) : LOC729121 (164297 downstream)																							AGTGTTCTTTGGGGGGAGAGT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108836458	108836458	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108836458delG								SLC5A7 (206019 upstream) : SULT1C3 (27193 downstream)																							TCTCAAaaccgagcagtttag	0.264													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109959822	109959822	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109959822delT	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						TCCTTGACTCTTTTTTTTTTC	0.473													5	3	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125232684	125232684	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125232684delT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGAGAATTCATTTTTTTTTTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126979271	126979272	+	IGR	DEL	CC	-	-	rs10617344		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126979271_126979272delCC								None (None upstream) : GYPC (434412 downstream)																							caggaaacagcccccaggaatc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129599025	129599025	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129599025delA								HS6ST1 (522854 upstream) : None (None downstream)																							GAGGCTCACTAAGACAGAatt	0.259													4	2	---	---	---	---	
RAB3GAP1	22930	broad.mit.edu	37	2	135877902	135877902	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135877902delT	uc002tuj.2	+						RAB3GAP1_uc010fnf.2_Intron|RAB3GAP1_uc010fng.2_Intron|RAB3GAP1_uc010fnh.1_Intron	NM_012233	NP_036365	Q15042	RB3GP_HUMAN	RAB3 GTPase-activating protein							centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.117)		TTTTTGAAACTTTTTTTTAGC	0.284													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	136886576	136886577	+	IGR	DEL	TG	-	-	rs148248796		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136886576_136886577delTG								CXCR4 (10851 upstream) : THSD7B (636538 downstream)																							cataaaaaactgtgataaaagc	0.064													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	136985859	136985859	+	IGR	DEL	T	-	-	rs68122582		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136985859delT								CXCR4 (110134 upstream) : THSD7B (537256 downstream)																							TGGACCCAGGTtagggtagtg	0.149													3	3	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142725998	142725998	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142725998delT	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)		AATTCCTTCATTTTTTTTGCT	0.338										TSP Lung(27;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177639630	177639630	+	IGR	DEL	G	-	-	rs149517980	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177639630delG								MIR1246 (173850 upstream) : HNRNPA3 (437792 downstream)																							ctacttgagaggctaaggtgg	0.000													4	2	---	---	---	---	
INPP1	3628	broad.mit.edu	37	2	191230786	191230789	+	Intron	DEL	TCTC	-	-	rs139867423		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191230786_191230789delTCTC	uc002ury.3	+						INPP1_uc010fsb.2_Intron|INPP1_uc002urx.3_Intron	NM_001128928	NP_001122400	P49441	INPP_HUMAN	inositol polyphosphate-1-phosphatase						signal transduction		inositol-1,4-bisphosphate 1-phosphatase activity|metal ion binding			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)		Lithium(DB01356)	gctctctctgtctctctgtctctt	0.000													4	2	---	---	---	---	
OBFC2A	64859	broad.mit.edu	37	2	192548205	192548206	+	Intron	INS	-	T	T	rs137973508	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192548205_192548206insT	uc002usx.2	+						OBFC2A_uc002usw.2_Intron|OBFC2A_uc002usy.2_Intron|OBFC2A_uc002usz.2_RNA|OBFC2A_uc002uta.2_Intron	NM_001031716	NP_001026886	Q96AH0	SOSB2_HUMAN	oligonucleotide/oligosaccharide-binding fold						double-strand break repair via homologous recombination|G2/M transition checkpoint|response to ionizing radiation	SOSS complex	single-stranded DNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.061)|Epithelial(96;0.244)			TTTTGATGTGATTTTTTTTTCA	0.302													4	2	---	---	---	---	
ANKRD44	91526	broad.mit.edu	37	2	197966775	197966775	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197966775delA	uc002uuc.2	-						ANKRD44_uc002utz.3_Intron|ANKRD44_uc002uua.1_Intron|ANKRD44_uc002uub.2_Intron|ANKRD44_uc010zgw.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)			ttcgctttgcaaaaaaaaaca	0.025													4	4	---	---	---	---	
CASP8	841	broad.mit.edu	37	2	202095893	202095894	+	5'Flank	INS	-	T	T	rs137889636	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202095893_202095894insT	uc002uxr.1	+						CASP8_uc010ftc.1_5'Flank|CASP8_uc002uxo.1_5'Flank|CASP8_uc002uxp.1_5'Flank|CASP8_uc002uxq.1_5'Flank|CASP8_uc002uxn.2_5'Flank	NM_033355	NP_203519	Q14790	CASP8_HUMAN	caspase 8 isoform B precursor						activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor	centrosome|cytosol|mitochondrial outer membrane	cysteine-type endopeptidase activity|protein binding|protein binding			upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5						gcttaaagataaaatgttaaaa	0.000										HNSCC(4;0.00038)			2	5	---	---	---	---	
PAX3	5077	broad.mit.edu	37	2	223097284	223097285	+	Intron	INS	-	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223097284_223097285insC	uc010fwo.2	-						PAX3_uc002vmt.1_Intron|PAX3_uc002vmy.1_Intron|PAX3_uc002vmv.1_Intron|PAX3_uc002vmw.1_Intron|PAX3_uc002vmx.1_Intron	NM_181457	NP_852122	P23760	PAX3_HUMAN	paired box 3 isoform PAX3						apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTATCTTTCTGCCCCCTAGGCA	0.292			T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						4	2	---	---	---	---	
FARSB	10056	broad.mit.edu	37	2	223460397	223460397	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223460397delA	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	GCTAAAGGGGAAAAAAAATCA	0.383													4	2	---	---	---	---	
GIGYF2	26058	broad.mit.edu	37	2	233652456	233652456	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233652456delT	uc002vti.3	+						GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		TATTCTTTCATTTTTTCCCTT	0.299													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236844396	236844396	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236844396delT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						AAGCCTGTAATTTTTTTTGAT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	18719531	18719532	+	IGR	INS	-	TACT	TACT	rs142022122	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18719531_18719532insTACT								SATB1 (239279 upstream) : KCNH8 (470485 downstream)																							agtttcttcaatacttatttcc	0.000													4	4	---	---	---	---	
KAT2B	8850	broad.mit.edu	37	3	20084037	20084037	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20084037delA	uc003cbq.2	+							NM_003884	NP_003875	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B						cell cycle arrest|cellular response to insulin stimulus|chromatin remodeling|histone H3 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|negative regulation of cell proliferation|transcription initiation from RNA polymerase I promoter	Ada2/Gcn5/Ada3 transcription activator complex|chromatin remodeling complex|PCAF complex	cyclin-dependent protein kinase inhibitor activity|histone acetyltransferase activity|histone deacetylase binding|protein kinase binding|transcription coactivator activity|transcription factor binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						aaaacctatgaaaaaaaagaG	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	22517566	22517566	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22517566delT								ZNF385D (103443 upstream) : UBE2E2 (727087 downstream)																							tccaatcctgttttcctcact	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	22939465	22939465	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22939465delA								ZNF385D (525342 upstream) : UBE2E2 (305188 downstream)																							ccgatgcctcaaaaatgtgac	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	24937049	24937049	+	IGR	DEL	T	-	-	rs72026327		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24937049delT								THRB (400596 upstream) : RARB (278774 downstream)																							AAATTTACGCTTTTTTTTTTC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	24982773	24982773	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24982773delT								THRB (446320 upstream) : RARB (233050 downstream)																							GGGTTGACAATTTTTACTACG	0.303													4	2	---	---	---	---	
NEK10	152110	broad.mit.edu	37	3	27168250	27168251	+	Intron	INS	-	A	A	rs149878878	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27168250_27168251insA	uc010hfk.2	-						NEK10_uc010hfj.2_Intron			Q6ZWH5	NEK10_HUMAN	RecName: Full=Serine/threonine-protein kinase Nek10;          EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10;								ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13						cacctgggagcaaaaaaAAAAC	0.099													4	2	---	---	---	---	
ARPP21	10777	broad.mit.edu	37	3	35706789	35706791	+	Intron	DEL	TAA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35706789_35706791delTAA	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc003cfz.2_Intron	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3						CTTTTTTTTTTAATATGATAACA	0.315													4	2	---	---	---	---	
SCN5A	6331	broad.mit.edu	37	3	38618501	38618502	+	Intron	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38618501_38618502insA	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron|SCN5A_uc010hhj.1_Intron	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha						blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)	GGAGTCTAAGGCTGGGGTGTGG	0.614													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	40912650	40912650	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40912650delA								ZNF621 (331607 upstream) : CTNNB1 (323751 downstream)																							TTGATGTTCCAGTGAAATATG	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	45795440	45795440	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45795440delC								SACM1L (8540 upstream) : SLC6A20 (1502 downstream)																							gcaccagcatccccccagcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	47578761	47578761	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47578761delG								C3orf75 (23562 upstream) : CSPG5 (24968 downstream)																							ATGCAAAATAGGGACACAGGT	0.512													4	2	---	---	---	---	
ARHGEF3	50650	broad.mit.edu	37	3	57012189	57012190	+	Intron	INS	-	T	T	rs143135019	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57012189_57012190insT	uc003dih.2	-							NM_001128615	NP_001122087	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		AATAAGCCTACTACCTTTATTT	0.431													4	2	---	---	---	---	
FAM19A1	407738	broad.mit.edu	37	3	68547552	68547553	+	Intron	INS	-	CA	CA	rs148420802	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68547552_68547553insCA	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		GGGTTATAAATCAGAGATTAAA	0.252													3	3	---	---	---	---	
LMOD3	56203	broad.mit.edu	37	3	69169385	69169389	+	Intron	DEL	TAAAA	-	-	rs111478601		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69169385_69169389delTAAAA	uc003dns.2	-						LMOD3_uc003dnt.2_Intron	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)							cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		TCCCATAAATTAAAATGAGTATTAA	0.234													4	4	---	---	---	---	
FRMD4B	23150	broad.mit.edu	37	3	69437237	69437237	+	5'Flank	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69437237delT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dny.2_5'Flank	NM_015123	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		GTGGTGGTACTTTTTTTTTTT	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	70809240	70809240	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70809240delG								MITF (791754 upstream) : FOXP1 (195497 downstream)																							gaaagttagtgggggaataag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75988307	75988308	+	IGR	INS	-	AC	AC	rs147036991		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75988307_75988308insAC								ZNF717 (153637 upstream) : None (None downstream)																							TTTCTGTGGCTATGAGTTGTTT	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	83881021	83881021	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83881021delT								None (None upstream) : None (None downstream)																							GAAGGTCAGCTTTTACTATAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	87043689	87043689	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87043689delA								VGLL3 (3432 upstream) : CHMP2B (232724 downstream)																							TTATGATGTTAAAAAAAAATA	0.338													3	4	---	---	---	---	
EPHA6	285220	broad.mit.edu	37	3	96803177	96803178	+	Intron	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96803177_96803178delAC	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						AGCCCTTATAacacacacacac	0.282													4	2	---	---	---	---	
DCBLD2	131566	broad.mit.edu	37	3	98558070	98558071	+	Intron	DEL	TC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98558070_98558071delTC	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron	NM_080927	NP_563615	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3						cttctttccttctctctctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	98633828	98633829	+	IGR	INS	-	T	T	rs145196735	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98633828_98633829insT								DCBLD2 (13295 upstream) : COL8A1 (723625 downstream)																							ATAAAAGTGCATTTTTTTGTCA	0.277													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	104642083	104642083	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104642083delT								None (None upstream) : ALCAM (443630 downstream)																							GTAAGACATCTTACCTTACTC	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	106465272	106465272	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106465272delT								CBLB (877006 upstream) : LOC100302640 (90388 downstream)																							TATTTCCCCCTTTTTTGTCAA	0.313													4	2	---	---	---	---	
SLC9A10	285335	broad.mit.edu	37	3	111967144	111967144	+	Intron	DEL	C	-	-	rs71134816		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111967144delC	uc003dyu.2	-						SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5						ccaatttatgcttaaatgcaa	0.000													6	5	---	---	---	---	
POLQ	10721	broad.mit.edu	37	3	121234012	121234012	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121234012delT	uc003eee.3	-							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)		cagatgtgcattttttttatt	0.000								DNA_polymerases_(catalytic_subunits)					4	2	---	---	---	---	
PDIA5	10954	broad.mit.edu	37	3	122817550	122817552	+	Intron	DEL	AAC	-	-	rs147330006		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122817550_122817552delAAC	uc003egc.1	+						PDIA5_uc003egd.1_Intron	NM_006810	NP_006801	Q14554	PDIA5_HUMAN	protein disulfide isomerase A5 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding|response to stress	endoplasmic reticulum lumen	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0427)		CATTCCTTGGAACAGTGGTGAGT	0.562													5	7	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	123966731	123966731	+	Intron	DEL	A	-	-	rs35683525		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123966731delA	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						ACTTGTATTGAAAAAAAAAAG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127259059	127259059	+	IGR	DEL	T	-	-	rs75073105		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127259059delT								PLXNA1 (502831 upstream) : TPRA1 (32849 downstream)																							cacaaatgtatttttttagat	0.030													4	2	---	---	---	---	
TMEM108	66000	broad.mit.edu	37	3	132957690	132957690	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132957690delT	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epj.1_Intron|TMEM108_uc003epk.2_Intron	NM_023943	NP_076432	Q6UXF1	TM108_HUMAN	transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4						CTTTTAGATGTTACAGACAAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	138966174	138966174	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138966174delT								PISRT1 (13810 upstream) : MRPS22 (96624 downstream)																							ccatcaagagttttttttttc	0.005													3	4	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	139905760	139905760	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139905760delA	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						GCAAGGAGTTAAAAAAACAAA	0.373										HNSCC(16;0.037)			4	2	---	---	---	---	
PCOLCE2	26577	broad.mit.edu	37	3	142609525	142609526	+	5'Flank	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142609525_142609526insA	uc003evd.2	-							NM_013363	NP_037495	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2							extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3						TTTATGACATTAAAAAAAAGGG	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	142705218	142705218	+	IGR	DEL	T	-	-	rs9880385	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142705218delT								PAQR9 (23040 upstream) : SR140 (15154 downstream)																							AGTGTATCGATTTTTTTTTTG	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	148477883	148477884	+	IGR	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148477883_148477884delCA								AGTR1 (17095 upstream) : CPB1 (67704 downstream)																							GCCCCTCCTCCACACACACATA	0.327													4	2	---	---	---	---	
C3orf55	152078	broad.mit.edu	37	3	157290029	157290029	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157290029delT	uc003fbp.3	+						C3orf55_uc003fbo.2_Intron|C3orf55_uc011bot.1_Intron|C3orf55_uc010hvv.2_Intron	NM_001130002	NP_001123474	A1A4F0	CC055_HUMAN	hypothetical protein LOC152078 isoform 1												0			Lung(72;0.0215)|LUSC - Lung squamous cell carcinoma(72;0.037)			TGTTATTACCTTTTTTTTTAA	0.308													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	160365681	160365681	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160365681delA								KPNA4 (82305 upstream) : ARL14 (29267 downstream)																							TAAAATGAGGAAAAAAAAAGA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	161744726	161744726	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161744726delT								OTOL1 (522998 upstream) : None (None downstream)																							TGTTTTTTTATTTTGAAGTCA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166472636	166472636	+	IGR	DEL	A	-	-	rs112654885		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166472636delA								BCHE (917383 upstream) : ZBBX (485445 downstream)																							caacaacaacaaaaaaaaaaa	0.000													2	7	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173499887	173499888	+	Intron	INS	-	C	C	rs142975028	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173499887_173499888insC	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TTTGGAAGTGTCTTTTTTTTTA	0.371													4	2	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173597429	173597429	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173597429delT	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			tttctgtgtgttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178793602	178793602	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178793602delT								ZMAT3 (4018 upstream) : PIK3CA (72709 downstream)																							TATTCTAACATTTTTTAGCCT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180305171	180305171	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180305171delA								PEX5L (550654 upstream) : TTC14 (14747 downstream)																							GCAGACCAGGAAAAAAAATCA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181933155	181933156	+	IGR	DEL	GA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181933155_181933156delGA								SOX2OT (474152 upstream) : ATP11B (578135 downstream)																							ggacagagaggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184132605	184132606	+	IGR	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184132605_184132606delTG								CHRD (24986 upstream) : EPHB3 (146981 downstream)																							tgtgtgtatatgtgtgtgtgtg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184179337	184179337	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184179337delG								CHRD (71718 upstream) : EPHB3 (100250 downstream)																							tagtttgcctggggatatgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184485290	184485290	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184485290delG								MAGEF1 (55454 upstream) : VPS8 (44641 downstream)																							CGGGGTAACTGGGAGCACTCA	0.468													4	2	---	---	---	---	
VPS8	23355	broad.mit.edu	37	3	184685881	184685881	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184685881delT	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			ttcaccattctttttctgaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191796905	191796905	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191796905delA								PYDC2 (617662 upstream) : FGF12 (62779 downstream)																							TTCAGGTTCCAAAAAAACCTT	0.428													4	2	---	---	---	---	
DLG1	1739	broad.mit.edu	37	3	196975605	196975606	+	Intron	INS	-	T	T	rs140581997	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196975605_196975606insT	uc003fxo.3	-						DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Intron|DLG1_uc010iam.1_Intron	NM_001098424	NP_001091894	Q12959	DLG1_HUMAN	discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		CAGGAAGTTTATTTTTTGTACC	0.252													4	2	---	---	---	---	
LOC220729	220729	broad.mit.edu	37	3	197325895	197325895	+	Intron	DEL	C	-	-	rs67421337		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197325895delC	uc011bug.1	-											Homo sapiens cDNA FLJ60865 complete cds, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1).												0						GAGCATGCCACCCCAGCGTTT	0.438											OREG0016019	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
LOC220729	220729	broad.mit.edu	37	3	197330753	197330753	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197330753delA	uc011bug.1	-											Homo sapiens cDNA FLJ60865 complete cds, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1).												0						CCCCACCCAGAAAAAAAAAAA	0.547													3	4	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	65736	65736	+	Intron	DEL	A	-	-	rs113723441		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65736delA	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		ggcctcccctaaagcagaagc	0.000													4	2	---	---	---	---	
RNF4	6047	broad.mit.edu	37	4	2499068	2499068	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2499068delA	uc003gfb.2	+						RNF4_uc010ici.1_Intron|RNF4_uc010icj.2_Intron|RNF4_uc003gfc.2_Intron	NM_002938	NP_002929	P78317	RNF4_HUMAN	ring finger protein 4						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination|regulation of kinetochore assembly|regulation of spindle assembly|response to arsenic-containing substance	cytoplasm|PML body	androgen receptor binding|DNA binding|nucleosome binding|sequence-specific DNA binding transcription factor activity|SUMO polymer binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(65;0.241)				GGATCCATTTAAAAAAAAATC	0.418													4	2	---	---	---	---	
PPP2R2C	5522	broad.mit.edu	37	4	6366210	6366210	+	Intron	DEL	T	-	-	rs4689421	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6366210delT	uc003gjc.2	-						PPP2R2C_uc003gjb.2_Intron|PPP2R2C_uc011bwd.1_Intron|PPP2R2C_uc011bwe.1_Intron|PPP2R2C_uc003gja.2_Intron|PPP2R2C_uc003gjd.1_Intron	NM_020416	NP_065149	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						gatcttgtcgttttttttttt	0.085													7	4	---	---	---	---	
TBC1D14	57533	broad.mit.edu	37	4	6969468	6969468	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6969468delT	uc011bwg.1	+						TBC1D14_uc003gjs.3_Intron	NM_001113361	NP_001106832	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14 isoform a							intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2						TGCAAATGTGTTTATCATCAA	0.398													4	2	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7501489	7501490	+	Intron	INS	-	G	G	rs72600609		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7501489_7501490insG	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						CTGGAGAGAAACCCCACAAGTC	0.584													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11826910	11826911	+	IGR	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11826910_11826911delTG								HS3ST1 (396373 upstream) : None (None downstream)																							tatgtgtatatgtgtgtgtgtg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	15761336	15761336	+	IGR	DEL	T	-	-	rs34949400		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15761336delT								BST1 (21403 upstream) : CD38 (18595 downstream)																							GGGGGTGTCATGGGGTACAGC	0.398													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	19163944	19163944	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19163944delA								None (None upstream) : None (None downstream)																							ATCTGTTGAGAAAAAAAAGGG	0.353													4	2	---	---	---	---	
CCDC149	91050	broad.mit.edu	37	4	24877915	24877920	+	Intron	DEL	ACACAC	-	-	rs71844079		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24877915_24877920delACACAC	uc011bxr.1	-						CCDC149_uc003grc.2_Intron|CCDC149_uc003grb.2_Intron|CCDC149_uc003grd.2_Intron|CCDC149_uc003gre.2_Intron	NM_173463	NP_775734	B4DZG3	B4DZG3_HUMAN	coiled-coil domain containing 149 isoform 1												0		Breast(46;0.173)				atacacacgtacacacacacacacac	0.209													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	31340502	31340503	+	IGR	INS	-	T	T	rs142431381	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31340502_31340503insT								PCDH7 (192081 upstream) : None (None downstream)																							GTTGATAAACATTTTTTTTTCA	0.322													4	2	---	---	---	---	
C4orf19	55286	broad.mit.edu	37	4	37562263	37562264	+	Intron	INS	-	C	C	rs144833476	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37562263_37562264insC	uc003gsw.3	+							NM_001104629	NP_001098099	Q8IY42	CD019_HUMAN	hypothetical protein LOC55286												0						CAGACACCTTGCCCCTACATCA	0.505													6	3	---	---	---	---	
TBC1D1	23216	broad.mit.edu	37	4	37951483	37951483	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37951483delG	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1						gacattgtgtgggttggattt	0.000													4	2	---	---	---	---	
ATP10D	57205	broad.mit.edu	37	4	47574662	47574667	+	Intron	DEL	GTGTGT	-	-	rs143303182		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47574662_47574667delGTGTGT	uc003gxk.1	+						ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D						ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3						TTGTGCGCACgtgtgtgtgtgtgtgt	0.189													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	48497036	48497036	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48497036delT								ZAR1 (616 upstream) : FRYL (2344 downstream)																							CTTCAAAGCCTTTTTTTTTTC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49154827	49154827	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49154827delG								CWH43 (90734 upstream) : None (None downstream)																							cattccactcgggttgattcc	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55214740	55214740	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55214740delT								PDGFRA (50329 upstream) : KIT (309355 downstream)																							ggggagccccttttttaagta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55250894	55250894	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55250894delG								PDGFRA (86483 upstream) : KIT (273201 downstream)																							TACTGCGCTTGGAAGTCCAGA	0.537											OREG0016198	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	4	69705867	69705867	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69705867delA								UGT2B10 (8128 upstream) : UGT2A3 (88310 downstream)																							tcatatgtggaaaaaaaattc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	74219742	74219742	+	IGR	DEL	T	-	-	rs77865983		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74219742delT								ANKRD17 (95240 upstream) : ALB (50230 downstream)																							accagacttatatatatctaa	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	74219744	74219746	+	IGR	DEL	TAT	-	-	rs71655746		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74219744_74219746delTAT								ANKRD17 (95242 upstream) : ALB (50226 downstream)																							cagacttatatatatctaagcag	0.000													2	5	---	---	---	---	
THAP6	152815	broad.mit.edu	37	4	76470369	76470369	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76470369delT	uc003hio.1	+									Q8TBB0	THAP6_HUMAN	Homo sapiens cDNA FLJ32397 fis, clone SKMUS2000243.							microtubule cytoskeleton	DNA binding|metal ion binding				0			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ataacatagatgaggaaattg	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90910739	90910739	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90910739delT								MMRN1 (34961 upstream) : FAM190A (137945 downstream)																							ATTTTATAGATTTTTTTTTTT	0.308													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91668636	91668636	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91668636delA	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						gagagcagagaaaaaaaaaga	0.085													4	2	---	---	---	---	
BMPR1B	658	broad.mit.edu	37	4	95971625	95971625	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95971625delA	uc003htm.3	+							NM_001203	NP_001194	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB						BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(4)|skin(2)|stomach(1)|breast(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		TTATCAAAACAAAAAAAACAT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111580147	111580147	+	IGR	DEL	T	-	-	rs34072616	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111580147delT								PITX2 (17030 upstream) : MIR297 (201591 downstream)																							TTCAACAGTGttttttttgtt	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	113688722	113688723	+	IGR	INS	-	AATA	AATA	rs139226825	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113688722_113688723insAATA								LARP7 (109981 upstream) : ANK2 (50516 downstream)																							gaccctgtctcaataaataaat	0.178													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	134773949	134773949	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134773949delA								PCDH10 (661218 upstream) : PABPC4L (343542 downstream)																							tgtttgctctaatattcatta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	135465360	135465360	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135465360delA								PABPC4L (342457 upstream) : None (None downstream)																							GTCTTCTTCTAAGGCATACGA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	138925387	138925387	+	IGR	DEL	A	-	-	rs111750562		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138925387delA								PCDH18 (471739 upstream) : SLC7A11 (159861 downstream)																							TGAAGAGTCCAAAAAAAAATG	0.373													4	2	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154514629	154514630	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154514629_154514630insT	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron|KIAA0922_uc010ipq.2_Intron	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				ttgagagtcactTTTTTTTTCA	0.124													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	161153617	161153618	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161153617_161153618insT								RAPGEF2 (872318 upstream) : None (None downstream)																							AAATATGTCTGTTTTTTTGGGG	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	164139226	164139227	+	IGR	DEL	AT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164139226_164139227delAT								NAF1 (51153 upstream) : NPY1R (105890 downstream)																							tctctgccacattttccacatc	0.000													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	165115025	165115025	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165115025delG	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)				AGAAGCAACTGGCTTTTGTTC	0.338													4	2	---	---	---	---	
PALLD	23022	broad.mit.edu	37	4	169704547	169704547	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169704547delA	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		TTTGGTCTTCAGGAGGAGGGG	0.428									Pancreatic_Cancer_Familial_Clustering_of				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	172349532	172349532	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172349532delT								None (None upstream) : GALNTL6 (385043 downstream)																							ACATGCATTCTTTTTTTTTCA	0.398													4	4	---	---	---	---	
GALNTL6	442117	broad.mit.edu	37	4	173862351	173862351	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173862351delA	uc003isv.2	+							NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4						TAATTGAGTCAGGTAGTCCCC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174419848	174419848	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174419848delC								SCRG1 (92320 upstream) : HAND2 (27804 downstream)																							AAACAGATCACCTAGATTAAA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180331474	180331474	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180331474delT								None (None upstream) : None (None downstream)																							ATTTGATTCATTTTTTTTTTA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182999909	182999910	+	Intron	DEL	AG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182999909_182999910delAG	uc003iva.1	-											Homo sapiens cDNA FLJ31634 fis, clone NT2RI2003419.																		cagaggaaatagagagagagag	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185832035	185832036	+	IGR	DEL	AG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185832035_185832036delAG								ACSL1 (84820 upstream) : HELT (107959 downstream)																							CTACTTACTTAGCTCTACATCT	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188205954	188205954	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188205954delT								FAT1 (558104 upstream) : ZFP42 (710971 downstream)																							CCCAAATTACTTGCCTGAGAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4723622	4723622	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4723622delT								None (None upstream) : LOC340094 (310850 downstream)																							TCTCTCACCCTTCCCCATCCT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6791775	6791775	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6791775delT								PAPD7 (34614 upstream) : ADCY2 (604568 downstream)																							TTGGAATTTCTtttttttgtg	0.209													4	2	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9548189	9548190	+	5'Flank	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9548189_9548190insA	uc003jek.2	-						SNORD123_uc010itp.1_5'Flank	NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						TACTTGAAAAGAAAAAAAAAAA	0.391													2	4	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11570758	11570758	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11570758delT	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						ttcttttttctttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13399878	13399878	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13399878delT								None (None upstream) : DNAH5 (290559 downstream)																							CTTCTCCAAATTTGACTGCTC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	16411710	16411711	+	IGR	INS	-	AG	AG	rs145742923		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16411710_16411711insAG								MARCH11 (231813 upstream) : ZNF622 (39918 downstream)																							cacagacacacacacacacaca	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24879081	24879081	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24879081delT								CDH10 (234170 upstream) : None (None downstream)																							CTCATAACTGTTTTTTTTTTA	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	28614113	28614114	+	IGR	INS	-	ACAA	ACAA	rs147488001	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28614113_28614114insACAA								None (None upstream) : None (None downstream)																							CACACACACTCacaaacaaaca	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	31153994	31153995	+	IGR	INS	-	CT	CT	rs149411330	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31153994_31153995insCT								None (None upstream) : CDH6 (39801 downstream)																							tattccttcagctctctctctC	0.213													5	4	---	---	---	---	
CDH6	1004	broad.mit.edu	37	5	31269993	31269993	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31269993delA	uc003jhe.1	+						CDH6_uc003jhd.1_Intron	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						TATTTGCTGGAAAAAAAAATC	0.443													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36419981	36419981	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36419981delT								RANBP3L (117970 upstream) : SLC1A3 (186476 downstream)																							aagacaccccttttgagaaaa	0.109													4	2	---	---	---	---	
GHR	2690	broad.mit.edu	37	5	42475360	42475360	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42475360delT	uc003jmt.2	+						uc003jmu.2_Intron|uc003jmv.1_Intron	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	GAGCACTGGATTTATGCTTGG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56720279	56720279	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56720279delT								GPBP1 (160869 upstream) : ACTBL2 (55565 downstream)																							TAGAATCCGCTTTTTTTTGTA	0.398													8	4	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59490365	59490365	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59490365delC	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	tgactctccaccaatgaatca	0.100													4	2	---	---	---	---	
POLK	51426	broad.mit.edu	37	5	74843762	74843762	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74843762delT	uc003kdw.2	+						POLK_uc003kdx.2_Intron|POLK_uc003kdy.2_Intron|POLK_uc003kdz.2_Intron|POLK_uc003kea.2_Intron|POLK_uc003keb.2_Intron|POLK_uc010izq.2_Intron|POLK_uc003kec.2_Intron|POLK_uc010izr.2_Intron|POLK_uc010izs.2_Intron|POLK_uc003ked.2_Intron|POLK_uc003kee.2_Intron	NM_016218	NP_057302	Q9UBT6	POLK_HUMAN	DNA-directed DNA polymerase kappa						DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		atatcttttcttttttttgag	0.000								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	82714453	82714453	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82714453delA								XRCC4 (64876 upstream) : VCAN (53040 downstream)																							AAGAAGGGGGAGGGCTGTGGC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	84551368	84551368	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84551368delT								EDIL3 (870757 upstream) : None (None downstream)																							CACCTCACAATTTTTTTTAAT	0.338													4	2	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	89930624	89930627	+	Intron	DEL	AGTT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89930624_89930627delAGTT	uc003kju.2	+						GPR98_uc003kjt.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TGTCTGTGGCAGTTAGTTATAATG	0.373													2	4	---	---	---	---	
MCTP1	79772	broad.mit.edu	37	5	94533734	94533734	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94533734delT	uc003kkx.2	-							NM_024717	NP_078993	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		agacacaaggttttttaagag	0.000													4	2	---	---	---	---	
ERAP2	64167	broad.mit.edu	37	5	96233248	96233249	+	Intron	INS	-	T	T	rs139679505	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96233248_96233249insT	uc003kmq.2	+						uc003kmo.1_Intron|ERAP2_uc003kmt.2_Intron|ERAP2_uc003kmr.2_Intron|ERAP2_uc003kms.2_Intron|ERAP2_uc003kmu.2_Intron	NM_022350	NP_071745	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2						antigen processing and presentation of endogenous peptide antigen via MHC class I|proteolysis|regulation of blood pressure	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding				0		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		tgtgtctattctttttttaatg	0.104													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	104051765	104051766	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104051765_104051766insT								None (None upstream) : RAB9BP1 (383409 downstream)																							ATATCGAACAATTTTTTTTTAG	0.257													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	104103155	104103155	+	IGR	DEL	T	-	-	rs139345066		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104103155delT								None (None upstream) : RAB9BP1 (332020 downstream)																							CTAGTCTCAGTTTTTTCAAGT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	125118158	125118161	+	IGR	DEL	TTTG	-	-	rs112937030		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125118158_125118161delTTTG								None (None upstream) : GRAMD3 (577627 downstream)																							gtcagctttttttgtttgtttgtt	0.000													2	5	---	---	---	---	
GRAMD3	65983	broad.mit.edu	37	5	125697760	125697760	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125697760delC	uc011cwt.1	+							NM_001146319	NP_001139791	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3 isoform 1											central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		TGGGTCTCCTCCTTTGTTTTT	0.303													4	2	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	130767211	130767214	+	Intron	DEL	GTAA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130767211_130767214delGTAA	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvm.1_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TATATTCCTTGTAAGTATTTAGTT	0.294													8	5	---	---	---	---	
C5orf56	441108	broad.mit.edu	37	5	131788122	131788122	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131788122delT	uc003kwy.1	+						C5orf56_uc003kwz.1_Intron|C5orf56_uc010jds.1_Intron|IRF1_uc003kxd.2_Intron	NM_001013717	NP_001013739	Q8N8D9	CE056_HUMAN	hypothetical protein LOC441108												0						gtttatactattttttgatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134590266	134590266	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134590266delA	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		TGTGTGAGGGAAAAAAAAATA	0.423													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134882320	134882321	+	IGR	INS	-	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134882320_134882321insC								NEUROG1 (10681 upstream) : CXCL14 (24052 downstream)																							GGTCGTTGCTGCCCCCTCATTC	0.441													4	2	---	---	---	---	
TRPC7	57113	broad.mit.edu	37	5	135582913	135582913	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135582913delT	uc003lbn.1	-						TRPC7_uc010jef.1_Intron|TRPC7_uc010jeg.1_Intron|TRPC7_uc010jeh.1_Intron|TRPC7_uc010jei.1_Intron|TRPC7_uc010jej.1_Intron	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,						axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ctacatgtgattttTTTTTTT	0.020													5	3	---	---	---	---	
SPOCK1	6695	broad.mit.edu	37	5	136335644	136335644	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136335644delA	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACCAAAGGATAAAAATAACCC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	140597417	140597418	+	IGR	DEL	GA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140597417_140597418delGA								PCDHB13 (424 upstream) : PCDHB14 (5513 downstream)																							GCATGTGTATGAGAGAGAGAGA	0.366													4	2	---	---	---	---	
PCDH12	51294	broad.mit.edu	37	5	141341589	141341589	+	5'Flank	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141341589delC	uc003llx.2	-							NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor						neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCGGCTTATCCCAGGTAGGG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	145746661	145746662	+	IGR	INS	-	CT	CT	rs148662018	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145746661_145746662insCT								POU4F3 (26578 upstream) : TCERG1 (80211 downstream)																							CTTGGCAGGAACTCTGCTCCAA	0.361													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	146581611	146581611	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146581611delA								PPP2R2B (120557 upstream) : STK32A (32968 downstream)																							gtgcagtggtaattgtaaatg	0.080													4	2	---	---	---	---	
SPINK14	408187	broad.mit.edu	37	5	147549507	147549508	+	Intron	INS	-	AT	AT	rs141153879	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147549507_147549508insAT	uc003loz.1	+							NM_001001325	NP_001001325	Q6IE38	ISK14_HUMAN	Kazal type serine protease inhibitor 5-like 2							extracellular region	serine-type endopeptidase inhibitor activity				0						tatccattgacgtgttgcagag	0.213													5	3	---	---	---	---	
GRIA1	2890	broad.mit.edu	37	5	153056891	153056891	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153056891delA	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_Intron|GRIA1_uc011dcy.1_Intron|GRIA1_uc011dcz.1_Intron|GRIA1_uc010jia.1_Intron	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AAGCTCATATAAAAAAAAAAT	0.348													5	3	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153632109	153632110	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153632109_153632110insT	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)			gtgataatctatttttttttcc	0.000													4	2	---	---	---	---	
GABRB2	2561	broad.mit.edu	37	5	160948719	160948719	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160948719delA	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron|GABRB2_uc011dei.1_Intron	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	CGCCACTGGTAAAACAGAGTA	0.343													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166968534	166968535	+	Intron	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166968534_166968535delAC	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		ATTTTAATCAACACACACACAC	0.332													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168713235	168713238	+	Intron	DEL	AAGC	-	-	rs72277881		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168713235_168713238delAAGC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						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)			ACTATAGAGGAAGCAAAATTATGT	0.343													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173659523	173659523	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173659523delC								HMP19 (123342 upstream) : MSX2 (492052 downstream)																							GATTGTGTTGCATAAGTTGAG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	8268038	8268038	+	IGR	DEL	A	-	-	rs34930790		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8268038delA								EEF1E1 (165210 upstream) : SLC35B3 (143695 downstream)																							TATATGCATGAAAAAAAAAAT	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	12208436	12208437	+	IGR	DEL	AG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12208436_12208437delAG								HIVEP1 (43205 upstream) : EDN1 (82092 downstream)																							TCATTAACTTAGCTACATGCCT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19714746	19714747	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19714746_19714747insT								None (None upstream) : ID4 (122870 downstream)																							ATCTTTTGACATTTTTTTTTTC	0.416													4	2	---	---	---	---	
FLJ22536	401237	broad.mit.edu	37	6	21802463	21802463	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21802463delT	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0						AGAAAGTTGCTTTTTTTTTCC	0.368													4	3	---	---	---	---	
GABBR1	2550	broad.mit.edu	37	6	29598612	29598612	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29598612delA	uc003nmt.3	-						GABBR1_uc003nmp.3_5'Flank|GABBR1_uc003nms.3_5'Flank|GABBR1_uc003nmu.3_Intron|GABBR1_uc011dlr.1_Intron|GABBR1_uc011dls.1_Intron	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1						gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)	TTCCCAAAAGAAAAAAAAAAT	0.418													4	2	---	---	---	---	
COL11A2	1302	broad.mit.edu	37	6	33136168	33136169	+	Intron	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33136168_33136169delCA	uc003ocx.1	-						COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Intron|COL11A2_uc003ocz.1_Intron	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1						cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						CCAGCTCCTGCACACACACACA	0.614													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	34169156	34169156	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34169156delA								GRM4 (55287 upstream) : HMGA1 (35421 downstream)																							cgaaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ANKS1A	23294	broad.mit.edu	37	6	34945424	34945425	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34945424_34945425insT	uc003ojx.3	+						ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Intron|ANKS1A_uc010jvp.1_Intron|ANKS1A_uc010jvr.1_Intron	NM_015245	NP_056060	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4						taaaccttccatttttttttgg	0.059													4	2	---	---	---	---	
PPARD	5467	broad.mit.edu	37	6	35391525	35391525	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35391525delA	uc003okm.2	+						PPARD_uc003okl.2_Intron|PPARD_uc003okn.2_Intron|PPARD_uc011dtb.1_Intron|PPARD_uc011dtc.1_Intron|PPARD_uc010jvv.1_Intron	NM_006238	NP_006229	Q03181	PPARD_HUMAN	peroxisome proliferative activated receptor,						apoptosis|axon ensheathment|cholesterol metabolic process|decidualization|embryo implantation|fatty acid beta-oxidation|fatty acid transport|generation of precursor metabolites and energy|glucose metabolic process|glucose transport|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fat cell differentiation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|linoleic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1					Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	aagATACACCAAAAAAAAAAA	0.358													6	3	---	---	---	---	
MAPK14	1432	broad.mit.edu	37	6	36034814	36034814	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36034814delT	uc003olp.2	+						MAPK14_uc011dth.1_Intron|MAPK14_uc003olo.2_Intron|MAPK14_uc003olq.2_Intron|MAPK14_uc003olr.2_Intron|MAPK14_uc011dti.1_Intron	NM_001315	NP_001306	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14 isoform 1						activation of MAPK activity|cellular component movement|cellular response to ionizing radiation|chemotaxis|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of muscle cell differentiation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|signal transduction in response to DNA damage|stress-activated MAPK cascade|stress-induced premature senescence|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|MAP kinase activity|MAP kinase kinase activity|protein binding			ovary(2)|stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	6						ATGTTTACAATTTTTTTTTTA	0.338													6	6	---	---	---	---	
FRS3	10817	broad.mit.edu	37	6	41745445	41745445	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41745445delG	uc003orc.1	-							NM_006653	NP_006644	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3						fibroblast growth factor receptor signaling pathway	plasma membrane	fibroblast growth factor receptor binding|insulin receptor binding			ovary(2)	2	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TTTTTCTGAAGGGGAGACCAG	0.398													4	2	---	---	---	---	
UBR2	23304	broad.mit.edu	37	6	42620554	42620554	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42620554delT	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc003osh.2_Intron	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			GCCAGACAGATTTTTTTATAC	0.358													4	2	---	---	---	---	
PEX6	5190	broad.mit.edu	37	6	42932348	42932348	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42932348delT	uc003otf.2	-						uc003ote.1_5'Flank|PEX6_uc010jya.2_Intron	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6						protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			CTCCCACTAGttttttttttc	0.279													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48963810	48963810	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48963810delA								C6orf138 (884867 upstream) : MUT (435184 downstream)																							gatgcagaccaaaagagtagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	49939182	49939182	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49939182delT								DEFB113 (1844 upstream) : DEFB110 (37671 downstream)																							TTTCTTTTTGTTTTTTAGGGA	0.244													4	2	---	---	---	---	
LRRC1	55227	broad.mit.edu	37	6	53677887	53677888	+	Intron	DEL	AG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53677887_53677888delAG	uc003pcd.1	+							NM_018214	NP_060684	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		GATGCTGTACAGAGAGAGAGAA	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	55914082	55914083	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55914082_55914083insT								BMP5 (173707 upstream) : COL21A1 (7306 downstream)																							TATTCTCTCAATTTTTTTTTTT	0.342													0	6	---	---	---	---	
DST	667	broad.mit.edu	37	6	56485734	56485734	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56485734delT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GAAGAATATCTTTTTGCCCCT	0.333													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57417082	57417091	+	Intron	DEL	TTGGCAAATG	-	-	rs140389069		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57417082_57417091delTTGGCAAATG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		aaagcaaatattggcaaatgggatctaatt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	68408758	68408758	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68408758delA								None (None upstream) : BAI3 (936874 downstream)																							aaagtgagagaaaaaaaaaat	0.100													4	3	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71171048	71171048	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71171048delA	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfk.2_Intron|FAM135A_uc003pfl.2_Intron	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						cttagactgtaaagggctgta	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77034270	77034270	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77034270delA								IMPG1 (251935 upstream) : None (None downstream)																							ACTTCTGGAGAAAAAAAGAAA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	78318172	78318173	+	IGR	DEL	TC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78318172_78318173delTC								HTR1B (145052 upstream) : None (None downstream)																							TTAAGGGAGTtctctctctctc	0.243													4	2	---	---	---	---	
RNGTT	8732	broad.mit.edu	37	6	89614282	89614282	+	Intron	DEL	A	-	-	rs113231405		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89614282delA	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	NM_003800	NP_003791	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		ctttctctccaaaaaaaaaaa	0.129													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91610936	91610936	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91610936delT								MAP3K7 (314029 upstream) : None (None downstream)																							CTACACTTCCTTTTTGAATCT	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92776205	92776208	+	IGR	DEL	AAAT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92776205_92776208delAAAT								None (None upstream) : None (None downstream)																							GGAAGACGaaaaataaataaataa	0.387													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	98932075	98932075	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98932075delT								MIR2113 (459578 upstream) : POU3F2 (350505 downstream)																							ATGCTGATAGTTTACTATTGC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	111820311	111820311	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111820311delG	uc003pvb.2	+											Homo sapiens cDNA clone IMAGE:5274708.																		AAGTAGGGGAGGGTCTGGAGA	0.264													4	2	---	---	---	---	
LAMA2	3908	broad.mit.edu	37	6	129613067	129613067	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129613067delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ACCTTAAACATTTTTTTTTGG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139617569	139617569	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139617569delT								TXLNB (4361 upstream) : CITED2 (75828 downstream)																							atatgatccattttttttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141025972	141025972	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141025972delT								None (None upstream) : None (None downstream)																							atggaatccatttcttccaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145364624	145364624	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145364624delT								UTRN (190456 upstream) : EPM2A (581822 downstream)																							CTGAAGACTGTTTTTTTTTCA	0.388													6	3	---	---	---	---	
RBM16	22828	broad.mit.edu	37	6	155055505	155055505	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155055505delG	uc003qqa.2	+						RBM16_uc011efj.1_Intron|RBM16_uc011efk.1_Intron|RBM16_uc003qpz.2_Intron|RBM16_uc010kji.2_Intron	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16						mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)		TGGGGGCGGTGGGGGAAATGA	0.522													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162992804	162992804	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162992804delA	uc003qtx.3	-						PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		CTCAACGAGGAAAGAGCCCAG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165494375	165494375	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165494375delA								None (None upstream) : C6orf118 (198780 downstream)																							actaaagatgaaaaaaaaaat	0.000													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3538364	3538365	+	Intron	DEL	TT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3538364_3538365delTT	uc003smx.2	+							NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		aggcctcatctttttttttttt	0.000													4	2	---	---	---	---	
THSD7A	221981	broad.mit.edu	37	7	11568472	11568472	+	Intron	DEL	T	-	-	rs12699201	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11568472delT	uc003ssf.3	-							NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TCCTGGTGACTTTTTTTTTGA	0.338										HNSCC(18;0.044)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	13486703	13486711	+	IGR	DEL	ATAAAAGCC	-	-	rs11271371		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13486703_13486711delATAAAAGCC								ARL4A (756147 upstream) : ETV1 (444147 downstream)																							TGAGAACAAAATAAAAGCCTCCCAATTTG	0.388													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17218967	17218968	+	IGR	INS	-	G	G	rs77442614		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17218967_17218968insG								AGR3 (297354 upstream) : AHR (119308 downstream)																							CCCCACCCCCCACACACACCAT	0.322													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	21147955	21147956	+	IGR	INS	-	GT	GT	rs137869382	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21147955_21147956insGT								RPL23P8 (280516 upstream) : SP4 (319733 downstream)																							CACAAGCCGGAGTGTGTGTGTG	0.495													4	8	---	---	---	---	
MGC87042	256227	broad.mit.edu	37	7	22478569	22478569	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22478569delA	uc003svh.2	-						MGC87042_uc010kum.1_Intron			Q6NZ63	STEAL_HUMAN	SubName: Full=cDNA FLJ60218, highly similar to Six transmembrane epithelial antigen ofprostate 1;							integral to membrane	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0						tgaataaaacaaaaaaaagtg	0.000													4	2	---	---	---	---	
AAA1	404744	broad.mit.edu	37	7	34528205	34528205	+	Intron	DEL	T	-	-	rs5883463		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34528205delT	uc010kwo.1	-						AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron					Homo sapiens AAA1 variant IA mRNA, complete cds; alternatively spliced.												0						CTCCAGCCTATTTTTTTTTTC	0.448													3	3	---	---	---	---	
ADCY1	107	broad.mit.edu	37	7	45674737	45674738	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45674737_45674738insT	uc003tne.3	+						ADCY1_uc003tnd.2_Intron	NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	agtgaggtcagttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65183816	65183817	+	Intron	INS	-	CTACTG	CTACTG			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65183816_65183817insCTACTG	uc003tud.1	-											Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																		TTGAATCTCAACTGAgtgtggt	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65631518	65631518	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65631518delT								CRCP (11967 upstream) : TPST1 (38741 downstream)																							tctttgggggtttttttttta	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68689933	68689933	+	IGR	DEL	A	-	-	rs113250115		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68689933delA								None (None upstream) : AUTS2 (373972 downstream)																							Ttgttaactgaaaaaaaaaaa	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81046533	81046533	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81046533delT								SEMA3C (494858 upstream) : HGF (284912 downstream)																							atatctactctttttttcagt	0.000													4	2	---	---	---	---	
ABCB4	5244	broad.mit.edu	37	7	87038329	87038329	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87038329delT	uc003uiv.1	-						ABCB4_uc003uiw.1_Intron|ABCB4_uc003uix.1_Intron	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4						cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					TGGTTTTCCCTTTTTTTTTTA	0.269													4	3	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90112357	90112358	+	Intron	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90112357_90112358delTG	uc003ukt.1	+							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						TCTGAAAAATTGTGTGTGTGTG	0.396													4	2	---	---	---	---	
CDK6	1021	broad.mit.edu	37	7	92254292	92254292	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92254292delT	uc011khw.1	-						CDK6_uc010lez.2_Intron	NM_001259	NP_001250	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6						cell dedifferentiation|cell division|G1 phase of mitotic cell cycle|gliogenesis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|negative regulation of osteoblast differentiation|positive regulation of cell-matrix adhesion|positive regulation of fibroblast proliferation|regulation of erythrocyte differentiation|regulation of gene expression|response to virus	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleus|ruffle	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			central_nervous_system(1)|skin(1)	2	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTTTTCAAGATTTTTTTTTGA	0.095			T	MLLT10	ALL								5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	97669962	97669962	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97669962delC								OCM2 (50546 upstream) : LMTK2 (66235 downstream)																							ACTTCTGACGCCCACTTCCTT	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98417694	98417694	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98417694delA								NPTX2 (158513 upstream) : TMEM130 (26418 downstream)																							gtagaggtggaaaaaaatgag	0.000													4	2	---	---	---	---	
SMURF1	57154	broad.mit.edu	37	7	98625240	98625240	+	3'UTR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98625240delA	uc003upu.1	-	19					SMURF1_uc003upv.1_3'UTR|SMURF1_uc003upt.2_3'UTR|TRRAP_uc003ups.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)			CAACTTTCACAAAATAAATCA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100618904	100618905	+	IGR	INS	-	T	T	rs142129470	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100618904_100618905insT								ACHE (124365 upstream) : MUC12 (29170 downstream)																							TGGGGCAGAAAGGCCACAGCCC	0.554													5	4	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101499799	101499799	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101499799delA	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						CTAGAGCTGGAAAACCCTTCA	0.488											OREG0018226	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103412760	103412763	+	Intron	DEL	AATG	-	-	rs112387970		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103412760_103412763delAATG	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ATAGTTGTCAaatgaatgaatgaa	0.083													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	107519149	107519149	+	IGR	DEL	A	-	-	rs80245797		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107519149delA								SLC26A3 (75471 upstream) : DLD (12437 downstream)																							aatgctgtggaaaaaaaaaag	0.000													4	2	---	---	---	---	
NRCAM	4897	broad.mit.edu	37	7	108023583	108023584	+	Intron	DEL	CA	-	-	rs36108849		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108023583_108023584delCA	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5						cacacgctctcacacacacaca	0.317													4	2	---	---	---	---	
MDFIC	29969	broad.mit.edu	37	7	114560882	114560882	+	5'Flank	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114560882delA	uc003vhf.2	+						MDFIC_uc003vhg.2_5'Flank	NM_199072	NP_951038	Q9P1T7	MDFIC_HUMAN	MyoD family inhibitor domain containing protein						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						TCTCCAAGTGAAAAAAAAATG	0.373													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	125441287	125441287	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125441287delA								POT1 (871250 upstream) : GRM8 (637365 downstream)																							ttgcctgaggaaatggtaata	0.000													4	2	---	---	---	---	
WDR91	29062	broad.mit.edu	37	7	134893948	134893948	+	Intron	DEL	C	-	-	rs112551663		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134893948delC	uc003vsp.2	-						WDR91_uc010lmq.2_5'Flank|WDR91_uc010lmr.2_5'Flank	NM_014149	NP_054868	A4D1P6	WDR91_HUMAN	WD repeat domain 91											breast(2)|ovary(1)|skin(1)	4						AGCTGAAGTTCTAATGATAAA	0.343													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	135749249	135749249	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135749249delT								LUZP6 (87045 upstream) : CHRM2 (804150 downstream)																							AAATAAGGACTTTATCTGGAT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136467209	136467209	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136467209delC								LUZP6 (805005 upstream) : CHRM2 (86190 downstream)																							accaccccagccccagtctcc	0.000													4	2	---	---	---	---	
ATP6V0A4	50617	broad.mit.edu	37	7	138459891	138459891	+	5'Flank	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138459891delT	uc003vuf.2	-						ATP6V0A4_uc003vug.2_Intron|ATP6V0A4_uc003vuh.2_Intron	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						AGGGGGGTGCTTTTTTTTAAC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	143227275	143227276	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143227275_143227276insT								TAS2R41 (51386 upstream) : LOC441294 (41614 downstream)																							CTTTCCTTTTCTTTTTTTTTAA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145320795	145320795	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145320795delT								TPK1 (787649 upstream) : CNTNAP2 (492658 downstream)																							ACTCATTCTCTTTCATCTCCA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148967342	148967342	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148967342delT	uc003wfr.3	+											Homo sapiens cDNA FLJ36716 fis, clone UTERU2010651.																		caccattgcatttttttTAGT	0.010													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151981093	151981096	+	Intron	DEL	TATT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151981093_151981096delTATT	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)		TAGCTTTAACTATTTAATACTAGT	0.235			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	858936	858936	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:858936delG	uc003wpj.1	+						uc003wpk.2_Intron					Homo sapiens cDNA clone IMAGE:4824304.																		TTAATTTGTTGGGATTTACTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2231755	2231756	+	IGR	INS	-	T	T	rs139458202	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2231755_2231756insT								MYOM2 (138376 upstream) : CSMD1 (561120 downstream)																							cagaatttggcttttttTTAAT	0.183													4	2	---	---	---	---	
SGK223	157285	broad.mit.edu	37	8	8186101	8186102	+	Intron	INS	-	TTTCTA	TTTCTA	rs143704562	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8186101_8186102insTTTCTA	uc003wsh.3	-							NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin								ATP binding|non-membrane spanning protein tyrosine kinase activity				0						ATGTTACTTCTTTTCTATTTCT	0.351													4	2	---	---	---	---	
C8orf79	57604	broad.mit.edu	37	8	12879694	12879695	+	3'UTR	INS	-	T	T	rs146268183	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12879694_12879695insT	uc010lsq.2	+	5					C8orf79_uc011kxw.1_Intron|C8orf79_uc003wwj.3_3'UTR|C8orf79_uc010lsr.2_3'UTR	NM_020844	NP_065895	Q9P272	K1456_HUMAN	hypothetical protein LOC57604 isoform 1								methyltransferase activity				0						TTATTTGGTTGTTTTGTTTTCA	0.327													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23718627	23718628	+	IGR	DEL	TC	-	-	rs79859200		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23718627_23718628delTC								STC1 (6307 upstream) : ADAM28 (432952 downstream)																							GCAAGCATTTTCTTGAACATGT	0.416													4	2	---	---	---	---	
CCDC25	55246	broad.mit.edu	37	8	27610328	27610329	+	Intron	INS	-	A	A	rs71553882		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27610328_27610329insA	uc003xgc.2	-						CCDC25_uc003xgd.2_Intron|CCDC25_uc011lan.1_Intron|CCDC25_uc011lao.1_Intron|CCDC25_uc003xge.2_Intron|CCDC25_uc003xgf.1_Intron	NM_018246	NP_060716	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25												0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		ACTTAATAAGTaaaaaaaaaaa	0.223													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	28166143	28166144	+	IGR	INS	-	G	G	rs146935033	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28166143_28166144insG								ELP3 (117476 upstream) : PNOC (8505 downstream)																							TTTCAGCAGGTCCGGTCAGTCA	0.515													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	53838876	53838877	+	IGR	DEL	TC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53838876_53838877delTC								RB1CC1 (211850 upstream) : NPBWR1 (13591 downstream)																							tatccacctatctctctctctg	0.000													4	2	---	---	---	---	
TCEA1	6917	broad.mit.edu	37	8	54924201	54924201	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54924201delA	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc003xrw.1_Intron	NM_006756	NP_006747	P23193	TCEA1_HUMAN	transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			CTATCCCCCCAAAAAAACAGA	0.343			T	PLAG1	salivary adenoma								4	2	---	---	---	---	
XKR4	114786	broad.mit.edu	37	8	56297126	56297126	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56297126delT	uc003xsf.2	+							NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			AGGACTCTCCTTTTTTTGCTG	0.393													4	2	---	---	---	---	
CA8	767	broad.mit.edu	37	8	61154308	61154308	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61154308delA	uc003xtz.1	-						CA8_uc003xua.1_Intron	NM_004056	NP_004047	P35219	CAH8_HUMAN	carbonic anhydrase VIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)				TTTATTTTCTAAAAAAAAAAA	0.249													4	2	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68396310	68396310	+	Intron	DEL	T	-	-	rs71554608		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68396310delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			ttgccttctcttttttttttt	0.055													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70813207	70813207	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70813207delT								SLCO5A1 (65908 upstream) : PRDM14 (150818 downstream)																							GAAAGAAGCCTTATCATGATA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72441171	72441171	+	Intron	DEL	A	-	-	rs35138779		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72441171delA	uc003xyw.2	-											Homo sapiens cDNA clone IMAGE:5264099.																		tgccctttccaAAAAGATGTT	0.085													4	2	---	---	---	---	
MRPS28	28957	broad.mit.edu	37	8	80875890	80875890	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80875890delA	uc003ybp.2	-						MRPS28_uc003ybo.2_Intron|TPD52_uc010lzr.2_Intron	NM_014018	NP_054737	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28							mitochondrial small ribosomal subunit					0	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			ACACCAGCACAAAGGAAATGA	0.473													4	2	---	---	---	---	
WWP1	11059	broad.mit.edu	37	8	87387532	87387532	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87387532delT	uc003ydt.2	+							NM_007013	NP_008944	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase						central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2						TCGTTTTCAGTTTTTTTTTTA	0.294													4	2	---	---	---	---	
SDC2	6383	broad.mit.edu	37	8	97618896	97618896	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97618896delT	uc003yhv.1	+						SDC2_uc011lgu.1_Intron	NM_002998	NP_002989	P34741	SDC2_HUMAN	syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)	taggactgtattttttttaat	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98381945	98381946	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98381945_98381946insT								TSPYL5 (91769 upstream) : MTDH (274461 downstream)																							TTTCAACTATCTTTTTTTTTAA	0.371													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102111179	102111179	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102111179delT								YWHAZ (145556 upstream) : ZNF706 (98089 downstream)																							aaatgaatccttggtgcttac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103540941	103540942	+	IGR	DEL	GT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103540941_103540942delGT								UBR5 (116446 upstream) : ODF1 (22906 downstream)																							tgtgctgcgcgtgtgtgctctg	0.074													4	2	---	---	---	---	
PKHD1L1	93035	broad.mit.edu	37	8	110394432	110394434	+	Intron	DEL	TTG	-	-	rs66554679		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110394432_110394434delTTG	uc003yne.2	+							NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GTTATTATACTTGTTGTCCTTTT	0.325										HNSCC(38;0.096)			3	4	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	114085933	114085934	+	Intron	INS	-	T	T	rs78437571		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114085933_114085934insT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						tctcacaattcttTTTTTTTtc	0.059										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	2	---	---	---	---	
EXT1	2131	broad.mit.edu	37	8	118890094	118890095	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118890094_118890095insT	uc003yok.1	-							NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			AAGTTTTAATGTTTTTTTCTCC	0.337			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124620926	124620926	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124620926delT								FBXO32 (67480 upstream) : KLHL38 (36989 downstream)																							GAGGTGGGCCTTCGCTTCTAT	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129534253	129534253	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129534253delC								MIR1208 (371819 upstream) : None (None downstream)																							CTTCACAACACCCCCCACCCT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134987031	134987031	+	IGR	DEL	T	-	-	rs112711998		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134987031delT								ST3GAL1 (402848 upstream) : ZFAT (503002 downstream)																							ccttacaggcttttttttttt	0.020													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138530646	138530646	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138530646delT								None (None upstream) : FAM135B (611622 downstream)																							TTATTGGAACttttttttttc	0.249													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138912709	138912709	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138912709delT								None (None upstream) : FAM135B (229559 downstream)																							ATGTTTTTAATTTTTTTTTGC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142649167	142649167	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142649167delA								FLJ43860 (131837 upstream) : MIR1302-7 (218436 downstream)																							agaaagaaagaaaaaaGGGAC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144018957	144018958	+	IGR	INS	-	TG	TG			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144018957_144018958insTG								CYP11B2 (19698 upstream) : LOC100133669 (44490 downstream)																							gtgtgtgtgtctgtgtgtgtgA	0.203													3	3	---	---	---	---	
DMRT1	1761	broad.mit.edu	37	9	922888	922888	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:922888delC	uc003zgv.2	+							NM_021951	NP_068770	Q9Y5R6	DMRT1_HUMAN	doublesex and mab-3 related transcription factor						cell differentiation|male gonad development|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)		CTACATTTTACCCAAAGGTCA	0.493													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	8285046	8285047	+	IGR	INS	-	AT	AT	rs141620319	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8285046_8285047insAT								C9orf123 (485247 upstream) : PTPRD (29200 downstream)																							GGGATTAAAACGTGCTGCGGCT	0.441													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	19925982	19925982	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19925982delT								SLC24A2 (137174 upstream) : MLLT3 (418986 downstream)																							TTGCACAGTATTTCGAATCAA	0.428											OREG0019121	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	9	20328329	20328329	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20328329delA								SLC24A2 (539521 upstream) : MLLT3 (16639 downstream)																							acaaacaaacaaaaaaaaccc	0.159													4	2	---	---	---	---	
KIAA1797	54914	broad.mit.edu	37	9	20952694	20952694	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20952694delT	uc003zog.1	+						KIAA1797_uc003zoh.1_Intron	NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)		GTGGAAAGGGTTTTTTTTTTT	0.413													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	32244773	32244773	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32244773delG								None (None upstream) : ACO1 (139828 downstream)																							CCATCAGCATGGGGACACTGT	0.463													4	2	---	---	---	---	
DNAJA1	3301	broad.mit.edu	37	9	33037313	33037315	+	Intron	DEL	AAC	-	-	rs145355099		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33037313_33037315delAAC	uc003zsd.1	+						DNAJA1_uc011lnt.1_Intron	NM_001539	NP_001530	P31689	DNJA1_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 1						protein folding|response to heat|response to unfolded protein	membrane	ATP binding|heat shock protein binding|low-density lipoprotein particle receptor binding|metal ion binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.102)		tctttaaaaaaacaaaaaaaaaa	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	36822633	36822633	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36822633delT								MELK (144955 upstream) : PAX5 (15898 downstream)																							TGTCTCTACATTTTAGTACTG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	41692633	41692633	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:41692633delA								FAM75A5 (365269 upstream) : MGC21881 (255883 downstream)																							caaaatcaccaaaaaagcata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69034058	69034058	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69034058delG								MIR1299 (31737 upstream) : PGM5P2 (46187 downstream)																							ATACACAATAGGGTAGGAATG	0.323													4	2	---	---	---	---	
PGM5	5239	broad.mit.edu	37	9	71051357	71051358	+	Intron	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71051357_71051358insA	uc004agr.2	+							NM_021965	NP_068800	Q15124	PGM5_HUMAN	phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2						ACCCGGAAGATAAAAAATGTAC	0.446													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	72972664	72972665	+	IGR	INS	-	A	A	rs144299191	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72972664_72972665insA								SMC5 (2875 upstream) : KLF9 (26850 downstream)																							ccctgtctcttaaaaaaaaaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82359974	82359975	+	IGR	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82359974_82359975delAC								TLE4 (18317 upstream) : None (None downstream)																							acacacacagacacacacacgc	0.322													4	2	---	---	---	---	
NXNL2	158046	broad.mit.edu	37	9	91175296	91175296	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91175296delA	uc004aqa.2	+							NM_145283	NP_660326	Q5VZ03	NXNL2_HUMAN	nucleoredoxin-like 2 isoform 2												0						aggagatgctaaacctcactt	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92887686	92887687	+	IGR	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92887686_92887687delCA								LOC100129066 (553012 upstream) : DIRAS2 (484427 downstream)																							AAGCAAAGTGcacacacacaca	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98869111	98869111	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98869111delT								NCRNA00092 (85074 upstream) : HSD17B3 (128478 downstream)																							ctttctctgctttttttcagg	0.000													4	2	---	---	---	---	
FSD1L	83856	broad.mit.edu	37	9	108223639	108223639	+	Intron	DEL	A	-	-	rs74836830		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108223639delA	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron|FSD1L_uc004bcp.2_Intron	NM_001145313	NP_001138785	Q9BXM9	FSD1L_HUMAN	fibronectin type III and SPRY domain containing												0						actccgtaccaaaaaaaaaga	0.000													4	3	---	---	---	---	
FSD1L	83856	broad.mit.edu	37	9	108269055	108269055	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108269055delT	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron	NM_001145313	NP_001138785	Q9BXM9	FSD1L_HUMAN	fibronectin type III and SPRY domain containing												0						AAGGAAACCCttttttttttt	0.149													3	3	---	---	---	---	
SUSD1	64420	broad.mit.edu	37	9	114931393	114931394	+	Intron	INS	-	A	A	rs113283670		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114931393_114931394insA	uc004bfu.2	-						SUSD1_uc010mui.2_Intron|SUSD1_uc010muj.2_Intron	NM_022486	NP_071931	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1 precursor							integral to membrane	calcium ion binding				0						acatccctgacaaaaaaaaaat	0.089													4	2	---	---	---	---	
DEC1	50514	broad.mit.edu	37	9	117977559	117977559	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117977559delT	uc004bjk.1	+							NM_017418	NP_059114	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1						catacacccatttttttgtgt	0.000													4	2	---	---	---	---	
RABGAP1	23637	broad.mit.edu	37	9	125817097	125817097	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125817097delT	uc011lzh.1	+						RABGAP1_uc004bnl.3_Intron|RABGAP1_uc011lzj.1_Intron	NM_012197	NP_036329	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1						cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5						atttgtctgatttttttttca	0.000													4	2	---	---	---	---	
PPP6C	5537	broad.mit.edu	37	9	127915561	127915561	+	Intron	DEL	A	-	-	rs79901818		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127915561delA	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712	O00743	PPP6_HUMAN	protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2						tctcaaaaacaaaaaaaaaag	0.134													4	2	---	---	---	---	
ABL1	25	broad.mit.edu	37	9	133742554	133742554	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133742554delT	uc004bzw.2	+						ABL1_uc004bzv.2_Intron	NM_005157	NP_005148	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)	GCAGGATATATTTTTTTGAAT	0.423			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL						OREG0019551	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
C9orf171	389799	broad.mit.edu	37	9	135326250	135326250	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135326250delG	uc004cbn.2	+						C9orf171_uc004cbo.2_Intron	NM_207417	NP_997300	Q6ZQR2	CI171_HUMAN	hypothetical protein LOC389799											ovary(4)|large_intestine(1)	5						gtgagtgagaggtaagcagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	135883624	135883624	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135883624delC								GFI1B (16541 upstream) : GTF3C5 (22438 downstream)																							CTGGCTCGGTCCTCTGTTCTC	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	136159269	136159273	+	IGR	DEL	AGGCC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136159269_136159273delAGGCC								ABO (8639 upstream) : SURF6 (38280 downstream)																							acattgcagaaggccaggccgcagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137891433	137891433	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137891433delC								FCN1 (81624 upstream) : OLFM1 (75656 downstream)																							ctcagactcaccccagggctg	0.000													4	2	---	---	---	---	
LARP4B	23185	broad.mit.edu	37	10	910364	910364	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:910364delA	uc001ifs.1	-							NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3						GTTCaaaattaaaaaaaaaaa	0.388													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2856879	2856879	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2856879delG								None (None upstream) : PFKP (252873 downstream)																							CAGTTTCACAGGGGAAAGGTT	0.498													4	2	---	---	---	---	
PRKCQ	5588	broad.mit.edu	37	10	6582860	6582860	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6582860delT	uc001ijj.1	-						PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248	Q04759	KPCT_HUMAN	protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6						ccaccttccctttttttggta	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10775400	10775400	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10775400delA								None (None upstream) : SFTA1P (51002 downstream)																							GGAGGTAGTGAAAAAAAAAAG	0.413													4	4	---	---	---	---	
MCM10	55388	broad.mit.edu	37	10	13233040	13233040	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13233040delT	uc001ima.2	+						MCM10_uc001imb.2_Intron|MCM10_uc001imc.2_Intron	NM_182751	NP_877428	Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						aagcattggctttttttttat	0.144													5	3	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14073873	14073873	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14073873delT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						CTGACTTAGATTTTTTTTTTT	0.393													5	3	---	---	---	---	
PTER	9317	broad.mit.edu	37	10	16497238	16497238	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16497238delA	uc001iog.1	+						PTER_uc001ioh.1_Intron|PTER_uc001ioi.1_Intron|PTER_uc009xjp.1_Intron	NM_030664	NP_109589	Q96BW5	PTER_HUMAN	phosphotriesterase related						catabolic process		hydrolase activity, acting on ester bonds|zinc ion binding			ovary(2)	2						aaaacaaaacaaaaaaaaaaT	0.214													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	23012202	23012202	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23012202delA								PIP4K2A (8699 upstream) : ARMC3 (204752 downstream)																							GGCAGTTCCCAGGGTCTCCAC	0.498													4	2	---	---	---	---	
APBB1IP	54518	broad.mit.edu	37	10	26818557	26818557	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26818557delT	uc001iss.2	+						APBB1IP_uc009xks.1_Intron	NM_019043	NP_061916	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding,						blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7						CTCTGGAGTCtttttttttct	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36647023	36647024	+	IGR	DEL	GT	-	-	rs72351102		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36647023_36647024delGT								FZD8 (716661 upstream) : ANKRD30A (767761 downstream)																							ACCATGTGGGgtgtgtgtgtgt	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42625686	42625686	+	IGR	DEL	T	-	-	rs9732807		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42625686delT								None (None upstream) : LOC441666 (201629 downstream)																							ttatgctaaatttttgaagaa	0.040													4	2	---	---	---	---	
BMS1	9790	broad.mit.edu	37	10	43328704	43328705	+	3'UTR	INS	-	A	A	rs147817749	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43328704_43328705insA	uc001jaj.2	+	23						NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein						ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3						TAAGATTATTTAAACTAAAGTT	0.292													4	2	---	---	---	---	
RASSF4	83937	broad.mit.edu	37	10	45464403	45464404	+	Intron	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45464403_45464404delTG	uc001jbo.2	+						RASSF4_uc001jbp.2_Intron|RASSF4_uc009xmn.2_Intron|RASSF4_uc001jbq.2_Intron	NM_032023	NP_114412	Q9H2L5	RASF4_HUMAN	Ras association domain family 4						cell cycle|signal transduction		protein binding			large_intestine(1)	1						CACTGGAGTAtgtgtgtgtgtg	0.302													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47058285	47058286	+	Intron	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47058285_47058286delCA	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						tgtgtgcattcacacacacaca	0.238													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47059869	47059870	+	Intron	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47059869_47059870delAC	uc001jed.3	-									P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						TATCACATAAACACACACACAC	0.351													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47113053	47113054	+	Intron	INS	-	C	C	rs11377933		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47113053_47113054insC	uc001jed.3	-						uc001jef.2_Intron			P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						TGGGACATGGGGGGACTcctgc	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	50208072	50208072	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50208072delG								WDFY4 (17072 upstream) : C10orf72 (14261 downstream)																							ATGGCCTAGTGGGGGGTGAGG	0.597													4	2	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	56011313	56011313	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56011313delT	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				TAGAGAGTGCTTTTTTTAACC	0.279										HNSCC(58;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	57870349	57870349	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57870349delT								PCDH15 (482647 upstream) : ZWINT (246850 downstream)																							gctaaagaagtttttttttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	60905438	60905438	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60905438delC								BICC1 (316593 upstream) : PHYHIPL (30910 downstream)																							acagagacaacccaggttcaa	0.000													4	2	---	---	---	---	
ANK3	288	broad.mit.edu	37	10	62288924	62288925	+	Intron	INS	-	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62288924_62288925insG	uc010qih.1	-						ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron	NM_001149	NP_001140	Q12955	ANK3_HUMAN	ankyrin 3 isoform 2						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						CGAGATAAAGTGGGGGTAGACA	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63387851	63387851	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63387851delA								TMEM26 (174643 upstream) : C10orf107 (34868 downstream)																							GCACACTCAGAAAAAAAAAAT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	66137651	66137651	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66137651delT								REEP3 (755680 upstream) : ANXA2P3 (447634 downstream)																							TTGTGTTTTCTTTTTTTTTTT	0.274													4	2	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68492043	68492044	+	Intron	DEL	CT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68492043_68492044delCT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_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						aaatctagacctctctctcTCT	0.213													4	2	---	---	---	---	
LRRC20	55222	broad.mit.edu	37	10	72108893	72108894	+	Intron	INS	-	TGC	TGC	rs143930060	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72108893_72108894insTGC	uc001jqx.1	-						LRRC20_uc001jqy.1_Intron|LRRC20_uc001jqz.1_Intron	NM_207119	NP_997002	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20 isoform 1												0						AGCACAGACAGTATATAGTTCA	0.510													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80102108	80102108	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80102108delG	uc010qlp.1	+						uc001jzw.1_Intron					SubName: Full=cDNA FLJ57363;																		TTAGGACAGAGGCCCTAGAGA	0.557													4	2	---	---	---	---	
MAT1A	4143	broad.mit.edu	37	10	82050233	82050233	+	5'Flank	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82050233delA	uc001kbw.2	-							NM_000429	NP_000420	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha						methylation|S-adenosylmethionine biosynthetic process|xenobiotic metabolic process	cytosol	ATP binding|metal ion binding|methionine adenosyltransferase activity				0			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TGCTTTGACCAAAAAAAGTAG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82768370	82768371	+	IGR	DEL	AG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82768370_82768371delAG								SH2D4B (362054 upstream) : NRG3 (866699 downstream)																							agagagagaaagagagagagag	0.000													4	3	---	---	---	---	
EXOC6	54536	broad.mit.edu	37	10	94596333	94596334	+	Intron	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94596333_94596334delAC	uc010qnr.1	+						EXOC6_uc001kie.2_Intron	NM_001013848	NP_001013870	Q8TAG9	EXOC6_HUMAN	SEC15-like 1 isoform b						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)				TACTGTTAAAACACACTGATGT	0.406													4	3	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97117177	97117178	+	Intron	INS	-	G	G	rs139904456	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97117177_97117178insG	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		AGAACAAGGTTGGGGGGTCAAA	0.317													3	4	---	---	---	---	
CNNM2	54805	broad.mit.edu	37	10	104708636	104708637	+	Intron	INS	-	ACTG	ACTG	rs140891082	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104708636_104708637insACTG	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron	NM_017649	NP_060119	Q9H8M5	CNNM2_HUMAN	cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CTTTCAATGATAGAGAGAGAGA	0.208													2	4	---	---	---	---	
NT5C2	22978	broad.mit.edu	37	10	104884529	104884529	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104884529delT	uc001kwo.2	-						NT5C2_uc010qqp.1_Intron|NT5C2_uc001kwq.2_Intron|NT5C2_uc001kwp.2_Intron	NM_012229	NP_036361	P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II						purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	caccatgaggtttttttccac	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109078749	109078750	+	IGR	INS	-	AGCAAAG	AGCAAAG	rs145794962	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109078749_109078750insAGCAAAG								SORCS1 (154457 upstream) : None (None downstream)																							agagaCTATTAAAAGAAAGTTT	0.198													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113059179	113059179	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113059179delT								ADRA2A (218519 upstream) : GPAM (850443 downstream)																							GGAGAACAGGTTTTTGGGTGA	0.418													4	2	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114425197	114425197	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114425197delA	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)		GTTAGAAATGAAAAAAGAATT	0.338													4	2	---	---	---	---	
HSPA12A	259217	broad.mit.edu	37	10	118456609	118456609	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118456609delA	uc001lct.2	-						HSPA12A_uc001lcu.2_Intron	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A								ATP binding			ovary(1)	1				all cancers(201;0.0158)		AAAGGTACTCAAAAAAACAGG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	119515992	119515992	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119515992delA								EMX2 (206936 upstream) : RAB11FIP2 (248437 downstream)																							ACAGAAAAAGAAAAAAAAAAA	0.383													8	4	---	---	---	---	
GRK5	2869	broad.mit.edu	37	10	121128705	121128705	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121128705delG	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		gtgtggcctaggagtttcact	0.209													4	2	---	---	---	---	
PPAPDC1A	196051	broad.mit.edu	37	10	122303011	122303011	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122303011delA	uc001lev.1	+						PPAPDC1A_uc010qtd.1_Intron|PPAPDC1A_uc009xzl.1_Intron|PPAPDC1A_uc001lew.1_Intron|PPAPDC1A_uc001lex.1_Intron|PPAPDC1A_uc001ley.1_Intron	NM_001030059	NP_001025230	Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain						phospholipid dephosphorylation	integral to membrane	phosphatidate phosphatase activity			breast(1)	1		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)		CAATGCAATTAAAAAAAAAAC	0.453													3	3	---	---	---	---	
WDR11	55717	broad.mit.edu	37	10	122649700	122649703	+	Intron	DEL	ATTT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122649700_122649703delATTT	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron|WDR11_uc009xzn.2_Intron	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2							integral to membrane					0						ACAACTCAAGatttatttatttat	0.137													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125461073	125461073	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125461073delT								GPR26 (4162 upstream) : CPXM2 (4656 downstream)																							AATTACCTTCTCCTCATTATG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125461075	125461076	+	IGR	DEL	CT	-	-	rs35958012		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125461075_125461076delCT								GPR26 (4164 upstream) : CPXM2 (4653 downstream)																							TTACCTTCTCCTCATTATGAAA	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	135446993	135446993	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135446993delA								FRG2B (6694 upstream) : LOC653544 (43286 downstream)																							AAAATGGAAGAAAAAATAGAA	0.204													4	2	---	---	---	---	
MUC6	4588	broad.mit.edu	37	11	1028187	1028188	+	Intron	INS	-	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1028187_1028188insG	uc001lsw.2	-							NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric						maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGTGGGCGCTGGGGGGGCAGC	0.703													4	2	---	---	---	---	
NUP98	4928	broad.mit.edu	37	11	3767790	3767790	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3767790delC	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyj.1_Intron|NUP98_uc001lyk.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)		TGGACGATGACCCATGAATCA	0.284			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								4	2	---	---	---	---	
TRIM22	10346	broad.mit.edu	37	11	5769987	5769987	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5769987delC	uc009yet.1	+						TRIM5_uc001mbq.1_Intron	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN	tripartite motif-containing 22						immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		CTTTTGATATCTTTCCCATAG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	13230854	13230854	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13230854delT								RASSF10 (198207 upstream) : ARNTL (68471 downstream)																							tgatcctccgttttttgtcat	0.075													4	2	---	---	---	---	
ARNTL	406	broad.mit.edu	37	11	13407913	13407914	+	Intron	INS	-	TG	TG	rs143415137	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13407913_13407914insTG	uc001mkr.2	+						ARNTL_uc001mko.2_Intron|ARNTL_uc001mkp.2_Intron|ARNTL_uc001mkq.2_Intron|ARNTL_uc001mks.2_Intron|ARNTL_uc001mkt.2_Intron|ARNTL_uc001mku.2_Intron|ARNTL_uc001mkw.2_Intron|ARNTL_uc001mkx.2_Intron|ARNTL_uc001mky.2_Intron	NM_001178	NP_001169	O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear						circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0				Epithelial(150;0.0243)		TTCCTTAGAGCTGTCTCTTCAC	0.287													1	5	---	---	---	---	
SLC17A6	57084	broad.mit.edu	37	11	22360359	22360360	+	Intron	DEL	GT	-	-	rs71861548		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22360359_22360360delGT	uc001mqk.2	+							NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent						sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4						AACCTGTCTGgtgtgtgtgtgt	0.332													4	2	---	---	---	---	
METT5D1	196074	broad.mit.edu	37	11	28331148	28331149	+	Intron	INS	-	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28331148_28331149insC	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron|METT5D1_uc001msi.2_Intron	NM_001113528	NP_001107000	A6NJ78	MET15_HUMAN	methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0						AAGTCCAGTTTCCCTAAGTCTG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35930652	35930652	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35930652delA								TRIM44 (99722 upstream) : LDLRAD3 (34960 downstream)																							tgTTAAACAGAAAAAAAAAAA	0.169													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	36703112	36703112	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36703112delA								C11orf74 (6722 upstream) : None (None downstream)																							TCCTCTTTATAAGGTTGAGTA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39677947	39677947	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39677947delC								None (None upstream) : LRRC4C (457806 downstream)																							agaagattttccccagtgcct	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43019703	43019704	+	IGR	INS	-	GTGT	GTGT	rs146001237	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43019703_43019704insGTGT								None (None upstream) : API5 (313801 downstream)																							caGTCACACACgtgtgtgtgtg	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43155933	43155934	+	IGR	INS	-	TGA	TGA	rs140396220	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43155933_43155934insTGA								None (None upstream) : API5 (177571 downstream)																							aagctgaaagttgagcagtgac	0.114													4	2	---	---	---	---	
CREB3L1	90993	broad.mit.edu	37	11	46300724	46300725	+	Intron	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46300724_46300725delCA	uc001ncf.2	+							NM_052854	NP_443086	Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like						response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L1(6)	soft_tissue(6)|ovary(2)	8				GBM - Glioblastoma multiforme(35;0.0285)		GTTCACACGCCACACACACACA	0.535			T	FUS	myxofibrosarcoma								6	3	---	---	---	---	
F2	2147	broad.mit.edu	37	11	46742602	46742602	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46742602delT	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497	P00734	THRB_HUMAN	coagulation factor II preproprotein						activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)	tgaattaatgttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56406625	56406625	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56406625delT								OR5M1 (25647 upstream) : OR5AP2 (2340 downstream)																							tcatatcttcttttttttttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	61938139	61938141	+	IGR	DEL	TTG	-	-	rs34672057		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61938139_61938141delTTG								INCENP (17504 upstream) : SCGB1D1 (19569 downstream)																							TGATGTGTACTTGTTGTTAACCA	0.493													3	3	---	---	---	---	
ASRGL1	80150	broad.mit.edu	37	11	62140935	62140935	+	Intron	DEL	T	-	-	rs112856978		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62140935delT	uc001nte.3	+						ASRGL1_uc001ntf.3_Intron|ASRGL1_uc001ntg.3_Intron|ASRGL1_uc001nth.1_Intron	NM_025080	NP_079356	Q7L266	ASGL1_HUMAN	asparaginase-like 1						asparagine catabolic process via L-aspartate|protein maturation	cytoplasm|microtubule cytoskeleton|nucleus	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	AATCTAGGTGTTTTTTTTTTC	0.378													3	4	---	---	---	---	
SCYL1	57410	broad.mit.edu	37	11	65304784	65304785	+	Intron	DEL	GC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65304784_65304785delGC	uc001oea.1	+						SCYL1_uc009yqk.2_Intron|SCYL1_uc001oeb.1_Intron|SCYL1_uc001oec.1_Intron|SCYL1_uc001oed.1_Intron|SCYL1_uc001oee.1_Intron	NM_020680	NP_065731	Q96KG9	NTKL_HUMAN	SCY1-like 1 isoform A						regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent	cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus	ATP binding|DNA binding|protein tyrosine kinase activity			skin(1)	1						TTCAACCCCAGCGGCCCCAGGG	0.634													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71262422	71262425	+	IGR	DEL	TAAC	-	-	rs149017437		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71262422_71262425delTAAC								KRTAP5-9 (1769 upstream) : KRTAP5-10 (14184 downstream)																							aaaactagattaactaactacatc	0.000													4	2	---	---	---	---	
PAAF1	80227	broad.mit.edu	37	11	73625741	73625742	+	Intron	DEL	TC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73625741_73625742delTC	uc001ouk.1	+						PAAF1_uc001oul.1_Intron|PAAF1_uc009ytx.1_Intron|PAAF1_uc001oum.1_Intron	NM_025155	NP_079431	Q9BRP4	PAAF1_HUMAN	proteasomal ATPase-associated factor 1						interspecies interaction between organisms	proteasome complex	protein binding			ovary(1)|skin(1)	2	Breast(11;7.42e-05)					AAATCCCAGttctttttttttt	0.208													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74034364	74034364	+	RNA	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74034364delA	uc001ova.2	+	5		c.992delA								Homo sapiens cDNA clone IMAGE:5270804.																		acctctagacaaaaaaaaacc	0.080													3	3	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	78443807	78443807	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78443807delT	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						TAGAAAGCAGTTTTTTTTTAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81895076	81895077	+	Intron	DEL	GT	-	-	rs11233032		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81895076_81895077delGT	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																		TCTGAAGTGGGTGTGTGTGTGT	0.347													4	2	---	---	---	---	
NAALAD2	10003	broad.mit.edu	37	11	89925063	89925063	+	3'UTR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89925063delT	uc001pdf.3	+	19					NAALAD2_uc009yvx.2_3'UTR|NAALAD2_uc009yvy.2_3'UTR	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				CTGCAAAGCCTTTTTTTTTTG	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101006502	101006502	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101006502delA	uc010rum.1	+											FJ515873																		taatatctgcaaaaaaaaccc	0.000													4	2	---	---	---	---	
ATM	472	broad.mit.edu	37	11	108100223	108100223	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108100223delT	uc001pkb.1	+						ATM_uc009yxr.1_Intron	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TATTAAAAGGTTTTTTTTTAG	0.114			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			4	2	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108679492	108679492	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108679492delA	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		gcccacctttaaaaaaaaaag	0.174			T	NUP98	AML*								4	2	---	---	---	---	
DIXDC1	85458	broad.mit.edu	37	11	111817764	111817765	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111817764_111817765insT	uc001pml.2	+						DIXDC1_uc001pmj.2_Intron|DIXDC1_uc001pmk.2_Intron	NM_001037954	NP_001033043	Q155Q3	DIXC1_HUMAN	DIX domain containing 1 isoform a						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytosol|focal adhesion	actin binding|gamma-tubulin binding|signal transducer activity			ovary(1)	1		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)		ACAAAATGCAGttttttttttc	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112591129	112591129	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112591129delG								PTS (450452 upstream) : NCAM1 (240866 downstream)																							TGCTTCCCCTGGGAAAATCCC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	113360072	113360073	+	IGR	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113360072_113360073delCA								DRD2 (13659 upstream) : TMPRSS5 (198196 downstream)																							TTACTCCAAGCACACACACACA	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119802624	119802624	+	IGR	DEL	A	-	-	rs35024480		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119802624delA								PVRL1 (203189 upstream) : TRIM29 (179371 downstream)																							gaaggagagcaagatagggag	0.005													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119884994	119884995	+	IGR	INS	-	T	T	rs141846231	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119884994_119884995insT								PVRL1 (285559 upstream) : TRIM29 (97000 downstream)																							CAGTTCTCAGCGCCCTTCCTGC	0.594													3	9	---	---	---	---	
ASAM	79827	broad.mit.edu	37	11	122971289	122971290	+	Intron	INS	-	CC	CC	rs139336115	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122971289_122971290insCC	uc001pyt.2	-							NM_024769	NP_079045	Q9H6B4	CLMP_HUMAN	adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		TCTTTCCCCAGGCGGCGCCTCC	0.520													2	4	---	---	---	---	
ASAM	79827	broad.mit.edu	37	11	123063686	123063686	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123063686delA	uc001pyt.2	-							NM_024769	NP_079045	Q9H6B4	CLMP_HUMAN	adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		ACAGGTGCTCAAAAAGTGCAA	0.448													4	2	---	---	---	---	
OR8B12	219858	broad.mit.edu	37	11	124416087	124416087	+	5'Flank	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124416087delA	uc010sam.1	-							NM_001005195	NP_001005195	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|skin(1)	3		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0213)		aaaaagaaagaaaaaaaaagg	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130635004	130635004	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130635004delT								ADAMTS15 (291289 upstream) : SNX19 (110763 downstream)																							TGGTTCCGGGTTTTTTTCTCT	0.443													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132340064	132340064	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132340064delA	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	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)		gaagggatgcaaaaatggaag	0.000													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132856000	132856000	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132856000delT	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)		gcatcagctctgaaaactttt	0.000													4	2	---	---	---	---	
ACAD8	27034	broad.mit.edu	37	11	134126723	134126723	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134126723delT	uc001qhk.2	+						ACAD8_uc009zdc.2_Intron|ACAD8_uc010sco.1_Intron|ACAD8_uc010scp.1_Intron|ACAD8_uc010scq.1_Intron|ACAD8_uc001qhl.2_Intron|ACAD8_uc010scr.1_Intron|ACAD8_uc009zde.1_5'Flank	NM_014384	NP_055199	Q9UKU7	ACAD8_HUMAN	acyl-Coenzyme A dehydrogenase family, member 8						branched chain family amino acid catabolic process|lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding				0	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)		TGTACATAACTTTTTTTTTGT	0.328													8	4	---	---	---	---	
RASSF8	11228	broad.mit.edu	37	12	26173458	26173458	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26173458delT	uc001rgx.2	+						RASSF8_uc001rgy.2_Intron|RASSF8_uc001rgz.2_Intron|RASSF8_uc009zjd.1_Intron|RASSF8_uc001rgw.1_Intron	NM_007211	NP_009142	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family						signal transduction						0	Colorectal(261;0.0847)					AGATTGAAACTTTTTTTTTAA	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30159871	30159871	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30159871delA								TMTC1 (222179 upstream) : IPO8 (622052 downstream)																							caggttcaataaaaattacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30748794	30748794	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30748794delA								TMTC1 (811102 upstream) : IPO8 (33129 downstream)																							actcatcaggaaaatgcaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	40868879	40868880	+	IGR	INS	-	A	A	rs145938364	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40868879_40868880insA								LRRK2 (105795 upstream) : CNTN1 (217478 downstream)																							GAGCCTGAACCATTGTTGTTGA	0.485													1	5	---	---	---	---	
SLC4A8	9498	broad.mit.edu	37	12	51845570	51845570	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51845570delA	uc001rys.1	+						SLC4A8_uc010sni.1_Intron|SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc001ryp.1_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryq.3_Intron|SLC4A8_uc001ryr.2_Intron|SLC4A8_uc010snk.1_Intron	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)		AAGCAAATGTAAAAAAAAAAA	0.294													4	3	---	---	---	---	
ATF7	11016	broad.mit.edu	37	12	53955221	53955221	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53955221delT	uc001sdy.2	-						ATF7_uc010sok.1_Intron|ATF7_uc001sdz.2_Intron|ATF7_uc010sol.1_Intron|ATF7_uc001sea.3_Intron|ATF7_uc001seb.3_Intron	NM_001130059	NP_001123531	P17544	ATF7_HUMAN	activating transcription factor 7 isoform 1						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2						ATAACTGATCTTTTTTTTGAA	0.333													4	2	---	---	---	---	
USP15	9958	broad.mit.edu	37	12	62749542	62749542	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62749542delA	uc001src.1	+						USP15_uc001srb.1_Intron	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15						protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AAAGGGAGGGAAAAAAAAGCA	0.274													4	2	---	---	---	---	
RPSAP52	204010	broad.mit.edu	37	12	66215958	66215958	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66215958delA	uc001sso.2	-						HMGA2_uc001ssw.1_5'Flank|HMGA2_uc001ssx.2_5'Flank|HMGA2_uc001ssp.1_5'Flank|HMGA2_uc010ssv.1_5'Flank|HMGA2_uc001sss.1_5'Flank|HMGA2_uc001sst.1_5'Flank|HMGA2_uc001ssu.1_5'Flank|HMGA2_uc001ssv.2_5'Flank	NR_026825				SubName: Full=Putative uncharacterized protein RPSAP52;												0						ATGTAAATGTAAAAAAAAAAT	0.279													4	2	---	---	---	---	
CPM	1368	broad.mit.edu	37	12	69252514	69252514	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69252514delT	uc001sup.2	-						CPM_uc001sur.2_Intron|CPM_uc001suq.2_Intron	NM_198320	NP_938079	P14384	CBPM_HUMAN	carboxypeptidase M precursor						anatomical structure morphogenesis|proteolysis	anchored to membrane|cytoplasm|nucleus|plasma membrane	metallocarboxypeptidase activity|zinc ion binding				0	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			ATTTTTGTGGTTTTTTTTTTT	0.323													6	3	---	---	---	---	
RAB3IP	117177	broad.mit.edu	37	12	70133945	70133945	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70133945delT	uc001svp.2	+						uc001svj.1_5'Flank|uc001svk.2_5'Flank|RAB3IP_uc001svl.1_Intron|RAB3IP_uc001svm.2_Intron|RAB3IP_uc001svn.2_Intron|RAB3IP_uc001svo.2_Intron|RAB3IP_uc001svq.2_Intron|RAB3IP_uc001svr.2_Intron|RAB3IP_uc001svs.2_Intron	NM_175623	NP_783322	Q96QF0	RAB3I_HUMAN	RAB3A interacting protein isoform alpha 2						cilium assembly|Golgi to plasma membrane transport|protein localization to organelle|protein transport	actin cortical patch|centrosome|cytosol|lamellipodium|microtubule basal body|nucleus	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			TTCATGAAGGTTTTTTTTTCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	71358170	71358171	+	IGR	DEL	CA	-	-	rs34922502		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71358170_71358171delCA								PTPRR (43586 upstream) : TSPAN8 (160706 downstream)																							CAGGAATGTGCATGGCAAGTAG	0.416													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77358209	77358209	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77358209delT								CSRP2 (85410 upstream) : E2F7 (56818 downstream)																							CCTGATTACATTTAGGAGAAT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82340953	82340956	+	IGR	DEL	CACA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82340953_82340956delCACA								PPFIA2 (187844 upstream) : CCDC59 (405134 downstream)																							CCCAAACCAGCACACACACACACA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	87236460	87236460	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87236460delA								MGAT4C (3779 upstream) : None (None downstream)																							gcagaaatataaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	87514274	87514275	+	IGR	DEL	TC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87514274_87514275delTC								MGAT4C (281593 upstream) : C12orf50 (859541 downstream)																							tcttatcagatctctctctctt	0.010													4	2	---	---	---	---	
CRADD	8738	broad.mit.edu	37	12	94227598	94227599	+	Intron	INS	-	T	T	rs146026428	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94227598_94227599insT	uc001tda.2	+						CRADD_uc010sur.1_Intron|CRADD_uc010sus.1_Intron	NM_003805	NP_003796	P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1						TTCATTTTGTGTTTTTTTTTCC	0.059													3	3	---	---	---	---	
NEDD1	121441	broad.mit.edu	37	12	97338264	97338265	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97338264_97338265insT	uc001teu.3	+						NEDD1_uc001tev.3_Intron|NEDD1_uc010svc.1_Intron|NEDD1_uc001tew.2_Intron|NEDD1_uc001tex.2_Intron	NM_152905	NP_690869	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally						cell division|G2/M transition of mitotic cell cycle|mitosis	cytosol					0						CTCCAGttctctttttcttttt	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	98420113	98420114	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98420113_98420114insT								RMST (461320 upstream) : LOC100128191 (486639 downstream)																							TGGCACTAGTGTTTTTTTTTTT	0.317													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	100094294	100094294	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100094294delT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		cgagcacgaattttttttcct	0.000													4	2	---	---	---	---	
ANO4	121601	broad.mit.edu	37	12	101299230	101299230	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101299230delA	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron|ANO4_uc001thx.2_Intron	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						aaagtttatcaagaagagaag	0.000										HNSCC(74;0.22)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	104500978	104500978	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104500978delC								HCFC2 (682 upstream) : NFYB (9880 downstream)																							gtctatggttcccttttttac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112760182	112760182	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112760182delA								C12orf51 (16144 upstream) : RPL6 (82813 downstream)																							ctcaaaaaagaaaaaaaaaag	0.144													3	3	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117996846	117996847	+	Intron	INS	-	GGAT	GGAT	rs71444628		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117996846_117996847insGGAT	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					gatggatggaaggatggatgga	0.074													4	2	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119497716	119497716	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119497716delT	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						GCAGAGTCCCTTCATGTTGGA	0.453													4	2	---	---	---	---	
CCDC60	160777	broad.mit.edu	37	12	119913953	119913954	+	Intron	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119913953_119913954insA	uc001txe.2	+						uc001txf.2_Intron	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		ACTATGCAGGGAAAAAAAAATC	0.386													4	2	---	---	---	---	
GCN1L1	10985	broad.mit.edu	37	12	120576813	120576814	+	Intron	INS	-	A	A	rs141247337	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120576813_120576814insA	uc001txo.2	-							NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TACTGTGAAATAAAAAAAAGGA	0.262													4	5	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124835399	124835400	+	Intron	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124835399_124835400delCA	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		CACGCGTGTCCACACACACACT	0.436													4	3	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	129069138	129069138	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129069138delC	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						TAACAGGCATCCCCAACGTGC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	20934442	20934442	+	IGR	DEL	T	-	-	rs142098283		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20934442delT								GJB6 (127908 upstream) : CRYL1 (43367 downstream)																							gatttgagtgttttttttttt	0.000													4	3	---	---	---	---	
ATP8A2	51761	broad.mit.edu	37	13	25991304	25991305	+	Intron	INS	-	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25991304_25991305insC	uc001uqk.2	+							NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		GTCCCCAGTTTCCCATTAATTC	0.406													4	2	---	---	---	---	
FLT3	2322	broad.mit.edu	37	13	28577937	28577937	+	3'UTR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28577937delA	uc001urw.2	-	24					FLT3_uc010aao.2_RNA|FLT3_uc010tdn.1_3'UTR	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)	CCAGCCTGAGAAGGCCTTGGA	0.363			Mis|O		AML|ALL								4	2	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33334087	33334088	+	Intron	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33334087_33334088insA	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)		AATATCAAGATAAAAAAAATCT	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	34299767	34299767	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34299767delG								STARD13 (48835 upstream) : RFC3 (92439 downstream)																							GTGCCTACCTGGAGCAGAATG	0.433													4	2	---	---	---	---	
KIAA0564	23078	broad.mit.edu	37	13	42179719	42179719	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42179719delA	uc001uyj.2	-							NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		agtgagttggaaaaaaatgtg	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	43720815	43720816	+	IGR	INS	-	G	G	rs151149404	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43720815_43720816insG								DNAJC15 (37511 upstream) : ENOX1 (66864 downstream)																							ATGTAAATCGTGAAAAAGATGA	0.282													4	7	---	---	---	---	
FAM194B	220081	broad.mit.edu	37	13	46160068	46160068	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46160068delC	uc001val.2	-						FAM194B_uc001vam.1_Intron	NM_182542	NP_872348	Q5W0A0	F194B_HUMAN	hypothetical protein LOC220081											central_nervous_system(1)	1						CTGTTGCATACCCCAGCCTTT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	47618678	47618678	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47618678delT								HTR2A (147628 upstream) : SUCLA2 (898114 downstream)																							ATCTTACAACTTTTTTTTTTT	0.383													4	2	---	---	---	---	
GUCY1B2	2974	broad.mit.edu	37	13	51570722	51570722	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51570722delC	uc001vfc.3	-							NR_003923				Homo sapiens soluble guanylyl cyclase subunit beta 2 (GUCY1B2) mRNA, complete cds.												0						TCATCTGCCTCCACATCCATC	0.428													4	2	---	---	---	---	
LMO7	4008	broad.mit.edu	37	13	76430509	76430509	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76430509delT	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjx.1_5'Flank	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TCTTTCGGCCTTTTTTTTTCT	0.403													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	80615353	80615353	+	IGR	DEL	T	-	-	rs112080979		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80615353delT								NDFIP2 (485148 upstream) : SPRY2 (294761 downstream)																							TAGGCAACGATTTTTTTTTAT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	85636499	85636500	+	IGR	INS	-	C	C	rs141016397	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85636499_85636500insC								None (None upstream) : SLITRK6 (730422 downstream)																							agggtgatcagccccatctaga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	89739885	89739885	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89739885delT								None (None upstream) : None (None downstream)																							ctcctccaacttttttttgaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	98157600	98157600	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98157600delC								RAP2A (37349 upstream) : IPO5 (448329 downstream)																							tcctgttcatcccctttccta	0.154													4	2	---	---	---	---	
STK24	8428	broad.mit.edu	37	13	99232010	99232010	+	5'Flank	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99232010delT	uc001vnn.1	-						STK24_uc010tim.1_5'Flank	NM_001032296	NP_001027467	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24 isoform b						cellular component disassembly involved in apoptosis|signal transduction	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CATTCACACCTTTTTTGAATA	0.433													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102743810	102743811	+	Intron	DEL	CC	-	-	rs35844908		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102743810_102743811delCC	uc001vpf.2	-							NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B						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)					gcttcagtcaccccccaccaac	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	104908519	104908519	+	IGR	DEL	T	-	-	rs111307004		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104908519delT								None (None upstream) : None (None downstream)																							AAAAATAAGGTTTTTTTTTTT	0.368													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107532991	107532991	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107532991delT								ARGLU1 (312477 upstream) : FAM155A (287889 downstream)																							TTCCTCTTAATTTTTTTTCTT	0.363													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	107861058	107861058	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107861058delA	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						GTCCCACAAGAAAAAAAAAAT	0.348													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	110323173	110323174	+	IGR	INS	-	G	G	rs141455995	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110323173_110323174insG								MYO16 (462818 upstream) : IRS2 (83012 downstream)																							AAGAGTCTTCAGGGCCACCAAG	0.446													4	3	---	---	---	---	
RASA3	22821	broad.mit.edu	37	13	114754134	114754134	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114754134delA	uc001vui.2	-						RASA3_uc010tkk.1_Intron|RASA3_uc001vuj.2_Intron	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			ctgtccatccatccatcactc	0.045													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19795889	19795890	+	IGR	DEL	TC	-	-	rs150326417		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19795889_19795890delTC								POTEG (210947 upstream) : P704P (188064 downstream)																							attgcaattttctctctctcaa	0.000													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	28309075	28309076	+	IGR	INS	-	TC	TC	rs137951977	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28309075_28309076insTC								None (None upstream) : FOXG1 (927211 downstream)																							gtctcaggtgttgttacagcaa	0.099													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	32500890	32500890	+	IGR	DEL	A	-	-	rs35799151		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32500890delA								NUBPL (170473 upstream) : C14orf128 (43736 downstream)																							ATGGGAAATGAAAAAAAAAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	38428662	38428663	+	Intron	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38428662_38428663delCA	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																		GAATGTTGTTCACAAATTGCTG	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	46801848	46801848	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46801848delA								None (None upstream) : RPL10L (318374 downstream)																							agaatgatacaaaaaaagaaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49673609	49673609	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49673609delA								None (None upstream) : SDCCAG1 (359418 downstream)																							TTTTGGAGTCAAAAAAAAAAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	55920398	55920398	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55920398delA								TBPL2 (13135 upstream) : C14orf33 (104292 downstream)																							GGTCTTGGGGAAAAAAAAAGA	0.254													4	2	---	---	---	---	
ZFYVE26	23503	broad.mit.edu	37	14	68222413	68222413	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68222413delT	uc001xka.2	-						ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkb.2_Intron	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26						cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CATTTATTTCTTTTTTTTACC	0.333													3	3	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	68953822	68953823	+	Intron	DEL	CT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68953822_68953823delCT	uc001xkf.1	+						RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193	O15315	RA51B_HUMAN	RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		tattcgtctgctcaggctgcat	0.228			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
PCNX	22990	broad.mit.edu	37	14	71518935	71518935	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71518935delT	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		ctttctttccttttttttttt	0.085													3	3	---	---	---	---	
SIPA1L1	26037	broad.mit.edu	37	14	72153951	72153951	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72153951delC	uc001xms.2	+						SIPA1L1_uc001xmt.2_Intron|SIPA1L1_uc001xmu.2_Intron|SIPA1L1_uc001xmv.2_Intron|SIPA1L1_uc010ttm.1_Intron	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AGTTTCCTCTCCCATAGTGGC	0.388													4	2	---	---	---	---	
RGS6	9628	broad.mit.edu	37	14	72855662	72855664	+	Intron	DEL	TAG	-	-	rs34503088		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72855662_72855664delTAG	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287	P49758	RGS6_HUMAN	regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		TTCCCATTATTAGTAGTAGTAGT	0.241													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	75681165	75681166	+	IGR	INS	-	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75681165_75681166insG								TMED10 (37816 upstream) : FOS (64315 downstream)																							aggtggaaaaaggctaggacca	0.000													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	78649188	78649189	+	Intron	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78649188_78649189insA	uc001xum.1	+									Q9Y4C0	NRX3A_HUMAN	Homo sapiens mRNA for KIAA0743 protein, partial cds.						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		ttgcaggtgagaaaaaaaaagt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	80786337	80786337	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80786337delA	uc001xuw.1	+											Homo sapiens, clone IMAGE:5167652, mRNA.																		atccagtgagaaaaaaaaatt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	83782235	83782236	+	IGR	INS	-	CTGT	CTGT	rs138512427	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83782235_83782236insCTGT								None (None upstream) : None (None downstream)																							atgatcttctcctgttgtctgc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	83818180	83818181	+	IGR	DEL	TC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83818180_83818181delTC								None (None upstream) : None (None downstream)																							tttgtgtgtttctctctctctc	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88179928	88179929	+	IGR	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88179928_88179929delCA								None (None upstream) : GALC (124235 downstream)																							GCTGGGGGTGCACAGTGTCAAT	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88630504	88630505	+	5'Flank	DEL	CT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88630504_88630505delCT	uc001xwl.2	+											DQ574857																		actgtcttacctctctctctga	0.054													4	2	---	---	---	---	
ZC3H14	79882	broad.mit.edu	37	14	89055340	89055340	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89055340delT	uc001xww.2	+						ZC3H14_uc010twd.1_Intron|ZC3H14_uc010twe.1_Intron|ZC3H14_uc001xwx.2_Intron|ZC3H14_uc010twf.1_Intron|ZC3H14_uc001xwy.2_Intron|ZC3H14_uc010twg.1_Intron|ZC3H14_uc001xxa.2_Intron	NM_024824	NP_079100	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14 isoform 1							cytoplasm|cytoplasm|nuclear speck	protein binding|RNA binding|zinc ion binding			ovary(2)|skin(1)	3						attaaagggattttttttttc	0.129													3	4	---	---	---	---	
C14orf159	80017	broad.mit.edu	37	14	91603314	91603314	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91603314delA	uc001xzb.2	+						C14orf159_uc010atu.1_Intron|C14orf159_uc010atv.1_Intron|C14orf159_uc001xyy.2_Intron|C14orf159_uc001xyx.2_Intron|C14orf159_uc001xyw.2_Intron|C14orf159_uc001xzc.2_Intron|C14orf159_uc001xza.2_Intron|C14orf159_uc001xyv.2_Intron|C14orf159_uc001xyz.2_Intron|C14orf159_uc010twj.1_Intron|C14orf159_uc001xze.2_Intron	NM_001102366	NP_001095836	Q7Z3D6	CN159_HUMAN	hypothetical protein LOC80017 isoform a							mitochondrion				central_nervous_system(2)|ovary(1)	3		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		actttgtctcaaaaaaaaaaa	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	94348014	94348014	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94348014delA								PRIMA1 (93248 upstream) : C14orf86 (23062 downstream)																							gctgtttcttaaaaaaattct	0.194													4	2	---	---	---	---	
SERPINA9	327657	broad.mit.edu	37	14	94938077	94938078	+	Intron	INS	-	CAAGA	CAAGA	rs142274377	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94938077_94938078insCAAGA	uc001ydf.2	-						SERPINA9_uc001yde.2_Intron|SERPINA9_uc010avc.2_Intron|SERPINA9_uc001ydg.2_Intron|SERPINA9_uc001ydh.1_Intron|SERPINA9_uc001ydi.1_Intron	NM_175739	NP_783866	Q86WD7	SPA9_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytoplasm|extracellular region|membrane	serine-type endopeptidase inhibitor activity			lung(1)|central_nervous_system(1)	2		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TGCCCCATCTCTCCCTTTCTCC	0.545													4	2	---	---	---	---	
SERPINA9	327657	broad.mit.edu	37	14	94938078	94938079	+	Intron	INS	-	GC	GC			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94938078_94938079insGC	uc001ydf.2	-						SERPINA9_uc001yde.2_Intron|SERPINA9_uc010avc.2_Intron|SERPINA9_uc001ydg.2_Intron|SERPINA9_uc001ydh.1_Intron|SERPINA9_uc001ydi.1_Intron	NM_175739	NP_783866	Q86WD7	SPA9_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytoplasm|extracellular region|membrane	serine-type endopeptidase inhibitor activity			lung(1)|central_nervous_system(1)	2		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		GCCCCATCTCTCCCTTTCTCCA	0.545													4	2	---	---	---	---	
BDKRB2	624	broad.mit.edu	37	14	96694033	96694034	+	Intron	DEL	CA	-	-	rs75828958	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96694033_96694034delCA	uc010avm.1	+						BDKRB2_uc010avl.1_Intron|BDKRB2_uc010twu.1_Intron|BDKRB2_uc001yfg.2_Intron	NM_000623	NP_000614	P30411	BKRB2_HUMAN	bradykinin receptor B2						arachidonic acid secretion|elevation of cytosolic calcium ion concentration|transmembrane receptor protein tyrosine kinase signaling pathway	endosome|integral to plasma membrane	bradykinin receptor activity|phosphatidylinositol phospholipase C activity|protease binding|protein heterodimerization activity|type 1 angiotensin receptor binding			ovary(3)|breast(1)|kidney(1)	5		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)		cacacacatgcacacacacaca	0.208													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97849694	97849695	+	IGR	INS	-	G	G			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97849694_97849695insG								VRK1 (501744 upstream) : C14orf64 (542252 downstream)																							TGCAGCTGGATGGGGTGCGGTA	0.431													4	2	---	---	---	---	
EML1	2009	broad.mit.edu	37	14	100314280	100314280	+	Intron	DEL	A	-	-	rs35039142		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100314280delA	uc001ygs.2	+						EML1_uc010avt.1_Intron|EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	NM_004434	NP_004425	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)				ttgcttttttaaaaaaaaaat	0.000													4	2	---	---	---	---	
AMN	81693	broad.mit.edu	37	14	103396005	103396005	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103396005delG	uc001ymg.3	+	8	807	c.774delG	c.(772-774)TTGfs	p.L258fs	AMN_uc001ymh.3_Frame_Shift_Del_p.L204fs	NM_030943	NP_112205	Q9BXJ7	AMNLS_HUMAN	amnionless protein precursor	258	Extracellular (Potential).				lipid metabolic process|lipoprotein metabolic process|multicellular organismal development	integral to membrane|plasma membrane					0				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCGTTGTGTTGCTGACCCACG	0.701													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106643112	106643113	+	Intron	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106643112_106643113delAC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						acacacacaaacacacacacac	0.381													4	2	---	---	---	---	
APBA2	321	broad.mit.edu	37	15	29351419	29351420	+	Intron	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29351419_29351420delTG	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		tttgttgatatgtgtgtgtgtg	0.000													2	4	---	---	---	---	
CHRFAM7A	89832	broad.mit.edu	37	15	30668188	30668188	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30668188delG	uc001zdt.1	-						CHRFAM7A_uc001zdu.1_Intron|CHRFAM7A_uc010azn.2_Intron|CHRFAM7A_uc001zdv.2_5'Flank	NM_139320	NP_647536	Q494W8	CRFM7_HUMAN	CHRNA7-FAM7A fusion isoform 1							integral to membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity			skin(1)	1		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		gttgagtcgtgggtggtatgt	0.000													4	2	---	---	---	---	
FMN1	342184	broad.mit.edu	37	15	33200379	33200379	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33200379delT	uc001zhf.3	-							NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GAACAATGCCTTCTTCCTTCC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37136992	37136992	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37136992delA								CSNK1A1P (26285 upstream) : LOC145845 (19652 downstream)																							CATATCACCCAAAAAAAAGTG	0.388													4	2	---	---	---	---	
FRMD5	84978	broad.mit.edu	37	15	44384929	44384929	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44384929delC	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		GACTTCTGCACCCAGAATCCT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46151513	46151513	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46151513delT								SQRDL (168035 upstream) : None (None downstream)																							ATCACATTGCTTTtttttgtt	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	53246688	53246688	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53246688delT								ONECUT1 (164479 upstream) : WDR72 (559250 downstream)																							ACCTCTTGTCTTTTTTTTTTT	0.413													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	54116869	54116869	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54116869delT								WDR72 (65010 upstream) : UNC13C (188232 downstream)																							gtcctgaaaatttttcctcta	0.000													4	2	---	---	---	---	
PIGB	9488	broad.mit.edu	37	15	55612211	55612211	+	Intron	DEL	T	-	-	rs77286116		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55612211delT	uc002act.2	+						uc002acs.2_5'Flank|PIGB_uc010ugg.1_Intron	NM_004855	NP_004846	Q92521	PIGB_HUMAN	phosphatidylinositol glycan, class B						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity				0				all cancers(107;0.0255)		TAACCCACTCttttttttttg	0.333													9	4	---	---	---	---	
FAM63B	54629	broad.mit.edu	37	15	59082785	59082785	+	Intron	DEL	A	-	-	rs113082743		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59082785delA	uc002afj.2	+						FAM63B_uc002afi.2_Intron|FAM63B_uc002afk.2_Intron|FAM63B_uc002afl.2_Intron	NM_001040450	NP_001035540	Q8NBR6	FA63B_HUMAN	hypothetical protein LOC54629 isoform a											central_nervous_system(1)	1						aatagaccttagtggggggta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63697652	63697652	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63697652delA								CA12 (23577 upstream) : USP3 (99158 downstream)																							TCATCCTTCTAAAAAAACTAA	0.478													4	2	---	---	---	---	
ZNF609	23060	broad.mit.edu	37	15	64949812	64949812	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64949812delA	uc002ann.2	+							NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609							nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						actccgtctcaaaaaaaaaCA	0.095													3	3	---	---	---	---	
RPL4	6124	broad.mit.edu	37	15	66796912	66796912	+	Intron	DEL	C	-	-	rs139436991	byFrequency	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66796912delC	uc002apv.2	-						RPL4_uc010bhr.2_Intron|RPL4_uc002apw.2_Intron|RPL4_uc002apx.2_Intron|RPL4_uc010ujq.1_Intron|SNORD18B_uc002apy.1_5'Flank|SNORD16_uc010bht.2_5'Flank|SNORD18A_uc002apz.1_5'Flank|ZWILCH_uc010bhu.1_5'Flank|ZWILCH_uc002aqb.2_5'Flank|ZWILCH_uc002aqa.2_5'Flank|ZWILCH_uc010bhv.2_5'Flank	NM_000968	NP_000959	P36578	RL4_HUMAN	ribosomal protein L4						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0						TCCACTACTGCTTCCCGGCGC	0.532													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70769954	70769954	+	IGR	DEL	A	-	-	rs36089300		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70769954delA								TLE3 (379698 upstream) : UACA (176941 downstream)																							ACTCCTGGGGAAGGGCAGCAT	0.388													2	5	---	---	---	---	
CT62	196993	broad.mit.edu	37	15	71406262	71406263	+	Intron	INS	-	T	T	rs34068489		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71406262_71406263insT	uc002ata.2	-							NM_001102658	NP_001096128	P0C5K7	CT62_HUMAN	cancer/testis antigen 62												0						agttgcgcaGGTTTTTTTTTTT	0.183													3	3	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	76913821	76913822	+	Intron	INS	-	CC	CC			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76913821_76913822insCC	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						atgagacagttctttgtgaggg	0.139													4	2	---	---	---	---	
PSTPIP1	9051	broad.mit.edu	37	15	77289235	77289236	+	Intron	DEL	CT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77289235_77289236delCT	uc002bcf.2	+						PSTPIP1_uc010bkt.1_Intron|PSTPIP1_uc010umo.1_Intron|PSTPIP1_uc010bku.1_Intron|PSTPIP1_uc002bcg.2_Intron|PSTPIP1_uc010bkv.1_Intron|PSTPIP1_uc010bkw.1_Intron	NM_003978	NP_003969	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting						cell adhesion|signal transduction	cleavage furrow|lamellipodium|perinuclear region of cytoplasm	catalytic activity			ovary(1)	1						GAGTCACCACCTAGCTGCCCTG	0.649													4	2	---	---	---	---	
HMG20A	10363	broad.mit.edu	37	15	77745079	77745079	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77745079delA	uc002bcr.2	+						HMG20A_uc002bcq.1_Intron|HMG20A_uc002bcs.2_Intron	NM_018200	NP_060670	Q9NP66	HM20A_HUMAN	high-mobility group 20A						chromatin modification	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						gcaaccaaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	86528741	86528742	+	IGR	DEL	CT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86528741_86528742delCT								KLHL25 (190552 upstream) : AGBL1 (156500 downstream)																							tctaatccccctctcagtgagg	0.000													4	2	---	---	---	---	
MCTP2	55784	broad.mit.edu	37	15	94927566	94927566	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94927566delG	uc002btj.2	+						MCTP2_uc002bti.2_Intron|MCTP2_uc010boj.2_Intron|MCTP2_uc010bok.2_Intron|MCTP2_uc002btk.3_Intron|MCTP2_uc002btl.2_Intron	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			GGAGGCATTTGTAAAGTAGAT	0.333													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7471998	7471998	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7471998delA	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|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.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)		AAAATAGAATAAAAACCCTCA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18083434	18083435	+	IGR	DEL	AC	-	-	rs10582421		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18083434_18083435delAC								XYLT1 (518696 upstream) : NOMO2 (427748 downstream)																							CACCTGTGGTACACACACACAC	0.277													4	2	---	---	---	---	
ARHGAP17	55114	broad.mit.edu	37	16	24953719	24953719	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24953719delA	uc002dnb.2	-						ARHGAP17_uc002dmz.2_5'Flank|ARHGAP17_uc002dna.2_Intron|ARHGAP17_uc002dnc.2_Intron|ARHGAP17_uc010vcf.1_Intron	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)		TCTTTTGTGGAAAAAAAATAA	0.318													4	2	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	27986833	27986834	+	Intron	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27986833_27986834delAC	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						CTTGTTTAGTACACGTGTCCTC	0.460													4	2	---	---	---	---	
BOLA2	552900	broad.mit.edu	37	16	29729110	29729110	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29729110delA	uc010bzb.1	-						uc002dtf.2_Intron			Q9H3K6	BOLA2_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0						agcttggaagaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32418182	32418182	+	IGR	DEL	G	-	-	rs150828843		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32418182delG								HERC2P4 (254308 upstream) : TP53TG3B (266659 downstream)																							gtctcaaaaaGTTTTTTTTAC	0.010													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32841066	32841066	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32841066delC								TP53TG3B (152188 upstream) : SLC6A10P (47731 downstream)																							ttaatttgggctaatcaatat	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33056620	33056621	+	IGR	INS	-	T	T	rs71247544		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33056620_33056621insT								SLC6A10P (160157 upstream) : MIR1826 (908887 downstream)																							accatgcccACtttttttttta	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54727202	54727202	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54727202delG								IRX3 (406824 upstream) : IRX5 (237909 downstream)																							aacctgcactggacacagaac	0.000													4	2	---	---	---	---	
CCDC135	84229	broad.mit.edu	37	16	57748547	57748548	+	Intron	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57748547_57748548delCA	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						CTCTCTCTGTCACACACACACA	0.252													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64265549	64265549	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64265549delA								None (None upstream) : CDH11 (715136 downstream)																							TATTTTCAGGAAAAAAAAAAT	0.254													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64762587	64762588	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64762587_64762588insT								None (None upstream) : CDH11 (218097 downstream)																							AAAGTGATACATTTTTTTTTTA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65699866	65699867	+	IGR	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65699866_65699867insA								LOC283867 (89663 upstream) : CDH5 (700658 downstream)																							TTTGTCCATATGGGCTGCTGGT	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	65925662	65925662	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65925662delG								LOC283867 (315459 upstream) : CDH5 (474863 downstream)																							tatcctgtttgggattcactc	0.000													4	2	---	---	---	---	
BEAN	146227	broad.mit.edu	37	16	66493219	66493219	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66493219delT	uc002eoq.2	+						BEAN_uc002eop.1_Intron	NM_001136106	NP_001129578	Q3B7T3	BEAN1_HUMAN	brain expressed, associated with Nedd4						cell death	integral to membrane					0						TCTCtttctctttttttttct	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66922813	66922813	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66922813delA								PDP2 (958 upstream) : CDH16 (19213 downstream)																							TCTAGTTAGTAATATTGAGAA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72756559	72756560	+	Intron	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72756559_72756560delAC	uc002fcj.1	+											Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100.																		TAACACATAGACACACACACCC	0.490													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	79031782	79031782	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79031782delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		ACAttctttctttttttttta	0.214													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85299286	85299286	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85299286delT								FAM92B (153172 upstream) : KIAA0182 (345743 downstream)																							AGACCATGTGTTTGGGGCAGG	0.343													4	3	---	---	---	---	
RPH3AL	9501	broad.mit.edu	37	17	95270	95271	+	Intron	DEL	GT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:95270_95271delGT	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		gtggatgtgagtgtgtgtgtat	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6994000	6994000	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6994000delA								CLEC10A (10400 upstream) : ASGR2 (10641 downstream)																							gaacagagagaaaaaaaaaat	0.000													3	3	---	---	---	---	
ASGR2	433	broad.mit.edu	37	17	7010880	7010881	+	Intron	DEL	AT	-	-	rs143843681		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7010880_7010881delAT	uc002gep.3	-						ASGR2_uc010vtk.1_Intron|ASGR2_uc002gem.1_Intron|ASGR2_uc002gen.1_Intron|ASGR2_uc002geo.1_Intron|ASGR2_uc002ger.3_Intron|ASGR2_uc002geq.3_Intron	NM_001181	NP_001172	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2 isoform a						cell surface receptor linked signaling pathway|endocytosis	focal adhesion|integral to membrane|nucleolus	asialoglycoprotein receptor activity|protein binding|sugar binding			ovary(1)	1					Antihemophilic Factor(DB00025)	gtacacacacatataccatacc	0.025													4	4	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	9968072	9968072	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9968072delT	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						gctgacactgtttgtttaagc	0.000			T	MLL	AML*								4	2	---	---	---	---	
HS3ST3A1	9955	broad.mit.edu	37	17	13479801	13479801	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13479801delT	uc002gob.1	-							NM_006042	NP_006033	Q9Y663	HS3SA_HUMAN	heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity			ovary(1)|central_nervous_system(1)	2		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		aagcacaatattttaacaagc	0.000													4	2	---	---	---	---	
CCDC144A	9720	broad.mit.edu	37	17	16658141	16658141	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16658141delG	uc002gqk.1	+						CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A												0						gtcagactatggagtccccat	0.000													4	2	---	---	---	---	
FAM83G	644815	broad.mit.edu	37	17	18898375	18898376	+	Intron	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18898375_18898376insA	uc002guw.2	-						SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815											ovary(1)|central_nervous_system(1)	2						atttaaaggagaaaacaaaaca	0.000													4	2	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	19969166	19969167	+	Intron	DEL	AG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19969166_19969167delAG	uc002gwq.2	+							NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						ggagaagttcagagagagagag	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21553270	21553270	+	IGR	DEL	G	-	-	rs112545936		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21553270delG								C17orf51 (75539 upstream) : FAM27L (272100 downstream)																							TTTATGTTCTGGGGGTCTCCA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25296374	25296374	+	IGR	DEL	C	-	-	rs145918287	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25296374delC								None (None upstream) : WSB1 (324732 downstream)																							GGTTGCATTGCCAGTGCCCAC	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25304671	25304671	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25304671delA								None (None upstream) : WSB1 (316435 downstream)																							TCTTGTAGGTAAGGGTAAATA	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25326814	25326815	+	IGR	INS	-	A	A	rs77693118		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25326814_25326815insA								None (None upstream) : WSB1 (294291 downstream)																							CTATATGGATCGCTTCCTCACA	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25326817	25326817	+	IGR	DEL	T	-	-	rs66857954		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25326817delT								None (None upstream) : WSB1 (294289 downstream)																							TATGGATCGCTTCCTCACATT	0.363													4	2	---	---	---	---	
KSR1	8844	broad.mit.edu	37	17	25938896	25938896	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25938896delT	uc010crg.2	+						KSR1_uc002gzm.2_Intron|KSR1_uc002gzn.2_Intron	NM_014238	NP_055053	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras						Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CCTTTCAGTCTTTTTTTTTTC	0.328													4	3	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31785758	31785758	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31785758delA	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)	tcagaatcctaatctattaat	0.114													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32085190	32085191	+	Intron	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32085190_32085191delTG	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)	ttttcttaaatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35152698	35152698	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35152698delA								MRM1 (187292 upstream) : LHX1 (141801 downstream)																							gcaactttgtatccattaaac	0.000													4	3	---	---	---	---	
CCR10	2826	broad.mit.edu	37	17	40831511	40831511	+	3'UTR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40831511delC	uc002iax.3	-	2					PLEKHH3_uc002iau.2_5'Flank|PLEKHH3_uc002iav.2_5'Flank|PLEKHH3_uc010cym.1_5'Flank|PLEKHH3_uc002iaw.2_5'Flank	NM_016602	NP_057686	P46092	CCR10_HUMAN	CC chemokine receptor 10							integral to plasma membrane					0		Breast(137;0.000153)		BRCA - Breast invasive adenocarcinoma(366;0.14)		TCTCAGTGTTCCCCCACCTAC	0.537													4	2	---	---	---	---	
NBR1	4077	broad.mit.edu	37	17	41348222	41348223	+	Intron	INS	-	A	A	rs35166890		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41348222_41348223insA	uc010czd.2	+						NBR1_uc010diz.2_Intron|NBR1_uc010whu.1_Intron|NBR1_uc010whv.1_Intron|NBR1_uc010whw.1_Intron	NM_031862	NP_114068	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1						macroautophagy|protein oligomerization	autophagic vacuole|cytoplasmic vesicle|cytosol|late endosome|lysosome|sarcomere	ubiquitin binding|zinc ion binding			skin(1)	1		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		TCCCTCTAGATACTTGTGTCCT	0.312													3	4	---	---	---	---	
FAM117A	81558	broad.mit.edu	37	17	47836766	47836767	+	Intron	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47836766_47836767delTG	uc002ipk.2	-						FAM117A_uc010wlz.1_Intron	NM_030802	NP_110429	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A											ovary(1)	1						CTGGCAAAGCTGTCAAAAGCAA	0.455													4	2	---	---	---	---	
TAC4	255061	broad.mit.edu	37	17	47918628	47918629	+	Intron	DEL	TC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47918628_47918629delTC	uc002ipo.1	-						TAC4_uc002ipp.1_Intron|TAC4_uc002ipq.1_Intron|TAC4_uc002ipr.1_Intron|TAC4_uc002ips.1_Intron	NM_170685	NP_733786	Q86UU9	TKN4_HUMAN	tachykinin 4 isoform alpha						regulation of blood pressure	extracellular region				breast(1)	1						tttttttttttCTAATTCCAGG	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	52100615	52100615	+	IGR	DEL	A	-	-	rs113582706		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52100615delA								KIF2B (198042 upstream) : TOM1L1 (877437 downstream)																							aaacaacaacaaaaaaaacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54574628	54574629	+	IGR	DEL	GT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54574628_54574629delGT								ANKFN1 (14621 upstream) : NOG (96431 downstream)																							AAATGGCTTAGTGTCTCCTCAT	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	55013886	55013886	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55013886delA								TRIM25 (22477 upstream) : COIL (1677 downstream)																							agaagatgacaggtttccagc	0.000													4	2	---	---	---	---	
DHX40	79665	broad.mit.edu	37	17	57663224	57663225	+	Intron	INS	-	AT	AT			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57663224_57663225insAT	uc002ixn.1	+						DHX40_uc010woe.1_Intron|DHX40_uc010wof.1_5'Flank	NM_024612	NP_078888	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GTAGACTTGACAGGCTGTGAAG	0.347													4	2	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	59421165	59421166	+	Intron	DEL	GA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59421165_59421166delGA	uc002iyv.3	+						BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.3_Intron|BCAS3_uc002izb.3_Intron|BCAS3_uc002izc.3_Intron	NM_001099432	NP_001092902	Q9H6U6	BCAS3_HUMAN	breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			ATTTTGCCTGGAGAGAGAGAAG	0.490													4	2	---	---	---	---	
PITPNC1	26207	broad.mit.edu	37	17	65669518	65669519	+	Intron	INS	-	AC	AC	rs142605380	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65669518_65669519insAC	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			cacacacgcagacacacacaca	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66759908	66759908	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66759908delG								FAM20A (162813 upstream) : ABCA8 (103525 downstream)																							ATGGACTATTGAACACAAATG	0.413													4	2	---	---	---	---	
ABCA10	10349	broad.mit.edu	37	17	67188453	67188454	+	Intron	INS	-	AAAC	AAAC	rs139772003	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67188453_67188454insAAAC	uc010dfa.1	-						ABCA10_uc010wqt.1_Intron|ABCA10_uc010dfb.1_Intron	NM_080282	NP_525021	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A, member 10						transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)					tgtctTcaaaaaaacaaacaaa	0.094													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68612022	68612022	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68612022delA								KCNJ2 (435841 upstream) : None (None downstream)																							TGGTACTGCCAAAAGCTGGAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70345155	70345155	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70345155delA								SOX9 (222603 upstream) : SLC39A11 (296931 downstream)																							gaaactctgtaaaaaaaaaac	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78431003	78431003	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78431003delC								FLJ35220 (19122 upstream) : NPTX1 (9630 downstream)																							accaaagcgtccattaccatc	0.209													4	2	---	---	---	---	
SLC38A10	124565	broad.mit.edu	37	17	79236362	79236362	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79236362delA	uc002jzz.1	-						SLC38A10_uc002jzy.1_Intron|SLC38A10_uc002kab.2_Intron	NM_001037984	NP_001033073	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10 isoform a						amino acid transport|sodium ion transport	integral to membrane				pancreas(1)|skin(1)	2	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GAGAAGCTACAAAAAAAAATT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	4582177	4582177	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4582177delA								DLGAP1 (126911 upstream) : LOC642597 (561495 downstream)																							AACAAAGAGGAAAAAAAAGAG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11671270	11671270	+	5'Flank	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11671270delT	uc002kpz.2	+						uc002kqa.1_5'Flank					DQ579650																		CCAAGAATGATTCATCTACAG	0.522													4	2	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	37213631	37213631	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37213631delA	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						ATCCACAGATAAAAAGCAGAT	0.408													4	2	---	---	---	---	
RIT2	6014	broad.mit.edu	37	18	40689504	40689504	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40689504delA	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1						cttcagcatcaaaaaaatcct	0.030													4	2	---	---	---	---	
KIAA0427	9811	broad.mit.edu	37	18	46184276	46184276	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46184276delG	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0						CTTCTTCTCTGTCCTCAGCTT	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49044593	49044593	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49044593delC	uc010xdq.1	+											Homo sapiens cDNA FLJ37617 fis, clone BRCOC2012229.																		AAAGGGAGTGCCTGAAGCAGT	0.383													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50595141	50595142	+	Intron	DEL	CT	-	-	rs141025596	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50595141_50595142delCT	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)		ACCTTTTAGACtgtgtgtgtgt	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53688046	53688046	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53688046delT								TCF4 (384861 upstream) : TXNL1 (582009 downstream)																							CCAAACACTCTTTTTTATTCA	0.358													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	56058215	56058215	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56058215delT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpn.2_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						AAGGCTGCTCTTTTTTTTTTT	0.353													5	3	---	---	---	---	
CDH19	28513	broad.mit.edu	37	18	64178570	64178571	+	Intron	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64178570_64178571delCA	uc002lkc.1	-						CDH19_uc010dql.1_Intron|CDH19_uc010xey.1_Intron	NM_021153	NP_066976	Q9H159	CAD19_HUMAN	cadherin 19, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)				AGCTTACAGCCATTGATAACTT	0.307													1	5	---	---	---	---	
CDH19	28513	broad.mit.edu	37	18	64178577	64178578	+	Intron	INS	-	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64178577_64178578insC	uc002lkc.1	-						CDH19_uc010dql.1_Intron|CDH19_uc010xey.1_Intron	NM_021153	NP_066976	Q9H159	CAD19_HUMAN	cadherin 19, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)				AGCCATTGATAACTTTAAAAAG	0.322													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	65042307	65042307	+	IGR	DEL	T	-	-	rs75002100		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65042307delT								CDH19 (771091 upstream) : DSEL (131512 downstream)																							gtcttcttcattttttttttt	0.184													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73700734	73700734	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73700734delG								C18orf62 (561145 upstream) : ZNF516 (370885 downstream)																							ATCATATTTTGGGCTTCAGTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75581525	75581525	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75581525delC								GALR1 (599431 upstream) : None (None downstream)																							GAGGTGGAGGCGGAGGAGGAG	0.483													4	2	---	---	---	---	
PQLC1	80148	broad.mit.edu	37	18	77682134	77682134	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77682134delA	uc002lnl.2	-						PQLC1_uc010dre.2_Intron|PQLC1_uc002lnk.2_Intron|PQLC1_uc010xfm.1_Intron	NM_025078	NP_079354	Q8N2U9	PQLC1_HUMAN	PQ loop repeat containing 1 isoform 1							integral to membrane				large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)		TGGTACAAATAATAACTCAAC	0.328													4	2	---	---	---	---	
ZNF69	7620	broad.mit.edu	37	19	12022630	12022632	+	Intron	DEL	ATA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12022630_12022632delATA	uc002mst.3	+							NM_021915	NP_068734	Q9UC07	ZNF69_HUMAN	zinc finger protein 69							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1				Lung(535;0.011)		aacttaaagtataataataataa	0.138													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13977703	13977704	+	IGR	DEL	AC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13977703_13977704delAC								MIR23A (30230 upstream) : MIR181C (7809 downstream)																							acacacacatacacacacacac	0.356													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14394656	14394656	+	IGR	DEL	A	-	-	rs74450856		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14394656delA								LPHN1 (77659 upstream) : CD97 (97557 downstream)																							accttgtctcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
NWD1	284434	broad.mit.edu	37	19	16909080	16909080	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16909080delT	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7						TGAAGTTCTCTTTTTTTCCCC	0.284													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29289946	29289947	+	IGR	INS	-	A	A	rs144973564	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29289946_29289947insA								None (None upstream) : LOC148145 (166093 downstream)																							agtttaaaaagaaaaaaaaact	0.000													6	3	---	---	---	---	
CCNE1	898	broad.mit.edu	37	19	30311985	30311985	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30311985delA	uc002nsn.2	+						CCNE1_uc002nso.2_Intron|CCNE1_uc002nsp.2_5'Flank	NM_001238	NP_001229	P24864	CCNE1_HUMAN	cyclin E1 isoform 1						androgen receptor signaling pathway|cell division|positive regulation of transcription, DNA-dependent|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm	androgen receptor binding|protein kinase binding|transcription coactivator activity			lung(2)	2	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			ACATTGAGCCAAAAAAAAAAA	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32221361	32221361	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32221361delA								TSHZ3 (381171 upstream) : ZNF507 (615153 downstream)																							TGCCATCTGGAAGGAGATAAC	0.473													4	2	---	---	---	---	
CCDC123	84902	broad.mit.edu	37	19	33450519	33450519	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33450519delC	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron|CCDC123_uc002nua.2_Intron|CCDC123_uc002nub.1_Intron	NM_032816	NP_116205	Q96ST8	CEP89_HUMAN	coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)					TAGCTCTGTGCCGCTGTGAAA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	34891255	34891255	+	IGR	DEL	T	-	-	rs78522905		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34891255delT								GPI (19 upstream) : PDCD2L (4048 downstream)																							CAGCCTCTGATTTTTTTTTTC	0.493													4	2	---	---	---	---	
HPN	3249	broad.mit.edu	37	19	35556034	35556034	+	Intron	DEL	T	-	-	rs113406953		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35556034delT	uc002nxq.1	+						HPN_uc002nxr.1_Intron|HPN_uc002nxs.1_Intron|HPN_uc010xsh.1_Intron|HPN_uc002nxt.1_Intron|LOC100128675_uc010xsi.1_Intron	NM_002151	NP_002142	P05981	HEPS_HUMAN	hepsin						cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	ccTATTGTGGTTTTTTTTTTA	0.299													7	4	---	---	---	---	
BCKDHA	593	broad.mit.edu	37	19	41884729	41884730	+	Intron	DEL	GA	-	-	rs2015924		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41884729_41884730delGA	uc002oqm.3	+						CYP2F1_uc010xvw.1_Intron|TMEM91_uc002oqi.2_Intron|TMEM91_uc010ehq.2_Intron|TMEM91_uc002oql.2_Intron|TMEM91_uc010ehr.2_Intron|TMEM91_uc010ehs.2_Intron|TMEM91_uc010eht.2_Intron|TMEM91_uc002oqk.3_Intron|TMEM91_uc002oqn.2_Intron	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0						GTGTGTGTGTgagagagagaga	0.267													3	3	---	---	---	---	
ZNF155	7711	broad.mit.edu	37	19	44489179	44489179	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44489179delA	uc002oxy.1	+						ZNF155_uc002oxz.1_Intron|ZNF155_uc010xwt.1_Intron	NM_003445	NP_003436	Q12901	ZN155_HUMAN	zinc finger protein 155							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2		Prostate(69;0.0352)				TTCTCTTTTTAAAAAAAAGTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	56891887	56891888	+	IGR	INS	-	C	C	rs141343973	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56891887_56891888insC								ZNF542 (693 upstream) : ZNF582 (2760 downstream)																							CTTGCTCAAATCCCAGATTTCC	0.302													4	3	---	---	---	---	
ZNF471	57573	broad.mit.edu	37	19	57019599	57019600	+	Intron	DEL	TG	-	-	rs72131854		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57019599_57019600delTG	uc002qnh.2	+							NM_020813	NP_065864	Q9BX82	ZN471_HUMAN	zinc finger protein 471						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		GTGTGGTTTCtgtgtgtgtgtg	0.520													4	2	---	---	---	---	
ZNF547	284306	broad.mit.edu	37	19	57968097	57968097	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57968097delT	uc002qpm.3	+						VN1R1_uc002qos.1_5'Flank			Q8IVP9	ZN547_HUMAN	RecName: Full=Zinc finger protein 547;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		tatactatagtttgcaaaatg	0.010													4	2	---	---	---	---	
TMC2	117532	broad.mit.edu	37	20	2597181	2597182	+	Intron	INS	-	AG	AG	rs151226434	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2597181_2597182insAG	uc002wgf.1	+						TMC2_uc002wgg.1_Intron	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2							integral to membrane				ovary(3)	3						aggagtaaagaagaggaggaaa	0.099													4	3	---	---	---	---	
RASSF2	9770	broad.mit.edu	37	20	4794429	4794430	+	Intron	DEL	GT	-	-	rs11468773		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4794429_4794430delGT	uc002wld.2	-						RASSF2_uc002wle.2_Intron|RASSF2_uc002wlf.2_Intron	NM_170774	NP_739580	P50749	RASF2_HUMAN	Ras association domain family 2						cell cycle|signal transduction	nucleus	protein binding			ovary(3)|lung(2)|large_intestine(1)	6						agtgtgtggcgtgtgtgtgtgt	0.094													4	2	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9289221	9289221	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9289221delG	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						CCTTTACCAAGAAGTTGAAAG	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	10659946	10659947	+	IGR	DEL	AG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10659946_10659947delAG								JAG1 (5252 upstream) : None (None downstream)																							TTGTGAAGCTAGAGTGTGGGAG	0.337													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12146588	12146588	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12146588delA								BTBD3 (239346 upstream) : SPTLC3 (843039 downstream)																							CAGTATCATTAAAAAATCGGC	0.284													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15383248	15383248	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15383248delC	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				AATATGTGAGCCGCCATGAGA	0.373													4	2	---	---	---	---	
RRBP1	6238	broad.mit.edu	37	20	17631582	17631582	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17631582delT	uc002wpv.1	-						RRBP1_uc002wpu.2_Intron|RRBP1_uc002wpw.1_Intron|RRBP1_uc010gcl.1_Intron	NM_001042576	NP_001036041	Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1						protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1						ACGTCTTGTGTTAGAAACTTG	0.418													4	2	---	---	---	---	
OVOL2	58495	broad.mit.edu	37	20	18031613	18031613	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18031613delA	uc002wqi.1	-							NM_021220	NP_067043	Q9BRP0	OVOL2_HUMAN	zinc finger protein 339						negative regulation of keratinocyte differentiation|negative regulation of Notch signaling pathway|negative regulation of transcription by competitive promoter binding|regulation of cell cycle|regulation of keratinocyte proliferation|transcription, DNA-dependent	nucleus	DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)	1						CTTGGGAGACAAAAAAACAAG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	18232255	18232255	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18232255delA								CSRP2BP (63240 upstream) : ZNF133 (36866 downstream)																							GGGCATCAGGAACCCCAGCCC	0.512													4	2	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19308770	19308770	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19308770delC	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						ggaagagcatccaggcagagg	0.000													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29624401	29624401	+	Intron	DEL	T	-	-	rs112995863		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29624401delT	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						TTAAACTCACTGTTTGGAAGT	0.294													10	5	---	---	---	---	
TM9SF4	9777	broad.mit.edu	37	20	30733590	30733590	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30733590delG	uc002wxj.2	+						TM9SF4_uc010ztr.1_Intron|TM9SF4_uc010zts.1_Intron|TM9SF4_uc002wxk.2_Intron|TM9SF4_uc010gdz.2_Intron	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4							integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			ttctagtggtgggagagaaac	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31636675	31636676	+	IGR	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31636675_31636676delTG								BPIL3 (4823 upstream) : C20orf185 (6554 downstream)																							GGCACATTCATGTGTGTGTGGG	0.564													4	2	---	---	---	---	
GDF5	8200	broad.mit.edu	37	20	33925843	33925843	+	Intron	DEL	C	-	-	rs2378349	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33925843delC	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron	NM_000557	NP_000548	P43026	GDF5_HUMAN	growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			TTAAAAAAAACACACAACCAA	0.408													4	3	---	---	---	---	
PHF20	51230	broad.mit.edu	37	20	34357098	34357098	+	5'Flank	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34357098delT	uc002xek.1	+						PHF20_uc002xei.1_5'Flank|PHF20_uc010gfo.1_5'Flank|PHF20_uc002xej.1_5'Flank|PHF20_uc002xeh.2_5'Flank	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					GGGCAGGTCATTCCTCTCTTC	0.502													4	2	---	---	---	---	
DLGAP4	22839	broad.mit.edu	37	20	34997065	34997066	+	Intron	DEL	TG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34997065_34997066delTG	uc002xff.2	+						DLGAP4_uc010zvp.1_Intron	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				GTCTGAGAGCTGTGTCTGTGGG	0.495													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36081697	36081697	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36081697delC								SRC (47878 upstream) : BLCAP (64123 downstream)																							TAGATTTGGTCCCCATGTTGC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37970069	37970069	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37970069delA								LOC339568 (116678 upstream) : None (None downstream)																							GCTACCAGCTAAGTAACAGAG	0.363													4	2	---	---	---	---	
ZHX3	23051	broad.mit.edu	37	20	39876962	39876962	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39876962delT	uc002xjs.1	-						ZHX3_uc002xjq.1_Intron|ZHX3_uc002xjr.1_Intron|ZHX3_uc002xjt.1_Intron|ZHX3_uc002xju.1_Intron|ZHX3_uc002xjv.1_Intron|ZHX3_uc002xjw.1_Intron	NM_015035	NP_055850	Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3						negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)				GTTTCTCCGGTTTTTTTTTTG	0.368													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41179091	41179092	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41179091_41179092insT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TTGGATTAGGGTTTTTTTTTAG	0.381													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41532691	41532691	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41532691delA	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				GTTCCTAAGCAAAAAAACAGA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42420933	42420933	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42420933delA								GTSF1L (65291 upstream) : TOX2 (122559 downstream)																							TACTCAGCATAAAAAAGGGTG	0.463													4	2	---	---	---	---	
STK4	6789	broad.mit.edu	37	20	43614694	43614695	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43614694_43614695insT	uc002xnb.2	+						STK4_uc010ggx.2_Intron|STK4_uc010ggy.2_Intron|STK4_uc010ggw.1_Intron	NM_006282	NP_006273	Q13043	STK4_HUMAN	serine/threonine kinase 4						apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)				ttcaacagatatttttttcagt	0.173													4	2	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45715571	45715572	+	Intron	DEL	AA	-	-	rs73624044		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45715571_45715572delAA	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				GGGGGCAAACAAATGTTTTCTA	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54014933	54014936	+	IGR	DEL	TCTC	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54014933_54014936delTCTC								DOK5 (747224 upstream) : CBLN4 (557561 downstream)																							cttcaagtcttctctctttttatc	0.000													2	4	---	---	---	---	
TFAP2C	7022	broad.mit.edu	37	20	55208253	55208253	+	Intron	DEL	T	-	-	rs72357061		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55208253delT	uc002xya.2	+						TFAP2C_uc010zzi.1_Intron	NM_003222	NP_003213	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma						cell-cell signaling|male gonad development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Colorectal(105;0.229)			actcttattattttttttttt	0.179													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57115237	57115237	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57115237delA	uc002xzg.1	+											Homo sapiens cDNA FLJ30075 fis, clone BGGI11000285.																		CAGTGATCCCACTCCTGTTTA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58908586	58908586	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58908586delC	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		ctcccaaaggccccacctcct	0.015													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60468549	60468549	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60468549delG	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			gatggtggatgggtaggtggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	62604379	62604380	+	IGR	INS	-	GTATTTGT	GTATTTGT	rs142567120	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62604379_62604380insGTATTTGT								ZNF512B (3161 upstream) : SAMD10 (1086 downstream)																							TCTGCATGCTAGTATTTGTGTA	0.475													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9415562	9415562	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9415562delG								None (None upstream) : None (None downstream)																							agtgtggatcgggacctcttt	0.015													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10130988	10130989	+	IGR	DEL	AT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10130988_10130989delAT								None (None upstream) : TPTE (775754 downstream)																							AGTTAAAAACATAAAATCCAGT	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10160325	10160326	+	IGR	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10160325_10160326insT								None (None upstream) : TPTE (746417 downstream)																							tttcttctaggttttttttttt	0.000													3	3	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	11009897	11009897	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11009897delT	uc002yis.1	-									P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ttccaattccttttttttttg	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11024346	11024347	+	Intron	INS	-	A	A	rs146206335	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11024346_11024347insA	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TAAGAGTAAACaaaaaaagaag	0.213													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11037534	11037537	+	Intron	DEL	AAAT	-	-	rs140499714		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037534_11037537delAAAT	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ACAAAACAAAAAATACTTACTGGA	0.270													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14362686	14362687	+	IGR	DEL	GT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14362686_14362687delGT								None (None upstream) : C21orf99 (47800 downstream)																							tacaaaaatagtgtttccaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	16116029	16116029	+	IGR	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16116029delG								SAMSN1 (160306 upstream) : NRIP1 (217527 downstream)																							cataaaatatggtgggggtgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	23047353	23047353	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23047353delT								NCAM2 (136139 upstream) : None (None downstream)																							ggtaaattccttcttcaagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	25702377	25702377	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25702377delA								None (None upstream) : None (None downstream)																							CAAGTTACATAAGCAGGCAGA	0.353													4	2	---	---	---	---	
ADAMTS1	9510	broad.mit.edu	37	21	28215013	28215013	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28215013delA	uc002ymf.2	-							NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1						integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)		TCCTGTAAAGAAAAAAAAAAG	0.408													17	8	---	---	---	---	
C21orf7	56911	broad.mit.edu	37	21	30496057	30496057	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30496057delT	uc002yne.2	+						C21orf7_uc011acr.1_Intron|C21orf7_uc002ynd.2_Intron|C21orf7_uc010gln.2_Intron|C21orf7_uc002ynf.2_Intron|C21orf7_uc010glo.2_Intron	NM_020152	NP_064537	P57077	TAK1L_HUMAN	chromosome 21 open reading frame 7							cytosol|nucleus	protein binding			ovary(2)	2				Colorectal(56;0.248)		tgttggggaattactgtggtg	0.000													4	2	---	---	---	---	
C21orf59	56683	broad.mit.edu	37	21	33957940	33957940	+	Intron	DEL	T	-	-	rs148817899		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33957940delT	uc002ypy.1	-						TCP10L_uc002ypw.3_5'Flank|C21orf59_uc002ypx.1_Intron|C21orf59_uc002ypz.1_Intron	NM_021254	NP_067077	P57076	CU059_HUMAN	hypothetical protein LOC56683							cytosol|nucleus					0						CCTGCAATTCTTAATATAGAA	0.413											OREG0003581	type=REGULATORY REGION|Gene=TCP10L|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35584259	35584259	+	IGR	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35584259delC								C21orf82 (22039 upstream) : KCNE2 (152064 downstream)																							GTTAGGCTTTCTATTGCGGTT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	38050029	38050030	+	IGR	INS	-	AG	AG	rs151236890	by1000genomes	TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38050029_38050030insAG								CLDN14 (101162 upstream) : SIM2 (21961 downstream)																							cgatgagagacagagagagaga	0.035													4	2	---	---	---	---	
DSCR9	257203	broad.mit.edu	37	21	38579595	38579595	+	5'Flank	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38579595delT	uc010gng.2	+						DSCR9_uc010gnh.2_5'Flank|DSCR9_uc010gni.2_5'Flank|DSCR9_uc010gnj.2_5'Flank|DSCR9_uc011aef.1_5'Flank					Homo sapiens DSCR9 mRNA, partial splicing variant form DSCR9a.												0						cattggcaaatgctGTTTTGC	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39424526	39424526	+	IGR	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39424526delA								KCNJ6 (135830 upstream) : DSCR4 (1788 downstream)																							TCTCTTTAGGAAAAAAAAATA	0.318													4	3	---	---	---	---	
C21orf70	85395	broad.mit.edu	37	21	46364231	46364231	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46364231delT	uc002zgl.2	+						C21orf70_uc002zgm.2_Intron	NM_058190	NP_478070	Q9NSI2	CU070_HUMAN	hypothetical protein LOC85395												0				Colorectal(79;0.248)		TGCGCAGCCCTTCCCGTCTCC	0.547													4	2	---	---	---	---	
C21orf70	85395	broad.mit.edu	37	21	46380413	46380413	+	Intron	DEL	G	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46380413delG	uc002zgl.2	+						C21orf70_uc002zgm.2_Intron	NM_058190	NP_478070	Q9NSI2	CU070_HUMAN	hypothetical protein LOC85395												0				Colorectal(79;0.248)		TCGGCTCCTTGTTTGTAAAAA	0.522													4	2	---	---	---	---	
LSS	4047	broad.mit.edu	37	21	47624536	47624537	+	Intron	INS	-	A	A			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47624536_47624537insA	uc002zij.2	-						LSS_uc011afv.1_Intron|LSS_uc002zil.2_Intron|LSS_uc002zik.2_Intron	NM_001001438	NP_001001438	P48449	ERG7_HUMAN	lanosterol synthase isoform 1						cholesterol biosynthetic process	endoplasmic reticulum membrane	lanosterol synthase activity				0	Breast(49;0.214)					gaacccatctcaaaaaaaaaag	0.000													4	3	---	---	---	---	
MICAL3	57553	broad.mit.edu	37	22	18382589	18382589	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18382589delA	uc002zng.3	-						MICAL3_uc011agl.1_Intron|MICAL3_uc002znh.2_Intron|MICAL3_uc002znj.1_Intron|MICAL3_uc002znk.1_Intron|MICAL3_uc002znl.1_Intron|MICAL3_uc010grf.2_Intron|MICAL3_uc011agm.1_Intron	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		CGAAACAAGCAAAAAAAAAAG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20975199	20975200	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20975199_20975200insT	uc002zsv.2	-											Homo sapiens, clone IMAGE:5171202, mRNA.																		AGAGATTTCCATTTTTTTTTCC	0.554													4	2	---	---	---	---	
TOP3B	8940	broad.mit.edu	37	22	22320704	22320706	+	Intron	DEL	GAG	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22320704_22320706delGAG	uc002zvs.2	-						TOP3B_uc010gtm.1_Intron|TOP3B_uc002zvr.2_Intron|TOP3B_uc010gtl.2_Intron|TOP3B_uc002zvt.3_Intron	NM_003935	NP_003926	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta						DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CTGGAAGATTGAGGAGGAGTCAG	0.384													2	6	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23208439	23208439	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23208439delA	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						cccttttactaaaaaggaata	0.184													4	2	---	---	---	---	
KREMEN1	83999	broad.mit.edu	37	22	29530563	29530564	+	Intron	INS	-	T	T			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29530563_29530564insT	uc011akm.1	+						KREMEN1_uc003ael.2_Intron|KREMEN1_uc011akn.1_Intron	NM_032045	NP_114434	Q96MU8	KREM1_HUMAN	kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5						ccctcccacccttgcttttata	0.000													4	2	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33743724	33743724	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33743724delA	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)				TGTAACCTGCACCTAGTTGCC	0.468													4	2	---	---	---	---	
EIF3D	8664	broad.mit.edu	37	22	36907942	36907943	+	Intron	DEL	TT	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36907942_36907943delTT	uc003apq.2	-						EIF3D_uc011amr.1_Intron|EIF3D_uc003apr.2_Intron|EIF3D_uc011ams.1_Intron|EIF3D_uc011amt.1_Intron	NM_003753	NP_003744	O15371	EIF3D_HUMAN	eukaryotic translation initiation factor 3							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			pancreas(1)	1						CTAttttttctttttttttttt	0.223													4	2	---	---	---	---	
MFNG	4242	broad.mit.edu	37	22	37877128	37877129	+	Intron	DEL	CA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37877128_37877129delCA	uc003ass.1	-						MFNG_uc011ani.1_Intron|MFNG_uc011anj.1_Intron|CARD10_uc003ast.1_Intron	NM_002405	NP_002396	O00587	MFNG_HUMAN	O-fucosylpeptide						pattern specification process	extracellular space|integral to Golgi membrane	O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity			lung(1)	1	Melanoma(58;0.0574)					cacacacaatcacacacacaca	0.421													6	3	---	---	---	---	
FAM83F	113828	broad.mit.edu	37	22	40409371	40409371	+	Intron	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40409371delT	uc003ayk.1	+							NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828											breast(1)	1						ctaaagggcattttttttctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41375490	41375490	+	IGR	DEL	T	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41375490delT								RBX1 (6824 upstream) : MIR1281 (113027 downstream)																							aaattctatgtttagcttttt	0.000													4	2	---	---	---	---	
MPPED1	758	broad.mit.edu	37	22	43894738	43894738	+	Intron	DEL	C	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43894738delC	uc011apv.1	+						MPPED1_uc011apw.1_Intron|MPPED1_uc011apx.1_Intron|MPPED1_uc011apy.1_Intron|MPPED1_uc011apz.1_Intron	NM_001044370	NP_001037835	O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1								hydrolase activity				0		all_neural(38;0.0244)|Ovarian(80;0.0694)				GCCTCCTCCACCCCTACTGTC	0.602													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	487602	487603	+	IGR	INS	-	C	C			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:487602_487603insC								PPP2R3B (139975 upstream) : SHOX (97476 downstream)																							TGGGATACTGTCCCTCTGGCGC	0.564													0	6	---	---	---	---	
EFHC2	80258	broad.mit.edu	37	X	44067039	44067041	+	Intron	DEL	CAA	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44067039_44067041delCAA	uc004dgb.3	-							NM_025184	NP_079460	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2								calcium ion binding			breast(3)|ovary(2)|central_nervous_system(1)	6						aaacttaaatcaacaacaacaac	0.000													4	2	---	---	---	---	
BRCC3	79184	broad.mit.edu	37	X	154327425	154327425	+	Intron	DEL	A	-	-			TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154327425delA	uc004fna.2	+						BRCC3_uc004fnb.2_Intron	NM_024332	NP_077308	P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3						double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|positive regulation of DNA repair|response to X-ray	BRCA1-A complex|BRISC complex|nuclear ubiquitin ligase complex	enzyme regulator activity|metal ion binding|metallopeptidase activity|polyubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(3)|ovary(1)|large_intestine(1)|breast(1)	6	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					catatattagaaaaaaaaatt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13436651	13436651	+	IGR	DEL	G	-	-	rs111751963		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13436651delG								None (None upstream) : None (None downstream)																							AATTATGAAAGTTTTTCTAAC	0.308													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59006024	59006028	+	IGR	DEL	TTATA	-	-	rs111313709		TCGA-B0-4700-01A-02D-1534-10	TCGA-B0-4700-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59006024_59006028delTTATA								None (None upstream) : None (None downstream)																							ttggatttctttatattatttctta	0.015													6	3	---	---	---	---	
