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
ATAD3C	219293	broad.mit.edu	37	1	1390889	1390889	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1390889T>C	uc001aft.2	+	5	1423	c.428T>C	c.(427-429)GTT>GCT	p.V143A		NM_001039211	NP_001034300	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	143							ATP binding|nucleoside-triphosphatase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CTGGAGGGTGTTGTGCTTAGT	0.687													5	203	---	---	---	---	PASS
TPRG1L	127262	broad.mit.edu	37	1	3542321	3542321	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3542321C>T	uc001akm.2	+	3	419	c.338C>T	c.(337-339)ACG>ATG	p.T113M	TPRG1L_uc009vlj.2_Intron	NM_182752	NP_877429	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	113						cell junction|synaptic vesicle					0	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)		GTGCTGGTCACGGAGCAGTCC	0.572													4	53	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16973784	16973784	+	5'Flank	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16973784C>T	uc001azg.1	-						CROCCL1_uc001azi.1_5'Flank|MST1P2_uc009vow.2_RNA|MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_5'Flank|MST1P2_uc001azm.3_5'Flank					Homo sapiens mRNA for FLJ00313 protein.												0						ATCTTCAGCACCCGCACCAGC	0.697													3	9	---	---	---	---	PASS
PLA2G2A	5320	broad.mit.edu	37	1	20302181	20302181	+	3'UTR	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20302181G>A	uc001bcu.2	-	5					PLA2G2A_uc001bcv.2_3'UTR|PLA2G2A_uc010oda.1_3'UTR|PLA2G2A_uc010odb.1_3'UTR	NM_001161729	NP_001155201	P14555	PA2GA_HUMAN	phospholipase A2, group IIA precursor						defense response to Gram-positive bacterium|lipid catabolic process|low-density lipoprotein particle remodeling|phosphatidic acid metabolic process|positive regulation of inflammatory response|positive regulation of macrophage derived foam cell differentiation	endoplasmic reticulum|extracellular space|membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|phospholipid binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AAGGTTTCCAGGGAAGAGGGG	0.502													4	207	---	---	---	---	PASS
TINAGL1	64129	broad.mit.edu	37	1	32051533	32051533	+	Intron	SNP	C	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32051533C>A	uc001bta.2	+						TINAGL1_uc001bsz.2_Intron|TINAGL1_uc010ogj.1_Intron|TINAGL1_uc010ogk.1_3'UTR	NM_022164	NP_071447	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1						endosome transport|immune response|proteolysis	extracellular region	cysteine-type endopeptidase activity|extracellular matrix structural constituent|polysaccharide binding|scavenger receptor activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		gctaggggctctggagcctgc	0.249													10	16	---	---	---	---	PASS
S100PBP	64766	broad.mit.edu	37	1	33292267	33292267	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33292267T>G	uc001bvz.2	+	3	844	c.567T>G	c.(565-567)AAT>AAG	p.N189K	S100PBP_uc001bwa.1_Missense_Mutation_p.N189K|S100PBP_uc001bwb.1_Missense_Mutation_p.N189K|S100PBP_uc001bwc.2_Missense_Mutation_p.N189K|S100PBP_uc001bwd.2_RNA	NM_022753	NP_073590	Q96BU1	S1PBP_HUMAN	S100P binding protein isoform a	189						nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TTAGCCCAAATGAAAGCAAAC	0.443													11	73	---	---	---	---	PASS
MTF1	4520	broad.mit.edu	37	1	38287859	38287859	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38287859C>T	uc001cce.1	-	9	1842	c.1701G>A	c.(1699-1701)ATG>ATA	p.M567I	MTF1_uc009vvj.1_Missense_Mutation_p.M258I	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	567						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TCTGTTCTCCCATGACTAGGC	0.448													8	797	---	---	---	---	PASS
OSBPL9	114883	broad.mit.edu	37	1	52253050	52253050	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52253050T>C	uc001cst.2	+	23	2045	c.2026T>C	c.(2026-2028)TTA>CTA	p.L676L	OSBPL9_uc001css.2_Silent_p.L681L|OSBPL9_uc001csx.2_RNA|OSBPL9_uc009vza.2_Silent_p.L677L|OSBPL9_uc001csu.2_Silent_p.L686L|OSBPL9_uc001csv.2_Silent_p.L511L|OSBPL9_uc001csw.2_Silent_p.L663L|OSBPL9_uc001csy.2_Silent_p.L498L|OSBPL9_uc001csz.2_Silent_p.L498L|OSBPL9_uc001cta.2_Silent_p.L566L|OSBPL9_uc001ctb.2_Silent_p.L461L	NM_024586	NP_078862	Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9 isoform e	676					lipid transport		lipid binding			central_nervous_system(1)	1						CACTTTCAACTTAAAAATCAG	0.418													5	278	---	---	---	---	PASS
ECHDC2	55268	broad.mit.edu	37	1	53387308	53387308	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53387308G>T	uc001cup.3	-	1	284	c.38C>A	c.(37-39)CCC>CAC	p.P13H	ECHDC2_uc001cun.2_5'UTR|ECHDC2_uc001cuo.3_Missense_Mutation_p.P13H|ECHDC2_uc010onk.1_5'UTR|ECHDC2_uc010onl.1_5'Flank|ECHDC2_uc010onm.1_5'UTR|ECHDC2_uc010onn.1_5'UTR	NM_018281	NP_060751	Q86YB7	ECHD2_HUMAN	enoyl Coenzyme A hydratase domain containing 2	13					fatty acid metabolic process	mitochondrion	lyase activity			central_nervous_system(1)	1						GGCCCGAAGGGGCCTCCAGGG	0.716													10	10	---	---	---	---	PASS
LRRC8B	23507	broad.mit.edu	37	1	90049487	90049487	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90049487T>C	uc001dni.2	+	7	1785	c.1278T>C	c.(1276-1278)CTT>CTC	p.L426L	LRRC8B_uc001dnh.2_Silent_p.L426L|LRRC8B_uc001dnj.2_Silent_p.L426L	NM_001134476	NP_001127948	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member	426						integral to membrane				ovary(2)	2		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		AACTGCATCTTTTTATGCTCA	0.418													33	41	---	---	---	---	PASS
KCNC4	3749	broad.mit.edu	37	1	110775595	110775595	+	3'UTR	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110775595A>G	uc001dzh.2	+	4					KCNC4_uc001dzg.2_3'UTR|KCNC4_uc001dzi.2_RNA	NM_004978	NP_004969	Q03721	KCNC4_HUMAN	Shaw-related voltage-gated potassium channel						synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		CCTCTCTTAAAGCGGCACCAA	0.537													5	162	---	---	---	---	PASS
KCND3	3752	broad.mit.edu	37	1	112524688	112524688	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112524688G>A	uc001ebu.1	-	2	1141	c.661C>T	c.(661-663)CGC>TGC	p.R221C	KCND3_uc001ebv.1_Missense_Mutation_p.R221C	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related	221						sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		ACCGAGTAGCGCTCCCCGCAC	0.657													4	21	---	---	---	---	PASS
MAGI3	260425	broad.mit.edu	37	1	114186372	114186372	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114186372T>C	uc001edk.2	+	11	2155	c.1974T>C	c.(1972-1974)CCT>CCC	p.P658P	MAGI3_uc001edh.3_Silent_p.P683P|MAGI3_uc001edi.3_Silent_p.P658P|MAGI3_uc010owm.1_Silent_p.P683P|MAGI3_uc001edj.2_Silent_p.P379P	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	683					apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAGGTCCTCCTTCACCAACCA	0.403													6	428	---	---	---	---	PASS
WDR3	10885	broad.mit.edu	37	1	118481109	118481109	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118481109A>G	uc010oxe.1	+	5	573	c.507A>G	c.(505-507)AAA>AAG	p.K169K	WDR3_uc001ehi.2_Intron|WDR3_uc001ehh.2_5'UTR	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3	169	WD 4.					nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		TTAGTGGGAAAGATACCATGG	0.423													8	469	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145296448	145296448	+	Missense_Mutation	SNP	T	A	A	rs4996268	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145296448T>A	uc001end.3	+	3	405	c.370T>A	c.(370-372)TAT>AAT	p.Y124N	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.Y124N|NBPF10_uc001emq.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	124											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CCGCTCATTGTATGAGCATCT	0.562													7	39	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145323656	145323656	+	Missense_Mutation	SNP	A	T	T	rs145276193	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145323656A>T	uc001end.3	+	29	3753	c.3718A>T	c.(3718-3720)ATT>TTT	p.I1240F	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc010oym.1_Intron|NBPF10_uc010oyn.1_Intron|NBPF10_uc010oyo.1_Intron|NBPF10_uc010oyp.1_5'Flank	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	1165											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TATTGCAGGAATTAAAAAGGA	0.473													3	34	---	---	---	---	PASS
IGSF9	57549	broad.mit.edu	37	1	159901558	159901558	+	Intron	SNP	T	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159901558T>G	uc001fur.2	-						IGSF9_uc001fuq.2_Intron|IGSF9_uc001fup.2_5'UTR	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a							cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GAGGCAGGGGTGTAGTGGGCG	0.642													6	37	---	---	---	---	PASS
SELP	6403	broad.mit.edu	37	1	169588443	169588443	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169588443T>C	uc001ggi.3	-	2	83	c.18A>G	c.(16-18)ATA>ATG	p.I6M	SELP_uc001ggh.2_Translation_Start_Site|SELP_uc009wvr.2_Missense_Mutation_p.I6M	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor	6					platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)	ACAAGATGGCTATTTGGCAGT	0.388													4	318	---	---	---	---	PASS
TSEN15	116461	broad.mit.edu	37	1	184023569	184023569	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184023569A>G	uc001gqt.3	+	2	296	c.217A>G	c.(217-219)AGC>GGC	p.S73G	TSEN15_uc009wyg.2_RNA|TSEN15_uc001gqu.3_Missense_Mutation_p.S73G	NM_052965	NP_443197	Q8WW01	SEN15_HUMAN	tRNA splicing endonuclease 15 isoform 1	73					mRNA processing|tRNA processing	nucleolus	protein binding				0						CCTCATGGAAAGTAAGTTGTT	0.333													7	758	---	---	---	---	PASS
ASPM	259266	broad.mit.edu	37	1	197087000	197087000	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197087000T>C	uc001gtu.2	-	17	4241	c.3984A>G	c.(3982-3984)AGA>AGG	p.R1328R	ASPM_uc001gtv.2_Silent_p.R1328R|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1328					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6						GTGCTAAGACTCTTCGCCAAT	0.323													8	666	---	---	---	---	PASS
C1orf116	79098	broad.mit.edu	37	1	207200938	207200938	+	Silent	SNP	G	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207200938G>C	uc001hfd.2	-	2	265	c.6C>G	c.(4-6)CCC>CCG	p.P2P	C1orf116_uc009xcb.1_Intron	NM_023938	NP_076427	Q9BW04	SARG_HUMAN	specifically androgen-regulated protein isoform	2						cytoplasm|plasma membrane	receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4	Prostate(682;0.19)					GCTCCCTCTCGGGCATCACCC	0.612													37	33	---	---	---	---	PASS
TP53BP2	7159	broad.mit.edu	37	1	223983623	223983623	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223983623G>A	uc010pvb.1	-	13	2910	c.2618C>T	c.(2617-2619)CCT>CTT	p.P873L	TP53BP2_uc001hod.2_Missense_Mutation_p.P744L|TP53BP2_uc010puz.1_Missense_Mutation_p.P106L|TP53BP2_uc010pva.1_Missense_Mutation_p.P512L	NM_001031685	NP_001026855	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein, 2 isoform 1	867	SH3-binding (Potential).|Pro-rich.				apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)		TGGGTATGGAGGGTACTCCTC	0.582													47	282	---	---	---	---	PASS
DNAH14	127602	broad.mit.edu	37	1	225288466	225288466	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225288466A>G	uc001how.2	+	23	3962	c.3747A>G	c.(3745-3747)AAA>AAG	p.K1249K		NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform	Error:Variant_position_missing_in_Q0VDD8_after_alignment					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						CCATGTGGAAAAAAATAATGT	0.313													60	62	---	---	---	---	PASS
PLD5	200150	broad.mit.edu	37	1	242287796	242287796	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242287796C>T	uc001hzn.1	-	6	1034	c.907G>A	c.(907-909)GAA>AAA	p.E303K	PLD5_uc001hzl.3_Missense_Mutation_p.E241K|PLD5_uc001hzm.3_Missense_Mutation_p.E93K|PLD5_uc001hzo.1_Missense_Mutation_p.E211K			Q8N7P1	PLD5_HUMAN	RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;	303						integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			GATTTGGTTTCATTCAACTGA	0.373													5	377	---	---	---	---	PASS
AHCTF1	25909	broad.mit.edu	37	1	247051711	247051711	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247051711A>G	uc001ibu.1	-	17	2260	c.2253T>C	c.(2251-2253)CCT>CCC	p.P751P	AHCTF1_uc001ibv.1_Silent_p.P760P|AHCTF1_uc009xgs.1_5'UTR	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	751	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GACTAGCAGGAGGATATTTTC	0.463													5	236	---	---	---	---	PASS
ZNF692	55657	broad.mit.edu	37	1	249152747	249152747	+	Intron	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249152747A>G	uc001ifc.1	-						ZNF692_uc001iez.1_5'Flank|ZNF692_uc001ifa.1_5'Flank|ZNF692_uc001ifb.1_5'UTR|ZNF692_uc001ifd.1_Intron|ZNF692_uc001ife.1_Intron|ZNF692_uc001iff.1_Intron|ZNF692_uc010pzr.1_5'UTR	NM_017865	NP_060335	Q9BU19	ZN692_HUMAN	zinc finger protein 692 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			AGGCAGACAGAAGCAGTCAGA	0.592											OREG0014373	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	137	---	---	---	---	PASS
SF3B14	51639	broad.mit.edu	37	2	24290658	24290658	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24290658C>T	uc002rev.2	-	4	567	c.352G>A	c.(352-354)GGC>AGC	p.G118S	SF3B14_uc010eyb.2_RNA	NM_016047	NP_057131	Q9Y3B4	PM14_HUMAN	splicing factor 3B, 14 kDa subunit	118					nuclear mRNA splicing, via spliceosome	nucleoplasm|U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTGTTGATGCCATATTTCTCC	0.343													6	770	---	---	---	---	PASS
FSHR	2492	broad.mit.edu	37	2	49190949	49190949	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49190949T>C	uc002rww.2	-	10	1085	c.1011A>G	c.(1009-1011)TTA>TTG	p.L337L	FSHR_uc002rwx.2_Silent_p.L275L|FSHR_uc010fbn.2_Silent_p.L311L	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	337	Extracellular (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)	CTTCATTGCATAAGTCATAGT	0.478									Gonadal_Dysgenesis_46_XX				5	504	---	---	---	---	PASS
SUCLG1	8802	broad.mit.edu	37	2	84652703	84652703	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84652703A>C	uc002son.2	-	8	1043	c.850T>G	c.(850-852)TCC>GCC	p.S284A		NM_003849	NP_003840	P53597	SUCA_HUMAN	succinate-CoA ligase, GDP-forming alpha subunit	284					tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)	GCAATGAAGGACACTACAGGC	0.433													60	74	---	---	---	---	PASS
POLR1A	25885	broad.mit.edu	37	2	86257417	86257417	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86257417G>A	uc002sqs.2	-	31	5060	c.4681C>T	c.(4681-4683)CGG>TGG	p.R1561W	POLR1A_uc010ytb.1_Missense_Mutation_p.R927W	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	1561					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						AGGAGGCACCGAGTGATGCCC	0.483													7	503	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96646519	96646519	+	RNA	SNP	T	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96646519T>A	uc010yug.1	-	5		c.693A>T								Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		AGTAACAGCATGTATGAGGGC	0.313													4	322	---	---	---	---	PASS
MRPS9	64965	broad.mit.edu	37	2	105665695	105665695	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105665695A>G	uc002tcn.3	+	2	270	c.202A>G	c.(202-204)ACT>GCT	p.T68A		NM_182640	NP_872578	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9 precursor	68					DNA damage response, detection of DNA damage|translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0						AAAACGTGAAACTTACACAGA	0.328													6	394	---	---	---	---	PASS
RGPD4	285190	broad.mit.edu	37	2	108479385	108479385	+	Intron	SNP	G	T	T	rs146539322	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108479385G>T	uc010ywk.1	+						RGPD4_uc002tdu.2_5'UTR|RGPD4_uc010ywl.1_Intron	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4						intracellular transport		binding			skin(2)	2						GCTCTTTTGTGATTTTTATTT	0.313													6	552	---	---	---	---	PASS
MIR663B	100302269	broad.mit.edu	37	2	133015519	133015519	+	5'Flank	SNP	G	T	T	rs77644836	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133015519G>T	hsa-mir-663b|MI0006336	-						NCRNA00164_uc002ttj.3_RNA																	0						GCCCCTCGGCGGCCGGCCGGC	0.682													7	51	---	---	---	---	PASS
GALNT13	114805	broad.mit.edu	37	2	155115568	155115568	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155115568G>T	uc002tyr.3	+	8	1459	c.892G>T	c.(892-894)GAC>TAC	p.D298Y	GALNT13_uc002tyt.3_Missense_Mutation_p.D298Y|GALNT13_uc010foc.1_Missense_Mutation_p.D117Y|GALNT13_uc010fod.2_Missense_Mutation_p.D51Y	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	298	Catalytic subdomain B.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						ATTTTCTATTGACAGAAACTA	0.343													65	547	---	---	---	---	PASS
RBM45	129831	broad.mit.edu	37	2	178981042	178981042	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178981042A>G	uc002ulv.2	+	2	446	c.354A>G	c.(352-354)GAA>GAG	p.E118E		NM_152945	NP_694453	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	118					cell differentiation|nervous system development	cytoplasm|nucleus	nucleotide binding|RNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			TTGAAGATGAAGAACTTACAA	0.338													9	623	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179587426	179587426	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179587426A>G	uc010zfg.1	-	73	18692	c.18468T>C	c.(18466-18468)AGT>AGC	p.S6156S	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.S2817S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7083							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)			CAGTTCCTATACTATTTTCTG	0.323													4	117	---	---	---	---	PASS
CD28	940	broad.mit.edu	37	2	204591400	204591400	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204591400G>A	uc002vah.3	+	2	319	c.97G>A	c.(97-99)GAC>AAC	p.D33N	CD28_uc002vag.1_RNA|CD28_uc010zio.1_RNA|CD28_uc010ftx.2_Intron|CD28_uc002vaj.3_RNA	NM_006139	NP_006130	P10747	CD28_HUMAN	CD28 antigen precursor	33	Extracellular (Potential).|Ig-like V-type.				cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0						TGTAGCGTACGACAATGCGGT	0.433													20	116	---	---	---	---	PASS
STK36	27148	broad.mit.edu	37	2	219566631	219566631	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219566631T>C	uc002viu.2	+	27	4113	c.3847T>C	c.(3847-3849)TCT>CCT	p.S1283P	STK36_uc002viv.2_Missense_Mutation_p.S1262P|STK36_uc002viw.2_Missense_Mutation_p.S461P|STK36_uc002vix.2_Missense_Mutation_p.S328P	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36	1283					cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		ATCCTTGCTCTCTCTGGGGAA	0.522													5	150	---	---	---	---	PASS
KIAA1486	57624	broad.mit.edu	37	2	226378271	226378271	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226378271C>T	uc002voe.2	+	3	581	c.406C>T	c.(406-408)CGG>TGG	p.R136W	KIAA1486_uc010fxa.1_Intron	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624	136										ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		CTGTGGCTCACGGAGACAACC	0.577													59	59	---	---	---	---	PASS
USP40	55230	broad.mit.edu	37	2	234389876	234389876	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234389876T>C	uc010zmr.1	-	30	3605	c.3605A>G	c.(3604-3606)AAA>AGA	p.K1202R	USP40_uc002vul.2_Missense_Mutation_p.K186R	NM_018218	NP_060688	Q9NVE5	UBP40_HUMAN	ubiquitin thioesterase 40	1190					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)|breast(1)	3		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		GGCCCGTTGTTTCTGCTTTTC	0.443													8	789	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238283513	238283513	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238283513T>C	uc002vwl.2	-	8	3506	c.3221A>G	c.(3220-3222)GAC>GGC	p.D1074G	COL6A3_uc002vwo.2_Missense_Mutation_p.D868G|COL6A3_uc010znj.1_Missense_Mutation_p.D467G|COL6A3_uc002vwq.2_Missense_Mutation_p.D868G|COL6A3_uc002vwr.2_Missense_Mutation_p.D667G	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1074	Nonhelical region.|VWFA 6.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CCTGGTCCGGTCGCTGTACTG	0.617													4	62	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191532	10191532	+	Nonsense_Mutation	SNP	C	A	A	rs5030835		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191532C>A	uc003bvc.2	+	3	738	c.525C>A	c.(523-525)TAC>TAA	p.Y175*	VHL_uc003bvd.2_Nonsense_Mutation_p.Y134*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	175			Y -> D (in VHLD; type I).		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.Y175fs*27(7)|p.Y175*(4)|p.Y175D(2)|p.P172fs*39(1)|p.Y175fs*1(1)|p.Y175fs*40(1)|p.Y175fs*28(1)|p.R176fs*36(1)|p.E173fs*26(1)		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)		CTGAGAATTACAGGAGACTGG	0.527		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				74	26	---	---	---	---	PASS
LTF	4057	broad.mit.edu	37	3	46477692	46477692	+	Silent	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46477692C>T	uc003cpq.2	-	17	2165	c.2127G>A	c.(2125-2127)AGG>AGA	p.R709R	LTF_uc003fzr.2_Silent_p.R665R|LTF_uc010hjh.2_Silent_p.R707R|LTF_uc003cpr.2_Silent_p.R696R	NM_002343	NP_002334	P02788	TRFL_HUMAN	lactotransferrin precursor	709					cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)	GGTTTTACTTCCTGAGGAATT	0.502													119	40	---	---	---	---	PASS
DOCK3	1795	broad.mit.edu	37	3	51246204	51246204	+	Splice_Site	SNP	G	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51246204G>C	uc011bds.1	+	13	1061	c.1038_splice	c.e13-1	p.T346_splice		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3							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)		TTCTGTTACAGGTGCAACAAC	0.468													104	38	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52584626	52584626	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52584626G>A	uc003des.2	-	29	4720	c.4708C>T	c.(4708-4710)CAG>TAG	p.Q1570*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.Q1463*|PBRM1_uc003der.2_Nonsense_Mutation_p.Q1483*|PBRM1_uc003det.2_Nonsense_Mutation_p.Q1478*|PBRM1_uc003deu.2_Nonsense_Mutation_p.Q1533*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.Q1515*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.Q1490*|PBRM1_uc003dey.2_Nonsense_Mutation_p.Q1463*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1570	Pro-rich.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GGTGGTGCCTGCTGCCCTGGA	0.557			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								125	62	---	---	---	---	PASS
IGSF10	285313	broad.mit.edu	37	3	151171490	151171490	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151171490G>A	uc011bod.1	-	3	397	c.397C>T	c.(397-399)CGA>TGA	p.R133*		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	133	LRR 4.				cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ATGTGCAATCGTGTCAAGCTC	0.368													4	149	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505763	195505763	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505763G>A	uc011bto.1	-	3	12764	c.12304C>T	c.(12304-12306)CTT>TTT	p.L4102F	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAAGGCTGGTGACA	0.582													4	158	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506983	195506983	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506983G>A	uc011bto.1	-	3	11544	c.11084C>T	c.(11083-11085)ACC>ATC	p.T3695I	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGAGGGGTGGTGTCACC	0.587													4	31	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195507717	195507717	+	Silent	SNP	G	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195507717G>T	uc011bto.1	-	3	10810	c.10350C>A	c.(10348-10350)TCC>TCA	p.S3450S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTCACCTGTGGATACTGAGG	0.587													25	35	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195507915	195507915	+	Silent	SNP	T	C	C	rs71635073	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195507915T>C	uc011bto.1	-	3	10612	c.10152A>G	c.(10150-10152)TCA>TCG	p.S3384S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGGTGGATGCTGAGGAAGCGC	0.587													13	136	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195507925	195507925	+	Missense_Mutation	SNP	C	T	T	rs71635074	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195507925C>T	uc011bto.1	-	3	10602	c.10142G>A	c.(10141-10143)GGC>GAC	p.G3381D	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	292					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGCGCCGGTGACAGG	0.597													10	127	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195508500	195508500	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195508500G>C	uc011bto.1	-	3	10027	c.9567C>G	c.(9565-9567)GAC>GAG	p.D3189E	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGCGTCGGTGACAA	0.577													10	48	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195509563	195509563	+	Missense_Mutation	SNP	A	T	T	rs28605870		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195509563A>T	uc011bto.1	-	3	8964	c.8504T>A	c.(8503-8505)GTC>GAC	p.V2835D	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGTGTCGGTGACAGGAAGAGA	0.587													6	68	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511525	195511525	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511525T>C	uc011bto.1	-	2	7386	c.6926A>G	c.(6925-6927)GAC>GGC	p.D2309G	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	195					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGCGTCGGTGACATG	0.582													8	22	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511526	195511526	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511526C>T	uc011bto.1	-	2	7385	c.6925G>A	c.(6925-6927)GAC>AAC	p.D2309N	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	195					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGCGTCGGTGACATGA	0.587													9	23	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195512629	195512629	+	Missense_Mutation	SNP	C	A	A	rs74830022	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195512629C>A	uc011bto.1	-	2	6282	c.5822G>T	c.(5821-5823)AGC>ATC	p.S1941I	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGCTAGTGACAGG	0.592													6	152	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513493	195513493	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513493C>A	uc011bto.1	-	2	5418	c.4958G>T	c.(4957-4959)AGC>ATC	p.S1653I	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	444					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGCTGGTGACATG	0.592													10	221	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513826	195513826	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513826G>A	uc011bto.1	-	2	5085	c.4625C>T	c.(4624-4626)CCT>CTT	p.P1542L	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGCTGAGGAAGGGCTAGTGAC	0.592													7	45	---	---	---	---	PASS
EPHA5	2044	broad.mit.edu	37	4	66213848	66213848	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66213848A>G	uc003hcy.2	-	15	2775	c.2582T>C	c.(2581-2583)GTC>GCC	p.V861A	EPHA5_uc003hcx.2_Missense_Mutation_p.V793A|EPHA5_uc003hcz.2_Missense_Mutation_p.V839A|EPHA5_uc011cah.1_Missense_Mutation_p.V862A|EPHA5_uc011cai.1_Missense_Mutation_p.V840A|EPHA5_uc003hda.2_Missense_Mutation_p.V862A	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	861	Cytoplasmic (Potential).|Protein kinase.				cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						ATAACTCCAGACATCACTGGC	0.403										TSP Lung(17;0.13)			6	314	---	---	---	---	PASS
ENAM	10117	broad.mit.edu	37	4	71495256	71495256	+	Silent	SNP	T	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71495256T>G	uc011caw.1	+	2	320	c.39T>G	c.(37-39)CCT>CCG	p.P13P		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	13					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)			CCTCTTTTCCTAAACTAGATA	0.353													101	335	---	---	---	---	PASS
DSPP	1834	broad.mit.edu	37	4	88536919	88536919	+	Silent	SNP	T	C	C	rs147223434	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88536919T>C	uc003hqu.2	+	5	3225	c.3105T>C	c.(3103-3105)GAT>GAC	p.D1035D		NM_014208	NP_055023	Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein preproprotein	1035	Asp/Ser-rich.				biomineral tissue development|ossification|skeletal system development	proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent			central_nervous_system(1)	1		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgatagcagtgaca	0.000													13	29	---	---	---	---	PASS
ADH1C	126	broad.mit.edu	37	4	100264013	100264013	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100264013T>C	uc003huu.2	-	8	852	c.767A>G	c.(766-768)AAG>AGG	p.K256R		NM_000669	NP_000660	P00326	ADH1G_HUMAN	class I alcohol dehydrogenase, gamma subunit	256					ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Fomepizole(DB01213)|NADH(DB00157)	AGTCATTTCCTTTAGCACTTC	0.458									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				7	483	---	---	---	---	PASS
CCDC109B	55013	broad.mit.edu	37	4	110603989	110603989	+	Intron	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110603989A>G	uc011cfs.1	+						CCDC109B_uc010imf.2_3'UTR	NM_017918	NP_060388	Q9NWR8	C109B_HUMAN	coiled-coil domain containing 109B							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		aatgctttccatatgctaatt	0.085													3	27	---	---	---	---	PASS
EXOSC9	5393	broad.mit.edu	37	4	122728760	122728760	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122728760T>A	uc003iea.2	+	6	696	c.588T>A	c.(586-588)TTT>TTA	p.F196L	EXOSC9_uc003idz.2_Missense_Mutation_p.F196L|EXOSC9_uc003ieb.2_Missense_Mutation_p.F180L|EXOSC9_uc010inp.1_RNA	NM_005033	NP_005024	Q06265	EXOS9_HUMAN	exosome component 9 isoform 2	196	ARE binding.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|immune response|nuclear mRNA surveillance|nuclear polyadenylation-dependent rRNA catabolic process|positive regulation of cell growth|rRNA processing	cytosol|nuclear exosome (RNase complex)|nucleolus|nucleolus|nucleus	3'-5'-exoribonuclease activity|AU-rich element binding|protein binding				0						GTGTCAGTTTTGCCTTTTTCC	0.363													108	323	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16711291	16711291	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16711291T>C	uc003jft.3	-	20	2461	c.1993A>G	c.(1993-1995)ACT>GCT	p.T665A	MYO10_uc011cnd.1_Missense_Mutation_p.T22A|MYO10_uc011cne.1_Missense_Mutation_p.T22A|MYO10_uc010itx.2_Missense_Mutation_p.T288A	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	665	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						ATTCTCACAGTCTCCAGCATC	0.473													4	107	---	---	---	---	PASS
RANBP3L	202151	broad.mit.edu	37	5	36301592	36301592	+	5'UTR	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36301592T>C	uc003jkh.2	-	1					RANBP3L_uc011cow.1_5'UTR	NM_145000	NP_659437	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like isoform 2						intracellular transport					ovary(1)	1	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			TAAAGTGGCCTTCACCAGACA	0.453													4	56	---	---	---	---	PASS
GHR	2690	broad.mit.edu	37	5	42719121	42719121	+	Silent	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42719121C>T	uc003jmt.2	+	10	1555	c.1512C>T	c.(1510-1512)GGC>GGT	p.G504G	GHR_uc011cpq.1_Silent_p.G317G	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor	504	Cytoplasmic (Potential).				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)	TTTCCCCGGGCCAAAAGAATA	0.488													5	100	---	---	---	---	PASS
ITGA1	3672	broad.mit.edu	37	5	52216231	52216231	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52216231A>G	uc003jou.2	+	17	2277	c.2225A>G	c.(2224-2226)GAG>GGG	p.E742G	ITGA1_uc003jov.2_RNA|ITGA1_uc003jow.2_Missense_Mutation_p.E273G	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor	742	Extracellular (Potential).				axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				GGAACTCAAGAGAGAAAGGTT	0.353													5	306	---	---	---	---	PASS
GZMA	3001	broad.mit.edu	37	5	54398561	54398561	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54398561T>C	uc003jpm.2	+	1	88	c.51T>C	c.(49-51)TCT>TCC	p.S17S		NM_006144	NP_006135	P12544	GRAA_HUMAN	granzyme A precursor	17					cleavage of lamin|cytolysis|immune response|negative regulation of DNA binding|negative regulation of endodeoxyribonuclease activity|negative regulation of oxidoreductase activity|positive regulation of apoptosis	extracellular region|immunological synapse|nucleus	protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|pancreas(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				TTGTCGTTTCTCTCCTGCTAA	0.403													6	411	---	---	---	---	PASS
ENC1	8507	broad.mit.edu	37	5	73931273	73931273	+	Silent	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73931273C>T	uc003kdc.3	-	2	2169	c.1038G>A	c.(1036-1038)GGG>GGA	p.G346G	ENC1_uc011css.1_Silent_p.G273G	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	346	Kelch 2.				nervous system development	cytoplasm|cytoskeleton|nuclear matrix	actin binding			ovary(1)|pancreas(1)|skin(1)	3		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		ACCCCCGCCCCCCAGTAATGT	0.522													3	82	---	---	---	---	PASS
GIN1	54826	broad.mit.edu	37	5	102433322	102433322	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102433322A>G	uc003koa.1	-	5	885	c.803T>C	c.(802-804)GTT>GCT	p.V268A	GIN1_uc003kob.1_Missense_Mutation_p.V121A|GIN1_uc003koc.1_Intron	NM_017676	NP_060146	Q9NXP7	GIN1_HUMAN	zinc finger, H2C2 domain containing	268	Integrase catalytic.				DNA integration		DNA binding			ovary(1)|skin(1)	2		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)		GGCAAATGAAACAGCTGATAG	0.373													6	578	---	---	---	---	PASS
ALDH7A1	501	broad.mit.edu	37	5	125930769	125930769	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125930769C>T	uc003ktx.2	-	1	314	c.122G>A	c.(121-123)TGG>TAG	p.W41*	ALDH7A1_uc003kty.2_RNA|ALDH7A1_uc011cxa.1_Nonsense_Mutation_p.W68*|ALDH7A1_uc003ktz.2_Nonsense_Mutation_p.W68*	NM_001182	NP_001173	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	41					cellular aldehyde metabolic process|lysine catabolic process|sensory perception of sound	cytosol|mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity|betaine-aldehyde dehydrogenase activity|L-aminoadipate-semialdehyde dehydrogenase activity			kidney(2)|ovary(1)	3		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)	NADH(DB00157)|Pyridoxine(DB00165)	CTCTTTCAGCCACGCATACTG	0.602													6	127	---	---	---	---	PASS
KIF4B	285643	broad.mit.edu	37	5	154394720	154394720	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154394720T>C	uc010jih.1	+	1	1461	c.1301T>C	c.(1300-1302)CTA>CCA	p.L434P		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	434	Potential.				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AACGCCAAGCTAGAAGAGCTC	0.443													5	264	---	---	---	---	PASS
CYFIP2	26999	broad.mit.edu	37	5	156820108	156820108	+	3'UTR	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156820108A>G	uc003lwq.2	+	33					CYFIP2_uc011ddn.1_3'UTR|CYFIP2_uc011ddo.1_3'UTR|CYFIP2_uc003lwr.2_3'UTR|CYFIP2_uc003lws.2_3'UTR|CYFIP2_uc003lwt.2_3'UTR|CYFIP2_uc011ddp.1_3'UTR|CYFIP2_uc003lwv.2_3'UTR	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AACGTGTGGGATGGACCTGGA	0.557													3	24	---	---	---	---	PASS
CLINT1	9685	broad.mit.edu	37	5	157233081	157233081	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157233081A>G	uc003lxj.1	-	7	925	c.735T>C	c.(733-735)TCT>TCC	p.S245S	CLINT1_uc003lxi.1_Silent_p.S227S|CLINT1_uc011ddv.1_Silent_p.S245S	NM_014666	NP_055481	Q14677	EPN4_HUMAN	epsin 4	245					endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CACCTTTGGGAGATCTGCCTC	0.423													8	597	---	---	---	---	PASS
MRPL2	51069	broad.mit.edu	37	6	43025965	43025965	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43025965T>C	uc003ots.1	-	2	226	c.103A>G	c.(103-105)AAC>GAC	p.N35D	KLC4_uc003otr.1_Intron|MRPL2_uc011dvc.1_Missense_Mutation_p.N35D|MRPL2_uc010jyi.2_Missense_Mutation_p.E70G|MRPL2_uc003ott.3_Missense_Mutation_p.N35D|KLC4_uc011dvd.1_5'Flank|KLC4_uc003otu.2_5'Flank|KLC4_uc003otv.1_5'Flank|KLC4_uc003otw.1_5'Flank|KLC4_uc003otx.1_5'Flank|KLC4_uc003oty.1_5'Flank|KLC4_uc003otz.1_5'Flank	NM_015950	NP_057034	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2 precursor	35					translation	mitochondrion|ribosome	structural constituent of ribosome				0		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		AGGCCATTGTTCATCATCTAG	0.468													5	237	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56401585	56401585	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56401585T>C	uc003pdf.2	-	56	10433	c.10405A>G	c.(10405-10407)AAT>GAT	p.N3469D	DST_uc003pcz.3_Missense_Mutation_p.N3291D|DST_uc011dxj.1_Missense_Mutation_p.N3320D|DST_uc011dxk.1_Missense_Mutation_p.N3331D|DST_uc003pcy.3_Missense_Mutation_p.N2965D	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5377	Spectrin 7.				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)			ACCTTCTTATTGAGAGTCTTC	0.433													51	126	---	---	---	---	PASS
BEND6	221336	broad.mit.edu	37	6	56857317	56857317	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56857317A>G	uc010kab.2	+	3	848	c.262A>G	c.(262-264)AAC>GAC	p.N88D	BEND6_uc003pdg.2_RNA	NM_152731	NP_689944	Q5SZJ8	BEND6_HUMAN	BEN domain containing 6	88	Potential.										0						CCGGAAAGAAAACAGCCGACT	0.378													7	310	---	---	---	---	PASS
KCNQ5	56479	broad.mit.edu	37	6	73904212	73904212	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73904212A>G	uc003pgk.2	+	14	2221	c.1874A>G	c.(1873-1875)GAC>GGC	p.D625G	KCNQ5_uc011dyh.1_Missense_Mutation_p.D644G|KCNQ5_uc011dyi.1_Missense_Mutation_p.D635G|KCNQ5_uc010kat.2_Missense_Mutation_p.D616G|KCNQ5_uc011dyj.1_Missense_Mutation_p.D515G|KCNQ5_uc011dyk.1_Missense_Mutation_p.D375G	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	625					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)		TGCCTACTAGACATCTATCAA	0.423													4	109	---	---	---	---	PASS
REV3L	5980	broad.mit.edu	37	6	111696867	111696867	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111696867A>G	uc003puy.3	-	13	3014	c.2691T>C	c.(2689-2691)TGT>TGC	p.C897C	REV3L_uc003pux.3_Silent_p.C819C|REV3L_uc003puz.3_Silent_p.C819C	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	897					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTCCAAAGTGACAGTCTATAA	0.373								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					5	190	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152720859	152720859	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152720859T>C	uc010kiw.2	-	48	7731	c.7129A>G	c.(7129-7131)AGC>GGC	p.S2377G	SYNE1_uc003qot.3_Missense_Mutation_p.S2384G|SYNE1_uc003qou.3_Missense_Mutation_p.S2377G|SYNE1_uc010kjb.1_Missense_Mutation_p.S2360G	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2377	Spectrin 3.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CGGCCCAGGCTCTCCAACTCA	0.473										HNSCC(10;0.0054)			6	340	---	---	---	---	PASS
ZNF735	730291	broad.mit.edu	37	7	63673489	63673489	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63673489A>G	uc011kdn.1	+	2	59	c.59A>G	c.(58-60)GAC>GGC	p.D20G		NM_001159524	NP_001152996	P0CB33	ZN735_HUMAN	zinc finger protein 735	20	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ACATTCAGAGACATAGCTATA	0.383													5	276	---	---	---	---	PASS
AUTS2	26053	broad.mit.edu	37	7	70255256	70255256	+	Silent	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70255256C>T	uc003tvw.3	+	19	3797	c.3054C>T	c.(3052-3054)CCC>CCT	p.P1018P	AUTS2_uc003tvx.3_Silent_p.P994P|AUTS2_uc011keg.1_Silent_p.P470P	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	1018										ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		ACCCGGGGCCCCTGGCCTCGA	0.677													3	29	---	---	---	---	PASS
GTF2IP1	2970	broad.mit.edu	37	7	72617487	72617487	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72617487A>G	uc003txo.3	+	21	2356	c.1475A>G	c.(1474-1476)AAA>AGA	p.K492R	FKBP6_uc003twz.2_Intron|GTF2IP1_uc011keq.1_Missense_Mutation_p.K492R	NR_003580				SubName: Full=cDNA FLJ61347, highly similar to General transcription factor II-I;												0						AGTGAGTCAAAAGGCCCCGTG	0.502													5	260	---	---	---	---	PASS
PHTF2	57157	broad.mit.edu	37	7	77531189	77531189	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77531189A>G	uc003ugs.3	+	6	523	c.397A>G	c.(397-399)ACA>GCA	p.T133A	PHTF2_uc003ugo.3_Missense_Mutation_p.T95A|PHTF2_uc003ugp.2_Missense_Mutation_p.T95A|PHTF2_uc003ugq.3_Missense_Mutation_p.T95A|PHTF2_uc010ldv.2_Missense_Mutation_p.T95A|PHTF2_uc003ugr.3_Missense_Mutation_p.T99A|PHTF2_uc003ugt.3_Missense_Mutation_p.T99A|PHTF2_uc003ugu.3_Missense_Mutation_p.T95A	NM_001127357	NP_001120829	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	133					regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1						GTTACAAGTAACATCAAAGGT	0.373													6	526	---	---	---	---	PASS
CACNA2D1	781	broad.mit.edu	37	7	81598283	81598283	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81598283C>T	uc003uhr.1	-	29	2571	c.2315G>A	c.(2314-2316)GGA>GAA	p.G772E	CACNA2D1_uc011kgy.1_Intron	NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	784	Extracellular (Potential).					voltage-gated calcium channel complex	metal ion binding	p.G772E(1)		ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	GGCACCAGGTCCACTTTCtaa	0.284													116	200	---	---	---	---	PASS
EPHB4	2050	broad.mit.edu	37	7	100410789	100410789	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100410789T>G	uc003uwn.1	-	11	2289	c.1798A>C	c.(1798-1800)AAT>CAT	p.N600H	EPHB4_uc003uwm.1_Missense_Mutation_p.N507H|EPHB4_uc010lhj.1_Missense_Mutation_p.N600H	NM_004444	NP_004435	P54760	EPHB4_HUMAN	EPH receptor B4 precursor	600	Cytoplasmic (Potential).				cell proliferation|organ morphogenesis|regulation of angiogenesis	cell surface|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1)	15	Lung NSC(181;0.041)|all_lung(186;0.0581)					ACAGCCTCATTAGGGTCTTCA	0.532													10	356	---	---	---	---	PASS
COG5	10466	broad.mit.edu	37	7	106888896	106888896	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106888896C>T	uc003ved.2	-	16	2353	c.1828G>A	c.(1828-1830)GTG>ATG	p.V610M	COG5_uc003vec.2_Missense_Mutation_p.V631M|COG5_uc003vee.2_Missense_Mutation_p.V631M	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform	610					intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						GCATCTCCCACAGAAGTGAGT	0.318													125	210	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151860719	151860719	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151860719G>A	uc003wla.2	-	43	10162	c.9943C>T	c.(9943-9945)CAG>TAG	p.Q3315*	MLL3_uc003wkz.2_Nonsense_Mutation_p.Q2376*|MLL3_uc003wky.2_Nonsense_Mutation_p.Q824*	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3315	Gln-rich.|Pro-rich.				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)		GTTGTGTGCTGCTGGTGCTGA	0.582			N		medulloblastoma								170	281	---	---	---	---	PASS
PRKDC	5591	broad.mit.edu	37	8	48706924	48706924	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48706924A>G	uc003xqi.2	-	75	10654	c.10597T>C	c.(10597-10599)TTC>CTC	p.F3533L	PRKDC_uc003xqj.2_Missense_Mutation_p.F3533L|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	3533	FAT.				cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				CTTATGATGAAGGGATAAACA	0.438								NHEJ					6	309	---	---	---	---	PASS
ZBTB10	65986	broad.mit.edu	37	8	81411751	81411751	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81411751A>G	uc003ybx.3	+	2	1593	c.995A>G	c.(994-996)GAG>GGG	p.E332G	ZBTB10_uc003ybv.3_Missense_Mutation_p.E40G|ZBTB10_uc003ybw.3_Missense_Mutation_p.E332G|ZBTB10_uc010lzt.2_Missense_Mutation_p.E332G	NM_001105539	NP_001099009	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10 isoform	332					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			CCATCAGAGGAGGGGTACTGT	0.323													6	235	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110432841	110432841	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110432841G>A	uc003yne.2	+	23	2723	c.2619G>A	c.(2617-2619)ATG>ATA	p.M873I		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	873	Extracellular (Potential).				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)			GGCCAACTATGACAAACCAAT	0.383										HNSCC(38;0.096)			139	242	---	---	---	---	PASS
SNTB1	6641	broad.mit.edu	37	8	121823811	121823811	+	Silent	SNP	G	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121823811G>C	uc010mdg.2	-	1	499	c.273C>G	c.(271-273)GTC>GTG	p.V91V	SNTB1_uc003ype.2_Silent_p.V91V	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin	91	PH 1.				muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			AAGCGGTGCGGAccccggcgg	0.453													9	12	---	---	---	---	PASS
ASAP1	50807	broad.mit.edu	37	8	131165021	131165021	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131165021A>G	uc003yta.1	-	12	1069	c.1041T>C	c.(1039-1041)TGT>TGC	p.C347C	ASAP1_uc003ysz.1_Silent_p.C158C|ASAP1_uc011liw.1_Silent_p.C340C	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor	347	PH.				cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						TCTTGACTGAACACTTCCTCC	0.433													5	218	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20414343A>G	uc003zoe.2	-	5	760	c.501T>C	c.(499-501)AGT>AGC	p.S167S	MLLT3_uc011lne.1_Silent_p.S135S|MLLT3_uc011lnf.1_Silent_p.S164S|MLLT3_uc003zof.2_5'UTR|MLLT3_uc011lng.1_Missense_Mutation_p.V129A	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	167	Poly-Ser.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.139			T	MLL	ALL								8	122	---	---	---	---	PASS
KIAA1797	54914	broad.mit.edu	37	9	20720379	20720379	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20720379A>G	uc003zog.1	+	6	496	c.133A>G	c.(133-135)ACT>GCT	p.T45A		NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914	45						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)		TTGGTTTCAGACTCCTGCTTT	0.458													6	296	---	---	---	---	PASS
AQP7	364	broad.mit.edu	37	9	33395267	33395267	+	Intron	SNP	C	A	A	rs149620724	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33395267C>A	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_5'Flank|AQP7_uc010mjt.2_5'UTR|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_5'UTR|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TCTTCAACTCCCAGCTGAGTT	0.592													4	31	---	---	---	---	PASS
EXOSC3	51010	broad.mit.edu	37	9	37780827	37780827	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37780827G>A	uc004aal.2	-	4	703	c.677C>T	c.(676-678)CCA>CTA	p.P226L	EXOSC3_uc010mly.1_Missense_Mutation_p.P226L|EXOSC3_uc004aam.2_3'UTR	NM_016042	NP_057126	Q9NQT5	EXOS3_HUMAN	exosome component 3 isoform 1	226					CUT catabolic process|DNA deamination|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|isotype switching|rRNA processing	cytoplasmic exosome (RNase complex)|cytosol|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5'-exoribonuclease activity|protein binding|RNA binding			breast(2)	2				GBM - Glioblastoma multiforme(29;0.00771)|Lung(182;0.221)		TATCTCCAGTGGATAGAGTTT	0.378													5	405	---	---	---	---	PASS
TXN	7295	broad.mit.edu	37	9	113018762	113018762	+	5'UTR	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113018762G>A	uc004bep.1	-	1					TXN_uc004beq.1_5'UTR|TXN_uc004ber.1_RNA	NM_003329	NP_003320	P10599	THIO_HUMAN	thioredoxin						cell proliferation|cell-cell signaling|cellular component movement|electron transport chain|glycerol ether metabolic process|nucleobase, nucleoside and nucleotide interconversion|positive regulation of DNA binding|regulation of protein import into nucleus, translocation|response to radiation|signal transduction|transcription, DNA-dependent|transport	cytosol|extracellular region|nucleoplasm	electron carrier activity|protein binding|protein disulfide oxidoreductase activity				0				OV - Ovarian serous cystadenocarcinoma(323;7.36e-07)		CGATGGAAATGGATCCAAAGC	0.517													10	34	---	---	---	---	PASS
ITIH5	80760	broad.mit.edu	37	10	7683905	7683905	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7683905A>G	uc001ijq.2	-	3	363	c.284T>C	c.(283-285)ATC>ACC	p.I95T	ITIH5_uc001ijr.1_Missense_Mutation_p.I95T	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	95	VIT.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4						GAAGTTGGTGATGAAAGCTGC	0.507													4	88	---	---	---	---	PASS
CTNNA3	29119	broad.mit.edu	37	10	68979386	68979386	+	Silent	SNP	T	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68979386T>A	uc009xpn.1	-	6	945	c.822A>T	c.(820-822)GGA>GGT	p.G274G	CTNNA3_uc001jmw.2_Silent_p.G274G|CTNNA3_uc001jmx.3_Silent_p.G274G|CTNNA3_uc009xpo.1_Silent_p.G134G|CTNNA3_uc001jna.2_Silent_p.G286G	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3	274					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						CAAGGGCACTTCCCAGGGTTG	0.403													5	217	---	---	---	---	PASS
DDX50	79009	broad.mit.edu	37	10	70670959	70670959	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70670959T>C	uc001jou.2	+	4	703	c.596T>C	c.(595-597)CTC>CCC	p.L199P	DDX50_uc001jot.2_Missense_Mutation_p.L199P|DDX50_uc010qjc.1_Missense_Mutation_p.L199P	NM_024045	NP_076950	Q9BQ39	DDX50_HUMAN	nucleolar protein GU2	199	Helicase ATP-binding.					nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1						ATTGAAAGACTCCAAAGAAAT	0.368													4	110	---	---	---	---	PASS
SUPV3L1	6832	broad.mit.edu	37	10	70951507	70951507	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70951507A>G	uc001jpe.1	+	6	893	c.838A>G	c.(838-840)AGT>GGT	p.S280G	SUPV3L1_uc010qjd.1_Missense_Mutation_p.S149G	NM_003171	NP_003162	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 precursor	280	Helicase ATP-binding.				DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2						TGAGATGTGCAGTGTTACAAC	0.328													6	296	---	---	---	---	PASS
MYOF	26509	broad.mit.edu	37	10	95066678	95066678	+	3'UTR	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95066678T>C	uc001kin.2	-	54					MYOF_uc001kio.2_3'UTR|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						GGCAGGATTCTCTCATTGCTG	0.443													162	64	---	---	---	---	PASS
CYP2C9	1559	broad.mit.edu	37	10	96701763	96701763	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96701763C>T	uc001kka.3	+	2	342	c.317C>T	c.(316-318)GCT>GTT	p.A106V	CYP2C9_uc009xut.2_Missense_Mutation_p.A106V|CYP2C9_uc001kjz.2_Missense_Mutation_p.A106V	NM_000771	NP_000762	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C,	106					exogenous drug catabolic process|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid metabolic process|urea metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|caffeine oxidase activity|drug binding|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(4)|ovary(2)	6		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Alosetron(DB00969)|Amiodarone(DB01118)|Antihemophilic Factor(DB00025)|Aprepitant(DB00673)|Bosentan(DB00559)|Carprofen(DB00821)|Carvedilol(DB01136)|Celecoxib(DB00482)|Clomipramine(DB01242)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Desogestrel(DB00304)|Diclofenac(DB00586)|Esomeprazole(DB00736)|Etodolac(DB00749)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Glibenclamide(DB01016)|Glimepiride(DB00222)|Glipizide(DB01067)|Guanfacine(DB01018)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Imipramine(DB00458)|Irbesartan(DB01029)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Losartan(DB00678)|Lumiracoxib(DB01283)|Marinol(DB00470)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mephenytoin(DB00532)|Metronidazole(DB00916)|Miconazole(DB01110)|Midazolam(DB00683)|Montelukast(DB00471)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Oxymorphone(DB01192)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pravastatin(DB00175)|Quinidine(DB00908)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Sertraline(DB01104)|Sildenafil(DB00203)|Sulfamethoxazole(DB01015)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tenoxicam(DB00469)|Terfenadine(DB00342)|Tolbutamide(DB01124)|Torasemide(DB00214)|Troleandomycin(DB01361)|Valdecoxib(DB00580)|Valsartan(DB00177)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)	GCTGAAAGAGCTAACAGAGGA	0.507													5	559	---	---	---	---	PASS
MMP21	118856	broad.mit.edu	37	10	127461203	127461203	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127461203C>T	uc001liu.2	-	3	814	c.814G>A	c.(814-816)GAC>AAC	p.D272N		NM_147191	NP_671724	Q8N119	MMP21_HUMAN	matrix metalloproteinase 21 preproprotein	272					proteolysis	extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				ATGCCCGTGTCACTGGTGGGA	0.572													73	20	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093437	1093437	+	Silent	SNP	G	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093437G>C	uc001lsx.1	+	31	12369	c.12342G>C	c.(12340-12342)ACG>ACC	p.T4114T		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4114						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|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;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccacggtgaccccaa	0.000													15	466	---	---	---	---	PASS
OR52I2	143502	broad.mit.edu	37	11	4608985	4608985	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4608985C>T	uc010qyh.1	+	1	943	c.943C>T	c.(943-945)CCA>TCA	p.P315S		NM_001005170	NP_001005170	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I,	315	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CGTGATCATCCCAGCCACCTT	0.512													120	164	---	---	---	---	PASS
OR51V1	283111	broad.mit.edu	37	11	5221867	5221867	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5221867G>T	uc010qyz.1	-	1	64	c.64C>A	c.(64-66)CTT>ATT	p.L22I		NM_001004760	NP_001004760	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V,	22	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCAGTGAGAAGAAAGGAAGAA	0.428													4	196	---	---	---	---	PASS
OR52B6	340980	broad.mit.edu	37	11	5603002	5603002	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5603002T>C	uc010qzi.1	+	1	896	c.896T>C	c.(895-897)CTC>CCC	p.L299P	HBG2_uc001mak.1_Intron	NM_001005162	NP_001005162	Q8NGF0	O52B6_HUMAN	olfactory receptor, family 52, subfamily B,	299	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;3.56e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGGCCAGCCTCTACGTTGTC	0.468													7	560	---	---	---	---	PASS
API5	8539	broad.mit.edu	37	11	43352069	43352069	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43352069A>G	uc010rfh.1	+	11	1406	c.1233A>G	c.(1231-1233)AAA>AAG	p.K411K	API5_uc010rfg.1_Silent_p.K400K|API5_uc001mxf.2_Silent_p.K411K|API5_uc010rfi.1_Silent_p.K357K|API5_uc001mxg.2_Silent_p.K285K	NM_001142930	NP_001136402	Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5 isoform a	411					anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3						ACAAGATTAAAGTCGTTGCAT	0.299													6	446	---	---	---	---	PASS
MADD	8567	broad.mit.edu	37	11	47331130	47331130	+	Silent	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47331130G>A	uc001ner.1	+	28	4316	c.4125G>A	c.(4123-4125)CTG>CTA	p.L1375L	MADD_uc001neq.2_Silent_p.L1316L|MADD_uc001nev.1_Silent_p.L1273L|MADD_uc001nes.1_Silent_p.L1293L|MADD_uc001net.1_Silent_p.L1336L|MADD_uc009yln.1_Silent_p.L1269L|MADD_uc001neu.1_Silent_p.L1273L|MADD_uc001nex.2_Silent_p.L1375L|MADD_uc001nez.2_Silent_p.L1272L|MADD_uc001new.2_Silent_p.L1315L|MADD_uc009ylo.2_Silent_p.L289L	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	1375	Death.				activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)		CCACACTTCTGCACAACCTCA	0.517													5	221	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62296991	62296991	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62296991T>C	uc001ntl.2	-	5	5198	c.4898A>G	c.(4897-4899)GAA>GGA	p.E1633G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1633					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				CAACTTCCCTTCTGGACCTTC	0.473													5	253	---	---	---	---	PASS
C11orf20	25858	broad.mit.edu	37	11	64071010	64071010	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64071010T>C	uc009ypm.2	+	3	429	c.409T>C	c.(409-411)TAC>CAC	p.Y137H	KCNK4_uc001nzm.3_RNA|ESRRA_uc001nzq.1_5'Flank|ESRRA_uc001nzr.1_5'Flank|ESRRA_uc001nzs.1_5'Flank	NM_001039496	NP_001034585	Q9NTU4	CK020_HUMAN	hypothetical protein LOC25858	137					cell differentiation|spermatogenesis	cytoplasm					0						CCATCGAGCCTACTGGGCAGA	0.532													4	311	---	---	---	---	PASS
MUS81	80198	broad.mit.edu	37	11	65629691	65629691	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65629691G>A	uc001ofv.3	+	5	813	c.460G>A	c.(460-462)GGT>AGT	p.G154S	CFL1_uc001oft.2_5'Flank|MUS81_uc001ofw.3_RNA|MUS81_uc001ofx.3_5'Flank	NM_025128	NP_079404	Q96NY9	MUS81_HUMAN	MUS81 endonuclease homolog	154	Interaction with BLM.				DNA recombination|DNA repair	nucleolus	3'-flap endonuclease activity|DNA binding|metal ion binding|protein binding				0				READ - Rectum adenocarcinoma(159;0.166)		GAATCCTAATGGTCACCACTT	0.577								Homologous_recombination					4	175	---	---	---	---	PASS
MMP12	4321	broad.mit.edu	37	11	102738000	102738000	+	Splice_Site	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102738000C>T	uc001phk.2	-	7	956	c.911_splice	c.e7+1	p.R304_splice		NM_002426	NP_002417	P39900	MMP12_HUMAN	matrix metalloproteinase 12 preproprotein						positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)	AATGATCCTACCTGTCTTTGA	0.338													5	429	---	---	---	---	PASS
DDI1	414301	broad.mit.edu	37	11	103908556	103908556	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103908556C>T	uc001phr.2	+	1	1249	c.1006C>T	c.(1006-1008)CGG>TGG	p.R336W	PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1	336					proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|upper_aerodigestive_tract(1)|pancreas(1)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		AGATATGCTCCGGAGACATCA	0.443													36	213	---	---	---	---	PASS
OR4D5	219875	broad.mit.edu	37	11	123810587	123810587	+	Silent	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123810587C>T	uc001pzk.1	+	1	264	c.264C>T	c.(262-264)GGC>GGT	p.G88G		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	88	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TGCTCTCAGGCAACCCTACCA	0.473													33	235	---	---	---	---	PASS
ST8SIA1	6489	broad.mit.edu	37	12	22408288	22408288	+	Silent	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22408288C>T	uc001rfo.3	-	3	899	c.417G>A	c.(415-417)GCG>GCA	p.A139A	ST8SIA1_uc009zix.2_Intron	NM_003034	NP_003025	Q92185	SIA8A_HUMAN	alpha-2,8-sialyltransferase 1	139	Lumenal (Potential).				glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(3)	3						TTCCCACCACCGCGCATTTCT	0.498													4	235	---	---	---	---	PASS
FAM19A2	338811	broad.mit.edu	37	12	62148719	62148719	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62148719C>A	uc001sqw.2	-	3	1706	c.193G>T	c.(193-195)GTC>TTC	p.V65F	FAM19A2_uc001sqv.2_RNA|FAM19A2_uc001sqx.2_Missense_Mutation_p.V65F|FAM19A2_uc001sqy.2_RNA	NM_178539	NP_848634	Q8N3H0	F19A2_HUMAN	family with sequence similarity 19 (chemokine	65						cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)		GAGCACTTGACTGTTTGTGAC	0.493													32	181	---	---	---	---	PASS
LEMD3	23592	broad.mit.edu	37	12	65564335	65564335	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65564335A>G	uc001ssl.1	+	1	965	c.959A>G	c.(958-960)GAC>GGC	p.D320G	LEMD3_uc009zqo.1_Missense_Mutation_p.D320G	NM_014319	NP_055134	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	320					negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		GCGATGAATGACAGGGCGGCG	0.652													4	64	---	---	---	---	PASS
C12orf50	160419	broad.mit.edu	37	12	88376922	88376922	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88376922G>A	uc001tam.1	-	12	1345	c.1177C>T	c.(1177-1179)CCT>TCT	p.P393S		NM_152589	NP_689802	Q8NA57	CL050_HUMAN	hypothetical protein LOC160419	393										skin(2)|ovary(1)	3						TTTGAAAAAGGAATTCGTTTT	0.259													10	416	---	---	---	---	PASS
GNPTAB	79158	broad.mit.edu	37	12	102161789	102161789	+	Intron	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102161789C>T	uc001tit.2	-						GNPTAB_uc001tiu.1_Silent_p.S478S	NM_024312	NP_077288	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase						cell differentiation	Golgi membrane|integral to membrane|nucleus	metal ion binding|transcription factor binding|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity			ovary(1)|skin(1)	2						TAAAAATGAACGAATTACAGT	0.328													89	135	---	---	---	---	PASS
TRAFD1	10906	broad.mit.edu	37	12	112590234	112590234	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112590234T>C	uc001ttp.2	+	11	1709	c.1623T>C	c.(1621-1623)GGT>GGC	p.G541G	TRAFD1_uc001tto.2_Silent_p.G541G	NM_006700	NP_006691	O14545	TRAD1_HUMAN	TRAF-type zinc finger domain containing 1	541					negative regulation of innate immune response	intracellular	protein binding|zinc ion binding				0						CTTTCAGTGGTAGGAGTGAAG	0.517													6	289	---	---	---	---	PASS
POSTN	10631	broad.mit.edu	37	13	38162097	38162097	+	Silent	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38162097G>A	uc001uwo.3	-	5	586	c.468C>T	c.(466-468)AAC>AAT	p.N156N	POSTN_uc001uwp.3_Silent_p.N156N|POSTN_uc001uwr.2_Silent_p.N156N|POSTN_uc001uwq.2_Silent_p.N156N|POSTN_uc010teu.1_Silent_p.N156N|POSTN_uc010tev.1_Silent_p.N156N|POSTN_uc010tew.1_Silent_p.N156N|POSTN_uc010tex.1_Silent_p.N71N	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	156	FAS1 1.				cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		CAACATTCACGTTGCTCTCCA	0.323													133	157	---	---	---	---	PASS
GUCY1B2	2974	broad.mit.edu	37	13	51602398	51602398	+	Intron	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51602398T>C	uc001vfd.3	-						GUCY1B2_uc010tgo.1_Intron|GUCY1B2_uc001vfc.3_RNA					SubName: Full=Guanylate cyclase 1, soluble, beta 2;												0						GCTTTGTCTTTCTCATCTTCC	0.433													6	730	---	---	---	---	PASS
DOCK9	23348	broad.mit.edu	37	13	99449450	99449450	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99449450T>C	uc001vnt.2	-	54	6175	c.6120A>G	c.(6118-6120)GAA>GAG	p.E2040E	DOCK9_uc001vnw.2_Silent_p.E2039E|DOCK9_uc001vnq.2_Silent_p.E587E|DOCK9_uc001vnr.2_Silent_p.E669E|DOCK9_uc010tin.1_Silent_p.E658E|DOCK9_uc001vns.2_Silent_p.E575E|DOCK9_uc010tio.1_Silent_p.E695E|DOCK9_uc010tip.1_Silent_p.E736E	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	2040	Potential.|DHR-2.				blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CGAGCTGGTCTTCTTTAATCA	0.502													5	318	---	---	---	---	PASS
OR10G3	26533	broad.mit.edu	37	14	22038220	22038220	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22038220T>C	uc010tmb.1	-	1	656	c.656A>G	c.(655-657)TAC>TGC	p.Y219C		NM_001005465	NP_001005465	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G,	219	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|central_nervous_system(1)	2	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		GATCTGTATGTAGGAGAGGAG	0.542													4	209	---	---	---	---	PASS
EFS	10278	broad.mit.edu	37	14	23826852	23826852	+	Silent	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23826852C>T	uc001wjo.2	-	6	1877	c.1269G>A	c.(1267-1269)GGG>GGA	p.G423G	EFS_uc001wjp.2_Silent_p.G330G|EFS_uc010tnm.1_Silent_p.G254G	NM_005864	NP_005855	O43281	EFS_HUMAN	embryonal Fyn-associated substrate isoform 1	423					cell adhesion|intracellular signal transduction	cytoplasm	SH3 domain binding			large_intestine(1)	1	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		CCAGTGGCTCCCCTGGGGACA	0.577													7	27	---	---	---	---	PASS
NYNRIN	57523	broad.mit.edu	37	14	24884470	24884470	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24884470C>T	uc001wpf.3	+	9	3833	c.3515C>T	c.(3514-3516)ACG>ATG	p.T1172M		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	1172					DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3						GTGGCCCTGACGGCCATCCTC	0.657													18	14	---	---	---	---	PASS
TIMM9	26520	broad.mit.edu	37	14	58877562	58877562	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58877562T>C	uc010aph.2	-	3	349	c.134A>G	c.(133-135)GAG>GGG	p.E45G	TIMM9_uc001xds.2_Missense_Mutation_p.E45G|TIMM9_uc010api.2_Missense_Mutation_p.E45G	NM_012460	NP_036592	Q9Y5J7	TIM9_HUMAN	translocase of inner mitochondrial membrane 9	45	Twin CX3C motif.				protein import into mitochondrial inner membrane|sensory perception of sound|transmembrane transport	mitochondrial inner membrane presequence translocase complex|mitochondrial intermembrane space protein transporter complex	zinc ion binding				0						TTTTCATACCTCTTCAGGTTT	0.358													6	462	---	---	---	---	PASS
ADAM21P1	145241	broad.mit.edu	37	14	70714259	70714259	+	5'UTR	SNP	A	G	G	rs7144638	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70714259A>G	uc010ttg.1	-	1						NR_003951				SubName: Full=ADAM21-like protein;												0						CACCACTTCCAGGGAAGTGAA	0.527													7	119	---	---	---	---	PASS
MLH3	27030	broad.mit.edu	37	14	75500151	75500151	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75500151T>C	uc001xrd.1	-	7	3902	c.3686A>G	c.(3685-3687)GAG>GGG	p.E1229G	MLH3_uc001xre.1_Intron|MLH3_uc010tuy.1_RNA	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	1229					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)		ACGTATACGCTCATGGGCAGC	0.478								MMR					4	72	---	---	---	---	PASS
DIO2	1734	broad.mit.edu	37	14	80669284	80669284	+	Silent	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80669284A>G	uc010tvq.1	-	4	972	c.570T>C	c.(568-570)GAT>GAC	p.D190D	DIO2_uc010tvp.1_Silent_p.D226D|DIO2_uc001xut.2_RNA|DIO2_uc010asx.2_3'UTR|DIO2_uc010tvr.1_Silent_p.D190D|DIO2_uc010asy.2_3'UTR	NM_000793	NP_000784	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II isoform a	190					hormone biosynthetic process|selenocysteine incorporation|thyroid hormone generation	integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|ubiquitin protein ligase binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0281)		CTGCACATCGATCTTCCTGGT	0.552											OREG0022848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	64	---	---	---	---	PASS
TDRD9	122402	broad.mit.edu	37	14	104436923	104436923	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104436923C>T	uc001yom.3	+	6	841	c.811C>T	c.(811-813)CGC>TGC	p.R271C	TDRD9_uc001yon.3_Missense_Mutation_p.R9C	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	271	Helicase ATP-binding.				cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				ATTGGTAGTCCGCAAACTCTT	0.373													6	382	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106208261	106208261	+	RNA	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106208261G>A	uc010tyt.1	-	3627		c.58953C>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Silent_p.A79A|uc001ysf.2_Silent_p.A79A					Parts of antibodies, mostly variable regions.												0						TCTCGATGGGGGCTGGGAGGG	0.622													7	276	---	---	---	---	PASS
SPTBN5	51332	broad.mit.edu	37	15	42150817	42150817	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42150817G>C	uc001zos.2	-	49	8437	c.8104C>G	c.(8104-8106)CAG>GAG	p.Q2702E		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2737	Spectrin 24.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		AGCTCCTGCTGTTGGTGCATG	0.627													10	8	---	---	---	---	PASS
VPS39	23339	broad.mit.edu	37	15	42476783	42476783	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42476783A>G	uc001zpd.2	-	9	834	c.683T>C	c.(682-684)GTA>GCA	p.V228A	VPS39_uc001zpc.2_Missense_Mutation_p.V217A	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39	228	CNH.				protein transport	HOPS complex|late endosome membrane|lysosomal membrane	small GTPase regulator activity			ovary(1)|pancreas(1)|skin(1)	3		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		CTCATTGAGTACCACGGTGAG	0.522													4	145	---	---	---	---	PASS
MYO5C	55930	broad.mit.edu	37	15	52564788	52564788	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52564788C>T	uc010bff.2	-	6	876	c.739G>A	c.(739-741)GTT>ATT	p.V247I	MYO5C_uc010uga.1_RNA|MYO5C_uc010ugb.1_RNA|MYO5C_uc010ugc.1_Missense_Mutation_p.V210I	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	247	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		TGAAAGACAACTCTGGATTTC	0.343													5	354	---	---	---	---	PASS
GOLGA6L5	374650	broad.mit.edu	37	15	85053208	85053208	+	RNA	SNP	A	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85053208A>C	uc002bkm.2	-	9		c.1839T>G			uc002bkl.1_5'Flank	NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						AAAGAATGGCATGCAGCCTCT	0.512													4	20	---	---	---	---	PASS
PDPK1	5170	broad.mit.edu	37	16	2652616	2652616	+	3'UTR	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2652616T>C	uc002cqs.2	+	14					PDPK1_uc002cqt.2_3'UTR|PDPK1_uc010bsn.2_3'UTR|PDPK1_uc002cqu.2_3'UTR|LOC652276_uc002cqx.2_5'Flank|LOC652276_uc002cqy.3_5'Flank	NM_002613	NP_002604	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase-1						actin cytoskeleton organization|activation of protein kinase B activity|insulin receptor signaling pathway|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|peptidyl-threonine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|synaptic transmission|T cell costimulation|T cell receptor signaling pathway	cytosol|nucleoplasm|plasma membrane	3-phosphoinositide-dependent protein kinase activity|ATP binding			central_nervous_system(2)|ovary(1)	3		Ovarian(90;0.17)			Celecoxib(DB00482)	AAGTTGGATGTTGGCAAAATT	0.413													5	293	---	---	---	---	PASS
SRRM2	23524	broad.mit.edu	37	16	2815556	2815556	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2815556C>A	uc002crk.2	+	11	5576	c.5027C>A	c.(5026-5028)CCA>CAA	p.P1676Q	SRRM2_uc002crj.1_Missense_Mutation_p.P1580Q|SRRM2_uc002crl.1_Missense_Mutation_p.P1676Q|SRRM2_uc010bsu.1_Missense_Mutation_p.P1580Q	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	1676	Arg-rich.|Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						AGGTCATCACCAGAGCCCAAG	0.572													3	95	---	---	---	---	PASS
A2BP1	54715	broad.mit.edu	37	16	7647386	7647386	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7647386C>T	uc002cys.2	+	9	1563	c.575C>T	c.(574-576)ACA>ATA	p.T192I	A2BP1_uc010buf.1_Missense_Mutation_p.T192I|A2BP1_uc002cyr.1_Missense_Mutation_p.T191I|A2BP1_uc002cyt.2_Missense_Mutation_p.T192I|A2BP1_uc010uxz.1_Missense_Mutation_p.T235I|A2BP1_uc010uya.1_Missense_Mutation_p.T149I|A2BP1_uc002cyv.1_Missense_Mutation_p.T192I|A2BP1_uc010uyb.1_Missense_Mutation_p.T192I|A2BP1_uc002cyw.2_Missense_Mutation_p.T212I|A2BP1_uc002cyy.2_Missense_Mutation_p.T212I|A2BP1_uc002cyx.2_Missense_Mutation_p.T212I|A2BP1_uc010uyc.1_Missense_Mutation_p.T212I	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4	192	RRM.				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)		AATAATGCCACAGCACGTGTA	0.363													13	468	---	---	---	---	PASS
USP7	7874	broad.mit.edu	37	16	9012898	9012898	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9012898T>G	uc002czl.2	-	6	909	c.710A>C	c.(709-711)CAG>CCG	p.Q237P	USP7_uc010uyk.1_Missense_Mutation_p.Q138P|USP7_uc010uyj.1_Missense_Mutation_p.Q138P|USP7_uc002czk.2_Missense_Mutation_p.Q221P|USP7_uc010uyl.1_RNA	NM_003470	NP_003461	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7	237					interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3						CTTTCGTAGCTGATTCGTGAA	0.468													43	71	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268121	70268121	+	RNA	SNP	C	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268121C>G	uc010cfp.1	-	3		c.294G>C								Homo sapiens cDNA, FLJ98908.																		AGACGGAAGACAGAATAAAGG	0.338													6	60	---	---	---	---	PASS
PSMD7	5713	broad.mit.edu	37	16	74336132	74336132	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74336132A>G	uc002fcq.2	+	5	512	c.380A>G	c.(379-381)AAG>AGG	p.K127R	PSMD7_uc010vmr.1_Missense_Mutation_p.K50R	NM_002811	NP_002802	P51665	PSD7_HUMAN	proteasome 26S non-ATPase subunit 7	127					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0						ATTGATGTGAAGCCGAAGGAC	0.458													6	303	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90168789	90168789	+	RNA	SNP	C	T	T	rs4273797		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90168789C>T	uc002fqr.2	+	1		c.88C>T								Homo sapiens cDNA FLJ35239 fis, clone PROST2002212.																		CCTGTGGCCTCGCAAACAAAA	0.343													5	239	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10419922	10419922	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10419922G>A	uc002gmo.2	-	3	132	c.38C>T	c.(37-39)GCT>GTT	p.A13V	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	13	Myosin head-like.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						GAAAGGAGCAGCCTCCCCAAA	0.502													53	81	---	---	---	---	PASS
TEKT3	64518	broad.mit.edu	37	17	15215686	15215686	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15215686C>A	uc002gon.2	-	7	1178	c.991G>T	c.(991-993)GTG>TTG	p.V331L		NM_031898	NP_114104	Q9BXF9	TEKT3_HUMAN	tektin 3	331					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		TTGGCAGTCACAACCAAGAGG	0.448													8	205	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	16735564	16735564	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16735564A>G	uc010vwr.1	-	1	584	c.142T>C	c.(142-144)TTC>CTC	p.F48L						SubName: Full=cDNA FLJ53570, highly similar to Keratin, type I cytoskeletal 16;																		ATGGTCTTGAAGTAGGGACTG	0.567													5	170	---	---	---	---	PASS
CCDC144NL	339184	broad.mit.edu	37	17	20768623	20768623	+	3'UTR	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20768623A>G	uc002gyf.2	-	4						NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,												0						CAGTTTAATAAAAGAGTTCAT	0.308													7	150	---	---	---	---	PASS
KRTAP1-1	81851	broad.mit.edu	37	17	39197549	39197549	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39197549G>C	uc002hvw.1	-	1	165	c.101C>G	c.(100-102)TCC>TGC	p.S34C		NM_030967	NP_112229	Q07627	KRA11_HUMAN	keratin associated protein 1-1	34			Missing (in allele KAP1.7).|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			extracellular region|keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGGAGCTGGTCTC	0.612													18	96	---	---	---	---	PASS
KRT17	3872	broad.mit.edu	37	17	39775697	39775697	+	3'UTR	SNP	C	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39775697C>G	uc002hxh.2	-	8					JUP_uc010wfs.1_Intron	NM_000422	NP_000413	Q04695	K1C17_HUMAN	keratin 17						epidermis development	cytoplasm|intermediate filament	protein binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2		Breast(137;0.000307)				CATTTCATAGCTGAGTCAACA	0.562									Steatocystoma_Multiplex				5	7	---	---	---	---	PASS
AARSD1	80755	broad.mit.edu	37	17	41123660	41123660	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41123660T>C	uc002icf.2	-	6	689	c.471A>G	c.(469-471)GAA>GAG	p.E157E	AARSD1_uc002icd.2_Silent_p.E96E|AARSD1_uc002ice.2_Intron|AARSD1_uc010whg.1_Silent_p.E157E|AARSD1_uc002icg.2_RNA|AARSD1_uc002ich.2_Silent_p.E119E|AARSD1_uc010whh.1_Silent_p.E124E	NM_025267	NP_079543	Q9BTE6	AASD1_HUMAN	alanyl-tRNA synthetase domain containing 1	Error:Variant_position_missing_in_Q9BTE6_after_alignment					alanyl-tRNA aminoacylation	cytoplasm	alanine-tRNA ligase activity|ATP binding|metal ion binding|nucleic acid binding				0		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		GCTCCATCTCTTCATCCCCTT	0.517													6	518	---	---	---	---	PASS
DHX8	1659	broad.mit.edu	37	17	41582097	41582097	+	Silent	SNP	G	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41582097G>T	uc002idu.1	+	12	1705	c.1632G>T	c.(1630-1632)GGG>GGT	p.G544G	DHX8_uc010wif.1_Silent_p.G453G|DHX8_uc010wig.1_Silent_p.G544G	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	544						catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		ATGCCTTTGGGGGCAACAAAG	0.498													72	112	---	---	---	---	PASS
GRN	2896	broad.mit.edu	37	17	42427606	42427606	+	Silent	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42427606C>T	uc002igp.1	+	5	579	c.360C>T	c.(358-360)TCC>TCT	p.S120S	GRN_uc002igq.1_3'UTR|GRN_uc002igr.1_5'Flank	NM_002087	NP_002078	P28799	GRN_HUMAN	granulin precursor	120			S -> Y.		signal transduction	extracellular space	cytokine activity|growth factor activity			ovary(2)|central_nervous_system(2)|skin(1)	5		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GTAACAACTCCGTGGGTGCCA	0.602													4	247	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60069951	60069951	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60069951A>G	uc002izo.2	-	11	2290	c.2213T>C	c.(2212-2214)TTA>TCA	p.L738S		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	738					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						TTCATGTGATAACACTGTTAC	0.279													5	424	---	---	---	---	PASS
SMURF2	64750	broad.mit.edu	37	17	62579640	62579640	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62579640A>G	uc002jep.1	-	7	896	c.508T>C	c.(508-510)TCT>CCT	p.S170P	SMURF2_uc002jeq.1_5'UTR|SMURF2_uc002jer.1_5'UTR	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	170	WW 1.				BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			ATTCTTCCAGAGGCGGTTCTC	0.403													6	599	---	---	---	---	PASS
OTOP2	92736	broad.mit.edu	37	17	72920812	72920812	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72920812C>G	uc010wrp.1	+	3	174	c.85C>G	c.(85-87)CGC>GGC	p.R29G	USH1G_uc002jme.1_5'Flank|USH1G_uc010wro.1_5'Flank|OTOP2_uc002jmf.1_Missense_Mutation_p.R29G	NM_178160	NP_835454	Q7RTS6	OTOP2_HUMAN	otopetrin 2	29						integral to membrane				ovary(3)|large_intestine(1)	4	all_lung(278;0.172)|Lung NSC(278;0.207)					GAAGGGTGGCCGCCTGCTGTC	0.706													18	14	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	18	109344	109344	+	RNA	SNP	T	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:109344T>A	uc002kke.2	+	1		c.280T>A								Homo sapiens Rho-associated, coiled-coil containing protein kinase 1, mRNA (cDNA clone IMAGE:5269982), complete cds.																		aggctttgcctacaggggaca	0.000													3	26	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	18	109348	109348	+	RNA	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:109348G>A	uc002kke.2	+	1		c.284G>A								Homo sapiens Rho-associated, coiled-coil containing protein kinase 1, mRNA (cDNA clone IMAGE:5269982), complete cds.																		tttgcctacaggggacattgt	0.000													3	27	---	---	---	---	PASS
LAMA1	284217	broad.mit.edu	37	18	7015803	7015803	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7015803A>G	uc002knm.2	-	22	3138	c.3044T>C	c.(3043-3045)GTC>GCC	p.V1015A	LAMA1_uc010wzj.1_Missense_Mutation_p.V491A	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1015	Laminin EGF-like 11.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGGGGGGCAGACACACTCTCC	0.542													5	177	---	---	---	---	PASS
MUM1	84939	broad.mit.edu	37	19	1367161	1367161	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1367161T>C	uc010xgm.1	+	8	1433	c.1364T>C	c.(1363-1365)TTC>TCC	p.F455S	MUM1_uc010dsi.2_Missense_Mutation_p.F387S|MUM1_uc002lrz.2_Missense_Mutation_p.F456S|MUM1_uc002lsb.2_Missense_Mutation_p.F387S			Q2TAK8	MUM1_HUMAN	SubName: Full=MUM1 protein;	455	PWWP.				chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTTCAAGTTTCACAGTGTCT	0.388													7	565	---	---	---	---	PASS
INSR	3643	broad.mit.edu	37	19	7267576	7267576	+	Silent	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7267576G>A	uc002mgd.1	-	2	541	c.432C>T	c.(430-432)GTC>GTT	p.V144V	INSR_uc002mge.1_Silent_p.V144V|INSR_uc002mgf.2_Silent_p.V144V	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor	144					activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TCTCGATGCGGACAGAACCCC	0.493													7	141	---	---	---	---	PASS
NR2C2AP	126382	broad.mit.edu	37	19	19313097	19313097	+	Intron	SNP	C	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19313097C>A	uc002nlx.2	-						NR2C2AP_uc010xqq.1_5'Flank|NR2C2AP_uc002nly.2_3'UTR	NM_176880	NP_795361	Q86WQ0	NR2CA_HUMAN	TR4 orphan receptor associated protein TRA16						cell adhesion|gene expression|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm				ovary(1)	1			Epithelial(12;0.00235)			tccaaagcTTCCAGAGGCACA	0.274													28	57	---	---	---	---	PASS
CD22	933	broad.mit.edu	37	19	35837721	35837721	+	3'UTR	SNP	G	A	A	rs149174052	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35837721G>A	uc010edt.2	+	14					CD22_uc010xst.1_3'UTR|CD22_uc010edu.2_3'UTR|CD22_uc010edv.2_3'UTR|CD22_uc002nzb.3_3'UTR|CD22_uc010edx.2_RNA	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule precursor						cell adhesion		protein binding|sugar binding			ovary(5)|lung(3)|breast(1)	9	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)	acacacacacgcacacacaca	0.502													3	21	---	---	---	---	PASS
NLRP13	126204	broad.mit.edu	37	19	56424222	56424222	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56424222A>G	uc010ygg.1	-	5	986	c.961T>C	c.(961-963)TCA>CCA	p.S321P		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	321	NACHT.						ATP binding			skin(4)|ovary(3)|pancreas(1)|lung(1)	9		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		TCAGAGCGTGACTCAGATATG	0.458													5	161	---	---	---	---	PASS
FAM182A	284800	broad.mit.edu	37	20	26063625	26063625	+	RNA	SNP	T	C	C	rs77830989	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26063625T>C	uc010gdq.2	+	5		c.1183T>C				NR_026713				Homo sapiens cDNA FLJ38374 fis, clone FEBRA2002552.												0						AGACCTACCATTTCTCGTTAT	0.468													7	68	---	---	---	---	PASS
DEFB115	245929	broad.mit.edu	37	20	29847316	29847316	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29847316A>G	uc002wvp.1	+	2	148	c.148A>G	c.(148-150)AAA>GAA	p.K50E		NM_001037730	NP_001032819	Q30KQ5	DB115_HUMAN	beta-defensin 115 precursor	50					defense response to bacterium	extracellular region				ovary(1)	1			Colorectal(19;0.00445)|COAD - Colon adenocarcinoma(19;0.0347)			GAAATCATGCAAAGAAATTGA	0.338													156	225	---	---	---	---	PASS
DSN1	79980	broad.mit.edu	37	20	35399333	35399333	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35399333T>C	uc010gfr.2	-	3	671	c.298A>G	c.(298-300)AGT>GGT	p.S100G	DSN1_uc002xfz.2_Missense_Mutation_p.S100G|DSN1_uc002xfy.3_Intron|DSN1_uc002xga.2_Missense_Mutation_p.S100G|DSN1_uc010zvs.1_Intron|DSN1_uc002xgc.2_Missense_Mutation_p.S84G|DSN1_uc002xgb.2_Missense_Mutation_p.S84G	NM_001145316	NP_001138788	Q9H410	DSN1_HUMAN	DSN1, MIND kinetochore complex component,	100					cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00874)				TCTTTCATACTTGCTCGCCGC	0.522													5	168	---	---	---	---	PASS
CHD6	84181	broad.mit.edu	37	20	40113060	40113060	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40113060T>C	uc002xka.1	-	15	2367	c.2189A>G	c.(2188-2190)AAC>AGC	p.N730S	CHD6_uc002xkd.2_Missense_Mutation_p.N708S	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	730					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				ATTGGGCATGTTGTGCTGATT	0.483													7	557	---	---	---	---	PASS
TH1L	51497	broad.mit.edu	37	20	57561223	57561223	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57561223G>A	uc002yag.2	+	2	190	c.163G>A	c.(163-165)GAT>AAT	p.D55N	TH1L_uc010zzu.1_Missense_Mutation_p.D55N|TH1L_uc002yaf.1_RNA|TH1L_uc002yah.2_Missense_Mutation_p.D55N	NM_198976	NP_945327	Q8IXH7	NELFD_HUMAN	TH1-like protein	55					negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	all_lung(29;0.00711)		Colorectal(105;0.109)			TTCCACCCGGGATTATATCAT	0.468													5	401	---	---	---	---	PASS
SFRS15	57466	broad.mit.edu	37	21	33076188	33076188	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33076188G>A	uc002ypd.2	-	4	637	c.211C>T	c.(211-213)CGA>TGA	p.R71*	SFRS15_uc002ype.2_Nonsense_Mutation_p.R71*|SFRS15_uc010glu.2_Nonsense_Mutation_p.R56*|SFRS15_uc002ypf.1_5'Flank|SFRS15_uc002ypg.2_Nonsense_Mutation_p.R71*	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	71	CID.					nucleus	nucleotide binding|RNA binding				0						CGAGACTGTCGCACAATTGAG	0.358													5	289	---	---	---	---	PASS
TRPM2	7226	broad.mit.edu	37	21	45797651	45797651	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45797651T>C	uc002zet.1	+	8	1222	c.1009T>C	c.(1009-1011)TTG>CTG	p.L337L	TRPM2_uc002zeu.1_Silent_p.L337L|TRPM2_uc002zew.1_Silent_p.L337L|TRPM2_uc010gpt.1_Silent_p.L337L|TRPM2_uc002zex.1_Silent_p.L123L	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	337	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						CCCGGGCACGTTGCACGTGAG	0.587													4	158	---	---	---	---	PASS
DIP2A	23181	broad.mit.edu	37	21	47969770	47969770	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47969770G>A	uc002zjo.2	+	22	2792	c.2609G>A	c.(2608-2610)AGC>AAC	p.S870N	DIP2A_uc011afy.1_Missense_Mutation_p.S806N|DIP2A_uc011afz.1_Missense_Mutation_p.S866N|DIP2A_uc002zjn.2_Missense_Mutation_p.S870N	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	870					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GAGGAGGACAGCTTCCAGTGG	0.647													20	30	---	---	---	---	PASS
MYO18B	84700	broad.mit.edu	37	22	26273924	26273924	+	Splice_Site	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26273924A>G	uc003abz.1	+	25	4475	c.4225_splice	c.e25-2	p.E1409_splice	MYO18B_uc003aca.1_Splice_Site_p.E1290_splice|MYO18B_uc010guy.1_Splice_Site_p.E1291_splice|MYO18B_uc010guz.1_Splice_Site_p.E1290_splice|MYO18B_uc011aka.1_Splice_Site_p.E563_splice|MYO18B_uc011akb.1_Splice_Site_p.E922_splice	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						TTGTTTTTGTAGGAGGAGCTT	0.383													5	548	---	---	---	---	PASS
ENTHD1	150350	broad.mit.edu	37	22	40161248	40161248	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40161248A>T	uc003ayg.2	-	6	1450	c.1199T>A	c.(1198-1200)ATC>AAC	p.I400N		NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	400										ovary(2)|skin(1)	3	Melanoma(58;0.0749)					TGTCTTGAGGATTTTATCATC	0.338													10	248	---	---	---	---	PASS
CLCN4	1183	broad.mit.edu	37	X	10176435	10176435	+	Silent	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:10176435T>C	uc004csy.3	+	9	1624	c.1194T>C	c.(1192-1194)ATT>ATC	p.I398I	CLCN4_uc011mid.1_Silent_p.I304I	NM_001830	NP_001821	P51793	CLCN4_HUMAN	chloride channel 4	398						early endosome membrane|integral to membrane|late endosome membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						GCGAGCTCATTTCTGAGCTGT	0.547													4	94	---	---	---	---	PASS
FAM47A	158724	broad.mit.edu	37	X	34148877	34148877	+	Missense_Mutation	SNP	C	G	G	rs5973088		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34148877C>G	uc004ddg.2	-	1	1552	c.1519G>C	c.(1519-1521)GAG>CAG	p.E507Q		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	507			Missing.							ovary(4)|central_nervous_system(1)	5						TTGGGAGGCTCCGAGCGGAGA	0.647													9	59	---	---	---	---	PASS
PHF16	9767	broad.mit.edu	37	X	46887437	46887437	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46887437C>T	uc004dgx.2	+	6	670	c.619C>T	c.(619-621)CGG>TGG	p.R207W	PHF16_uc004dgy.2_Missense_Mutation_p.R207W	NM_001077445	NP_001070913	Q92613	JADE3_HUMAN	PHD finger protein 16	207	PHD-type.				histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0						TGATGTGTGCCGGTCTCCAGA	0.468													59	649	---	---	---	---	PASS
OGT	8473	broad.mit.edu	37	X	70775903	70775903	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70775903A>G	uc004eaa.1	+	8	1241	c.1024A>G	c.(1024-1026)AAC>GAC	p.N342D	BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.1_Missense_Mutation_p.N332D|OGT_uc004eac.2_Missense_Mutation_p.N203D|OGT_uc004ead.2_5'UTR	NM_181672	NP_858058	O15294	OGT1_HUMAN	O-linked GlcNAc transferase isoform 1	342	TPR 9.				cellular response to retinoic acid|positive regulation of granulocyte differentiation|positive regulation of histone H3-K4 methylation|positive regulation of proteolysis|protein O-linked glycosylation|signal transduction	cytosol|MLL5-L complex	enzyme activator activity|protein binding|protein N-acetylglucosaminyltransferase activity			ovary(3)|kidney(1)|pancreas(1)	5	Renal(35;0.156)					AGAACAGGGAAACATTGAAGA	0.443													6	397	---	---	---	---	PASS
KIAA2022	340533	broad.mit.edu	37	X	73965524	73965524	+	5'UTR	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73965524C>T	uc004eby.2	-	2						NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533						base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15						AGTCCAAATGCTGTCCAACCT	0.338													4	283	---	---	---	---	PASS
UPRT	139596	broad.mit.edu	37	X	74494134	74494134	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74494134C>A	uc004ecb.1	+	1	174	c.45C>A	c.(43-45)AAC>AAA	p.N15K	UPRT_uc010nlu.1_Missense_Mutation_p.N15K|UPRT_uc004ecc.1_RNA|UPRT_uc004ecd.1_Missense_Mutation_p.N15K|UPRT_uc004ece.1_5'Flank	NM_145052	NP_659489	Q96BW1	UPP_HUMAN	uracil phosphoribosyltransferase (FUR1) homolog	15					nucleoside metabolic process	cytoplasm|nucleus					0						CCTGTCACAACCAGCAAGTAA	0.597													5	106	---	---	---	---	PASS
COX7B	1349	broad.mit.edu	37	X	77160816	77160816	+	3'UTR	SNP	A	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77160816A>G	uc004ecu.1	+	3						NM_001866	NP_001857	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb precursor						respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TTGATGCCAAATTAAAGCACT	0.343													5	194	---	---	---	---	PASS
COX7B	1349	broad.mit.edu	37	X	77160852	77160852	+	3'UTR	SNP	T	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77160852T>A	uc004ecu.1	+	3						NM_001866	NP_001857	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb precursor						respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TATGGCATTATTGAAGAAATA	0.299													5	124	---	---	---	---	PASS
ZCCHC5	203430	broad.mit.edu	37	X	77912865	77912865	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77912865G>T	uc004edc.1	-	2	1349	c.1053C>A	c.(1051-1053)AAC>AAA	p.N351K		NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	351							nucleic acid binding|zinc ion binding			ovary(1)	1						TTTCATCCCAGTTCAGCTCTT	0.478													7	188	---	---	---	---	PASS
HMGN5	79366	broad.mit.edu	37	X	80370532	80370532	+	Silent	SNP	T	C	C	rs147858164	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80370532T>C	uc004eee.1	-	7	794	c.465A>G	c.(463-465)GAA>GAG	p.E155E		NM_030763	NP_110390	P82970	HMGN5_HUMAN	high-mobility group nucleosome binding domain 5	155					chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleolus	chromatin binding|DNA binding			lung(1)	1						cttttccatcttcttcccctt	0.005													9	886	---	---	---	---	PASS
TGIF2LX	90316	broad.mit.edu	37	X	89177557	89177557	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89177557C>A	uc004efe.2	+	2	522	c.473C>A	c.(472-474)CCC>CAC	p.P158H		NM_138960	NP_620410	Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	158						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2						CAAAGCCTGCCCCTGTGGCCC	0.602													91	114	---	---	---	---	PASS
TBC1D8B	54885	broad.mit.edu	37	X	106093257	106093257	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106093257G>A	uc004emo.2	+	12	2005	c.1840G>A	c.(1840-1842)GCC>ACC	p.A614T	MORC4_uc004emp.3_Intron	NM_017752	NP_060222	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	614	Rab-GAP TBC.					intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4						TTCTGTAGGTGCCTTGGTGGA	0.383													193	272	---	---	---	---	PASS
MOSPD1	56180	broad.mit.edu	37	X	134030784	134030784	+	Intron	SNP	G	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134030784G>C	uc004eyb.2	-						MOSPD1_uc004eya.2_Intron|MOSPD1_uc010nrv.2_Intron|MOSPD1_uc011mvr.1_3'UTR	NM_019556	NP_062456	Q9UJG1	MSPD1_HUMAN	motile sperm domain containing 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	integral to membrane|nucleus|perinuclear region of cytoplasm	structural molecule activity			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(192;0.000127)					TTAGCTGCCTGATTATTTTAA	0.338													16	159	---	---	---	---	PASS
TAZ	6901	broad.mit.edu	37	X	153649068	153649068	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153649068G>T	uc004fkx.2	+	10	1075	c.771G>T	c.(769-771)AAG>AAT	p.K257N	TAZ_uc004fky.2_Missense_Mutation_p.K243N|TAZ_uc004fkz.2_RNA|TAZ_uc004fla.2_Missense_Mutation_p.K227N|TAZ_uc004flb.2_Missense_Mutation_p.K213N|TAZ_uc010nuy.2_Missense_Mutation_p.K261N|TAZ_uc004flc.3_Missense_Mutation_p.K227N	NM_000116	NP_000107	Q16635	TAZ_HUMAN	tafazzin isoform 1	257					cardiac muscle contraction|cardiac muscle tissue development|cardiolipin biosynthetic process|cristae formation|hemopoiesis|mitochondrial ATP synthesis coupled electron transport|mitochondrial respiratory chain complex I assembly|skeletal muscle tissue development	integral to membrane|mitochondrion	1-acylglycerophosphocholine O-acyltransferase activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CGGAGAACAAGTCGGCTGTGA	0.647													46	65	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	155252868	155252868	+	Silent	SNP	T	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									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													5	26	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	7013	7013	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:7013G>A	uc011mfh.1	+	1	1160	c.112G>A	c.(112-114)GTA>ATA	p.V38I	uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		CTACACGACACGTACTACGTT	0.458													164	227	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	8200	8200	+	RNA	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:8200T>C	uc004cou.3	+	1		c.615T>C			uc011mfi.1_5'Flank|uc004cov.3_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP42.																		GCAAACCACAGTTTCATGCCC	0.488													6	420	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14310	14310	+	RNA	SNP	C	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14310C>T	uc004cox.3	+	1		c.1974C>T			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TATTCAGCTTCCTACACTATT	0.463													442	118	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14569	14569	+	RNA	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14569G>A	uc004cox.3	+	1		c.2233G>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CCGACCACACCGCTAACAATC	0.383													157	634	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14601	14601	+	RNA	SNP	G	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14601G>A	uc004cox.3	+	1		c.2265G>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CCCATAAATAGGAGAAGGCTT	0.398													7	812	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15718	15718	+	3'UTR	SNP	T	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15718T>C	uc004coy.2	+	1					uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		AGCCAATCACTTTATTGACTC	0.438													20	575	---	---	---	---	PASS
AGRN	375790	broad.mit.edu	37	1	985444	985444	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:985444delG	uc001ack.1	+							NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin precursor						axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TCTCGGGGCAGGGGGGGGGGG	0.657													8	6	---	---	---	---	
SCNN1D	6339	broad.mit.edu	37	1	1219477	1219478	+	Intron	INS	-	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1219477_1219478insG	uc001adu.1	+						SCNN1D_uc001adt.1_Intron|SCNN1D_uc001adw.2_Intron|SCNN1D_uc001adx.2_Intron|SCNN1D_uc001adv.2_Intron	NM_002978	NP_002969			sodium channel, nonvoltage-gated 1, delta												0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		CCAGGTACCgtgggggggggtg	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2615410	2615410	+	IGR	DEL	A	-	-	rs5772074		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2615410delA								MMEL1 (50929 upstream) : ACTRT2 (322636 downstream)																							TGAGCATCTGACAGCCTGGAG	0.622													16	8	---	---	---	---	
AGTRAP	57085	broad.mit.edu	37	1	11800907	11800908	+	Intron	DEL	GT	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11800907_11800908delGT	uc001asv.2	+						AGTRAP_uc001ast.2_Intron|AGTRAP_uc001asu.2_Intron|AGTRAP_uc001asw.2_Intron|AGTRAP_uc001asx.2_Intron	NM_020350	NP_065083	Q6RW13	ATRAP_HUMAN	angiotensin II receptor-associated protein							cytoplasmic vesicle membrane|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding		AGTRAP/BRAF(2)	stomach(2)	2	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		GAGGAAAGGGGTGATGGGAGCT	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17007764	17007764	+	IGR	DEL	G	-	-	rs68158629		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17007764delG								MST1P2 (30850 upstream) : ESPNP (9949 downstream)																							GATAAGTTATGGGGGCTTCTG	0.438													14	7	---	---	---	---	
IFFO2	126917	broad.mit.edu	37	1	19252495	19252495	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19252495delT	uc001bbd.2	-							NM_001136265	NP_001129737	Q5TF58	IFFO2_HUMAN	intermediate filament family orphan 2												0						gatggatggattggttggatg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20804020	20804022	+	IGR	DEL	TCC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20804020_20804022delTCC								VWA5B1 (122633 upstream) : CAMK2N1 (4863 downstream)																							ATTGCCTGGGTCCTCCTCCTCCC	0.601													4	2	---	---	---	---	
TRIM63	84676	broad.mit.edu	37	1	26380728	26380729	+	Intron	INS	-	T	T	rs140200094	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26380728_26380729insT	uc001bli.1	-							NM_032588	NP_115977	Q969Q1	TRI63_HUMAN	muscle specific ring finger protein 1							cytoplasm|microtubule|nucleus	ligase activity|signal transducer activity|titin binding|zinc ion binding			kidney(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		ATCACCTGCTCGCCTGTGACCA	0.584													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31973123	31973133	+	3'UTR	DEL	TGGAGTCTGTC	-	-	rs112889748		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31973123_31973133delTGGAGTCTGTC	uc001bsw.1	+	2					uc001bsx.2_Frame_Shift_Del_p.V94fs					Homo sapiens hypothetical protein LOC149086, mRNA (cDNA clone IMAGE:5171562), with apparent retained intron.																		TGCTTCTATGTGGAGTCTGTCTGCATGGCCG	0.626													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37172136	37172137	+	IGR	DEL	AC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37172136_37172137delAC								CSF3R (223627 upstream) : GRIK3 (88991 downstream)																							AGATTTGACAACACACACAAGG	0.584													4	2	---	---	---	---	
GRIK3	2899	broad.mit.edu	37	1	37376603	37376603	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37376603delG	uc001caz.2	-						GRIK3_uc001cba.1_Intron	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3						negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)	acgtcttcatgggggaggcag	0.224													4	2	---	---	---	---	
SNIP1	79753	broad.mit.edu	37	1	38011071	38011072	+	Intron	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38011071_38011072insA	uc001cbi.2	-						SNIP1_uc010oid.1_Intron	NM_024700	NP_078976	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein						production of miRNAs involved in gene silencing by miRNA	nucleus	protein binding			upper_aerodigestive_tract(1)|lung(1)	2		Myeloproliferative disorder(586;0.0393)				CCGCCCCCACCaaaaaaaaaaa	0.322													4	3	---	---	---	---	
BMP8B	656	broad.mit.edu	37	1	40245614	40245614	+	Intron	DEL	G	-	-	rs11288385		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40245614delG	uc001cdz.1	-						BMP8B_uc001cea.1_Intron	NM_001720	NP_001711	P34820	BMP8B_HUMAN	bone morphogenetic protein 8B preproprotein						cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			tcacagtcaagctgtcagcta	0.000													4	4	---	---	---	---	
STIL	6491	broad.mit.edu	37	1	47732210	47732210	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47732210delT	uc001crc.1	-						TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Intron|STIL_uc010omo.1_Intron|STIL_uc001crd.1_Intron|STIL_uc001cre.1_Intron|STIL_uc001crf.1_Intron|STIL_uc001crg.1_Intron	NM_003035	NP_003026	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 2						cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				agttaaaatatttttttatag	0.075													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	85992847	85992848	+	Intron	DEL	CT	-	-	rs142998762		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85992847_85992848delCT	uc001dlc.2	-							NM_001134445	NP_001127917	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)	CTGCTGGAAACTCTGCCTCACT	0.421													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88115339	88115339	+	IGR	DEL	T	-	-	rs35110823		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88115339delT								LMO4 (300736 upstream) : None (None downstream)																							ctatttattCTTTTTTTTTCC	0.149													6	4	---	---	---	---	
FNBP1L	54874	broad.mit.edu	37	1	93919893	93919894	+	Intron	INS	-	TG	TG	rs139478746	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93919893_93919894insTG	uc001dpw.2	+						FNBP1L_uc001dpv.2_Intron	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		atgggtgtgtctgtgtgtgtgt	0.292													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96331341	96331341	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96331341delT								RWDD3 (618568 upstream) : PTBP2 (855834 downstream)																							cttagtaagatttttTTGGAT	0.169													4	2	---	---	---	---	
COL11A1	1301	broad.mit.edu	37	1	103553904	103553904	+	Intron	DEL	T	-	-	rs67074206		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103553904delT	uc001dul.2	-						COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		cttcaaagagtttttttttgt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	110335299	110335300	+	IGR	INS	-	C	C	rs142064069	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110335299_110335300insC								EPS8L3 (28735 upstream) : CSF1 (117933 downstream)																							GCCAAGGGAGTCAGCATGGAGT	0.644													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	110969578	110969579	+	IGR	DEL	GA	-	-	rs67471926		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110969578_110969579delGA								HBXIP (19032 upstream) : PROK1 (24209 downstream)																							GAGCAAGCAGGAGAGAGAGAGA	0.525													1	8	---	---	---	---	
RAP1A	5906	broad.mit.edu	37	1	112148962	112148963	+	Intron	DEL	AA	-	-	rs72087801		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112148962_112148963delAA	uc001ebi.2	+						uc001ebj.1_Intron	NM_002884	NP_002875	P62834	RAP1A_HUMAN	RAP1A, member of RAS oncogene family precursor						activation of MAPKK activity|blood coagulation|energy reserve metabolic process|nerve growth factor receptor signaling pathway|regulation of insulin secretion	cytosol|plasma membrane	GTP binding|GTPase activity				0		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)		AGGAACCTTTAAAAAAAAAATG	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	115057164	115057166	+	IGR	DEL	TAA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115057164_115057166delTAA								TRIM33 (3383 upstream) : DENND2C (6852 downstream)																							tgtaaaacgttaataacagcacc	0.163													4	2	---	---	---	---	
HMGCS2	3158	broad.mit.edu	37	1	120296501	120296501	+	Intron	DEL	T	-	-	rs71752516		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120296501delT	uc001eid.2	-						HMGCS2_uc010oxj.1_Intron|HMGCS2_uc001eie.2_Intron	NM_005518	NP_005509	P54868	HMCS2_HUMAN	hydroxymethylglutaryl-CoA synthase 2 isoform 1						acetoacetic acid biosynthetic process|cholesterol biosynthetic process|isoprenoid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA synthase activity			ovary(2)	2	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		TTCCTGCCCGttttttttttc	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142544110	142544110	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142544110delG								None (None upstream) : None (None downstream)																							CAGAGTTTTAGAATGTTAAGG	0.313													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142615927	142615927	+	5'Flank	DEL	T	-	-	rs111980196		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142615927delT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		ccaTGGTTTGTTTTTTGtttt	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142644515	142644515	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142644515delT	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		cctttctttctttttttttga	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143519491	143519492	+	IGR	INS	-	GA	GA			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143519491_143519492insGA								None (None upstream) : LOC100286793 (128147 downstream)																							tatgtgtgtttgagagtgtgtg	0.139													6	3	---	---	---	---	
BCL9	607	broad.mit.edu	37	1	147086643	147086643	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147086643delC	uc001epq.2	+						BCL9_uc010ozr.1_Intron	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9						Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					ATCTCtttttctttttttttt	0.184			T	IGH@|IGL@	B-ALL								4	2	---	---	---	---	
BCL9	607	broad.mit.edu	37	1	147086644	147086644	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147086644delT	uc001epq.2	+						BCL9_uc010ozr.1_Intron	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9						Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					TCTCtttttcttttttttttt	0.179			T	IGH@|IGL@	B-ALL								4	2	---	---	---	---	
GATAD2B	57459	broad.mit.edu	37	1	153809853	153809854	+	Intron	INS	-	A	A	rs12404347		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153809853_153809854insA	uc001fdb.3	-							NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ACAAAACAAACAAAAAAAAAAA	0.050													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163235927	163235928	+	IGR	INS	-	CT	CT	rs148816018	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163235927_163235928insCT								RGS5 (63055 upstream) : NUF2 (55795 downstream)																							gggatctgctcctgtttttatt	0.000													3	3	---	---	---	---	
RXRG	6258	broad.mit.edu	37	1	165399443	165399443	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165399443delT	uc001gda.2	-							NM_006917	NP_008848	P48443	RXRG_HUMAN	retinoid X receptor, gamma isoform a						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tretinoin(DB00755)	GTCAGACACCTTGCCAAGCAG	0.388													4	2	---	---	---	---	
C1orf129	80133	broad.mit.edu	37	1	170922870	170922874	+	Intron	DEL	AAAGA	-	-	rs71646206		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170922870_170922874delAAAGA	uc001ghg.2	+						C1orf129_uc009wvy.2_Intron|C1orf129_uc010plz.1_Intron	NM_025063	NP_079339	Q5TGP6	CA129_HUMAN	hypothetical protein LOC80133 isoform 2								binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TAGATTAGGGaaagaaaagaaaaga	0.137													2	4	---	---	---	---	
FMO2	2327	broad.mit.edu	37	1	171178336	171178336	+	3'UTR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171178336delA	uc001ghk.1	+	9					FMO2_uc010pmd.1_3'UTR	NM_001460	NP_001451	Q99518	FMO2_HUMAN	flavin containing monooxygenase 2						drug metabolic process|NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|host cell microsome|integral to membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCTCCTAAAGAAAAAAAAAAA	0.348													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181773614	181773614	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181773614delT								CACNA1E (2901 upstream) : ZNF648 (250093 downstream)																							AGGTACAGAATTTTTTCAGGA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	188036272	188036272	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188036272delT								None (None upstream) : None (None downstream)																							tttctgcatgtgtgtttgcac	0.005													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	189471579	189471579	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189471579delA								None (None upstream) : FAM5C (595218 downstream)																							TAGTAGCTGGAAAAAAAAAAT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	191945292	191945292	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191945292delG								None (None upstream) : RGS18 (182300 downstream)																							GTGGAGTAGTGGGGACAGGAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193667067	193667068	+	IGR	INS	-	A	A	rs138705287	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193667067_193667068insA								CDC73 (443127 upstream) : None (None downstream)																							GTGATGGTTTCATTTACTGGAA	0.089													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	195234599	195234599	+	IGR	DEL	A	-	-	rs10713008		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195234599delA								None (None upstream) : KCNT2 (960314 downstream)																							tgtaaaatagaaaaaaaaaaa	0.104													4	2	---	---	---	---	
LGR6	59352	broad.mit.edu	37	1	202269786	202269786	+	Intron	DEL	A	-	-	rs111707317		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202269786delA	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron|LGR6_uc001gxw.2_Intron|LGR6_uc009xac.1_Intron	NM_001017403	NP_001017403	Q9HBX8	LGR6_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10						cctgtctcagaaaaaaaaaaa	0.159													3	3	---	---	---	---	
PLXNA2	5362	broad.mit.edu	37	1	208223334	208223334	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208223334delA	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)		ATCATGTTTCAAAAAATATTG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209262485	209262486	+	IGR	DEL	TG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209262485_209262486delTG								PLXNA2 (844820 upstream) : LOC642587 (339682 downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.178													5	4	---	---	---	---	
IARS2	55699	broad.mit.edu	37	1	220308110	220308110	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220308110delG	uc001hmc.2	+						IARS2_uc001hmd.2_5'Flank	NM_018060	NP_060530	Q9NSE4	SYIM_HUMAN	mitochondrial isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	tgttgttgttgtttttttttt	0.179													4	2	---	---	---	---	
C1orf35	79169	broad.mit.edu	37	1	228294012	228294012	+	5'Flank	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228294012delG	uc001hrx.2	-						C1orf35_uc009xew.2_5'Flank	NM_024319	NP_077295	Q9BU76	MMTA2_HUMAN	hypothetical protein LOC79169												0		Prostate(94;0.0488)				TGCAGGGCCAGGGCAGGGAGC	0.637													4	2	---	---	---	---	
AKT3	10000	broad.mit.edu	37	1	243791929	243791929	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243791929delT	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)			ccagatcaactttggaaccat	0.000													4	2	---	---	---	---	
TPO	7173	broad.mit.edu	37	2	1479744	1479745	+	Intron	INS	-	CTGG	CTGG	rs141415061	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1479744_1479745insCTGG	uc002qww.2	+						TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Intron|TPO_uc002qwr.2_Intron|TPO_uc002qwx.2_Intron|TPO_uc010yio.1_Intron|TPO_uc010yip.1_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a						cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	ACCTCCTGTGCCTGGGTCCATC	0.639													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	8620532	8620532	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8620532delA								LOC339788 (503555 upstream) : ID2 (198808 downstream)																							TCGTTTGTCCAAAAATGTAGA	0.378													4	2	---	---	---	---	
DDX1	1653	broad.mit.edu	37	2	15740149	15740153	+	Intron	DEL	TCATA	-	-	rs112848455		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15740149_15740153delTCATA	uc002rce.2	+						DDX1_uc010yjq.1_Intron	NM_004939	NP_004930	Q92499	DDX1_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 1						DNA duplex unwinding|double-strand break repair|multicellular organismal development|regulation of transcription, DNA-dependent|regulation of translational initiation|spliceosome assembly|transcription, DNA-dependent	cleavage body|stress granule|tRNA-splicing ligase complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|DNA/RNA helicase activity|exonuclease activity|poly(A) RNA binding|protein binding|RNA helicase activity|transcription cofactor activity			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)		gacttctatctcatatcataattag	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20876628	20876628	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20876628delA								GDF7 (5378 upstream) : C2orf43 (7175 downstream)																							ACAGTTGCTGAAAAAGCAAAA	0.483													4	2	---	---	---	---	
C2orf39	92749	broad.mit.edu	37	2	26673737	26673737	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26673737delT	uc002rhg.2	+							NM_145038	NP_659475	Q96MC2	CC164_HUMAN	hypothetical protein LOC92749												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					cctaatgttatccctccccta	0.000													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28174127	28174127	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28174127delA	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					cttttttcctaatattggtgt	0.000													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28518370	28518370	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28518370delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron|BRE_uc002rlx.2_5'Flank	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					GTGAATAGGCttttttttttg	0.164													3	3	---	---	---	---	
CAPN14	440854	broad.mit.edu	37	2	31437682	31437682	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31437682delG	uc010yms.1	-						CAPN14_uc002rnt.1_Intron	NM_001145122	NP_001138594	A8MX76	CAN14_HUMAN	calpain 14						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0						CGGCCTTTGTGGAAGTTGCAC	0.378													4	2	---	---	---	---	
BIRC6	57448	broad.mit.edu	37	2	32714098	32714098	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32714098delT	uc010ezu.2	+							NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					ttttttattattttttttttt	0.343													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34300531	34300531	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34300531delC								MYADML (347247 upstream) : None (None downstream)																							TAGATGGTCTCCAGGGCTTTA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37970359	37970359	+	IGR	DEL	T	-	-	rs62842460		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37970359delT								CDC42EP3 (71033 upstream) : FAM82A1 (182103 downstream)																							gtagtggcagtgatggtggtg	0.164													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	38065465	38065465	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38065465delA								CDC42EP3 (166139 upstream) : FAM82A1 (86997 downstream)																							CAGAGACGGGAATAAGCACAT	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43057240	43057240	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43057240delC								HAAO (37489 upstream) : ZFP36L2 (392302 downstream)																							GCCACTTCTTCCCAGAGTTCC	0.562													4	2	---	---	---	---	
PRKCE	5581	broad.mit.edu	37	2	46248974	46248975	+	Intron	DEL	TG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46248974_46248975delTG	uc002rut.2	+							NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			TTTACCTTTTTGTGTGTGTGTG	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48217841	48217843	+	IGR	DEL	CAT	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48217841_48217843delCAT								FBXO11 (85027 upstream) : FOXN2 (323952 downstream)																							TCATTGCTGAcatcatcatcatc	0.138													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	52798286	52798287	+	IGR	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52798286_52798287insA								None (None upstream) : None (None downstream)																							ACGTGCACCAGAAAAAAGTCTT	0.515													70	31	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56013493	56013496	+	IGR	DEL	AAAC	-	-	rs112069206		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56013493_56013496delAAAC								PNPT1 (92482 upstream) : EFEMP1 (79607 downstream)																							ATAAGCAAAGAAACAAAGGTAACA	0.304													9	7	---	---	---	---	
CCT4	10575	broad.mit.edu	37	2	62110909	62110914	+	Intron	DEL	ACACAC	-	-	rs72272622	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62110909_62110914delACACAC	uc002sbo.2	-						CCT4_uc010ypp.1_Intron|CCT4_uc010ypq.1_Intron|CCT4_uc010ypr.1_Intron|CCT4_uc010yps.1_Intron	NM_006430	NP_006421	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)						'de novo' posttranslational protein folding	melanosome|microtubule organizing center|nucleus	ATP binding|unfolded protein binding			ovary(2)	2	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			AGAAATGTAGacacacacacacacac	0.223													4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71845644	71845645	+	Intron	DEL	GT	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71845644_71845645delGT	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						tttggtagaggtgtgtgtgtgg	0.054													6	3	---	---	---	---	
DOK1	1796	broad.mit.edu	37	2	74782263	74782264	+	Intron	DEL	CT	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74782263_74782264delCT	uc002sms.2	+						LOXL3_uc010ffm.1_5'Flank|LOXL3_uc002smp.1_5'Flank|LOXL3_uc002smq.1_5'Flank|LOXL3_uc010ffn.1_5'Flank|DOK1_uc002smr.2_Intron|DOK1_uc010ffo.2_Intron|DOK1_uc002smt.2_Intron|DOK1_uc002smu.2_Intron|DOK1_uc010yrz.1_Intron|DOK1_uc002smv.2_5'UTR|DOK1_uc002smw.1_5'Flank	NM_001381	NP_001372	Q99704	DOK1_HUMAN	docking protein 1						fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	cytosol|perinuclear region of cytoplasm	insulin receptor binding				0						CTCTCGAGCACTCTCTCTCTCT	0.658													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76852471	76852471	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76852471delC								C2orf3 (914360 upstream) : LRRTM4 (122387 downstream)																							tgtcaaatctccaggaagatc	0.000													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	79862576	79862576	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79862576delA	uc010yse.1	+						CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						cagaaaaaagaaaaaaaaaag	0.000													5	3	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87744249	87744250	+	Intron	DEL	TC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87744249_87744250delTC	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						ctccacatattctctctctctc	0.000													4	2	---	---	---	---	
FLJ40330	645784	broad.mit.edu	37	2	89083543	89083543	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89083543delG	uc010fhf.2	+						FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TACACCACATGGGTGTGAGAA	0.363													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89879994	89879995	+	IGR	INS	-	GA	GA			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89879994_89879995insGA								FLJ40330 (773869 upstream) : None (None downstream)																							ggaatggaatgAGGGAATGTCA	0.248													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91774918	91774919	+	IGR	INS	-	AAAC	AAAC	rs141351243		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91774918_91774919insAAAC								None (None upstream) : LOC654342 (30273 downstream)																							ctccatctcaaaaacaaacaaa	0.144													4	2	---	---	---	---	
REV1	51455	broad.mit.edu	37	2	100037693	100037693	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100037693delA	uc002tad.2	-						REV1_uc002tac.2_Intron	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1						DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2						CACTTTTGGGAAAAAAAAAAC	0.343								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	5	---	---	---	---	
SLC20A1	6574	broad.mit.edu	37	2	113407841	113407841	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113407841delT	uc002tib.2	+							NM_005415	NP_005406	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate						phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to plasma membrane	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity			ovary(2)	2						TATTGAGAAGTCCCCACATAA	0.308													4	2	---	---	---	---	
IL1F9	56300	broad.mit.edu	37	2	113738761	113738761	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113738761delT	uc002tio.1	+						IL1F9_uc010fkr.1_Intron	NM_019618	NP_062564	Q9NZH8	IL36G_HUMAN	interleukin 1 family, member 9						cell-cell signaling	extracellular space	cytokine activity|interleukin-1 receptor antagonist activity				0						CTGCAGCACCTTCAGCTTTCT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132892025	132892026	+	IGR	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132892025_132892026insT								C2orf27B (332791 upstream) : NCRNA00164 (13138 downstream)																							GAttttttttcttttttttttt	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133045165	133045166	+	IGR	DEL	GA	-	-	rs112889460		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133045165_133045166delGA								NCRNA00164 (29623 upstream) : GPR39 (128981 downstream)																							ggcatgtttggagagtagctgg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133046453	133046454	+	IGR	INS	-	GACA	GACA	rs146739177		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133046453_133046454insGACA								NCRNA00164 (30911 upstream) : GPR39 (127693 downstream)																							CAAACCAATGTGACAGACAGAG	0.386													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133086349	133086350	+	IGR	INS	-	A	A	rs145771742	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133086349_133086350insA								NCRNA00164 (70807 upstream) : GPR39 (87797 downstream)																							GAACACAAAACAAACAAAACTG	0.243													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134838930	134838930	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134838930delA								NCKAP5 (512899 upstream) : MGAT5 (172900 downstream)																							AACTGGTAGGAAAAAAAAAAT	0.423													3	3	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	138334595	138334595	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138334595delC	uc002tva.1	+						THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		GTATTTGTCTCTGGAGGAGGT	0.398													4	2	---	---	---	---	
MBD5	55777	broad.mit.edu	37	2	148924292	148924295	+	Intron	DEL	TGTG	-	-	rs80268789		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148924292_148924295delTGTG	uc002twm.3	+							NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		CTATGTTTTCTGTGTGTGTGTGTG	0.368													4	2	---	---	---	---	
GPD2	2820	broad.mit.edu	37	2	157303851	157303851	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157303851delT	uc002tzf.3	+						GPD2_uc010zch.1_Intron|GPD2_uc002tzd.3_Intron	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,						cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						AATCTCTCTCttttttttttt	0.189													1	5	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	159881701	159881701	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159881701delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						tttttctttcttttctttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	160765214	160765217	+	IGR	DEL	TTAA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160765214_160765217delTTAA								LY75 (3952 upstream) : PLA2R1 (32795 downstream)																							GTCACGttttttaattataaaata	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162136904	162136905	+	IGR	INS	-	TTTT	TTTT	rs113191395		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162136904_162136905insTTTT								TANK (44222 upstream) : PSMD14 (27881 downstream)																							gacatttcccattgtatttttc	0.000													12	10	---	---	---	---	
SCN9A	6335	broad.mit.edu	37	2	167202043	167202044	+	Intron	INS	-	G	G	rs149071831	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167202043_167202044insG	uc010fpl.2	-							NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)	AACAAAAAAAAGTAGGGAAAAG	0.347													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173170109	173170112	+	IGR	DEL	GTTT	-	-	rs72279825		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173170109_173170112delGTTT								DLX2 (202631 upstream) : ITGA6 (121970 downstream)																							CCTGAAACTCgtttgtttgtttgt	0.275													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173389505	173389505	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173389505delG								ITGA6 (18324 upstream) : PDK1 (30596 downstream)																							aagattctgtggtgacaaaca	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	178063145	178063168	+	IGR	DEL	TGGGCTCCAGCTTTGGCTCTGGCG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178063145_178063168delTGGGCTCCAGCTTTGGCTCTGGCG								MIR1246 (597365 upstream) : HNRNPA3 (14254 downstream)																							AGCTACGGCCTGGGCTCCAGCTTTGGCTCTGGCGTGGGCTCCAG	0.598													5	6	---	---	---	---	
NCKAP1	10787	broad.mit.edu	37	2	183791862	183791870	+	Intron	DEL	TGGTCTTTA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183791862_183791870delTGGTCTTTA	uc002upc.2	-						NCKAP1_uc002upb.2_Intron	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1						apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			ATATTCTTATTGGTCTTTAAAACTGATTT	0.282													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193416773	193416773	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193416773delC								TMEFF2 (357129 upstream) : PCGEM1 (197798 downstream)																							actctggaagccccagtgcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200961512	200961513	+	IGR	DEL	TT	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200961512_200961513delTT								C2orf47 (132667 upstream) : SPATS2L (209091 downstream)																							cacacatgcatttttttttttt	0.000													4	2	---	---	---	---	
C2orf67	151050	broad.mit.edu	37	2	210913457	210913457	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210913457delT	uc002vds.2	-						C2orf67_uc002vdt.2_Intron|C2orf67_uc002vdw.2_Intron|uc002vdu.1_Intron|C2orf67_uc002vdv.2_Intron|C2orf67_uc002vdx.1_Intron	NM_152519	NP_689732	A0AUZ9	CB067_HUMAN	hypothetical protein LOC151050											ovary(3)	3		Renal(323;0.202)		Epithelial(149;0.00435)|Lung(261;0.0529)|LUSC - Lung squamous cell carcinoma(261;0.0551)|all cancers(144;0.0696)		tgttctgtgattttttttttc	0.000													4	4	---	---	---	---	
ABCA12	26154	broad.mit.edu	37	2	215961884	215961884	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215961884delT	uc002vew.2	-						ABCA12_uc010zjn.1_Intron	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AAATAAGCCCTTTACCCCCAC	0.388													4	2	---	---	---	---	
SMARCAL1	50485	broad.mit.edu	37	2	217310839	217310840	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217310839_217310840insT	uc002vgc.3	+						SMARCAL1_uc010fvf.2_Intron|SMARCAL1_uc002vgd.3_Intron|SMARCAL1_uc010fvg.2_Intron	NM_014140	NP_054859	Q9NZC9	SMAL1_HUMAN	SWI/SNF-related matrix-associated						chromatin modification|DNA metabolic process|regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity			ovary(3)|breast(3)|skin(1)	7		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		GGAAGAGTCTCTTTTTTTTTTT	0.441									Schimke_Immuno-Osseous_Dysplasia				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	221422997	221422997	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221422997delA								SLC4A3 (916296 upstream) : EPHA4 (859752 downstream)																							actccgtctcaaaaaaaaaTT	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	231703098	231703099	+	IGR	DEL	TA	-	-	rs56996961		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231703098_231703099delTA								CAB39 (17309 upstream) : ITM2C (26522 downstream)																							tcagactccctatgatttcgtc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239833378	239833379	+	IGR	DEL	AC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239833378_239833379delAC								TWIST2 (1141 upstream) : HDAC4 (136486 downstream)																							AAGcacacagacacacacacac	0.272													8	4	---	---	---	---	
RFTN1	23180	broad.mit.edu	37	3	16434582	16434582	+	Intron	DEL	C	-	-	rs73818401	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16434582delC	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4						aacaaacaaacaaaAAATgac	0.174													4	2	---	---	---	---	
RFTN1	23180	broad.mit.edu	37	3	16434587	16434589	+	Intron	DEL	AAT	-	-	rs58587574		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16434587_16434589delAAT	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4						acaaacaaaAAATgacaagaaac	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23241240	23241241	+	IGR	DEL	AG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23241240_23241241delAG								ZNF385D (827117 upstream) : UBE2E2 (3412 downstream)																							gtgacagcaaagagagagagag	0.000													4	2	---	---	---	---	
UBE2E2	7325	broad.mit.edu	37	3	23586911	23586911	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23586911delC	uc003ccg.2	+						UBE2E2_uc010hfc.2_Intron	NM_152653	NP_689866	Q96LR5	UB2E2_HUMAN	ubiquitin-conjugating enzyme E2E 2						ISG15-protein conjugation|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination	nucleolus	ATP binding|ISG15 ligase activity|ubiquitin-protein ligase activity				0						atctgtttaacaaagcacatc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	30602693	30602694	+	IGR	INS	-	T	T	rs144156794	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30602693_30602694insT								RBMS3 (556074 upstream) : TGFBR2 (45300 downstream)																							CTTTGTTTTTCTTGCTTTACTT	0.252													1	5	---	---	---	---	
FBXL2	25827	broad.mit.edu	37	3	33427849	33427849	+	3'UTR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33427849delA	uc003cfp.2	+	15					FBXL2_uc011axo.1_3'UTR|FBXL2_uc011axp.1_3'UTR|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron	NM_012157	NP_036289	Q9UKC9	FBXL2_HUMAN	F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1						TTACTAAAGGAAAAAAGCTAA	0.388													4	2	---	---	---	---	
C3orf67	200844	broad.mit.edu	37	3	58856317	58856317	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58856317delA	uc003dkt.1	-						C3orf67_uc003dks.1_5'Flank|uc003dku.1_Intron|C3orf67_uc003dkv.1_Intron|C3orf67_uc003dkw.2_Intron	NM_198463	NP_940865	Q6ZVT6	CC067_HUMAN	hypothetical protein LOC200844												0		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		GTTTTTCTTTAAAAAAAAAAA	0.040													4	3	---	---	---	---	
FAM55C	91775	broad.mit.edu	37	3	101535115	101535116	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101535115_101535116insT	uc003dvn.2	+						FAM55C_uc010hpn.2_Intron	NM_145037	NP_659474	Q969Y0	FA55C_HUMAN	hypothetical protein LOC91775 precursor							extracellular region				ovary(1)|pancreas(1)|skin(1)	3						AAAGGAAAACCttttttttttt	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105063244	105063245	+	IGR	INS	-	AG	AG	rs144197143	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105063244_105063245insAG								None (None upstream) : ALCAM (22468 downstream)																							agcagcacaaaagaggccaaca	0.000													1	5	---	---	---	---	
MYH15	22989	broad.mit.edu	37	3	108189919	108189920	+	Intron	INS	-	AAGA	AAGA	rs3996014		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108189919_108189920insAAGA	uc003dxa.1	-							NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						agggagggagggaggaaggaag	0.035													9	4	---	---	---	---	
SIDT1	54847	broad.mit.edu	37	3	113315275	113315275	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113315275delA	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						CAACTATAATAAAAAGCAAAA	0.373													4	2	---	---	---	---	
FAM162A	26355	broad.mit.edu	37	3	122103819	122103819	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122103819delT	uc003eez.2	+						CCDC58_uc003eey.2_5'Flank|FAM162A_uc011bjq.1_Intron	NM_014367	NP_055182	Q96A26	F162A_HUMAN	growth and transformation-dependent protein							integral to membrane				ovary(1)	1						AGCTTAATTCTTTTTTTTTGG	0.398													4	2	---	---	---	---	
UMPS	7372	broad.mit.edu	37	3	124454339	124454339	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124454339delT	uc003ehl.3	+						UMPS_uc003ehm.3_Intron|UMPS_uc011bka.1_Intron|UMPS_uc011bkb.1_Intron|UMPS_uc011bkc.1_Intron|UMPS_uc003ehn.3_Intron|UMPS_uc011bkd.1_Intron	NM_000373	NP_000364	P11172	UMPS_HUMAN	uridine monophosphate synthase						'de novo' pyrimidine base biosynthetic process|'de novo' UMP biosynthetic process|pyrimidine nucleoside biosynthetic process	cytosol|nucleus	orotate phosphoribosyltransferase activity|orotidine-5'-phosphate decarboxylase activity			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.146)		AACTCCAACATTTTTTTTTTT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	135022656	135022657	+	IGR	INS	-	GA	GA	rs139394633	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135022656_135022657insGA								EPHB1 (43351 upstream) : PPP2R3A (661910 downstream)																							AAAAAAGGAAGGAGTGATCCCC	0.411													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137183871	137183871	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137183871delA								IL20RB (453951 upstream) : SOX14 (299708 downstream)																							ttttcactagaaaaaaaaaat	0.000													4	2	---	---	---	---	
MRPS22	56945	broad.mit.edu	37	3	139069524	139069524	+	Intron	DEL	G	-	-	rs112795230		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139069524delG	uc003etb.2	+						MRPS22_uc003etc.2_Intron|MRPS22_uc003etd.2_Intron|MRPS22_uc003ete.2_Intron	NM_020191	NP_064576	P82650	RT22_HUMAN	mitochondrial ribosomal protein S22							mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome			ovary(2)|skin(1)	3						ccccccccccgcaatccgact	0.095													1	5	---	---	---	---	
SLC25A36	55186	broad.mit.edu	37	3	140695478	140695479	+	3'UTR	INS	-	A	A	rs112628499		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140695478_140695479insA	uc003etr.2	+	7					SLC25A36_uc003ets.2_3'UTR|SLC25A36_uc003etq.2_3'UTR|SLC25A36_uc011bmz.1_3'UTR	NM_001104647	NP_001098117	Q96CQ1	S2536_HUMAN	solute carrier family 25, member 36 isoform a						response to estradiol stimulus|transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0						TCGGTAATGTGAAAAAAAAAAA	0.386													10	6	---	---	---	---	
XRN1	54464	broad.mit.edu	37	3	142066444	142066444	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142066444delT	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3						aaaatgctacttttttttttt	0.000													6	3	---	---	---	---	
XRN1	54464	broad.mit.edu	37	3	142089817	142089817	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142089817delA	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3						cctaggagtcaaaaaaaaaaa	0.020													7	4	---	---	---	---	
C3orf16	389161	broad.mit.edu	37	3	149509830	149509830	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149509830delT	uc003exl.2	-						C3orf16_uc011bnt.1_Intron|C3orf16_uc003exm.2_5'Flank	NM_001144960	NP_001138432	E9PHT4	E9PHT4_HUMAN	hypothetical protein LOC389161												0						GAAGTCAGACTTTTTTTTTTT	0.343													5	3	---	---	---	---	
ZBBX	79740	broad.mit.edu	37	3	167090743	167090743	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167090743delA	uc003fep.2	-						ZBBX_uc011bpc.1_Intron|ZBBX_uc003feq.2_Intron	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing							intracellular	zinc ion binding			ovary(2)	2						ACACTTCTGTAAAAGTAACAA	0.308													127	69	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180546925	180546926	+	Intron	INS	-	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180546925_180546926insG	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																		CGGCTTGCTCAGCACTAGCCCA	0.698													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181481334	181481334	+	IGR	DEL	A	-	-	rs10572514		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181481334delA								SOX2OT (22331 upstream) : None (None downstream)																							acctcatctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184481846	184481846	+	IGR	DEL	G	-	-	rs141213550		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184481846delG								MAGEF1 (52010 upstream) : VPS8 (48085 downstream)																							cttaaaacaaggctatgagat	0.085													3	3	---	---	---	---	
HRG	3273	broad.mit.edu	37	3	186389741	186389742	+	Intron	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186389741_186389742insA	uc003fqq.2	+							NM_000412	NP_000403	P04196	HRG_HUMAN	histidine-rich glycoprotein precursor						fibrinolysis|platelet activation|platelet degranulation	extracellular region|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding			ovary(1)|central_nervous_system(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		TTAAAAAATACAAAAAAATTGC	0.391													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191340022	191340022	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191340022delA								PYDC2 (160779 upstream) : FGF12 (519662 downstream)																							gcattgtggtaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194773967	194773967	+	IGR	DEL	T	-	-	rs113969500		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194773967delT								FAM43A (364203 upstream) : C3orf21 (15048 downstream)																							ttgtgcattcttttttcttgg	0.000													5	3	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195490843	195490846	+	Intron	DEL	GATG	-	-	rs34858176		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195490843_195490846delGATG	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TCCTTATCCAGATGCCACCTCCCG	0.632													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27530	27530	+	IGR	DEL	T	-	-	rs113321029		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27530delT								None (None upstream) : ZNF595 (25697 downstream)																							TAAAAAGGCCTTTTTTTTTGG	0.433													10	5	---	---	---	---	
TMEM175	84286	broad.mit.edu	37	4	946417	946418	+	Intron	DEL	TG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:946417_946418delTG	uc003gbq.2	+						TMEM175_uc010ibl.1_Intron|TMEM175_uc003gbp.1_Intron|TMEM175_uc003gbr.2_Intron|TMEM175_uc003gbu.2_Intron|TMEM175_uc003gbs.2_Intron|TMEM175_uc003gbt.2_Intron|TMEM175_uc003gbv.2_Intron|TMEM175_uc010ibm.2_Intron	NM_032326	NP_115702	Q9BSA9	TM175_HUMAN	transmembrane protein 175							integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGTCCtgtgctgtgtgtgtgtg	0.386													22	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	4893268	4893269	+	IGR	DEL	GT	-	-	rs141953709		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4893268_4893269delGT								MSX1 (27610 upstream) : CYTL1 (123047 downstream)																							TCTTCCTAGGgtgtgtgtgtgt	0.272													1	5	---	---	---	---	
FAM184B	27146	broad.mit.edu	37	4	17783284	17783284	+	5'Flank	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17783284delG	uc003gpm.3	-							NM_015688	NP_056503	Q9ULE4	F184B_HUMAN	hypothetical protein LOC27146											central_nervous_system(1)	1						TGCCGGCCTTGGGGGGTTTGC	0.711													4	2	---	---	---	---	
RHOH	399	broad.mit.edu	37	4	40211710	40211711	+	Intron	DEL	GT	-	-	rs34283631		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40211710_40211711delGT	uc003guz.2	+							NM_004310	NP_004301	Q15669	RHOH_HUMAN	ras homolog gene family, member H precursor						negative regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|T cell differentiation	cytosol|mitochondrion|plasma membrane	GTP binding|GTPase inhibitor activity|kinase inhibitor activity|Rho GTPase binding			ovary(1)|lung(1)	2						CATtgtgtgcgtgtgtgtgtgt	0.252													4	3	---	---	---	---	
RBM47	54502	broad.mit.edu	37	4	40568994	40568994	+	Intron	DEL	T	-	-	rs35644743		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40568994delT	uc003gvc.2	-						RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3						TTATCCTCTCTTTTTTTTCTC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49506430	49506430	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49506430delT								CWH43 (442337 upstream) : None (None downstream)																							TTCTTCTCTATTTTTTTGTAC	0.279													5	3	---	---	---	---	
RASL11B	65997	broad.mit.edu	37	4	53729814	53729814	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53729814delA	uc003gzt.2	+							NM_023940	NP_076429	Q9BPW5	RSLBB_HUMAN	RAS-like family 11 member B						small GTPase mediated signal transduction	membrane	GTP binding|GTPase activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0302)			CAAAAGTCGTAAAAAAAAAAA	0.458													2	4	---	---	---	---	
STAP1	26228	broad.mit.edu	37	4	68454071	68454072	+	Intron	INS	-	GAT	GAT	rs112837903		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68454071_68454072insGAT	uc003hde.3	+						STAP1_uc003hdf.2_Intron	NM_012108	NP_036240	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1						cellular membrane fusion|intracellular protein transport	cytoplasm					0						acgacgacgacgatgatgatga	0.208													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	70172663	70172664	+	IGR	INS	-	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70172663_70172664insC								UGT2B28 (11896 upstream) : UGT2B4 (173220 downstream)																							TGGCATATGGACACCTCAAATT	0.381													18	8	---	---	---	---	
CSN1S1	1446	broad.mit.edu	37	4	70799577	70799577	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70799577delG	uc003hep.1	+						CSN1S1_uc003heq.1_Intron|CSN1S1_uc003her.1_Intron	NM_001890	NP_001881	P47710	CASA1_HUMAN	casein alpha s1 isoform 1							extracellular region	protein binding|transporter activity				0						TTAGAACTATGGTGTAATATA	0.229													4	2	---	---	---	---	
RUFY3	22902	broad.mit.edu	37	4	71588132	71588132	+	5'UTR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71588132delT	uc003hfq.2	+	1					RUFY3_uc003hfp.3_Intron|RUFY3_uc011cax.1_5'UTR|RUFY3_uc003hfr.2_5'UTR	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			GTATTTTTCCTTTTTTTTTTT	0.323													9	5	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	78990366	78990366	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78990366delA	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						tttatggatgaggaaactggg	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84935986	84935986	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84935986delG	uc010ikd.1	-						uc003hoz.1_Intron					Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																		TATATATTGCGTAAAGCAAGG	0.338													4	2	---	---	---	---	
WDFY3	23001	broad.mit.edu	37	4	85661783	85661783	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85661783delA	uc003hpd.2	-							NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		agggctacataaaaaaaaaga	0.055													7	4	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	92111198	92111198	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92111198delT	uc003hsv.3	+							NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						ggcaccactgttgaaatctgt	0.134													4	2	---	---	---	---	
SCOC	60592	broad.mit.edu	37	4	141195011	141195011	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141195011delA	uc003iib.2	+							NM_032547	NP_115936	Q9UIL1	SCOC_HUMAN	short coiled-coil protein isoform 4							Golgi apparatus|nucleus	protein binding				0	all_hematologic(180;0.162)					TCAAAAGTGTAACAGTTTAAA	0.299													4	2	---	---	---	---	
TBC1D9	23158	broad.mit.edu	37	4	141600640	141600641	+	Intron	INS	-	A	A	rs144405227	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141600640_141600641insA	uc010ioj.2	-							NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				ACTTCAGTAGTAAAAAAAAATT	0.267													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174536901	174536901	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174536901delA								NBLA00301 (30022 upstream) : MORF4 (187 downstream)																							CTTTGAAATGaaaaaaaaaaa	0.313													5	6	---	---	---	---	
ENPP6	133121	broad.mit.edu	37	4	185097374	185097374	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185097374delT	uc003iwc.2	-							NM_153343	NP_699174	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						lipid catabolic process	extracellular region|integral to membrane|plasma membrane				central_nervous_system(1)	1		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		AAGCAGCACCTTTGGCCAACA	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189119722	189119722	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189119722delT								TRIML1 (51073 upstream) : None (None downstream)																							tcactgaatatttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189677233	189677233	+	IGR	DEL	T	-	-	rs147949065		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189677233delT								TRIML1 (608584 upstream) : None (None downstream)																							TATAttttccttttttttttt	0.224													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190551719	190551720	+	IGR	INS	-	CTCCCA	CTCCCA	rs150684825		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190551719_190551720insCTCCCA								None (None upstream) : FRG1 (310254 downstream)																							AGCCATTTCTCCCCCCGCCAAA	0.450													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	723042	723043	+	IGR	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:723042_723043insA								TPPP (29532 upstream) : ZDHHC11 (72677 downstream)																							tcctttctgttaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2145935	2145936	+	IGR	INS	-	C	C	rs144120416		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2145935_2145936insC								IRX4 (263055 upstream) : IRX2 (600345 downstream)																							CCTAATCACTTCCAGATCCTCC	0.540													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3084603	3084604	+	IGR	INS	-	AG	AG			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3084603_3084604insAG								C5orf38 (329091 upstream) : IRX1 (511564 downstream)																							TACTGAAAAACAGagagagaga	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10437892	10437892	+	RNA	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10437892delT	uc003jev.1	+	1		c.2011delT			uc003jew.2_5'Flank					Homo sapiens clone FBD3 Cri-du-chat critical region mRNA.																		AAATGCTCCCTTTTTAATGTG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10530902	10530903	+	IGR	DEL	GT	-	-	rs111992505		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10530902_10530903delGT								ROPN1L (65765 upstream) : DAP (148440 downstream)																							gtgtatgtccgtgtgtgtgtgt	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	13676841	13676843	+	IGR	DEL	GAT	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13676841_13676843delGAT								None (None upstream) : DNAH5 (13594 downstream)																							tgattatgacgatgatgatgatg	0.261													4	2	---	---	---	---	
DNAH5	1767	broad.mit.edu	37	5	13818110	13818110	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13818110delA	uc003jfd.2	-							NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					TTCATGGCTCAAAAAAAATCT	0.328									Kartagener_syndrome				5	4	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21551804	21551804	+	Intron	DEL	A	-	-	rs5866509		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21551804delA	uc003jgh.3	+							NR_027026				Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						GTGAAATGACAAAAAAAAAGT	0.398													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	21658788	21658789	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21658788_21658789insT	uc003jgj.2	+											Homo sapiens, clone IMAGE:5171606, mRNA.																		TGCTTTGATGATTTTTTTTTCT	0.238													4	2	---	---	---	---	
CDH10	1008	broad.mit.edu	37	5	24596480	24596480	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24596480delT	uc003jgr.1	-						CDH10_uc011cnu.1_Intron	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		CTCAGCTGTCTTTTTTTTTTG	0.378										HNSCC(23;0.051)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25242992	25242992	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25242992delT								CDH10 (598081 upstream) : None (None downstream)																							gaccaattccttttttttcct	0.000													4	2	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33626762	33626764	+	Intron	DEL	GTG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33626762_33626764delGTG	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						tggtggtgatgtggtaatggtgg	0.094										HNSCC(64;0.19)			8	4	---	---	---	---	
PRLR	5618	broad.mit.edu	37	5	35086663	35086664	+	Intron	DEL	GT	-	-	rs73767508	byFrequency	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35086663_35086664delGT	uc003jjm.2	-						PRLR_uc003jjg.1_Intron|PRLR_uc003jjh.1_Intron|PRLR_uc003jji.1_Intron|PRLR_uc003jjj.1_Intron|PRLR_uc003jjk.1_Intron|PRLR_uc003jjl.3_Intron|PRLR_uc010iuw.1_5'Flank	NM_000949	NP_000940	P16471	PRLR_HUMAN	prolactin receptor precursor						activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	CATTTTGCTGgtgtgtgtgtgt	0.386													6	3	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	36882368	36882368	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36882368delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			agtttagggaTTTTTTTTGTG	0.169													4	2	---	---	---	---	
PARP8	79668	broad.mit.edu	37	5	50035259	50035259	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50035259delT	uc003jon.3	+						PARP8_uc011cpz.1_Intron|PARP8_uc003joo.2_Intron|PARP8_uc003jop.2_Intron	NM_024615	NP_078891	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8							intracellular	NAD+ ADP-ribosyltransferase activity			lung(3)|large_intestine(1)|ovary(1)	5		Lung NSC(810;0.0305)|Breast(144;0.222)				TGAGAAATCATTTTTTTGATC	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63676825	63676825	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63676825delA								RNF180 (8131 upstream) : RGS7BP (125627 downstream)																							cactcaggataatcttcttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	68474723	68474723	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68474723delT								CCNB1 (657 upstream) : CENPH (10652 downstream)																							tttgtttttgttttttttttt	0.159													3	3	---	---	---	---	
CKMT2	1160	broad.mit.edu	37	5	80538123	80538123	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80538123delT	uc003khc.3	+						RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Intron|CKMT2_uc003khd.3_Intron|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase						creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	GTTTGTGGGCTTTTTTTTTGT	0.363													8	4	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93437675	93437676	+	Intron	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93437675_93437676insA	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron|FAM172A_uc003kkm.3_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						GAATAACCAGGAAAAAAAAAAG	0.163													4	2	---	---	---	---	
ERAP1	51752	broad.mit.edu	37	5	96111993	96111993	+	3'UTR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96111993delA	uc003kmm.2	-	19					CAST_uc003kmk.2_Intron|ERAP1_uc003kml.2_Intron|ERAP1_uc010jbm.1_Intron|ERAP1_uc003kmn.2_3'UTR	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding						angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		AGTTGAAGGGAAAAAAGTATC	0.393													128	85	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	102118755	102118755	+	IGR	DEL	A	-	-	rs11329963		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102118755delA								SLCO6A1 (284035 upstream) : PAM (82772 downstream)																							GGCAGGAAAGAAAAAAAACTC	0.363													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111532819	111532820	+	Intron	INS	-	AT	AT	rs72545062		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111532819_111532820insAT	uc003kpv.1	-						EPB41L4A_uc003kpp.1_Intron	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		acctctcacacagtcaccttgc	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115679969	115679970	+	IGR	INS	-	CAGT	CAGT	rs147577010	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115679969_115679970insCAGT								COMMD10 (50991 upstream) : SEMA6A (99282 downstream)																							tggggaaatgacagagctccct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119582043	119582043	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119582043delA								FAM170A (610527 upstream) : PRR16 (217976 downstream)																							AGAGAACTGGAAAAAAAAAGG	0.318													6	6	---	---	---	---	
CSNK1G3	1456	broad.mit.edu	37	5	122945604	122945605	+	Intron	INS	-	C	C	rs150055420	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122945604_122945605insC	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Intron|CSNK1G3_uc003ktn.2_Intron|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Intron	NM_004384	NP_004375	Q9Y6M4	KC1G3_HUMAN	casein kinase 1, gamma 3 isoform 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)		AAAGGGCATGGCATATTTATGA	0.431													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	126477257	126477257	+	IGR	DEL	A	-	-	rs112435935		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126477257delA								FLJ44606 (68085 upstream) : MEGF10 (149199 downstream)																							tgaaggcattaaaaaaaagtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134590265	134590266	+	Intron	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134590265_134590266insA	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		ATGTGTGAGGGAAAAAAAAATA	0.421													4	2	---	---	---	---	
CSF1R	1436	broad.mit.edu	37	5	149439931	149439931	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149439931delA	uc003lrl.2	-						CSF1R_uc011dcd.1_Intron|CSF1R_uc010jhc.2_Intron|CSF1R_uc003lrm.2_Intron	NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor						cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity			haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	AGACAACCTTAAAAAAAATGT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151913909	151913910	+	IGR	INS	-	T	T	rs142965260	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151913909_151913910insT								NMUR2 (129069 upstream) : GRIA1 (955265 downstream)																							TTTTGCTGACATTTTTTTTGTC	0.332													3	3	---	---	---	---	
GRIA1	2890	broad.mit.edu	37	5	153056890	153056891	+	Intron	INS	-	A	A	rs150898364	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153056890_153056891insA	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)	GAAGCTCATATAAAAAAAAAAT	0.347													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	159554373	159554373	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159554373delG								PWWP2A (7921 upstream) : FABP6 (60001 downstream)																							ggtgtcagctgggggtgtggt	0.000													4	2	---	---	---	---	
CCNJL	79616	broad.mit.edu	37	5	159754128	159754128	+	Intron	DEL	A	-	-	rs113991220		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159754128delA	uc003lyc.1	-									Q8IV13	CCNJL_HUMAN	Homo sapiens cDNA FLJ14166 fis, clone NT2RP1000796.							nucleus					0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTTTGTATTTAAAAAAAAAaa	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174845383	174845383	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174845383delG								MSX2 (687482 upstream) : DRD1 (22293 downstream)																							CAGAGAATTAGGCCAGAGTCA	0.453													4	2	---	---	---	---	
C5orf45	51149	broad.mit.edu	37	5	179281773	179281773	+	Intron	DEL	A	-	-	rs140386814		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179281773delA	uc003mla.2	-						C5orf45_uc003mky.2_Intron|C5orf45_uc011dgt.1_Intron|C5orf45_uc011dgu.1_Intron|C5orf45_uc003mlc.2_Intron|C5orf45_uc003mlb.2_Intron	NM_016175	NP_057259	Q6NTE8	CE045_HUMAN	hypothetical protein LOC51149 isoform 1												0						CATAATATTTAAATTCTTGTT	0.284													3	3	---	---	---	---	
RNF130	55819	broad.mit.edu	37	5	179397171	179397171	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179397171delA	uc003mll.1	-						RNF130_uc003mlm.1_Intron	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ttaaaaaaagaaaaaaaaaGG	0.189													5	3	---	---	---	---	
GFPT2	9945	broad.mit.edu	37	5	179757376	179757378	+	Intron	DEL	CAC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179757376_179757378delCAC	uc003mlw.1	-							NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	tctctctgcacaccaccaccAAG	0.202													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9453282	9453282	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9453282delT								HULC (799205 upstream) : TFAP2A (943635 downstream)																							TACAAAAAAATTATCATTTTA	0.318													4	2	---	---	---	---	
KIF13A	63971	broad.mit.edu	37	6	17836992	17836998	+	Intron	DEL	AGAGACA	-	-	rs12525646	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17836992_17836998delAGAGACA	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron|KIF13A_uc003ncj.2_Intron	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			agatttgggtagagacataaatcgaaa	0.208													15	14	---	---	---	---	
FAM65B	9750	broad.mit.edu	37	6	24843927	24843930	+	Intron	DEL	GTGT	-	-	rs34540028		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24843927_24843930delGTGT	uc003neo.1	-						FAM65B_uc011djs.1_Intron|FAM65B_uc011dju.1_Intron|FAM65B_uc003nep.2_Intron|FAM65B_uc011djt.1_Intron	NM_014722	NP_055537	Q9Y4F9	FA65B_HUMAN	hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1						TGTTGATGCCgtgtgtgtgtgtgt	0.275													5	3	---	---	---	---	
C6orf222	389384	broad.mit.edu	37	6	36298522	36298525	+	Intron	DEL	TTTG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36298522_36298525delTTTG	uc003oly.2	-							NM_001010903	NP_001010903	P0C671	CF222_HUMAN	hypothetical protein LOC389384											skin(2)|ovary(1)|breast(1)	4						tttgttttgatttgtttgtttgtt	0.216													7	6	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38927600	38927600	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38927600delA	uc003ooe.1	+						DNAH8_uc003oog.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						cttgagcattaaaaaaaaaag	0.000													4	2	---	---	---	---	
GPR116	221395	broad.mit.edu	37	6	46868031	46868031	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46868031delT	uc003oyo.3	-						GPR116_uc003oyp.3_Intron|GPR116_uc003oyq.3_Intron|GPR116_uc003oyr.2_Intron	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			TAGGAATTCATTTTTTTTTAG	0.408													5	6	---	---	---	---	
BEND6	221336	broad.mit.edu	37	6	56882435	56882435	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56882435delA	uc010kab.2	+						BEND6_uc003pdi.3_Intron	NM_152731	NP_689944	Q5SZJ8	BEND6_HUMAN	BEN domain containing 6												0						CAATTCATACAATTTATAGCT	0.229													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57369607	57369607	+	Intron	DEL	A	-	-	rs10716522		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57369607delA	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)		CTATAAAAAGAAAAAAAAATT	0.338													4	4	---	---	---	---	
MYO6	4646	broad.mit.edu	37	6	76532235	76532237	+	Intron	DEL	CTT	-	-	rs151140767		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76532235_76532237delCTT	uc003pih.1	+						MYO6_uc003pig.1_Intron|MYO6_uc003pii.1_Intron	NM_004999	NP_004990	Q9UM54	MYO6_HUMAN	myosin VI						actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TTTTTTTGTCCTTCTTTAGGTGT	0.227													6	3	---	---	---	---	
C6orf167	253714	broad.mit.edu	37	6	97715518	97715519	+	Intron	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97715518_97715519insA	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron|C6orf167_uc010kcn.1_Intron|C6orf167_uc010kco.1_Intron|C6orf167_uc003ppc.2_Intron	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		CTATTTTTCTTaaaaaaaaaaa	0.262													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100691412	100691413	+	IGR	DEL	AA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100691412_100691413delAA								MCHR2 (249298 upstream) : SIM1 (145338 downstream)																							ccatcagaggaaaagaggagTC	0.188													4	2	---	---	---	---	
ARMC2	84071	broad.mit.edu	37	6	109285993	109285993	+	Intron	DEL	A	-	-	rs77214837		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109285993delA	uc003pss.3	+						ARMC2_uc011eao.1_Intron	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2								binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		actctgtctcaaaaaaaaaaa	0.114													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112647042	112647042	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112647042delT								LAMA4 (71214 upstream) : RFPL4B (21490 downstream)																							GCTTTGCAGCTTTTTTTTTTC	0.453													9	4	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162851202	162851203	+	Intron	INS	-	GAT	GAT	rs73783531		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162851202_162851203insGAT	uc003qtx.3	-						PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|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)		acgacgacgacgacgatgatga	0.134													6	4	---	---	---	---	
PDE10A	10846	broad.mit.edu	37	6	166066852	166066852	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166066852delA	uc003qun.2	-						PDE10A_uc003quo.2_Intron	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	ggatggaagcacggatgagcg	0.124													4	2	---	---	---	---	
GNA12	2768	broad.mit.edu	37	7	2774749	2774750	+	Intron	INS	-	C	C	rs141758784	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2774749_2774750insC	uc003smu.2	-						GNA12_uc011jwb.1_Intron|GNA12_uc003smt.2_Intron	NM_007353	NP_031379	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein)						G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|Rho protein signal transduction	brush border membrane|heterotrimeric G-protein complex	D5 dopamine receptor binding|G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		GTGCACTCACTCCCTGATTTAC	0.634													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	10035471	10035471	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10035471delA								PER4 (360024 upstream) : NDUFA4 (937344 downstream)																							ACCAAAATTGAAAAAAAAAAT	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	10476559	10476562	+	IGR	DEL	TCCA	-	-	rs34217520		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10476559_10476562delTCCA								PER4 (801112 upstream) : NDUFA4 (496253 downstream)																							CCATCTTCACTCCATCTATACTCT	0.475													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	10915539	10915539	+	IGR	DEL	A	-	-	rs11361374		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10915539delA								None (None upstream) : NDUFA4 (57276 downstream)																							GACTTTGAACAAAAAAAAAAA	0.234													5	3	---	---	---	---	
VWDE	221806	broad.mit.edu	37	7	12396086	12396087	+	Intron	DEL	AC	-	-	rs143598907		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12396086_12396087delAC	uc003ssj.2	-						VWDE_uc011jxl.1_Intron|VWDE_uc011jxm.1_Intron	NM_001135924	NP_001129396	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains							extracellular region					0						TGATATATATACACACACACAC	0.282													6	4	---	---	---	---	
KLHL7	55975	broad.mit.edu	37	7	23188718	23188718	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23188718delA	uc003svs.3	+						KLHL7_uc003svr.3_Intron|KLHL7_uc011jys.1_Intron|KLHL7_uc011jyt.1_Intron|KLHL7_uc003svt.2_Intron|KLHL7_uc011jyv.1_Intron	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	kelch-like 7 isoform 1							Golgi apparatus|nucleolus|plasma membrane					0						AAAATTTTACATCCAAAAGAA	0.343													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23933222	23933223	+	Intron	INS	-	GTGT	GTGT	rs138007377	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23933222_23933223insGTGT	uc003swv.1	+									Q9BXU1	STK31_HUMAN	SubName: Full=Putative uncharacterized protein STK31;								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						TCCCTGATGCAgtgtgtgtgtg	0.332													3	3	---	---	---	---	
ADCYAP1R1	117	broad.mit.edu	37	7	31107832	31107833	+	Intron	DEL	CA	-	-	rs115664664	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31107832_31107833delCA	uc003tca.1	+						ADCYAP1R1_uc003tcb.1_Intron|ADCYAP1R1_uc003tcc.1_Intron|ADCYAP1R1_uc003tcd.1_Intron|ADCYAP1R1_uc003tce.1_Intron	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						tgtgcgcgcgcacacacacaca	0.233													3	3	---	---	---	---	
NPSR1	387129	broad.mit.edu	37	7	34717758	34717758	+	Intron	DEL	A	-	-	rs35522392		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34717758delA	uc003teg.1	+						AAA1_uc010kwo.1_Intron|AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron|AAA1_uc003teb.1_Intron|AAA1_uc011kaq.1_Intron|NPSR1_uc003teh.1_Intron|NPSR1_uc010kwt.1_Intron|NPSR1_uc010kwu.1_Intron|NPSR1_uc010kwv.1_Intron|NPSR1_uc003tei.1_Intron|NPSR1_uc010kww.1_Intron|NPSR1_uc011kar.1_Intron	NM_207172	NP_997055	Q6W5P4	NPSR1_HUMAN	G protein-coupled receptor for asthma							cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity			skin(3)|pancreas(1)	4					Halothane(DB01159)	GGACAAGTGCAAGAAATAAAC	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54099421	54099422	+	IGR	INS	-	GA	GA	rs76678014	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54099421_54099422insGA								POM121L12 (994804 upstream) : HPVC1 (169495 downstream)																							tgtgtgtgtgtgtgagagagag	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63016132	63016133	+	IGR	INS	-	G	G	rs138696627		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63016132_63016133insG								LOC100287704 (203981 upstream) : ZNF727 (489688 downstream)																							ACATGACCACTAGCTCACAGCA	0.653													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63363859	63363859	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63363859delT	uc003tsv.2	+											Homo sapiens cDNA clone IMAGE:5296015.																		TTAGGTGTGATTTTTTTTCTT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67611542	67611543	+	IGR	INS	-	T	T	rs145927864	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67611542_67611543insT								STAG3L4 (825030 upstream) : None (None downstream)																							TTCTTTTGTCCTTTTTTTTGTT	0.233													3	3	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	69961452	69961453	+	Intron	DEL	CA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69961452_69961453delCA	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		cgtacacagtcacacacacaca	0.040													5	3	---	---	---	---	
TYW1B	441250	broad.mit.edu	37	7	72026303	72026303	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72026303delC	uc011keh.1	-							NM_001145441	NP_001138913	Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0						CCAACCCCTACCCCAGGAATT	0.299													4	2	---	---	---	---	
STAG3L2	442582	broad.mit.edu	37	7	74303583	74303592	+	Intron	DEL	ACAGAAAGAG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74303583_74303592delACAGAAAGAG	uc003ubj.3	-						STAG3L2_uc011kfj.1_Intron	NM_001025202	NP_001020373	P0CL84	ST3L2_HUMAN	STAG3-like							nucleus	binding				0						agcctgggcaacagaaagagactgtctcaa	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	88163119	88163119	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88163119delT								STEAP4 (226910 upstream) : ZNF804B (225634 downstream)																							tactcagatatttttctatcc	0.000													4	2	---	---	---	---	
STEAP2	261729	broad.mit.edu	37	7	89822205	89822205	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89822205delC	uc003ujy.2	+							NM_001040666	NP_001035756	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the						electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)					agtaccttttcttgaaacttt	0.000													4	2	---	---	---	---	
CLDN12	9069	broad.mit.edu	37	7	90032544	90032544	+	Intron	DEL	T	-	-	rs67527055		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90032544delT	uc003ukp.2	+						CLDN12_uc003ukq.2_Intron|CLDN12_uc010leq.2_5'Flank|CLDN12_uc003ukr.2_5'Flank|CLDN12_uc003uks.2_5'Flank	NM_012129	NP_036261	P56749	CLD12_HUMAN	claudin 12						calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity				0						TCGTTTTGCCTTTTTTTTTTC	0.433											OREG0003800	type=REGULATORY REGION|Gene=CLDN12|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	6	3	---	---	---	---	
PDK4	5166	broad.mit.edu	37	7	95225789	95225790	+	5'UTR	INS	-	GG	GG	rs146716475	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95225789_95225790insGG	uc003uoa.2	-	1						NM_002612	NP_002603	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase 4 precursor						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity				0	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			GTCTGGGCAGAGTCGGAGATGC	0.663													4	4	---	---	---	---	
TFR2	7036	broad.mit.edu	37	7	100229247	100229247	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100229247delA	uc003uvv.1	-						TFR2_uc010lhc.1_Intron|TFR2_uc003uvu.1_Intron	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2						cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					actccatctcaaaaaaaaaaa	0.035													8	5	---	---	---	---	
LRWD1	222229	broad.mit.edu	37	7	102106858	102106861	+	Intron	DEL	TTTA	-	-	rs66463732		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102106858_102106861delTTTA	uc003uzn.2	+						ALKBH4_uc003uzl.2_5'Flank|ALKBH4_uc003uzm.2_5'Flank|LRWD1_uc003uzo.2_Intron	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain						chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding			skin(1)	1						GATGTGCTACtttatttatttatt	0.260													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109856082	109856082	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109856082delA								EIF3IP1 (255812 upstream) : IMMP2L (447028 downstream)																							CAGAGAACATAAAAATACAGG	0.313													4	2	---	---	---	---	
ST7	7982	broad.mit.edu	37	7	116600233	116600233	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116600233delT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		gctggGATTCttttttttttg	0.010													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117707231	117707231	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117707231delT								CTTNBP2 (193670 upstream) : NAA38 (116855 downstream)																							CCTTTGTTCCTTTCCTTTGCT	0.388													4	2	---	---	---	---	
SLC13A1	6561	broad.mit.edu	37	7	122787592	122787595	+	Intron	DEL	CTCT	-	-	rs72058039		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122787592_122787595delCTCT	uc003vkm.2	-						SLC13A1_uc010lks.2_Intron	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate							integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)	agcttgattcctctctctctctct	0.000													5	4	---	---	---	---	
WASL	8976	broad.mit.edu	37	7	123332231	123332231	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123332231delA	uc003vkz.2	-							NM_003941	NP_003932	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome gene-like protein						actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity				0						aagctgaattaaaaatttgtg	0.080													4	2	---	---	---	---	
WASL	8976	broad.mit.edu	37	7	123360650	123360650	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123360650delG	uc003vkz.2	-							NM_003941	NP_003932	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome gene-like protein						actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity				0						GAAATGACTAGGCAAATGAAG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127058812	127058814	+	IGR	DEL	CAC	-	-	rs72204773		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127058812_127058814delCAC								ZNF800 (26045 upstream) : GCC1 (161869 downstream)																							ctaccagcatcaccaccaccacc	0.113													7	6	---	---	---	---	
SLC37A3	84255	broad.mit.edu	37	7	140048263	140048263	+	Intron	DEL	T	-	-	rs112515175		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140048263delT	uc003vvo.2	-						SLC37A3_uc003vvp.2_Intron|SLC37A3_uc010lnh.2_Intron	NM_207113	NP_996996	Q8NCC5	SPX3_HUMAN	solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(3)	3	Melanoma(164;0.0142)					ttttcttttcttttttttttt	0.303													6	3	---	---	---	---	
DENND2A	27147	broad.mit.edu	37	7	140266731	140266731	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140266731delT	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)					AGCAGCAGCATTTTTTTTTCA	0.368													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142407690	142407690	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142407690delT	uc011krp.1	+						uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc011ksg.1_Intron					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		GGACATCCAATTTTTATGCAA	0.358													4	2	---	---	---	---	
GIMAP5	55340	broad.mit.edu	37	7	150438330	150438330	+	Intron	DEL	G	-	-	rs13235400	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150438330delG	uc003whr.1	+						GIMAP5_uc010lpu.2_Intron	NM_018384	NP_060854	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5							integral to membrane|mitochondrial outer membrane	GTP binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGCTCAAAAAGAAAAGGTCCC	0.393													8	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152103075	152103075	+	Intron	DEL	G	-	-	rs66994474		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152103075delG	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ctctgtctcagaaaaaaaaaa	0.114			N		medulloblastoma								6	5	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152110157	152110157	+	Intron	DEL	A	-	-	rs11335639		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152110157delA	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)		CACTTCTGAGAAAAAAAACAA	0.254			N		medulloblastoma								10	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152672793	152672794	+	IGR	DEL	AA	-	-	rs36107891		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152672793_152672794delAA								ACTR3B (120330 upstream) : DPP6 (911625 downstream)																							ATATATTTGTAAAAAAAAAAAA	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155650868	155650868	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155650868delT								SHH (45901 upstream) : C7orf4 (682317 downstream)																							tgtgcatgtatgagtgtatat	0.045													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	17719403	17719403	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17719403delT								MTUS1 (60977 upstream) : FGL1 (2499 downstream)																							tgtggaatcattttttttctc	0.065													4	2	---	---	---	---	
ADAM32	203102	broad.mit.edu	37	8	39125784	39125784	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39125784delT	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron|ADAM32_uc003xmv.2_Intron	NM_145004	NP_659441	Q8TC27	ADA32_HUMAN	a disintegrin and metalloprotease domain 32						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			tgtggtctcattttttttaac	0.000													4	2	---	---	---	---	
DKK4	27121	broad.mit.edu	37	8	42233038	42233038	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42233038delA	uc003xpb.2	-							NM_014420	NP_055235	Q9UBT3	DKK4_HUMAN	dickkopf homolog 4 precursor						multicellular organismal development|negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular region				ovary(1)	1	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|Lung(22;0.00597)|LUSC - Lung squamous cell carcinoma(45;0.024)			TCCGCCTCAGAAAAAAAAAAA	0.264													8	6	---	---	---	---	
ATP6V1H	51606	broad.mit.edu	37	8	54729798	54729799	+	Intron	DEL	AA	-	-	rs35983124		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54729798_54729799delAA	uc003xrl.2	-						ATP6V1H_uc003xrk.2_Intron|ATP6V1H_uc003xrm.2_Intron|ATP6V1H_uc003xrn.2_Intron|ATP6V1H_uc011ldv.1_Intron|ATP6V1H_uc010lyd.2_Intron	NM_213620	NP_998785	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			CTTTGtatttaaaaaaaaaaaa	0.099													4	4	---	---	---	---	
PLAG1	5324	broad.mit.edu	37	8	57107136	57107137	+	Intron	DEL	GT	-	-	rs36079543	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57107136_57107137delGT	uc003xsr.3	-						PLAG1_uc010lyi.2_Intron|PLAG1_uc010lyj.2_Intron	NM_002655	NP_002646	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1 isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding		CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3)	salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1)	129		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			TCAGCACTGGgtgtgtgtgtgt	0.332			T	TCEA1|LIFR|CTNNB1|CHCHD7	salivary adenoma								6	3	---	---	---	---	
DNAJC5B	85479	broad.mit.edu	37	8	66993834	66993834	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66993834delT	uc003xvs.1	+						DNAJC5B_uc003xvt.1_Intron	NM_033105	NP_149096	Q9UF47	DNJ5B_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5						protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)			tccacacaccttttattccct	0.000													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	68864143	68864144	+	5'Flank	INS	-	GCGC	GCGC			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68864143_68864144insGCGC	uc003xxv.1	+						PREX2_uc003xxu.1_5'Flank|PREX2_uc011lez.1_5'Flank|PREX2_uc003xxt.2_5'Flank	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						tgtgtgtgtgtgtgtgtgtgcg	0.351													5	3	---	---	---	---	
KCNB2	9312	broad.mit.edu	37	8	73777986	73777987	+	Intron	INS	-	T	T	rs147496191	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73777986_73777987insT	uc003xzb.2	+							NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related						regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)			ctcactgcctcttacttatcct	0.168													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102490069	102490071	+	IGR	DEL	TCC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102490069_102490071delTCC								NACAP1 (105134 upstream) : GRHL2 (14597 downstream)																							ctcttcctcttcctcctcctcct	0.143													4	2	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	113848040	113848040	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113848040delC	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ggaatcagagccagaagctgt	0.159										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117444304	117444304	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117444304delC								TRPS1 (763076 upstream) : EIF3H (212752 downstream)																							AAGCAGTTTTCCCCCAGTAAC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125147734	125147734	+	Intron	DEL	A	-	-	rs74943309		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125147734delA	uc003yqy.1	-											Homo sapiens cDNA FLJ32770 fis, clone TESTI2001898.																		TGGAAACAAGAAAAAAAAAAT	0.060													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	140816344	140816346	+	Intron	DEL	CAC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140816344_140816346delCAC	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						caccaccactcaccaccaccacc	0.039													5	3	---	---	---	---	
PDCD1LG2	80380	broad.mit.edu	37	9	5551875	5551876	+	Intron	DEL	CC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5551875_5551876delCC	uc003zjg.3	+						C9orf46_uc003zjd.2_Intron|PDCD1LG2_uc011lmc.1_Intron|PDCD1LG2_uc011lmd.1_Intron|PDCD1LG2_uc010mhp.1_Intron|PDCD1LG2_uc010mho.1_Intron	NM_025239	NP_079515	Q9BQ51	PD1L2_HUMAN	programmed cell death 1 ligand 2 precursor						immune response|T cell costimulation	endomembrane system|extracellular region|integral to membrane|plasma membrane	receptor activity				0	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000767)|Lung(218;0.112)		TGGGAGGCAGCCACAATCTCTG	0.282													4	2	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	7128976	7128976	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7128976delT	uc003zkh.2	+						KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						CCACAGAGGGTTTTTTTTGAC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	15000747	15000748	+	Intron	INS	-	C	C	rs150813539	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15000747_15000748insC	uc003zln.1	-						LOC389705_uc010mid.1_Intron					Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																		TTCCTTATAAAATTTTTTTTCC	0.366													2	6	---	---	---	---	
IFT74	80173	broad.mit.edu	37	9	27057541	27057541	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27057541delA	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqg.3_Intron	NM_001099223	NP_001092693	Q96LB3	IFT74_HUMAN	coiled-coil domain containing 2 isoform a							cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum				skin(1)	1		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		CACATGGTTTAAAACCCTAAA	0.184													4	2	---	---	---	---	
TOMM5	401505	broad.mit.edu	37	9	37595393	37595394	+	5'Flank	DEL	GT	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37595393_37595394delGT	uc010mlx.2	-						TOMM5_uc004aae.3_5'Flank|TOMM5_uc011lql.1_5'Flank|TOMM5_uc004aaf.2_5'Flank	NM_001001790	NP_001001790	Q8N4H5	TOM5_HUMAN	translocase of outer mitochondrial membrane 5							integral to membrane|mitochondrial outer membrane translocase complex					0						AAAATGGTCAGTGTGTGTGTGT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67337092	67337092	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67337092delT								AQP7P1 (47600 upstream) : FAM27B (455838 downstream)																							ataaaaatgcttcaacaagca	0.005													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68418203	68418204	+	IGR	INS	-	TG	TG	rs145604244		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68418203_68418204insTG								FAM27B (624014 upstream) : MIR1299 (584035 downstream)																							AGAAAATTAGATGTGTGTGTTT	0.262													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70087183	70087184	+	IGR	INS	-	T	T	rs148242551		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70087183_70087184insT								LOC100133920 (422234 upstream) : FOXD4L5 (88525 downstream)																							ACATGATGGGGTGGGGGGGGGG	0.416													21	22	---	---	---	---	
NCBP1	4686	broad.mit.edu	37	9	100417677	100417677	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100417677delT	uc004axq.2	+							NM_002486	NP_002477	Q09161	NCBP1_HUMAN	nuclear cap binding protein subunit 1, 80kDa						gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)				tttcataaaattttttttttt	0.000													4	2	---	---	---	---	
INVS	27130	broad.mit.edu	37	9	103039871	103039871	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103039871delT	uc004bap.1	+						INVS_uc011lve.1_Intron|INVS_uc004bao.1_Intron|INVS_uc004baq.1_Intron|INVS_uc004bar.1_Intron|INVS_uc010mtb.1_Intron	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a						negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|membrane|microtubule|nucleus|spindle	calmodulin binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.056)				gatctatagatttttttttat	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111009767	111009767	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111009767delC								KLF4 (757720 upstream) : ACTL7B (607104 downstream)																							AAACTGTTTACAGCACACACA	0.348													4	2	---	---	---	---	
INPP5E	56623	broad.mit.edu	37	9	139333050	139333053	+	Intron	DEL	CCCT	-	-	rs66749537		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139333050_139333053delCCCT	uc004cho.2	-						INPP5E_uc010nbm.2_Intron	NM_019892	NP_063945	Q9NRR6	INP5E_HUMAN	inositol polyphosphate-5-phosphatase E							cilium axoneme|cytoskeleton|Golgi cisterna membrane	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity			skin(1)	1		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		ACCCGCCAGGCCCTCCCTACCTGC	0.657													3	5	---	---	---	---	
LCN6	158062	broad.mit.edu	37	9	139642142	139642142	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139642142delC	uc004ciy.2	-						LCN10_uc004ciw.2_Intron|uc004ciz.1_RNA	NM_198946	NP_945184	P62502	LCN6_HUMAN	lipocalin 6 precursor						single fertilization	extracellular region	binding				0	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		aaccatccagccctccagcct	0.015													4	3	---	---	---	---	
LCN6	158062	broad.mit.edu	37	9	139642146	139642146	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139642146delC	uc004ciy.2	-						LCN10_uc004ciw.2_Intron|uc004ciz.1_RNA	NM_198946	NP_945184	P62502	LCN6_HUMAN	lipocalin 6 precursor						single fertilization	extracellular region	binding				0	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		atccagccctccagcctccag	0.000													4	3	---	---	---	---	
CACNA1B	774	broad.mit.edu	37	9	140918171	140918185	+	In_Frame_Del	DEL	GGAGAAGGAGACCAC	-	-	rs11137342		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140918171_140918185delGGAGAAGGAGACCAC	uc004cog.2	+	19	3121_3135	c.2976_2990delGGAGAAGGAGACCAC	c.(2974-2991)GTGGAGAAGGAGACCACG>GTG	p.EKETT993del	CACNA1B_uc011mfd.1_In_Frame_Del_p.EKETT523del|CACNA1B_uc004coi.2_In_Frame_Del_p.EKETT203del	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	993_997	Cytoplasmic (Potential).				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	ACGAGGCTGTGGAGAAGGAGACCACGGAGAAGGAG	0.433													6	3	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11325868	11325869	+	Intron	DEL	TG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11325868_11325869delTG	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbk.1_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc010qbo.1_Intron|CELF2_uc010qbp.1_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						gatggatgactgtgtggtaggt	0.000													3	3	---	---	---	---	
ARHGAP21	57584	broad.mit.edu	37	10	24996733	24996733	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24996733delC	uc001isb.2	-						ARHGAP21_uc009xkl.1_Intron|ARHGAP21_uc001isc.1_Intron|ARHGAP21_uc001isd.1_Intron	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21						signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8						taaattcagacccccatcaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31424135	31424135	+	IGR	DEL	T	-	-	rs111717554		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31424135delT								ZNF438 (103269 upstream) : LOC220930 (181323 downstream)																							GTGGAAGGCCTTTTTTTTTTC	0.368													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37598246	37598246	+	IGR	DEL	A	-	-	rs12261580	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37598246delA								ANKRD30A (76751 upstream) : ZNF248 (492201 downstream)																							ATTATTTTTTAAAAAAAAAAG	0.279													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42386460	42386460	+	IGR	DEL	G	-	-	rs113515963		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42386460delG								None (None upstream) : LOC441666 (440855 downstream)																							aacatcgaatggaatcgaatg	0.000													14	28	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76303614	76303614	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76303614delT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712	P55263	ADK_HUMAN	adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)	CTCTTTTATCTTTTTTTTTTC	0.284													3	3	---	---	---	---	
MYST4	23522	broad.mit.edu	37	10	76788042	76788046	+	Intron	DEL	TACTC	-	-	rs139379243	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76788042_76788046delTACTC	uc001jwn.1	+						MYST4_uc001jwo.1_Intron|MYST4_uc001jwp.1_Intron	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic						histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)					CCCAATATGTTACTCTCCCAGGCCT	0.346			T	CREBBP	AML								7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81632948	81632948	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81632948delT								LOC650623 (184300 upstream) : MBL1P (31706 downstream)																							TCTTCAtttcttttttttttt	0.214													4	3	---	---	---	---	
GHITM	27069	broad.mit.edu	37	10	85904422	85904422	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85904422delT	uc001kcs.1	+						GHITM_uc010qma.1_Intron|GHITM_uc010qmb.1_Intron	NM_014394	NP_055209	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0						AAATATGTTGTTTTTTATATG	0.025													4	2	---	---	---	---	
PAPSS2	9060	broad.mit.edu	37	10	89419638	89419639	+	5'UTR	INS	-	GCT	GCT			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89419638_89419639insGCT	uc001kex.2	+	1					PAPSS2_uc001kew.2_5'UTR|PAPSS2_uc009xtg.1_5'Flank	NM_004670	NP_004661	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|protein binding|sulfate adenylyltransferase (ATP) activity			central_nervous_system(1)|skin(1)	2		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		GTCCGGCAgccgctgctgctgc	0.530													2	13	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97271718	97271718	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97271718delC	uc001kkw.2	-						SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron|SORBS1_uc001kkx.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		aatcaggtcacccccatccta	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102324998	102325001	+	IGR	DEL	TTTG	-	-	rs67232845		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102324998_102325001delTTTG								HIF1AN (11318 upstream) : PAX2 (180467 downstream)																							TTGTGAAGAATTTGTTTGGGAGTC	0.554													1	5	---	---	---	---	
CYP17A1	1586	broad.mit.edu	37	10	104594232	104594232	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104594232delG	uc001kwg.2	-							NM_000102	NP_000093	P05093	CP17A_HUMAN	cytochrome P450, family 17						androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	NADH(DB00157)|Progesterone(DB00396)	cctgcacaatggggataataa	0.134													4	2	---	---	---	---	
MXI1	4601	broad.mit.edu	37	10	111987683	111987684	+	Intron	INS	-	AAAA	AAAA			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111987683_111987684insAAAA	uc001kza.2	+						MXI1_uc001kyy.2_Intron|MXI1_uc001kyz.2_Intron|MXI1_uc010qrc.1_Intron|MXI1_uc009xxu.2_Intron|MXI1_uc009xxv.2_Intron	NM_005962	NP_005953	P50539	MXI1_HUMAN	MAX interactor 1 isoform a						cytoplasmic sequestering of transcription factor|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription corepressor activity				0		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;1.33e-05)|all cancers(201;0.000277)|BRCA - Breast invasive adenocarcinoma(275;0.127)		TCTGAAATCTCAAGTTCTTGGG	0.416													2	4	---	---	---	---	
TRUB1	142940	broad.mit.edu	37	10	116734443	116734443	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116734443delA	uc001lcd.2	+						TRUB1_uc010qsl.1_Intron	NM_139169	NP_631908	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase homolog 1						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding				0		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		ACTAGGGATCAAAAAAAAAAA	0.284													6	4	---	---	---	---	
TUB	7275	broad.mit.edu	37	11	8054234	8054242	+	Intron	DEL	CGCACATCT	-	-	rs11469029		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8054234_8054242delCGCACATCT	uc010rbk.1	+							NM_177972	NP_813977	P50607	TUB_HUMAN	tubby isoform b						phagocytosis|positive regulation of phagocytosis|response to stimulus	cytoplasm|extracellular region|nucleus|plasma membrane				ovary(1)	1		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		TTGCACCTCCCGCACATCTGGCTCACGCC	0.531											OREG0020728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
FAR1	84188	broad.mit.edu	37	11	13733839	13733839	+	Intron	DEL	A	-	-	rs72447632		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13733839delA	uc001mld.2	+						FAR1_uc009ygp.2_Intron	NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2						CTTAAAAATGAAAAAAAAAAA	0.289													6	3	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16337654	16337655	+	Intron	INS	-	T	T	rs145059669		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16337654_16337655insT	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron|SOX6_uc001mmh.1_Intron|SOX6_uc009ygs.2_Intron|SOX6_uc001mmi.3_3'UTR	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						aaactcataggttttttttttt	0.000													4	3	---	---	---	---	
PLEKHA7	144100	broad.mit.edu	37	11	17002230	17002231	+	Intron	DEL	GA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17002230_17002231delGA	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						tgcactttgggaggccaaagtg	0.114													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21481024	21481024	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21481024delA	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						AGTAAAGGATAAAAAAAAGAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	30909660	30909661	+	Intron	DEL	AG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30909660_30909661delAG	uc001mss.1	-						uc009yjk.1_Intron|uc009yjj.1_Intron					Homo sapiens mRNA for KIAA1493 protein, partial cds.																		aaagaaagaaagaaagaaagaa	0.015													10	5	---	---	---	---	
PAX6	5080	broad.mit.edu	37	11	31815986	31815986	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31815986delA	uc001mtd.3	-						PAX6_uc001mte.3_Intron|PAX6_uc001mtg.3_Intron|PAX6_uc001mtf.3_Intron|PAX6_uc001mth.3_Intron|PAX6_uc009yjr.2_Intron	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a						blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)					acacacacacacacacacaca	0.179									Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35677607	35677608	+	IGR	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35677607_35677608insA								FJX1 (35188 upstream) : TRIM44 (6745 downstream)																							CATGCACTCAGAAAACAGCTGC	0.465													4	2	---	---	---	---	
ATL3	25923	broad.mit.edu	37	11	63426922	63426922	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63426922delC	uc001nxk.1	-						ATL3_uc010rms.1_Intron|ATL3_uc001nxl.1_Intron	NM_015459	NP_056274	Q6DD88	ATLA3_HUMAN	atlastin 3						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			pancreas(1)	1						aacggtgaaacccagcgctat	0.000													4	2	---	---	---	---	
PC	5091	broad.mit.edu	37	11	66623500	66623501	+	Intron	INS	-	CT	CT	rs139110664	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66623500_66623501insCT	uc001ojn.1	-						PC_uc001ojo.1_Intron|PC_uc001ojp.1_Intron|LRFN4_uc001ojq.1_5'Flank|LRFN4_uc001ojr.2_5'Flank|LRFN4_uc001ojs.2_5'Flank	NM_022172	NP_071504	P11498	PYC_HUMAN	pyruvate carboxylase precursor						gluconeogenesis|lipid biosynthetic process	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|pyruvate carboxylase activity			ovary(2)|lung(1)|kidney(1)	4		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	GTGGTGACTTCCTGTTTCCCAA	0.619													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81354635	81354635	+	IGR	DEL	A	-	-	rs72502447		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81354635delA								None (None upstream) : None (None downstream)																							TCTAAACTGGAAAAAAAAAAA	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	86057652	86057652	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86057652delT								C11orf73 (668 upstream) : CCDC81 (28126 downstream)																							aagaaaaggattttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	89847249	89847249	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89847249delA								UBTFL1 (26951 upstream) : NAALAD2 (20569 downstream)																							aactcAAAAGAAAAAAAAAAG	0.080													1	5	---	---	---	---	
AMOTL1	154810	broad.mit.edu	37	11	94602123	94602123	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94602123delA	uc001pfb.2	+						AMOTL1_uc001pfc.2_Intron	NM_130847	NP_570899	Q8IY63	AMOL1_HUMAN	angiomotin like 1							cytoplasm|tight junction	identical protein binding			ovary(1)|breast(1)	2		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				aaaaaaaaacaaaaaaaacac	0.264													4	2	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	103104605	103104608	+	Intron	DEL	GTGG	-	-	rs72297113	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103104605_103104608delGTGG	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		gtgtgtgtgtgtgGGTTTGTCTCT	0.240													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	104128732	104128732	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104128732delG								PDGFD (93705 upstream) : CASP12 (627710 downstream)																							ATGAAATGTAGGGGGACAGAG	0.393													4	2	---	---	---	---	
CASP1	834	broad.mit.edu	37	11	104938142	104938142	+	Intron	DEL	T	-	-	rs5794377		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104938142delT	uc010rve.1	-						CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Intron|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron|uc001piq.1_Intron	NM_033292	NP_150634	P29466	CASP1_HUMAN	caspase 1 isoform alpha precursor						cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction	cytosol	caspase activator activity|cysteine-type endopeptidase activity|protein binding			ovary(2)	2		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)|Penicillamine(DB00859)	GATACAGGAATTTTTTTTTTT	0.343													6	4	---	---	---	---	
ELMOD1	55531	broad.mit.edu	37	11	107533731	107533732	+	Intron	INS	-	CC	CC	rs139070974	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107533731_107533732insCC	uc010rvs.1	+						ELMOD1_uc001pjm.2_Intron|ELMOD1_uc010rvt.1_Intron	NM_018712	NP_061182	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1 isoform 1						phagocytosis	cytoskeleton	GTPase activator activity				0		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		ttgagattacaggtgtgagcca	0.168													2	5	---	---	---	---	
VSIG2	23584	broad.mit.edu	37	11	124621017	124621018	+	Intron	INS	-	TC	TC	rs145936470	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124621017_124621018insTC	uc001qas.2	-						VSIG2_uc001qat.2_Intron	NM_014312	NP_055127	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2							integral to plasma membrane|membrane fraction				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.215)	Breast(109;0.00663)|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;0.0215)		TGATCCATTGGTCTCTCTCTCT	0.490													7	6	---	---	---	---	
DCPS	28960	broad.mit.edu	37	11	126176268	126176268	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126176268delA	uc001qdp.2	+							NM_014026	NP_054745	Q96C86	DCPS_HUMAN	mRNA decapping enzyme						deadenylation-dependent decapping of nuclear-transcribed mRNA|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	exoribonuclease activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		actccatctcaaaaaaaaaaa	0.209													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127709571	127709571	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127709571delT								KIRREL3 (836216 upstream) : ETS1 (619085 downstream)																							tctctgaatcttttttccacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127999011	127999011	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127999011delA								None (None upstream) : ETS1 (329645 downstream)																							aaaagaagagaaaaaaacaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128747593	128747593	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128747593delA								KCNJ1 (10325 upstream) : KCNJ5 (13720 downstream)																							AAGGTCTACCAAAAAAAATGT	0.363													5	3	---	---	---	---	
ADIPOR2	79602	broad.mit.edu	37	12	1863865	1863866	+	Intron	INS	-	TAC	TAC	rs10082811	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1863865_1863866insTAC	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827	Q86V24	ADR2_HUMAN	adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			attattattattactactacta	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4303151	4303151	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4303151delC								PARP11 (320543 upstream) : CCND2 (79751 downstream)																							GGGTTAAGGACCATGTGCATC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	11486257	11486258	+	IGR	INS	-	T	T	rs146257086	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11486257_11486258insT								PRB4 (22891 upstream) : PRB1 (18499 downstream)																							cagtgattttcTTTTTTTTCTT	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	11665599	11665599	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11665599delA								PRB2 (117101 upstream) : ETV6 (137189 downstream)																							actccatctcaaaaaaaaaaT	0.189													9	4	---	---	---	---	
SLCO1A2	6579	broad.mit.edu	37	12	21453028	21453032	+	Intron	DEL	GAGAG	-	-	rs150349340		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21453028_21453032delGAGAG	uc001rer.2	-						SLCO1A2_uc001res.2_Intron|SLCO1A2_uc010siq.1_Intron|SLCO1A2_uc010sio.1_Intron|SLCO1A2_uc010sip.1_Intron|SLCO1A2_uc001ret.2_Intron|SLCO1A2_uc001reu.2_Intron	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A						bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						AAGAGAGAGAGAGAGGAGAGTGCCA	0.185													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	22993802	22993803	+	IGR	INS	-	AGAG	AGAG	rs147011346	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22993802_22993803insAGAG								ETNK1 (150195 upstream) : SOX5 (691429 downstream)																							AAAGAAATAAAAGCTAAattca	0.094													3	3	---	---	---	---	
BCAT1	586	broad.mit.edu	37	12	25015649	25015650	+	Intron	DEL	CT	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25015649_25015650delCT	uc001rgd.3	-						BCAT1_uc001rgc.2_Intron|BCAT1_uc010six.1_Intron|BCAT1_uc010siy.1_Intron|BCAT1_uc001rge.3_Intron	NM_005504	NP_005495	P54687	BCAT1_HUMAN	branched chain aminotransferase 1, cytosolic						branched chain family amino acid biosynthetic process|branched chain family amino acid catabolic process|cell proliferation|G1/S transition of mitotic cell cycle	cytosol	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			lung(1)|breast(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)|Pyridoxal Phosphate(DB00114)	ctcttttcccctctctctcctt	0.094													4	2	---	---	---	---	
TMTC1	83857	broad.mit.edu	37	12	29818084	29818084	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29818084delA	uc001rjb.2	-						TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					ACCCAATTTCAAAAAAAAAGA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	53081607	53081607	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53081607delC								KRT1 (7416 upstream) : KRT77 (1805 downstream)																							tgccacatctcccccagagac	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69593469	69593469	+	IGR	DEL	C	-	-	rs4761264	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69593469delC								CPM (236449 upstream) : CPSF6 (39848 downstream)																							tgctctgtgtcttttttttct	0.005													4	2	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78347756	78347757	+	Intron	INS	-	GC	GC			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78347756_78347757insGC	uc001syp.2	+						NAV3_uc001syo.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						tgggctggaatcaaggtgtcag	0.000										HNSCC(70;0.22)			4	2	---	---	---	---	
RASSF9	9182	broad.mit.edu	37	12	86216533	86216534	+	Intron	DEL	TC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86216533_86216534delTC	uc001taf.1	-							NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family						endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						TCTGCCTTTTTCTCTGGTTCTT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93854494	93854495	+	IGR	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93854494_93854495insT								UBE2N (18468 upstream) : MRPL42 (6775 downstream)																							TTATTTGTTAATTTTTTTTTag	0.149													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96558225	96558226	+	IGR	INS	-	AC	AC	rs142860399	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96558225_96558226insAC								LTA4H (120927 upstream) : ELK3 (29981 downstream)																							tcacacacactacacacacaca	0.000													4	2	---	---	---	---	
UHRF1BP1L	23074	broad.mit.edu	37	12	100490858	100490858	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100490858delA	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2						atctcatctcaaaaaaaataa	0.090													4	2	---	---	---	---	
TDG	6996	broad.mit.edu	37	12	104378858	104378859	+	Intron	INS	-	AC	AC	rs61937634		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104378858_104378859insAC	uc001tkg.2	+						TDG_uc009zuk.2_Intron|TDG_uc010swi.1_Intron|TDG_uc010swj.1_Intron	NM_003211	NP_003202	Q13569	TDG_HUMAN	thymine-DNA glycosylase						depyrimidination|mismatch repair	nucleoplasm	damaged DNA binding|mismatched DNA binding|protein binding|pyrimidine-specific mismatch base pair DNA N-glycosylase activity			ovary(3)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(302;0.00114)		tatacatatatacacataagta	0.069								BER_DNA_glycosylases					5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108972832	108972834	+	IGR	DEL	CAC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108972832_108972834delCAC								ISCU (9674 upstream) : TMEM119 (10790 downstream)																							ttaccacctacaccaccaccact	0.000													4	2	---	---	---	---	
ALDH2	217	broad.mit.edu	37	12	112220688	112220688	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112220688delA	uc001tst.2	+						ALDH2_uc010syi.1_Intron|ALDH2_uc009zvy.2_Intron	NM_000690	NP_000681	P05091	ALDH2_HUMAN	mitochondrial aldehyde dehydrogenase 2						carbohydrate metabolic process|ethanol oxidation|neurotransmitter biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase|electron carrier activity			skin(2)|ovary(1)|central_nervous_system(1)	4					Disulfiram(DB00822)|Guanidine(DB00536)|NADH(DB00157)|Nitroglycerin(DB00727)	atttcgtctcaaaaaaaaaac	0.164			T	HMGA2	leiomyoma								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115926613	115926613	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115926613delT								TBX3 (804644 upstream) : MED13L (469770 downstream)																							ggggctgctatttttttttat	0.025													3	3	---	---	---	---	
GPR81	27198	broad.mit.edu	37	12	123184238	123184238	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123184238delC	uc001ucw.1	-							NM_032554		Q9BXC0	HCAR1_HUMAN	G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)		ctgcctgtctccccactccaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127641815	127641815	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127641815delT								LOC100128554 (684485 upstream) : None (None downstream)																							ttaatacctgttttttttcct	0.000													4	2	---	---	---	---	
FBRSL1	57666	broad.mit.edu	37	12	133079217	133079217	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133079217delG	uc001ukf.2	+							NM_001142641	NP_001136113	Q9HCM7	FBSL_HUMAN	fibrosin-like 1											central_nervous_system(2)	2						CTGGAACCCTGGGATAAAACC	0.632													4	2	---	---	---	---	
FBRSL1	57666	broad.mit.edu	37	12	133095349	133095352	+	Intron	DEL	CATC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133095349_133095352delCATC	uc001ukf.2	+							NM_001142641	NP_001136113	Q9HCM7	FBSL_HUMAN	fibrosin-like 1											central_nervous_system(2)	2						tacatccacacatccatccatcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23246005	23246005	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23246005delT								FGF9 (967365 upstream) : SGCG (509055 downstream)																							actcggactgtttgatgattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	26596020	26596021	+	IGR	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26596020_26596021insT								ATP8A2 (601 upstream) : SHISA2 (22714 downstream)																							CTTCCTAACCCTTTTTTGTCAG	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30490711	30490712	+	IGR	INS	-	CTC	CTC	rs144889767	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30490711_30490712insCTC								UBL3 (65891 upstream) : KATNAL1 (286056 downstream)																							AGCTGCCACATCTCTGCTTAGC	0.436													4	2	---	---	---	---	
KATNAL1	84056	broad.mit.edu	37	13	30784928	30784928	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30784928delA	uc001uss.2	-						KATNAL1_uc001ust.2_Intron	NM_001014380	NP_001014402	Q9BW62	KATL1_HUMAN	katanin p60 subunit A-like 1							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity				0		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		AATGCTTCTCAAAAAAAAAAT	0.333													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	33563036	33563036	+	IGR	DEL	T	-	-	rs111937242		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33563036delT								PDS5B (210881 upstream) : KL (27165 downstream)																							ATGGCTTACATTTTTTTTTTT	0.378													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35297158	35297158	+	IGR	DEL	T	-	-	rs142222870		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35297158delT								RFC3 (756464 upstream) : NBEA (219298 downstream)																							TGAGGGGTGATTTTTTTTTTC	0.358													4	2	---	---	---	---	
DCLK1	9201	broad.mit.edu	37	13	36367862	36367863	+	Intron	INS	-	A	A	rs35264802		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36367862_36367863insA	uc001uvf.2	-						DCLK1_uc001uve.3_Intron|DCLK1_uc010teh.1_Intron|DCLK1_uc010abk.2_Intron	NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		GTCTCTAAATTAAAAAAAAAAA	0.327													12	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	40224686	40224686	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40224686delA								LHFP (47330 upstream) : COG6 (5078 downstream)																							agtcctaggtaatatctgatt	0.000													4	2	---	---	---	---	
NUFIP1	26747	broad.mit.edu	37	13	45551217	45551217	+	Intron	DEL	C	-	-	rs34872832		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45551217delC	uc001uzp.2	-							NM_012345	NP_036477	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein						box C/D snoRNP assembly|positive regulation of transcription from RNA polymerase II promoter|RNA processing	actin cytoskeleton|cytosolic ribosome|nuclear matrix|nucleolus|perichromatin fibrils|pre-snoRNP complex|presynaptic active zone|transcription elongation factor complex	DNA binding|identical protein binding|protein binding, bridging|RNA binding|zinc ion binding				0		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		CACACTCCTTCAACTTCTAAG	0.219													5	5	---	---	---	---	
VPS36	51028	broad.mit.edu	37	13	52992422	52992423	+	Intron	INS	-	A	A	rs137939288	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52992422_52992423insA	uc001vgs.2	-						VPS36_uc001vgq.2_Intron	NM_016075	NP_057159	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36						cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|late endosome|membrane|nucleus	lipid binding			skin(1)	1		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		attaaaaaaataaaaagaggcc	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	53972538	53972538	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53972538delA								OLFM4 (346352 upstream) : MIR1297 (913569 downstream)																							TCTCTAACTTAAAAAAAAAGT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	61296506	61296509	+	IGR	DEL	CGTA	-	-	rs148675039		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61296506_61296509delCGTA								TDRD3 (148494 upstream) : PCDH20 (687312 downstream)																							tgcgtgcgtgcgtatgtgtgtgtg	0.387													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63621302	63621303	+	IGR	INS	-	C	C	rs112606463		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63621302_63621303insC								None (None upstream) : OR7E156P (690265 downstream)																							AGAATTTATTGCTTTTTTATGA	0.342													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	69560508	69560509	+	IGR	INS	-	ATA	ATA	rs138891114	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69560508_69560509insATA								None (None upstream) : KLHL1 (714217 downstream)																							TATGAGATGCTATAATGAGCTA	0.307													6	4	---	---	---	---	
RNF219	79596	broad.mit.edu	37	13	79233435	79233436	+	5'Flank	INS	-	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79233435_79233436insG	uc001vkw.1	-						RNF219_uc010afb.1_Intron|RNF219_uc010afc.2_5'Flank	NM_024546	NP_078822	Q5W0B1	RN219_HUMAN	ring finger protein 219								zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)		TTCATTAaaaaaaaaaaaaaaa	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	89607837	89607837	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89607837delT								None (None upstream) : None (None downstream)																							TTATTTCATCTTTTTTTCCCA	0.323													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94419232	94419232	+	Intron	DEL	T	-	-	rs80001617		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94419232delT	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				ATGCACTTAATTTTTTTTTTT	0.388													4	2	---	---	---	---	
HS6ST3	266722	broad.mit.edu	37	13	97104433	97104433	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97104433delA	uc001vmw.2	+							NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					GTGGAGCATTAACTAACCAAG	0.318													4	2	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	101828983	101828983	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101828983delT	uc001vox.1	-						NALCN_uc001voy.2_Intron	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AAGAAAAAGGTTTTtttgaac	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106924682	106924682	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106924682delA								DAOA (781300 upstream) : EFNB2 (217416 downstream)																							AACAAAAAACAAAAAAAAAAA	0.398													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	111293683	111293684	+	IGR	INS	-	ATCG	ATCG	rs138202676	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111293683_111293684insATCG								CARKD (1343 upstream) : CARS2 (73 downstream)																							TACTTCACTCAATCGACGGTGA	0.525													20	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112252765	112252766	+	IGR	DEL	GA	-	-	rs71131432		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112252765_112252766delGA								C13orf16 (256172 upstream) : SOX1 (469147 downstream)																							gagagagagtgaggaagagaga	0.480													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26424543	26424544	+	IGR	INS	-	GT	GT	rs141322821	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26424543_26424544insGT								STXBP6 (905372 upstream) : NOVA1 (490546 downstream)																							agacacattcagtgcacatctt	0.188													4	2	---	---	---	---	
RALGAPA1	253959	broad.mit.edu	37	14	36217585	36217585	+	Intron	DEL	T	-	-	rs67932961		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36217585delT	uc001wti.2	-						RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron|RALGAPA1_uc001wtk.1_Intron	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						TCTCTCGCTCTTttttttttt	0.114													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	36507294	36507294	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36507294delT								BRMS1L (166126 upstream) : MBIP (260470 downstream)																							gcgctgactcttggaactttg	0.000													4	2	---	---	---	---	
SEC23A	10484	broad.mit.edu	37	14	39514144	39514144	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39514144delA	uc001wup.1	-						SEC23A_uc010tqa.1_Intron|SEC23A_uc010tqb.1_Intron	NM_006364	NP_006355	Q15436	SC23A_HUMAN	SEC23-related protein A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		catctcCTTTAAAAAAAAAAA	0.045													6	3	---	---	---	---	
GPR137C	283554	broad.mit.edu	37	14	53065277	53065278	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53065277_53065278insT	uc001wzu.3	+						GPR137C_uc001wzt.3_Intron	NM_001099652	NP_001093122	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C							integral to membrane					0	Breast(41;0.0716)					CTAATTTTTTGTTTTTTTGCTG	0.376													4	2	---	---	---	---	
PELI2	57161	broad.mit.edu	37	14	56665308	56665308	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56665308delT	uc001xch.2	+							NM_021255	NP_067078	Q9HAT8	PELI2_HUMAN	pellino 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1						ggggacagtgtccagcatgga	0.000													4	2	---	---	---	---	
KIAA0586	9786	broad.mit.edu	37	14	58979035	58979035	+	Intron	DEL	T	-	-	rs36123151		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58979035delT	uc001xdv.3	+						KIAA0586_uc010trr.1_Intron|KIAA0586_uc001xdt.3_Intron|KIAA0586_uc001xdu.3_Intron|KIAA0586_uc010trs.1_Intron|KIAA0586_uc010trt.1_Intron	NM_014749	NP_055564	E9PGW8	E9PGW8_HUMAN	talpid3 protein											ovary(1)	1						TTTTTAAAGGTTTTTTTTTGC	0.284													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	60550711	60550711	+	IGR	DEL	A	-	-	rs34096885		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60550711delA								RTN1 (213154 upstream) : C14orf135 (7918 downstream)																							CAGCCTAGAGAAAAGAACGAA	0.383													2	5	---	---	---	---	
C14orf135	64430	broad.mit.edu	37	14	60617037	60617037	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60617037delT	uc001xeq.2	+						DHRS7_uc001xes.2_Intron|DHRS7_uc001xet.2_Intron|DHRS7_uc001xeu.2_Intron	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)		TATTAGGCACttttttttatt	0.164													6	3	---	---	---	---	
DCAF4	26094	broad.mit.edu	37	14	73418334	73418334	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73418334delA	uc001xng.2	+						DCAF4_uc001xnj.2_Intron|DCAF4_uc010ttr.1_Intron|DCAF4_uc001xnh.2_Intron|DCAF4_uc010tts.1_Intron|DCAF4_uc010ttt.1_Intron|DCAF4_uc001xni.2_Intron|DCAF4_uc001xnk.2_Intron	NM_015604	NP_056419	Q8WV16	DCAF4_HUMAN	DDB1 and CUL4 associated factor 4 isoform 1							CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)|skin(1)	3						acaaacaaacaaaaaaaaaaC	0.224													9	4	---	---	---	---	
PTPN21	11099	broad.mit.edu	37	14	88964644	88964644	+	Intron	DEL	A	-	-	rs72318023		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88964644delA	uc001xwv.3	-						PTPN21_uc010twc.1_Intron|PTPN21_uc010atf.1_Intron	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4						cagaaaaaagaaaaaaaaAAA	0.144													4	2	---	---	---	---	
SMEK1	55671	broad.mit.edu	37	14	91925455	91925455	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91925455delT	uc001xzn.2	-						SMEK1_uc001xzm.2_Intron|SMEK1_uc001xzo.2_Intron|SMEK1_uc010atz.2_Intron	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		AAAGCAAAAAttttttttttc	0.030													4	2	---	---	---	---	
OTUB2	78990	broad.mit.edu	37	14	94510651	94510652	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94510651_94510652insT	uc001yci.2	+							NM_023112	NP_075601	Q96DC9	OTUB2_HUMAN	OTU domain, ubiquitin aldehyde binding 2						cellular amino acid metabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination		omega peptidase activity|protein binding|ubiquitin-specific protease activity				0		all_cancers(154;0.12)		Epithelial(152;0.124)|all cancers(159;0.21)|COAD - Colon adenocarcinoma(157;0.215)		GCTTGCCACTCTGAGTGTGCAC	0.545													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97616946	97616946	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97616946delG								VRK1 (268996 upstream) : C14orf64 (775001 downstream)																							TGAGGTCACAGGGGTGCGGGA	0.557													4	2	---	---	---	---	
BCL11B	64919	broad.mit.edu	37	14	99707356	99707356	+	Intron	DEL	T	-	-	rs77305482		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99707356delT	uc001yga.2	-						BCL11B_uc001ygb.2_Intron	NM_138576	NP_612808	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B isoform 1							nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)|lung(1)	10		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		TTTGTTGTAATTTTTTTTTTT	0.428			T	TLX3	T-ALL								3	6	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106414648	106414651	+	Intron	DEL	ATCC	-	-	rs145527262		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106414648_106414651delATCC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ccatccatctatccatccatccat	0.123													4	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106790869	106790870	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106790869_106790870insT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						CTGACAGGAAACAGCCTCCATC	0.530													16	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20515672	20515674	+	IGR	DEL	ATG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20515672_20515674delATG								None (None upstream) : GOLGA6L6 (221420 downstream)																							atgagatgaaatgatgagataaa	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21926084	21926084	+	IGR	DEL	G	-	-	rs77197518		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21926084delG								NF1P1 (791459 upstream) : LOC646214 (6430 downstream)																							ATAGGAGTCTGGGTTCACAGC	0.468													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21960584	21960585	+	IGR	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21960584_21960585insT								LOC646214 (19845 upstream) : CXADRP2 (53835 downstream)																							ttctTTTTCTCTTTTTTCAAAG	0.119													2	4	---	---	---	---	
HERC2P2	400322	broad.mit.edu	37	15	23338033	23338033	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23338033delA	uc001yvr.2	-						HERC2P2_uc010ayf.1_Intron					RecName: Full=Putative HERC2-like protein 3;												0						atggttagttaaaaaaaAAAA	0.199													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	28871660	28871660	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28871660delT								GOLGA8G (234489 upstream) : WHAMML2 (111069 downstream)																							ggtaattatcttttttttttt	0.000													3	4	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33602510	33602511	+	5'Flank	INS	-	TC	TC	rs138144348	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33602510_33602511insTC	uc001zhi.2	+						RYR3_uc010bar.2_5'Flank	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TCGAGTCCAGAtctctctctct	0.262													6	3	---	---	---	---	
PPIP5K1	9677	broad.mit.edu	37	15	43831398	43831398	+	Intron	DEL	A	-	-	rs67877426		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43831398delA	uc001zrw.2	-						PPIP5K1_uc001zrx.1_Intron|PPIP5K1_uc001zru.2_Intron|PPIP5K1_uc001zry.3_Intron|PPIP5K1_uc001zrv.2_Intron	NM_001130858	NP_001124330	Q6PFW1	VIP1_HUMAN	histidine acid phosphatase domain containing 2A						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity				0						tctgtctctcaaaaaaaaaaa	0.154													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	45902861	45902861	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45902861delA								PLDN (953 upstream) : SQRDL (20485 downstream)																							Ctattttattaaaaaaaaaaa	0.338													10	5	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62253641	62253641	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62253641delC	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						cacacacacacaaaacaatga	0.124													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63380307	63380308	+	IGR	INS	-	A	A	rs150860625	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63380307_63380308insA								TPM1 (16196 upstream) : LACTB (33724 downstream)																							gaaaaggaaagaaaaaaaaaga	0.218													4	2	---	---	---	---	
MEGF11	84465	broad.mit.edu	37	15	66422534	66422534	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66422534delG	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1						gagcctgcccgggacatggca	0.149													4	2	---	---	---	---	
NEO1	4756	broad.mit.edu	37	15	73410985	73410985	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73410985delT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor						axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1						TCAGGAAGCATTTTTTTGACC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	74019486	74019489	+	IGR	DEL	CTGA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74019486_74019489delCTGA								CD276 (12627 upstream) : C15orf59 (12654 downstream)																							ACACACTGAGCTGACTGTGGTCAC	0.549													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82243932	82243932	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82243932delA								TMC3 (577514 upstream) : MEX3B (90196 downstream)																							AGTCATTTCCAAAGGCCTCGA	0.502													4	2	---	---	---	---	
ACAN	176	broad.mit.edu	37	15	89417837	89417837	+	3'UTR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89417837delA	uc010upo.1	+	18					ACAN_uc010upp.1_3'UTR|ACAN_uc002bna.2_RNA	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor						cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TTAAAGAAGGAAAAAAATAAA	0.478													12	6	---	---	---	---	
CRTC3	64784	broad.mit.edu	37	15	91116868	91116868	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91116868delT	uc002bpp.2	+						CRTC3_uc002bpn.2_Intron|CRTC3_uc002bpo.2_Intron	NM_022769	NP_073606	Q6UUV7	CRTC3_HUMAN	transducer of regulated CREB protein 3 isoform						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus			CRTC3/MAML2(26)	salivary_gland(26)|ovary(1)	27	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			TTTTTTACTGTTTTTTTTCCC	0.289			T	MAML2	salivary gland mucoepidermoid								4	2	---	---	---	---	
FAM174B	400451	broad.mit.edu	37	15	93198679	93198684	+	In_Frame_Del	DEL	TGGAGC	-	-	rs68056278		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93198679_93198684delTGGAGC	uc010boe.2	-	1	348_353	c.206_211delGCTCCA	c.(205-213)AGCTCCAAC>AAC	p.SS69del	FAM174B_uc002bsl.3_Intron	NM_207446	NP_997329	Q3ZCQ3	F174B_HUMAN	hypothetical protein LOC400451	69_70	Extracellular (Potential).					integral to membrane					0						CCACTGCTGTTGGAGCTGGAGCTGCC	0.578													8	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98677460	98677462	+	IGR	DEL	AGG	-	-	rs139005344		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98677460_98677462delAGG								ARRDC4 (160393 upstream) : FAM169B (302929 downstream)																							TGGGAAGGGCAGGAGAAGTTCAG	0.463													3	3	---	---	---	---	
SLC9A3R2	9351	broad.mit.edu	37	16	2079331	2079336	+	Intron	DEL	AAGGGC	-	-	rs56176915		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2079331_2079336delAAGGGC	uc002coi.2	+						SLC9A3R2_uc002coj.2_Intron	NM_001130012	NP_001123484	Q15599	NHRF2_HUMAN	solute carrier family 9 isoform 3 regulator 2						protein complex assembly	apical plasma membrane|endomembrane system|nucleus	beta-catenin binding|phosphatase binding|protein C-terminus binding|receptor binding			central_nervous_system(1)	1						ACCCTGGGCTAAGGGCAAGGCTCTGG	0.660													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5175962	5175963	+	IGR	DEL	GA	-	-	rs140879394		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5175962_5175963delGA								FAM86A (28173 upstream) : A2BP1 (893169 downstream)																							CAATCCCTCGGAGAGAGAGAGA	0.401													7	5	---	---	---	---	
RUNDC2A	84127	broad.mit.edu	37	16	12078956	12078956	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12078956delC	uc002dbw.1	+							NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A											ovary(1)	1						acttttgaTTCCTTTTTTTTT	0.169			T	CIITA	PMBL|Hodgkin Lymphona|								5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20018974	20018974	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20018974delA								GPRC5B (122142 upstream) : GPR139 (24069 downstream)																							AAAGCCCCCCAAAGTTTTACA	0.473													4	2	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	27986381	27986381	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27986381delT	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						GAATCAGAACTTAAGCATCtc	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32399155	32399155	+	IGR	DEL	C	-	-	rs149453033		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32399155delC								HERC2P4 (235281 upstream) : TP53TG3B (285686 downstream)																							tgtgatccagcccacctcagc	0.040													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33041839	33041840	+	IGR	INS	-	T	T	rs145761951		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33041839_33041840insT								SLC6A10P (145376 upstream) : MIR1826 (923668 downstream)																							GTTCTTTGCAATTTTTTTTTTT	0.282													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33535051	33535053	+	IGR	DEL	AAC	-	-	rs148130679		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33535051_33535053delAAC								SLC6A10P (638588 upstream) : MIR1826 (430455 downstream)																							GAACAAAACTAACAATAAAAAGT	0.241													15	8	---	---	---	---	
VPS35	55737	broad.mit.edu	37	16	46714944	46714945	+	Intron	INS	-	AC	AC	rs148688318	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46714944_46714945insAC	uc002eef.3	-						VPS35_uc002eed.2_5'Flank|VPS35_uc002eee.2_Intron	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35						protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AAAAAAACTATacacacacaca	0.223													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46876402	46876402	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46876402delA								C16orf87 (11328 upstream) : GPT2 (41906 downstream)																							TCTTACCATTAAAAAAAAAAA	0.363													5	3	---	---	---	---	
PAPD5	64282	broad.mit.edu	37	16	50263428	50263428	+	3'UTR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50263428delA	uc010vgo.1	+	13					PAPD5_uc010cbi.2_Intron|PAPD5_uc002efz.2_3'UTR|PAPD5_uc002ega.2_3'UTR	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a						cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		aaaacaaaacaaaaaaaaaag	0.299													6	3	---	---	---	---	
CNGB1	1258	broad.mit.edu	37	16	57982509	57982509	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57982509delC	uc002emt.2	-						CNGB1_uc010cdh.2_Intron	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform						sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4						cacactcgctccctgggcatc	0.000													4	2	---	---	---	---	
GINS3	64785	broad.mit.edu	37	16	58426272	58426273	+	5'Flank	INS	-	C	C	rs141830137	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58426272_58426273insC	uc002enh.3	+						GINS3_uc010cdj.2_5'Flank|GINS3_uc002enj.3_5'Flank|GINS3_uc002eni.3_5'Flank	NM_022770	NP_073607	Q9BRX5	PSF3_HUMAN	GINS complex subunit 3 isoform b						DNA replication	nucleus					0						CCGCTCCCCAGCCGTGTCCCGC	0.624													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73437843	73437843	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73437843delT	uc002fco.1	+											Homo sapiens cDNA clone IMAGE:5272469.																		GATCTTGGGATTTTTTTTTTC	0.458													3	3	---	---	---	---	
PLCG2	5336	broad.mit.edu	37	16	81865710	81865710	+	Intron	DEL	A	-	-	rs143908658		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81865710delA	uc002fgt.2	+						PLCG2_uc010chg.1_Intron	NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						tgataaatggagggggggaat	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86751604	86751606	+	IGR	DEL	GAG	-	-	rs144157809		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86751604_86751606delGAG								FOXL1 (136301 upstream) : FBXO31 (611338 downstream)																							AGGCAGTGATGAGGAGATCCAAG	0.606													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87563287	87563287	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87563287delA								ZCCHC14 (37827 upstream) : JPH3 (72154 downstream)																							AGAATTTTTCAAAAAAAAAGG	0.323													5	4	---	---	---	---	
UBE2G1	7326	broad.mit.edu	37	17	4179079	4179079	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4179079delA	uc002fxs.2	-							NM_003342	NP_003333	P62253	UB2G1_HUMAN	ubiquitin-conjugating enzyme E2G 1						protein K48-linked ubiquitination|protein K63-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity				0						TACCCTTCACAAAAAAATGCT	0.423													7	4	---	---	---	---	
RICH2	9912	broad.mit.edu	37	17	12814654	12814654	+	Intron	DEL	C	-	-	rs112683376		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12814654delC	uc002gnr.3	+						RICH2_uc010vvk.1_Intron|RICH2_uc010vvl.1_Intron|RICH2_uc002gns.3_Intron|RICH2_uc010vvm.1_Intron|RICH2_uc010vvn.1_Intron	NM_014859	NP_055674	Q17R89	RHG44_HUMAN	Rho GTPase-activating protein RICH2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						ttttttttttccttaaaagac	0.000													4	2	---	---	---	---	
TRIM16	10626	broad.mit.edu	37	17	15516424	15516424	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15516424delA	uc002gor.1	-						CDRT1_uc002gov.3_Intron			O95361	TRI16_HUMAN	SubName: Full=Putative uncharacterized protein; Flags: Fragment;						histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		TCTGCTGGGGAAAAAAAAAAA	0.463													8	5	---	---	---	---	
SLC5A10	125206	broad.mit.edu	37	17	18874150	18874150	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18874150delA	uc002guu.1	+						SLC5A10_uc002gur.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001042450	NP_001035915	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/glucose						sodium ion transport|transmembrane transport	integral to membrane	transporter activity			ovary(1)	1						AATACACCTTAAAAAAAAAAA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	19504275	19504276	+	IGR	INS	-	C	C			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19504275_19504276insC								SLC47A1 (21929 upstream) : ALDH3A2 (47788 downstream)																							CTCTTACttctttttttttttt	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20488023	20488025	+	IGR	DEL	CTC	-	-	rs76850913		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20488023_20488025delCTC								LGALS9B (117175 upstream) : CCDC144NL (278685 downstream)																							GAGATGAGTTCTCCCTCCTCCTC	0.557													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21225026	21225027	+	IGR	INS	-	T	T	rs5819752		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21225026_21225027insT								MAP2K3 (6477 upstream) : KCNJ12 (54672 downstream)																							AGCGCTGGTGGTTCCCCACAGT	0.525													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21797890	21797890	+	IGR	DEL	A	-	-	rs112906700		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21797890delA								C17orf51 (320159 upstream) : FAM27L (27480 downstream)																							tcccccCCCCACAACTATGTG	0.338													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25298950	25298950	+	IGR	DEL	A	-	-	rs77602219		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25298950delA								None (None upstream) : WSB1 (322156 downstream)																							gttgataaatatttttcttgg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25988693	25988702	+	IGR	DEL	CACAGGTGGC	-	-	rs3217511		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25988693_25988702delCACAGGTGGC								LGALS9 (12108 upstream) : NOS2 (95091 downstream)																							GATGTAAAAGCACAGGTGGCCACAGGTTAC	0.500													16	9	---	---	---	---	
MYO1D	4642	broad.mit.edu	37	17	31168144	31168144	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31168144delT	uc002hho.1	-						MYO1D_uc002hhp.1_Intron|MYO1D_uc010wcb.1_Intron	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)			attaaatacctttttgactta	0.000													4	2	---	---	---	---	
ARHGAP23	57636	broad.mit.edu	37	17	36640843	36640850	+	Intron	DEL	GGGCATTG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36640843_36640850delGGGCATTG	uc010wdp.1	+						ARHGAP23_uc002hqc.2_Intron	NM_020876	NP_065927	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23						signal transduction	intracellular	GTPase activator activity			lung(1)	1						GCACTGGCCAGGGCATTGGGTTTGGCAG	0.644													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	42595438	42595438	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42595438delT								GPATCH8 (14636 upstream) : FZD2 (39487 downstream)																							tcggctaatgttttttttttt	0.055													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	44486669	44486669	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44486669delT								ARL17A (47506 upstream) : LRRC37A2 (103407 downstream)																							tttttttttcttttttttttt	0.119													4	2	---	---	---	---	
CDC27	996	broad.mit.edu	37	17	45198679	45198679	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45198679delA	uc002ild.3	-						CDC27_uc002ile.3_Intron|CDC27_uc002ilf.3_Intron|CDC27_uc010wkp.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						CTGAGACATTAAAAAAAAAAA	0.373													4	2	---	---	---	---	
EPN3	55040	broad.mit.edu	37	17	48617904	48617904	+	Intron	DEL	A	-	-	rs66736597		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48617904delA	uc002ira.3	+						SPATA20_uc002irc.2_5'Flank|EPN3_uc010wms.1_Intron|EPN3_uc010wmt.1_Intron|EPN3_uc010wmu.1_Intron	NM_017957	NP_060427	Q9H201	EPN3_HUMAN	epsin 3							clathrin-coated vesicle|nucleus|perinuclear region of cytoplasm	lipid binding			ovary(1)	1	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			GAAACGCAGCAAAATGTTCTC	0.577													4	9	---	---	---	---	
SPAG9	9043	broad.mit.edu	37	17	49094881	49094888	+	Intron	DEL	GAGAGAGA	-	-	rs72176610		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49094881_49094888delGAGAGAGA	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron|SPAG9_uc002ita.2_Intron|SPAG9_uc002ite.2_Intron	NM_001130528	NP_001124000	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GAACCTGTCTgagagagagagagagaga	0.067													3	4	---	---	---	---	
SPAG9	9043	broad.mit.edu	37	17	49193401	49193401	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49193401delT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron	NM_001130528	NP_001124000	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			CAGAAGtttcttttttttttc	0.154													4	2	---	---	---	---	
HEATR6	63897	broad.mit.edu	37	17	58124955	58124955	+	Intron	DEL	A	-	-	rs66526922		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58124955delA	uc002iyk.1	-						HEATR6_uc010ddk.1_Intron|HEATR6_uc010wos.1_Intron	NM_022070	NP_071353	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6								binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			ggaatgtctcaaaaaaaaaaa	0.000													6	4	---	---	---	---	
BCAS3	54828	broad.mit.edu	37	17	59320271	59320271	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59320271delT	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_5'Flank	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)			agctatacacttttttttttt	0.070													3	4	---	---	---	---	
HELZ	9931	broad.mit.edu	37	17	65182277	65182277	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65182277delA	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					ataaagaaacaaaaaaaaaac	0.318													4	2	---	---	---	---	
ARSG	22901	broad.mit.edu	37	17	66269127	66269127	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66269127delT	uc002jhc.2	+						SLC16A6_uc002jgz.1_Intron|SLC16A6_uc002jha.1_Intron	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAAATATAACTTTTTTTTTTT	0.264													5	3	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71335353	71335353	+	Intron	DEL	T	-	-	rs11290598		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71335353delT	uc010dfm.2	-						SDK2_uc002jjt.3_Intron	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						AAGACCTGAGtttttttttgt	0.279													9	5	---	---	---	---	
SRP68	6730	broad.mit.edu	37	17	74068229	74068230	+	Intron	INS	-	C	C	rs146512359	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74068229_74068230insC	uc002jqk.1	-						SRP68_uc010wsu.1_Intron|SRP68_uc002jql.1_Intron|GALR2_uc002jqm.1_5'Flank	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa						response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1						CGAGAGACAGACCCCCCCCGGA	0.629													19	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78950793	78950793	+	IGR	DEL	A	-	-	rs112496455		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78950793delA								RPTOR (10620 upstream) : CHMP6 (14848 downstream)																							tttgacaattaaaaaaaaaaa	0.129													8	4	---	---	---	---	
CSNK1D	1453	broad.mit.edu	37	17	80228540	80228540	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80228540delA	uc002kej.2	-						CSNK1D_uc002kef.2_Intron|CSNK1D_uc002kei.2_Intron|CSNK1D_uc010wvj.1_Intron	NM_001893	NP_001884	P48730	KC1D_HUMAN	casein kinase 1, delta isoform 1						circadian regulation of gene expression|DNA repair|G2/M transition of mitotic cell cycle|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|regulation of circadian rhythm|Wnt receptor signaling pathway	centrosome|cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			breast(2)	2	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			AAACTGCCTTACTCCGGCTAA	0.502													4	2	---	---	---	---	
SLC14A2	8170	broad.mit.edu	37	18	42973829	42973829	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42973829delC	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4						ctgaaatcctccccaaatccc	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58608453	58608453	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58608453delA								MC4R (568452 upstream) : CDH20 (392535 downstream)																							TTGTACTTCTAAAAAAAAAAG	0.383													4	2	---	---	---	---	
PHLPP1	23239	broad.mit.edu	37	18	60458212	60458212	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60458212delT	uc002lis.2	+							NM_194449	NP_919431	O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein						apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0						AGGCAGCTGATTTTGCAGGGA	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	70641750	70641751	+	IGR	INS	-	CTT	CTT	rs144677484	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70641750_70641751insCTT								NETO1 (106940 upstream) : None (None downstream)																							tctcatgtctcctccacagcta	0.050													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	74491855	74491855	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74491855delG								LOC284276 (220072 upstream) : ZNF236 (44261 downstream)																							ctgtgcagatggaggaagggg	0.000													4	2	---	---	---	---	
ZNF236	7776	broad.mit.edu	37	18	74679398	74679399	+	Intron	INS	-	GGT	GGT	rs145977669		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74679398_74679399insGGT	uc002lmi.2	+						ZNF236_uc002lmj.2_Intron	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236						cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		TTGTTGTTGGAGGTGGTGTGCT	0.262													3	7	---	---	---	---	
STK11	6794	broad.mit.edu	37	19	1227454	1227454	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1227454delC	uc002lrl.1	+							NM_000455	NP_000446	Q15831	STK11_HUMAN	serine/threonine protein kinase 11						anoikis|cell cycle arrest|energy reserve metabolic process|insulin receptor signaling pathway|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(174)|cervix(35)|skin(15)|large_intestine(12)|pancreas(6)|gastrointestinal_tract_(site_indeterminate)(5)|stomach(4)|ovary(4)|breast(2)|upper_aerodigestive_tract(1)|testis(1)|liver(1)|biliary_tract(1)|small_intestine(1)|urinary_tract(1)|oesophagus(1)|prostate(1)|kidney(1)	266		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGTGGCCTTCCCTGGCCTCC	0.672		14	D|Mis|N|F|S		NSCLC|pancreatic	jejunal harmartoma|ovarian|testicular|pancreatic			Peutz-Jeghers_syndrome	TSP Lung(3;<1E-08)			4	2	---	---	---	---	
WDR83	84292	broad.mit.edu	37	19	12781791	12781792	+	Intron	DEL	AA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12781791_12781792delAA	uc002mue.3	+						WDR83_uc002muc.2_Intron|C19orf56_uc002mud.2_5'Flank|WDR83_uc010dyw.2_Intron	NM_001099737	NP_001093207	Q9BRX9	WDR83_HUMAN	mitogen-activated protein kinase organizer 1						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|cytoplasm				lung(1)|breast(1)	2						acttgagtccaagagttcgagg	0.069													4	10	---	---	---	---	
ZSWIM4	65249	broad.mit.edu	37	19	13927882	13927882	+	Intron	DEL	A	-	-	rs76852888		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13927882delA	uc002mxh.1	+						ZSWIM4_uc010xng.1_Intron	NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4								zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			accccacctcaaaaaaaaaaG	0.254													3	3	---	---	---	---	
USHBP1	83878	broad.mit.edu	37	19	17369974	17369974	+	Intron	DEL	A	-	-	rs80351288		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17369974delA	uc002nfs.1	-						USHBP1_uc002nfr.1_5'Flank|USHBP1_uc002nft.1_Intron|USHBP1_uc010xpk.1_Intron|USHBP1_uc010eam.1_Intron	NM_031941	NP_114147	Q8N6Y0	USBP1_HUMAN	Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1						attctgtctcaaaaaaaaaaa	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	17511446	17511447	+	IGR	INS	-	A	A	rs143087072	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17511446_17511447insA								PLVAP (23309 upstream) : BST2 (2309 downstream)																							aaaaaacaaacaaaaaaaaccc	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	21087998	21087999	+	IGR	DEL	TG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21087998_21087999delTG								ZNF626 (243596 upstream) : ZNF85 (18081 downstream)																							ACCTGTTCATTGTCAGCCTCTC	0.495													4	2	---	---	---	---	
ZNF257	113835	broad.mit.edu	37	19	22269453	22269453	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22269453delT	uc010ecx.2	+						ZNF257_uc010ecy.2_Intron	NM_033468	NP_258429	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.0961)|Lung NSC(12;0.103)				ttagaaggtctttttttttta	0.005													6	3	---	---	---	---	
ZNF780A	284323	broad.mit.edu	37	19	40587440	40587440	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40587440delA	uc002omy.2	-						ZNF780A_uc002omw.3_Intron|ZNF780A_uc002omz.2_Intron|ZNF780A_uc010xvh.1_Intron	NM_001010880	NP_001010880	O75290	Z780A_HUMAN	zinc finger protein 780A isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					attccaccttaaaaaaaaaaa	0.154													5	5	---	---	---	---	
RSPH6A	81492	broad.mit.edu	37	19	46305051	46305052	+	Intron	INS	-	CA	CA	rs35295101		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46305051_46305052insCA	uc002pdm.2	-						RSPH6A_uc002pdl.2_Intron	NM_030785	NP_110412	Q9H0K4	RSH6A_HUMAN	radial spokehead-like 1							intracellular				ovary(1)|central_nervous_system(1)	2						ACCACCACCACcacacacacac	0.223													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	47120658	47120658	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47120658delT								CALM3 (6620 upstream) : PTGIR (3068 downstream)																							CTCTGGCCTGTTAGACAGTGT	0.592													4	2	---	---	---	---	
NPAS1	4861	broad.mit.edu	37	19	47542084	47542084	+	Intron	DEL	A	-	-	rs75714385		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47542084delA	uc002pfw.2	+						NPAS1_uc002pfx.2_Intron|NPAS1_uc002pfy.2_Intron|NPAS1_uc010xyj.1_Intron	NM_002517	NP_002508	Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1						central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		attcagtctcaaaaaaaaaaa	0.249													4	11	---	---	---	---	
DHX34	9704	broad.mit.edu	37	19	47875892	47875903	+	Intron	DEL	GGAGGGCAGGCG	-	-	rs11270236		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47875892_47875903delGGAGGGCAGGCG	uc010xyn.1	+						DHX34_uc010elc.1_Intron	NM_014681	NP_055496	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34							intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		GGTGGGAGCAGGAGGGCAGGCGGGAGGGCAGG	0.509													6	4	---	---	---	---	
IZUMO1	284359	broad.mit.edu	37	19	49247998	49247999	+	Intron	INS	-	C	C	rs150963534	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49247998_49247999insC	uc002pkj.2	-						IZUMO1_uc010eme.2_Intron|IZUMO1_uc010emf.2_Intron	NM_182575	NP_872381	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1 precursor						fusion of sperm to egg plasma membrane	integral to membrane				ovary(1)	1		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		aggctggagtgtgtggtgtaat	0.188													3	6	---	---	---	---	
TSKS	60385	broad.mit.edu	37	19	50265062	50265062	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50265062delA	uc002ppm.2	-							NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate								protein binding			large_intestine(1)|skin(1)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		ctaaaggaagaaaaaaaaAAG	0.234													4	2	---	---	---	---	
SIGLEC5	8778	broad.mit.edu	37	19	52132021	52132022	+	Intron	DEL	GT	-	-	rs34312547		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52132021_52132022delGT	uc002pxe.2	-							NM_003830	NP_003821	O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5 precursor						cell adhesion	integral to membrane	sugar binding			skin(2)|breast(1)|central_nervous_system(1)	4		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		gtgtatgtgcgtgtgtgtgtgg	0.000													7	5	---	---	---	---	
PPP1R12C	54776	broad.mit.edu	37	19	55605558	55605559	+	Intron	INS	-	TTA	TTA			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55605558_55605559insTTA	uc002qix.2	-						PPP1R12C_uc010yfs.1_Intron|PPP1R12C_uc002qiy.2_Intron	NM_017607	NP_060077	Q9BZL4	PP12C_HUMAN	protein phosphatase 1, regulatory subunit 12C							cytoplasm				ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		acctccagcccctcctccctca	0.000													2	6	---	---	---	---	
UBE2S	27338	broad.mit.edu	37	19	55914296	55914296	+	Intron	DEL	T	-	-	rs112400318		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55914296delT	uc002qkx.1	-							NM_014501	NP_055316	Q16763	UBE2S_HUMAN	ubiquitin-conjugating enzyme E2S						activation of anaphase-promoting complex activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|exit from mitosis|free ubiquitin chain polymerization|protein K11-linked ubiquitination|protein K27-linked ubiquitination|protein K29-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination	anaphase-promoting complex	ATP binding|ubiquitin-protein ligase activity				0	Breast(117;0.155)		LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.11)		TTTGGTTAACTTTTTTTTTTT	0.458													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7118199	7118199	+	IGR	DEL	A	-	-	rs35091756		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7118199delA								BMP2 (357289 upstream) : HAO1 (745432 downstream)																							TCATATGATTAAAAAAAAAAA	0.368													3	4	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15918375	15918376	+	Intron	DEL	TA	-	-	rs76061067		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15918375_15918376delTA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.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)				ATAGAAAATTtatatatatata	0.243													6	3	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19576793	19576793	+	Intron	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19576793delG	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						tttatattctgggaatatcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19804034	19804035	+	IGR	INS	-	C	C	rs57730958		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19804034_19804035insC								SLC24A3 (100494 upstream) : RIN2 (66175 downstream)																							TCTGCCTGCTTTTTTTTTTTTC	0.386													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	20701759	20701760	+	IGR	INS	-	A	A			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20701759_20701760insA								RALGAPA2 (8493 upstream) : PLK1S1 (404864 downstream)																							atcttgtctctaaaaaaaaaaa	0.134													9	4	---	---	---	---	
XRN2	22803	broad.mit.edu	37	20	21362930	21362930	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21362930delT	uc002wsf.1	+						XRN2_uc002wsg.1_Intron|XRN2_uc010zsk.1_Intron|XRN2_uc002wsh.1_Intron	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2						cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1						TTATTGATGCTTTTGAGATGC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	23315967	23315969	+	IGR	DEL	AGC	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23315967_23315969delAGC								CD93 (248990 upstream) : NXT1 (15404 downstream)																							tagcagtagtagcagcagcagca	0.197													8	4	---	---	---	---	
GINS1	9837	broad.mit.edu	37	20	25398092	25398092	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25398092delT	uc002wuv.1	+						GINS1_uc010zte.1_Intron	NM_021067	NP_066545	Q14691	PSF1_HUMAN	GINS complex subunit 1						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				ovary(1)|central_nervous_system(1)	2						TTTTGCCATATTTTTTTCATC	0.318													4	2	---	---	---	---	
DLGAP4	22839	broad.mit.edu	37	20	35022815	35022815	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35022815delA	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)				GGGAGTACCCAGGAGCCCTGG	0.657													4	4	---	---	---	---	
C20orf117	140710	broad.mit.edu	37	20	35425723	35425723	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35425723delT	uc002xgd.1	-						C20orf117_uc002xge.1_Intron	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)				GGTGGTTGGGTTTTTTTTTTA	0.522													10	6	---	---	---	---	
C20orf132	140699	broad.mit.edu	37	20	35760447	35760447	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35760447delA	uc010zvu.1	-						C20orf132_uc002xgk.2_Intron|C20orf132_uc002xgm.2_Intron|C20orf132_uc002xgn.2_Intron	NM_152503	NP_689716	Q9H579	CT132_HUMAN	hypothetical protein LOC140699 isoform 1												0		Myeloproliferative disorder(115;0.00878)				AAGCCAGGCTAATCAGAGTCC	0.448													4	2	---	---	---	---	
PPP1R16B	26051	broad.mit.edu	37	20	37439805	37439805	+	Intron	DEL	A	-	-	rs11310073		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37439805delA	uc002xje.2	+						PPP1R16B_uc010ggb.1_Intron	NM_015568	NP_056383	Q96T49	PP16B_HUMAN	protein phosphatase 1 regulatory inhibitor						regulation of filopodium assembly|signal transduction	nucleus|plasma membrane	protein phosphatase binding			upper_aerodigestive_tract(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				TTGATGTGGCAAGATGGTGGC	0.512													3	3	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41018504	41018505	+	Intron	INS	-	G	G			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41018504_41018505insG	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)				aaaaaaaaaaaaaaaagaaaga	0.000													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41060947	41060948	+	Intron	DEL	CA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41060947_41060948delCA	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)				TCTGCACCTCCACACACAGGCT	0.480													4	2	---	---	---	---	
DNTTIP1	116092	broad.mit.edu	37	20	44423157	44423157	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44423157delA	uc002xpk.2	+						WFDC3_uc002xpf.1_5'Flank|WFDC3_uc002xpj.1_5'Flank|WFDC3_uc002xph.1_5'Flank|WFDC3_uc010ghh.1_5'Flank	NM_052951	NP_443183	Q9H147	TDIF1_HUMAN	terminal deoxynucleotidyltransferase interacting							nucleus				ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.0122)				TTTTTTTTTTAAAATCTGCCC	0.204													4	2	---	---	---	---	
BCAS1	8537	broad.mit.edu	37	20	52581339	52581339	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52581339delT	uc002xws.2	-						BCAS1_uc010zza.1_Intron|BCAS1_uc010zzb.1_Intron|BCAS1_uc010gim.2_Intron|BCAS1_uc002xwt.2_Intron|BCAS1_uc010gil.1_Intron	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1							cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			GGTTTAGAGGTTTTTTTTTTT	0.328													4	3	---	---	---	---	
CYP24A1	1591	broad.mit.edu	37	20	52773545	52773545	+	Intron	DEL	A	-	-	rs113497239		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52773545delA	uc002xwv.2	-						CYP24A1_uc002xwu.1_Intron|CYP24A1_uc002xww.2_Intron	NM_000782	NP_000773	Q07973	CP24A_HUMAN	cytochrome P450 family 24 subfamily A						hormone biosynthetic process|osteoblast differentiation|vitamin D catabolic process|vitamin D receptor signaling pathway|xenobiotic metabolic process	mitochondrial inner membrane	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity|electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	tttacaaatgaaaaaaaaaaa	0.000													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55430721	55430721	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55430721delC								TFAP2C (216385 upstream) : BMP7 (313088 downstream)																							TTGAAGGGTTCCCCCAAGAGA	0.149													4	2	---	---	---	---	
PHACTR3	116154	broad.mit.edu	37	20	58363838	58363838	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58363838delC	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_Intron|PHACTR3_uc002yax.2_Intron	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			cgctcaacttcccagatcctc	0.154													4	2	---	---	---	---	
LAMA5	3911	broad.mit.edu	37	20	60904422	60904426	+	Intron	DEL	CAGCC	-	-	rs3065756		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60904422_60904426delCAGCC	uc002ycq.2	-							NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTGGCAGCAGcagcccagcccagcc	0.600													17	8	---	---	---	---	
RPS21	6227	broad.mit.edu	37	20	60963180	60963181	+	Intron	INS	-	C	C	rs140197118	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60963180_60963181insC	uc002ycr.2	+						RPS21_uc002ycs.2_Intron|RPS21_uc002yct.2_3'UTR|RPS21_uc002ycu.2_Intron	NM_001024	NP_001015	P63220	RS21_HUMAN	ribosomal protein S21						endocrine pancreas development|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein N-terminus binding|structural constituent of ribosome				0	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			ACTAGGAGGTGCCCCCCCGACC	0.668													19	15	---	---	---	---	
RPS21	6227	broad.mit.edu	37	20	60963416	60963419	+	Frame_Shift_Del	DEL	TCAA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60963416_60963419delTCAA	uc002ycr.2	+	5	328_331	c.238_241delTCAA	c.(238-243)TCAAAGfs	p.S80fs	RPS21_uc002ycs.2_Frame_Shift_Del_p.S80fs|RPS21_uc002yct.2_3'UTR|RPS21_uc002ycu.2_Frame_Shift_Del_p.S80fs	NM_001024	NP_001015	P63220	RS21_HUMAN	ribosomal protein S21	80_81					endocrine pancreas development|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein N-terminus binding|structural constituent of ribosome				0	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			TGGCATCGTCTCAAAGTAAGGTTG	0.485													269	135	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62076856	62076857	+	Intron	INS	-	CCCCAAAGGG	CCCCAAAGGG	rs138698925	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62076856_62076857insCCCCAAAGGG	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	GCAAGCTGACCCCCCCACCCCT	0.678													4	15	---	---	---	---	
ZGPAT	84619	broad.mit.edu	37	20	62346001	62346002	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62346001_62346002insT	uc002ygk.2	+						ZGPAT_uc002ygi.2_Intron|ZGPAT_uc002ygj.2_Intron|ZGPAT_uc010gkk.1_Intron|ZGPAT_uc010gkl.1_Intron|ZGPAT_uc002ygm.2_Intron|ZGPAT_uc002ygn.3_Intron	NM_032527	NP_115916	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain						negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					aagggtgttgatttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9831913	9831913	+	IGR	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9831913delC								None (None upstream) : None (None downstream)																							GCTAGCATGACCCTCCTACCT	0.512													7	6	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11064722	11064722	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11064722delA	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gccaataggcagtaagaaaat	0.000													15	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	30372065	30372066	+	IGR	INS	-	T	T	rs141380897	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30372065_30372066insT								RNF160 (6788 upstream) : RWDD2B (6016 downstream)																							ttgttttcagcttttttttttc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	31428321	31428321	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31428321delT								GRIK1 (116039 upstream) : CLDN17 (109942 downstream)																							catcatgggattattagaata	0.000													4	2	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37541193	37541193	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37541193delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						tccctgtgggtttTTTTTTTT	0.045													4	2	---	---	---	---	
PRDM15	63977	broad.mit.edu	37	21	43257865	43257882	+	Intron	DEL	TCCTGAGCTCCAGAACAT	-	-	rs71969131		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43257865_43257882delTCCTGAGCTCCAGAACAT	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398	P57071	PRD15_HUMAN	PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ACCATTAAACTCCTGAGCTCCAGAACATTCCTGAGCTC	0.381													7	9	---	---	---	---	
PDXK	8566	broad.mit.edu	37	21	45170614	45170615	+	Intron	INS	-	TG	TG	rs138835795	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45170614_45170615insTG	uc002zdm.3	+						PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Intron|PDXK_uc002zdq.3_Intron	NM_003681	NP_003672	O00764	PDXK_HUMAN	pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	atgtttgtgcatgtgtgtgtgt	0.173													4	4	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45390356	45390357	+	Intron	DEL	TG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45390356_45390357delTG	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron|AGPAT3_uc002zdx.2_Intron|AGPAT3_uc002zdy.2_Intron	NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		GAGTGCAGACTGTGGCCCTAGA	0.480													8	8	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45843708	45843710	+	Intron	DEL	GAG	-	-	rs143108860		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45843708_45843710delGAG	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron|uc011afe.1_Intron|TRPM2_uc011aff.1_5'Flank	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						GGAGGGCTCTGAGGAGTGATGGT	0.650													10	13	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	23161844	23161845	+	Intron	DEL	CC	-	-	rs72002333		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23161844_23161845delCC	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						TGCTCATGGTCCCCTGAGGACA	0.554													5	6	---	---	---	---	
ADRBK2	157	broad.mit.edu	37	22	25980838	25980838	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25980838delA	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)	TTTATTAATGAAAACATGGCT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27848424	27848425	+	IGR	INS	-	TGGA	TGGA	rs150249380	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27848424_27848425insTGGA								MIAT (733475 upstream) : MN1 (295841 downstream)																							ggataaataagtggatggatgg	0.015													4	3	---	---	---	---	
MN1	4330	broad.mit.edu	37	22	28171608	28171608	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28171608delA	uc003adj.2	-						MN1_uc010gvg.2_Intron	NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1								binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10						GTGCTGATGGAACCAAAACTC	0.552			T	ETV6	AML|meningioma								4	2	---	---	---	---	
RFPL2	10739	broad.mit.edu	37	22	32595898	32595899	+	Intron	INS	-	C	C	rs150809092	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32595898_32595899insC	uc003amg.3	-						RFPL2_uc003amf.3_Intron|RFPL2_uc003amh.3_Intron	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2								zinc ion binding			skin(1)	1						CCGCTCGCCCACTCACAGGCCA	0.634													16	7	---	---	---	---	
TRIOBP	11078	broad.mit.edu	37	22	38161835	38161836	+	Intron	INS	-	G	G	rs138412450	by1000genomes	TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38161835_38161836insG	uc003atr.2	+						TRIOBP_uc003atu.2_Intron|TRIOBP_uc003atw.2_Intron|TRIOBP_uc003atx.1_Intron|TRIOBP_uc010gxh.2_Intron	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GTATGGACCCTGGGGGGGGCAC	0.629													7	6	---	---	---	---	
ST13	6767	broad.mit.edu	37	22	41225553	41225555	+	Intron	DEL	ATA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41225553_41225555delATA	uc003aze.2	-						ST13_uc011aow.1_Intron	NM_003932	NP_003923	P50502	F10A1_HUMAN	heat shock 70kD protein binding protein								protein binding, bridging				0						ATATCACtttataataaatatta	0.246													4	2	---	---	---	---	
ARFGAP3	26286	broad.mit.edu	37	22	43219942	43219942	+	Intron	DEL	T	-	-	rs71696984		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43219942delT	uc003bdd.2	-						ARFGAP3_uc010gzf.2_Intron|ARFGAP3_uc011apu.1_Intron	NM_014570	NP_055385	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating						intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1						AGAAAATGTATTTTTTTTTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48465284	48465284	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48465284delA								TBC1D22A (895562 upstream) : FAM19A5 (420004 downstream)																							tgaaggattgaaatccactga	0.000													4	2	---	---	---	---	
C22orf34	348645	broad.mit.edu	37	22	50016360	50016360	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50016360delC	uc003bit.3	-						C22orf34_uc003biq.2_Intron					RecName: Full=Uncharacterized protein C22orf34;												0						GAGGCTGGGGCCACAGGCAGC	0.652													4	2	---	---	---	---	
P2RY8	286530	broad.mit.edu	37	X	1643816	1643817	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1643816_1643817insT	uc004cpz.2	-							NM_178129	NP_835230	Q86VZ1	P2RY8_HUMAN	G-protein coupled purinergic receptor P2Y8							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ccatccatccacccacccatcc	0.203			T	CRLF2	B-ALL|Downs associated ALL								4	2	---	---	---	---	
P2RY8	286530	broad.mit.edu	37	X	1643817	1643818	+	Intron	INS	-	CAT	CAT			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1643817_1643818insCAT	uc004cpz.2	-							NM_178129	NP_835230	Q86VZ1	P2RY8_HUMAN	G-protein coupled purinergic receptor P2Y8							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				catccatccacccacccatcca	0.208			T	CRLF2	B-ALL|Downs associated ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	2511406	2511406	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2511406delG								DHRSX (92391 upstream) : CD99 (97822 downstream)																							TGATGGCGCTGAAGAATGATG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	4571982	4571985	+	IGR	DEL	AGAG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4571982_4571985delAGAG								PRKX (940321 upstream) : None (None downstream)																							AGCTggagacagagagagagagag	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	5481721	5481722	+	IGR	DEL	CA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5481721_5481722delCA								None (None upstream) : NLGN4X (326362 downstream)																							ttcctttcttcaaacctgctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	37148384	37148385	+	IGR	DEL	TG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37148384_37148385delTG								FAM47C (118645 upstream) : PRRG1 (60143 downstream)																							tgtgtatgcttgtgtgtgtgtg	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	38832932	38832933	+	IGR	INS	-	T	T	rs75145514		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38832932_38832933insT								MID1IP1 (167151 upstream) : None (None downstream)																							GCTGCCAGGAATTTTTTTTTTT	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	40861135	40861136	+	IGR	DEL	CA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40861135_40861136delCA								LOC100132831 (168686 upstream) : USP9X (83752 downstream)																							ATTCTAATGGCACACACACACA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	42935256	42935256	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42935256delG								PPP1R2P9 (297770 upstream) : MAOA (580153 downstream)																							TCCCCAGAATGGGAAGAAATA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	50884729	50884729	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50884729delT								BMP15 (225123 upstream) : NUDT10 (190354 downstream)																							ttaggactggtttttttttct	0.000													4	2	---	---	---	---	
ATRX	546	broad.mit.edu	37	X	76972814	76972815	+	Intron	INS	-	T	T			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76972814_76972815insT	uc004ecp.3	-						ATRX_uc004ecq.3_Intron|ATRX_uc004eco.3_Intron|ATRX_uc004ecr.2_Intron|ATRX_uc010nlx.1_Intron|ATRX_uc010nly.1_Intron	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TAGCCATACTGTAAGTCGTGTA	0.292			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						83	55	---	---	---	---	
BRWD3	254065	broad.mit.edu	37	X	80065199	80065200	+	5'UTR	INS	-	GA	GA			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80065199_80065200insGA	uc004edt.2	-	1					BRWD3_uc004edo.2_5'Flank|BRWD3_uc004edp.2_5'Flank|BRWD3_uc004edq.2_5'Flank|BRWD3_uc010nmj.1_5'Flank|BRWD3_uc004edr.2_5'Flank|BRWD3_uc004eds.2_5'Flank|BRWD3_uc004edu.2_5'UTR|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_5'UTR|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_5'UTR|BRWD3_uc004edz.2_5'UTR|BRWD3_uc004eea.2_5'UTR|BRWD3_uc004eeb.2_5'UTR	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3											ovary(4)	4						agagggagagggagagagagag	0.213													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	100216251	100216251	+	IGR	DEL	G	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100216251delG								XKRX (32353 upstream) : ARL13A (8446 downstream)																							aaaaaaaaaagaatcgtggct	0.010													4	4	---	---	---	---	
RNF128	79589	broad.mit.edu	37	X	106017150	106017150	+	Intron	DEL	C	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106017150delC	uc004eml.2	+						RNF128_uc004emk.2_Intron	NM_194463	NP_919445	Q8TEB7	RN128_HUMAN	ring finger protein 128 isoform 1							endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding			ovary(1)|central_nervous_system(1)	2						catacatcttcagttcccgtg	0.000													4	2	---	---	---	---	
NUP62CL	54830	broad.mit.edu	37	X	106398912	106398912	+	Intron	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106398912delA	uc004ena.2	-						NUP62CL_uc004enb.2_Intron	NM_017681	NP_060151	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like						protein transport	nuclear pore	structural constituent of nuclear pore				0						atgcttgatgaaaaaaaaata	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	106663862	106663864	+	IGR	DEL	CTG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106663862_106663864delCTG								CXorf41 (176390 upstream) : PRPS1 (207790 downstream)																							CTACTTGAGCctgctgctgctgc	0.399													4	2	---	---	---	---	
TSC22D3	1831	broad.mit.edu	37	X	107021243	107021243	+	5'Flank	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107021243delT	uc004enh.2	-						TSC22D3_uc004eni.2_5'Flank|TSC22D3_uc004enj.2_5'Flank	NM_198057	NP_932174	Q99576	T22D3_HUMAN	TSC22 domain family, member 3 isoform 1								sequence-specific DNA binding transcription factor activity				0						TCTTCTTCGCTTTTTTTTTTT	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	112688938	112688938	+	IGR	DEL	A	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112688938delA								AMOT (604895 upstream) : None (None downstream)																							caacaacaacaaaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	114759377	114759377	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114759377delT	uc004eqc.1	-											Homo sapiens cDNA FLJ45456 fis, clone BRSTN2009917.																		catgcctggcttttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	122098450	122098452	+	IGR	DEL	AAG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122098450_122098452delAAG								None (None upstream) : GRIA3 (219644 downstream)																							ACTTGTTTTCAAGAAGACTTCTA	0.379													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	123439381	123439384	+	IGR	DEL	TTTG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123439381_123439384delTTTG								STAG2 (202878 upstream) : SH2D1A (40764 downstream)																							CCTTCTAGTTtttgtttgtttgtt	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	123460024	123460024	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123460024delT								STAG2 (223521 upstream) : SH2D1A (20124 downstream)																							ATAAAAGAGGTTTAGTCAAAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	127189606	127189607	+	IGR	INS	-	T	T	rs113173625		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127189606_127189607insT								ACTRT1 (3224 upstream) : None (None downstream)																							tttgttttttgttttttttgaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	134823014	134823016	+	IGR	DEL	GTG	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134823014_134823016delGTG								DDX26B (106555 upstream) : CT45A1 (24169 downstream)																							ACCCTTGGTTGTGGTGGTGGTGG	0.507													4	2	---	---	---	---	
ARHGEF6	9459	broad.mit.edu	37	X	135773735	135773735	+	Intron	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135773735delT	uc004fab.2	-						ARHGEF6_uc011mwd.1_Intron|ARHGEF6_uc011mwe.1_Intron	NM_004840	NP_004831	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor 6						apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)					AAGTGACAGCTTATGTTGAAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	144414970	144414970	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144414970delT								SPANXN1 (77242 upstream) : SLITRK2 (484377 downstream)																							cttcaatgggttttttctcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	144622471	144622471	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144622471delT								SPANXN1 (284743 upstream) : SLITRK2 (276876 downstream)																							attgtctgccttttttttcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	148092829	148092829	+	IGR	DEL	T	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148092829delT								AFF2 (10637 upstream) : IDS (467468 downstream)																							CAGATAGGGATTTTTTTTCCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	150262518	150262524	+	IGR	DEL	TTTGAAA	-	-	rs74886728		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150262518_150262524delTTTGAAA								HMGB3 (103272 upstream) : GPR50 (82535 downstream)																							ttagtttatttttgAAAtatcagccac	0.000													4	2	---	---	---	---	
MAGEA3	4102	broad.mit.edu	37	X	151939271	151939284	+	5'Flank	DEL	TTTTGTTGCGTAGA	-	-			TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151939271_151939284delTTTTGTTGCGTAGA	uc004fgp.2	-							NM_005362	NP_005353	P43357	MAGA3_HUMAN	melanoma antigen family A, 3												0	Acute lymphoblastic leukemia(192;6.56e-05)					GCTTTCCCTGTTTTGTTGCGTAGATTTTGTTGCT	0.449													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13445900	13445900	+	IGR	DEL	C	-	-	rs149511831		TCGA-BP-4164-01A-02D-1386-10	TCGA-BP-4164-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13445900delC								None (None upstream) : None (None downstream)																							AAAGTCCCAACAAACTTCTCA	0.244													16	8	---	---	---	---	
