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
APITD1	378708	broad.mit.edu	37	1	10493929	10493929	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10493929G>T	uc001are.2	+	2	498	c.82G>T	c.(82-84)GGT>TGT	p.G28C	APITD1_uc001arf.2_Missense_Mutation_p.G28C|APITD1_uc001arg.2_Missense_Mutation_p.G107V|APITD1_uc001arh.2_5'UTR	NM_199294	NP_954988	Q8N2Z9	CENPS_HUMAN	apoptosis-inducing, TAF9-like domain 1 isoform	28					DNA repair|mitotic prometaphase|transcription initiation, DNA-dependent	chromosome, centromeric region|cytosol|Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.31e-07)|COAD - Colon adenocarcinoma(227;7.32e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		CTATACTGTGGGTTGTCTTTG	0.443													5	127	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16975045	16975045	+	RNA	SNP	G	A	A	rs55763726	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16975045G>A	uc010och.1	+	7		c.1505G>A			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						CCTCCGAACCGCATGCACAAC	0.587													5	27	---	---	---	---	PASS
PIGV	55650	broad.mit.edu	37	1	27121005	27121005	+	Silent	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27121005C>A	uc001bmz.2	+	3	811	c.480C>A	c.(478-480)GCC>GCA	p.A160A	PIGV_uc001bmy.2_Intron|PIGV_uc009vso.2_Silent_p.A160A|PIGV_uc010ofg.1_Intron|PIGV_uc001bna.2_Silent_p.A160A	NM_017837	NP_060307	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan class V	160	Cytoplasmic (Potential).				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	glycolipid mannosyltransferase activity			ovary(1)	1		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		TCAGCCCTGCCAATGTCTTCC	0.537													5	67	---	---	---	---	PASS
PABPC4	8761	broad.mit.edu	37	1	40035558	40035558	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40035558A>G	uc010oiv.1	-	4	1518	c.620T>C	c.(619-621)CTG>CCG	p.L207P	PABPC4_uc001cdl.2_Missense_Mutation_p.L207P|PABPC4_uc001cdm.2_Missense_Mutation_p.L207P|SNORA55_uc001cdo.1_5'Flank	NM_003819	NP_003810	Q13310	PABP4_HUMAN	poly A binding protein, cytoplasmic 4 isoform 2	207	RRM 3.				blood coagulation|RNA catabolic process|RNA processing|translation	cytoplasm|ribonucleoprotein complex	nucleotide binding|poly(A) RNA binding|poly(U) RNA binding|protein binding				0	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TAGCTCTTTCAGACTCTCATC	0.453													6	132	---	---	---	---	PASS
KIAA0467	23334	broad.mit.edu	37	1	43897031	43897031	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43897031C>T	uc001cjk.1	+	19	2777	c.2315C>T	c.(2314-2316)CCA>CTA	p.P772L		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	1671						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTGCCACCCCCAGAAGAGGAG	0.463													8	40	---	---	---	---	PASS
CYP2J2	1573	broad.mit.edu	37	1	60359336	60359336	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60359336A>T	uc001czq.2	-	9	1501	c.1496T>A	c.(1495-1497)GTT>GAT	p.V499D		NM_000775	NP_000766	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J,	499					epoxygenase P450 pathway|linoleic acid metabolic process|regulation of heart contraction|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	arachidonic acid 11,12-epoxygenase activity|arachidonic acid 14,15-epoxygenase activity|aromatase activity|electron carrier activity|heme binding|linoleic acid epoxygenase activity			ovary(1)	1	all_cancers(7;0.000396)					CACCTGAGGAACAGCGCAGAG	0.468													15	45	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	146398425	146398425	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146398425C>A	uc001emp.3	+	13	2422	c.1224C>A	c.(1222-1224)GAC>GAA	p.D408E	uc010ozk.1_5'UTR	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672	137											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATGAGCCGGACAAGTCCCAGG	0.587													5	37	---	---	---	---	PASS
ILF2	3608	broad.mit.edu	37	1	153637769	153637769	+	Silent	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153637769A>G	uc001fcr.2	-	8	585	c.504T>C	c.(502-504)TCT>TCC	p.S168S	ILF2_uc010pdy.1_Silent_p.S130S|ILF2_uc009wok.2_Silent_p.S146S|ILF2_uc009wol.1_3'UTR	NM_004515	NP_004506	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2	168	DZF.				immune response|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|ribonucleoprotein complex	ATP binding|DNA binding|double-stranded RNA binding|protein binding|transferase activity				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TAGCATCAGAAGAACTGATTT	0.358													64	215	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	154031095	154031095	+	Silent	SNP	T	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154031095T>A	uc001fdw.2	-	21	2997	c.2925A>T	c.(2923-2925)ACA>ACT	p.T975T	NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Silent_p.T975T	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	975						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TGAGGTGGGCTGTTGCTGGAC	0.413													5	69	---	---	---	---	PASS
NME7	29922	broad.mit.edu	37	1	169101886	169101886	+	3'UTR	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169101886C>T	uc001gfu.2	-	12					ATP1B1_uc001gfs.1_RNA|NME7_uc010plq.1_RNA|NME7_uc001gft.2_3'UTR	NM_013330	NP_037462	Q9Y5B8	NDK7_HUMAN	nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)					TAATAATTGCCAGGAGTACAG	0.348													11	34	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	185972856	185972856	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185972856C>A	uc001grq.1	+	29	4584	c.4355C>A	c.(4354-4356)CCC>CAC	p.P1452H		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	1452	Ig-like C2-type 12.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						CAAGTTCCACCCACCATAATA	0.428													5	125	---	---	---	---	PASS
C1orf27	54953	broad.mit.edu	37	1	186375284	186375284	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186375284T>C	uc001grw.2	+	13	1306	c.1070T>C	c.(1069-1071)TTG>TCG	p.L357S	C1orf27_uc010poq.1_Missense_Mutation_p.L334S|C1orf27_uc010por.1_Missense_Mutation_p.L325S	NM_017847	NP_060317	Q5SWX8	ODR4_HUMAN	odorant response abnormal 4 isoform 1	357						integral to membrane	oxidoreductase activity|zinc ion binding			ovary(1)	1						ACTGTAATGTTGTGTGATTAT	0.353													6	235	---	---	---	---	PASS
PTPN14	5784	broad.mit.edu	37	1	214656184	214656184	+	Intron	SNP	C	T	T	rs145642282	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214656184C>T	uc001hkk.1	-						PTPN14_uc010pty.1_Intron|uc010ptz.1_RNA	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CACTTTTATACTGATGTCACC	0.413													6	128	---	---	---	---	PASS
TAF5L	27097	broad.mit.edu	37	1	229738474	229738474	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229738474T>G	uc001htq.2	-	4	606	c.440A>C	c.(439-441)CAG>CCG	p.Q147P	TAF5L_uc001htr.2_Missense_Mutation_p.Q147P	NM_014409	NP_055224	O75529	TAF5L_HUMAN	PCAF associated factor 65 beta isoform a	147					histone H3 acetylation|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				TAGGATGTCCTGGATGGTTTG	0.463													20	63	---	---	---	---	PASS
HPCAL1	3241	broad.mit.edu	37	2	10560058	10560058	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10560058G>A	uc002raj.2	+	3	549	c.175G>A	c.(175-177)GGC>AGC	p.G59S	HPCAL1_uc002rak.2_Missense_Mutation_p.G59S|HPCAL1_uc002ral.2_Missense_Mutation_p.G59S|HPCAL1_uc010exe.2_RNA|HPCAL1_uc010exf.2_Missense_Mutation_p.G59S	NM_002149	NP_002140	P37235	HPCL1_HUMAN	hippocalcin-like 1	59							calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)		CTTCCCCTACGGCGACGCTTC	0.607													3	20	---	---	---	---	PASS
ABCG5	64240	broad.mit.edu	37	2	44040208	44040208	+	3'UTR	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44040208A>G	uc002rtn.2	-	13					ABCG5_uc002rtm.2_3'UTR|ABCG5_uc002rto.2_3'UTR|ABCG5_uc002rtp.2_3'UTR	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CAGAGCAGTCATGCACAGTCG	0.423													9	100	---	---	---	---	PASS
MRPL35	51318	broad.mit.edu	37	2	86437759	86437759	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86437759A>G	uc002srg.3	+	4	593	c.535A>G	c.(535-537)AAG>GAG	p.K179E	MRPL35_uc002srf.3_Intron	NM_016622	NP_057706	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35 isoform a	179					translation	mitochondrial ribosome	structural constituent of ribosome				0						TCCTTATCAGAAGTATCATGA	0.358													5	147	---	---	---	---	PASS
MARCH7	64844	broad.mit.edu	37	2	160605273	160605273	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160605273C>A	uc002uax.2	+	5	1594	c.1472C>A	c.(1471-1473)GCA>GAA	p.A491E	MARCH7_uc010foq.2_Missense_Mutation_p.A491E|MARCH7_uc010zcn.1_Missense_Mutation_p.A435E|MARCH7_uc010for.2_Missense_Mutation_p.A453E|MARCH7_uc002uay.2_RNA	NM_022826	NP_073737	Q9H992	MARH7_HUMAN	axotrophin	491							ligase activity|zinc ion binding				0						GTCCCTCCAGCACTTGGGAGT	0.428													5	78	---	---	---	---	PASS
FASTKD1	79675	broad.mit.edu	37	2	170413697	170413697	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170413697C>A	uc002uev.3	-	6	1470	c.1082G>T	c.(1081-1083)AGA>ATA	p.R361I	FASTKD1_uc002uew.3_RNA|FASTKD1_uc002uex.3_Missense_Mutation_p.R347I	NM_024622	NP_078898	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	361					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(4)	4						GAAAAGATACCTTTTAATCAG	0.378													7	281	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179468975	179468975	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179468975A>G	uc010zfg.1	-	231	46959	c.46735T>C	c.(46735-46737)TAT>CAT	p.Y15579H	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.Y9274H|TTN_uc010zfi.1_Missense_Mutation_p.Y9207H|TTN_uc010zfj.1_Missense_Mutation_p.Y9082H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16506							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)			CTGATTCCATATTTATTCACT	0.383													10	63	---	---	---	---	PASS
NHEJ1	79840	broad.mit.edu	37	2	219942000	219942000	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219942000G>A	uc002vjp.3	-	7	939	c.793C>T	c.(793-795)CCA>TCA	p.P265S	NHEJ1_uc002vjq.3_RNA	NM_024782	NP_079058	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	265					B cell differentiation|central nervous system development|DNA recombination|double-strand break repair via nonhomologous end joining|positive regulation of ligase activity|response to ionizing radiation|T cell differentiation	nonhomologous end joining complex|nucleus	DNA binding|identical protein binding			lung(1)	1		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		GAGAGGGTTGGGGCTGAGGAG	0.522								Direct_reversal_of_damage|NHEJ					34	119	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228882779	228882779	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228882779C>T	uc002vpq.2	-	7	2838	c.2791G>A	c.(2791-2793)GAA>AAA	p.E931K	SPHKAP_uc002vpp.2_Missense_Mutation_p.E931K|SPHKAP_uc010zlx.1_Missense_Mutation_p.E931K	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	931	PKA-RII subunit binding domain (By similarity).					cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GCTAATTCTTCCGCAAAGTCT	0.473													30	83	---	---	---	---	PASS
TMEM111	55831	broad.mit.edu	37	3	10012345	10012345	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10012345C>A	uc003bun.2	-	6	674	c.495G>T	c.(493-495)TGG>TGT	p.W165C	CIDEC_uc003bto.2_Intron|TMEM111_uc003buo.2_Missense_Mutation_p.W165C	NM_018447	NP_060917	Q9P0I2	TM111_HUMAN	transmembrane protein 111	165						integral to membrane					0						CAGAACTCACCCTGGCAAAGC	0.418													5	149	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188321	10188321	+	Splice_Site	SNP	G	C	C	rs5030814		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188321G>C	uc003bvc.2	+	2	676	c.463_splice	c.e2+1	p.V155_splice	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(9)		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)		ACACTGCCAGGTACTGACGTT	0.403		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				56	95	---	---	---	---	PASS
LAMB2	3913	broad.mit.edu	37	3	49168474	49168474	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49168474T>C	uc003cwe.2	-	7	1123	c.824A>G	c.(823-825)TAT>TGT	p.Y275C	LAMB2_uc003cwf.1_Missense_Mutation_p.Y275C	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	275	Laminin N-terminal.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AACCAGCTCATAGAGGGCATA	0.587													4	32	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52649414	52649414	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52649414C>A	uc003des.2	-	15	1889	c.1877G>T	c.(1876-1878)GGC>GTC	p.G626V	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.G626V|PBRM1_uc003der.2_Missense_Mutation_p.G594V|PBRM1_uc003det.2_Missense_Mutation_p.G641V|PBRM1_uc003deu.2_Missense_Mutation_p.G641V|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.G626V|PBRM1_uc010hmk.1_Missense_Mutation_p.G626V|PBRM1_uc003dey.2_Missense_Mutation_p.G626V|PBRM1_uc003dez.1_Missense_Mutation_p.G626V|PBRM1_uc003dfb.1_Missense_Mutation_p.G539V|PBRM1_uc003dfc.2_5'UTR	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	626					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)		AGGCAGTGGGCCCAGCTCTTT	0.378			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								37	78	---	---	---	---	PASS
OR5H1	26341	broad.mit.edu	37	3	97851689	97851689	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97851689T>C	uc011bgt.1	+	1	148	c.148T>C	c.(148-150)TGG>CGG	p.W50R		NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,	50	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						TGCTGTCATCTGGAAAGACCC	0.418													6	48	---	---	---	---	PASS
IGSF10	285313	broad.mit.edu	37	3	151160939	151160939	+	Silent	SNP	A	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151160939A>C	uc011bod.1	-	5	5796	c.5796T>G	c.(5794-5796)CTT>CTG	p.L1932L	IGSF10_uc011bob.1_5'Flank|IGSF10_uc011boc.1_5'Flank	NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	1932	Ig-like C2-type 5.				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)			CTTCCATTGTAAGCATTACTA	0.463													14	100	---	---	---	---	PASS
KCNAB1	7881	broad.mit.edu	37	3	156009685	156009685	+	Intron	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156009685C>T	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_5'UTR|KCNAB1_uc010hvt.1_5'UTR	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CCGTGCGCTGCCTGGGGAAGC	0.567													4	8	---	---	---	---	PASS
KCNAB1	7881	broad.mit.edu	37	3	156009745	156009745	+	Intron	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156009745G>T	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Missense_Mutation_p.G17C|KCNAB1_uc010hvt.1_Missense_Mutation_p.G17C	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GAGTCGGAATGGTGAGGACCG	0.597													7	13	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195510108	195510108	+	Silent	SNP	G	A	A	rs142152945	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195510108G>A	uc011bto.1	-	3	8419	c.7959C>T	c.(7957-7959)CAC>CAT	p.H2653H	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)		GAGGGGTGGCGTGACCTGTGG	0.592													11	143	---	---	---	---	PASS
RASGEF1B	153020	broad.mit.edu	37	4	82377759	82377759	+	Intron	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82377759C>A	uc003hmi.1	-						RASGEF1B_uc003hmj.1_Intron|RASGEF1B_uc010ijq.1_Intron|RASGEF1B_uc003hmk.2_Missense_Mutation_p.A162S	NM_152545	NP_689758	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0						CCCACCCAGGCTCTGCCTGGG	0.483													5	44	---	---	---	---	PASS
WDFY3	23001	broad.mit.edu	37	4	85657456	85657456	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85657456C>A	uc003hpd.2	-	42	7190	c.6782G>T	c.(6781-6783)CGA>CTA	p.R2261L	WDFY3_uc003hpe.1_5'Flank	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2261						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)		AGCTTCTCCTCGACTTATGCA	0.353													9	438	---	---	---	---	PASS
HSPA4L	22824	broad.mit.edu	37	4	128729255	128729255	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128729255A>T	uc003ifm.2	+	11	1602	c.1349A>T	c.(1348-1350)CAT>CTT	p.H450L	HSPA4L_uc010iny.1_Missense_Mutation_p.H409L|HSPA4L_uc011cgr.1_Missense_Mutation_p.H417L	NM_014278	NP_055093	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	450					protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						ACTAATTTACATGAAGTGCCT	0.318													33	109	---	---	---	---	PASS
AADAT	51166	broad.mit.edu	37	4	170985920	170985920	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170985920C>A	uc003isr.2	-	11	1426	c.1084G>T	c.(1084-1086)GGC>TGC	p.G362C	AADAT_uc003iss.2_Missense_Mutation_p.G362C|AADAT_uc003ist.2_Missense_Mutation_p.G366C	NM_016228	NP_057312	Q8N5Z0	AADAT_HUMAN	kynurenine aminotransferase II	362					2-oxoglutarate metabolic process|biosynthetic process|glutamate metabolic process|lysine catabolic process	mitochondrial matrix	2-aminoadipate transaminase activity|kynurenine-oxoglutarate transaminase activity|protein homodimerization activity				0		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	TCATTAATGCCTTTAACTTTA	0.383													6	290	---	---	---	---	PASS
PAIP1	10605	broad.mit.edu	37	5	43555944	43555944	+	Silent	SNP	A	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43555944A>T	uc003job.2	-	2	670	c.423T>A	c.(421-423)TCT>TCA	p.S141S	PAIP1_uc003joa.2_Silent_p.S62S|PAIP1_uc010ivp.2_Silent_p.S62S|PAIP1_uc010ivo.2_RNA|PAIP1_uc003joc.2_Silent_p.S29S	NM_006451	NP_006442	Q9H074	PAIP1_HUMAN	poly(A) binding protein interacting protein 1	141	PABPC1-interacting motif-2 (PAM2).				mRNA stabilization|nuclear-transcribed mRNA poly(A) tail shortening|translational initiation	cytosol	protein binding|RNA binding|translation activator activity			ovary(1)	1	Lung NSC(6;2.07e-05)					TGTAACTGGAAGAATAACCTG	0.408													26	66	---	---	---	---	PASS
SFRS12	140890	broad.mit.edu	37	5	65455125	65455125	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65455125G>T	uc003juo.2	+	4	686	c.26G>T	c.(25-27)GGA>GTA	p.G9V	SFRS12_uc003jun.2_Missense_Mutation_p.G125V|SFRS12_uc010iwy.2_Missense_Mutation_p.G9V	NM_139168	NP_631907	Q8WXA9	SREK1_HUMAN	splicing factor, arginine/serine-rich 12 isoform	9					mRNA processing|RNA splicing	spliceosomal complex	nucleic acid binding|nucleotide binding|protein binding				0		Lung NSC(167;9.34e-06)|Prostate(74;0.00187)|Ovarian(174;0.0545)|Breast(144;0.0928)|Colorectal(97;0.234)		Lung(70;0.00449)		CCTGGTGCAGGATTGCTTCCA	0.453													8	93	---	---	---	---	PASS
RAD17	5884	broad.mit.edu	37	5	68684924	68684924	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68684924G>T	uc003jwo.2	+	9	1053	c.991G>T	c.(991-993)GGT>TGT	p.G331C	RAD17_uc003jwg.2_Missense_Mutation_p.G320C|RAD17_uc003jwh.2_Missense_Mutation_p.G320C|RAD17_uc003jwi.2_Missense_Mutation_p.G320C|RAD17_uc003jwj.2_Missense_Mutation_p.G320C|RAD17_uc003jwk.2_Missense_Mutation_p.G320C|RAD17_uc003jwl.2_Missense_Mutation_p.G320C|RAD17_uc003jwm.2_Missense_Mutation_p.G155C|RAD17_uc003jwn.2_Missense_Mutation_p.G234C	NM_133339	NP_579917	O75943	RAD17_HUMAN	RAD17 homolog isoform 2	331					cell cycle|DNA damage checkpoint|DNA repair|DNA replication|DNA replication checkpoint|mitotic cell cycle checkpoint|negative regulation of DNA replication|regulation of phosphorylation	nucleoplasm	ATP binding|nucleoside-triphosphatase activity|protein binding				0		Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		GGGATGTTCTGGTGATATCAG	0.328								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					7	401	---	---	---	---	PASS
MEF2C	4208	broad.mit.edu	37	5	88119552	88119552	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88119552C>A	uc003kjj.2	-	2	727	c.54G>T	c.(52-54)CAG>CAT	p.Q18H	MEF2C_uc003kji.2_Missense_Mutation_p.Q18H|MEF2C_uc003kjk.2_Missense_Mutation_p.Q18H|MEF2C_uc003kjm.2_Missense_Mutation_p.Q18H|MEF2C_uc003kjl.2_Missense_Mutation_p.Q18H	NM_002397	NP_002388	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C isoform 1	18	Lys-rich (basic).|MADS-box.				apoptosis|B cell proliferation|innate immune response|learning or memory|muscle cell differentiation|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|neuron development|positive regulation of muscle cell differentiation|positive regulation of survival gene product expression|positive regulation of transcription from RNA polymerase II promoter|regulation of germinal center formation|regulation of megakaryocyte differentiation|regulation of synaptic activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	nuclear speck	activating transcription factor binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			lung(3)|breast(2)|ovary(1)|large_intestine(1)	7		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		CTCCACTCACCTGTCTGTTAC	0.313										HNSCC(66;0.2)			5	115	---	---	---	---	PASS
LNPEP	4012	broad.mit.edu	37	5	96350753	96350753	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96350753A>G	uc003kmv.1	+	13	2844	c.2330A>G	c.(2329-2331)AAC>AGC	p.N777S	LNPEP_uc003kmw.1_Missense_Mutation_p.N763S	NM_005575	NP_005566	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase isoform 1	777	Extracellular (Potential).				cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		CTCATCTATAACCTCCTTGAA	0.418													4	42	---	---	---	---	PASS
MCC	4163	broad.mit.edu	37	5	112458491	112458491	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112458491T>G	uc003kqj.3	-	4	877	c.347A>C	c.(346-348)GAA>GCA	p.E116A	MCC_uc003kqk.3_RNA|MCC_uc003kql.3_Missense_Mutation_p.E306A|MCC_uc011cwb.1_Missense_Mutation_p.E116A|MCC_uc010jcd.1_Missense_Mutation_p.E78A	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2	116					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CTGGCTGAGTTCTGATCGCAG	0.478													17	95	---	---	---	---	PASS
YTHDC2	64848	broad.mit.edu	37	5	112899071	112899071	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112899071A>T	uc003kqn.2	+	19	2507	c.2324A>T	c.(2323-2325)GAA>GTA	p.E775V		NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	775	Helicase C-terminal.						ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GGTTTATAGGAACTTTGCTTA	0.328													14	110	---	---	---	---	PASS
SNX2	6643	broad.mit.edu	37	5	122137630	122137630	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122137630G>T	uc003kte.2	+	4	506	c.457G>T	c.(457-459)GGT>TGT	p.G153C	SNX2_uc011cwn.1_Missense_Mutation_p.G36C	NM_003100	NP_003091	O60749	SNX2_HUMAN	sorting nexin 2	153	PX.				cell communication|endocytosis|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding|protein transporter activity			kidney(1)	1		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		AGAAAAAGTTGGTGAGTCAAT	0.244													8	493	---	---	---	---	PASS
DOCK2	1794	broad.mit.edu	37	5	169138938	169138938	+	Splice_Site	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169138938G>A	uc003maf.2	+	16	1563	c.1483_splice	c.e16-1	p.V495_splice	DOCK2_uc011der.1_Splice_Site|DOCK2_uc010jjm.2_Splice_Site_p.R21_splice|DOCK2_uc010jjl.1_Splice_Site_p.V13_splice	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGTCTGCTGAGGTGGCTGTCC	0.498													9	173	---	---	---	---	PASS
BNIP1	662	broad.mit.edu	37	5	172578691	172578691	+	Intron	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172578691C>A	uc003mcj.3	+						BNIP1_uc003mci.3_Silent_p.T100T|BNIP1_uc003mck.3_Silent_p.T100T|BNIP1_uc003mcl.3_Intron	NM_001205	NP_001196	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kD interacting protein 1						anti-apoptosis|apoptosis|endoplasmic reticulum membrane fusion|endoplasmic reticulum organization|induction of apoptosis|vesicle-mediated transport	integral to endoplasmic reticulum membrane|nuclear envelope|SNARE complex	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CACCTGTTACCTTCAGTGTGA	0.373													10	447	---	---	---	---	PASS
SKIV2L	6499	broad.mit.edu	37	6	31928300	31928300	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31928300C>T	uc003nyn.1	+	5	835	c.446C>T	c.(445-447)CCA>CTA	p.P149L	RDBP_uc003nyk.2_5'Flank|RDBP_uc011dot.1_5'Flank|RDBP_uc003nyl.1_5'Flank|RDBP_uc003nym.1_5'Flank|SKIV2L_uc011dou.1_5'UTR|SKIV2L_uc011dov.1_Intron	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	149						nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						TGGGGAAATCCAACTCAGTAT	0.532													12	42	---	---	---	---	PASS
CENPQ	55166	broad.mit.edu	37	6	49437896	49437896	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49437896G>T	uc003ozh.1	+	2	96	c.7G>T	c.(7-9)GGT>TGT	p.G3C		NM_018132	NP_060602	Q7L2Z9	CENPQ_HUMAN	centromere protein Q	3					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)					CAAGATGTCTGGTAAAGCAAA	0.303													7	252	---	---	---	---	PASS
MCM3	4172	broad.mit.edu	37	6	52129392	52129392	+	Silent	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52129392G>A	uc003pan.1	-	17	2531	c.2421C>T	c.(2419-2421)CTC>CTT	p.L807L	MCM3_uc011dwu.1_Silent_p.L761L	NM_002388	NP_002379	P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	807					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	alpha DNA polymerase:primase complex|centrosome|MCM complex|perinuclear region of cytoplasm	ATP binding|DNA binding|helicase activity|protein binding			ovary(1)|lung(1)|skin(1)	3	Lung NSC(77;0.0931)					CTCCTCAGATGAGGAAGATGA	0.532													9	25	---	---	---	---	PASS
GFRAL	389400	broad.mit.edu	37	6	55266626	55266626	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55266626C>A	uc003pcm.1	+	9	1246	c.1160C>A	c.(1159-1161)TCG>TAG	p.S387*		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	387	Cytoplasmic (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			GATCCTTCATCGATCCAAATA	0.264													6	308	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64423285	64423285	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64423285G>T	uc003pep.1	+	15	5827	c.5801G>T	c.(5800-5802)CGA>CTA	p.R1934L	PHF3_uc003pen.2_Missense_Mutation_p.R1846L|PHF3_uc011dxs.1_Missense_Mutation_p.R1203L	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	1934					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			AAAAGAGAGCGACATGAAAAG	0.308													5	88	---	---	---	---	PASS
SNX14	57231	broad.mit.edu	37	6	86215537	86215537	+	3'UTR	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86215537G>A	uc003pkr.2	-	29					SNX14_uc003pkp.2_3'UTR|SNX14_uc003pkq.2_3'UTR|SNX14_uc011dzg.1_3'UTR|SNX14_uc003pks.2_3'UTR|SNX14_uc003pkt.2_3'UTR	NM_153816	NP_722523	Q9Y5W7	SNX14_HUMAN	sorting nexin 14 isoform a						cell communication|protein transport	integral to membrane	phosphatidylinositol binding|signal transducer activity				0		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		CATTAAGTTTGTGTTAGTCTT	0.264													7	18	---	---	---	---	PASS
FAM184A	79632	broad.mit.edu	37	6	119345803	119345803	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119345803T>C	uc003pyj.2	-	2	683	c.335A>G	c.(334-336)GAA>GGA	p.E112G	FAM184A_uc003pyk.3_5'UTR|FAM184A_uc003pyl.3_5'UTR	NM_024581	NP_078857	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 1	112	Potential.									ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7						TAATGATGATTCTAAAACTTG	0.348													13	166	---	---	---	---	PASS
C7orf46	340277	broad.mit.edu	37	7	23728936	23728936	+	Silent	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23728936C>T	uc003swo.3	+	3	377	c.288C>T	c.(286-288)CCC>CCT	p.P96P	C7orf46_uc003swq.3_Silent_p.P96P|C7orf46_uc003swr.3_Silent_p.P38P|C7orf46_uc003swp.3_RNA|C7orf46_uc010kup.2_RNA	NM_199136	NP_954587	A4D161	CG046_HUMAN	hypothetical protein LOC340277 isoform 1	96											0						AGCAGTGCCCCATTGATCTGC	0.448													9	20	---	---	---	---	PASS
SPDYE6	729597	broad.mit.edu	37	7	101991206	101991206	+	Silent	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101991206G>A	uc011kkp.1	-	5	1138	c.717C>T	c.(715-717)CCC>CCT	p.P239P	SPDYE6_uc003uzb.2_Silent_p.P95P	NM_001146210	NP_001139682	P0CI01	SPDE6_HUMAN	speedy homolog E6	239											0						ATTGCCAGGAGGGGAAGCCAG	0.532													10	28	---	---	---	---	PASS
POT1	25913	broad.mit.edu	37	7	124487019	124487019	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124487019C>A	uc003vlm.2	-	12	1584	c.983G>T	c.(982-984)AGA>ATA	p.R328I	POT1_uc011koe.1_RNA|POT1_uc003vlk.2_RNA|POT1_uc003vll.2_RNA|POT1_uc003vlo.2_Missense_Mutation_p.R197I|POT1_uc003vln.2_RNA	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1	328					DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						CTGTTGACATCTTTCTACCTC	0.328													35	183	---	---	---	---	PASS
FAM86B1	85002	broad.mit.edu	37	8	12040786	12040786	+	3'UTR	SNP	C	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12040786C>G	uc010lse.2	-	7					FAM66D_uc011kxp.1_Intron|FAM86B1_uc003wvf.3_RNA|FAM86B1_uc003wvi.3_3'UTR|FAM86B1_uc010lsd.2_RNA|FAM86B1_uc003wvh.3_3'UTR|FAM86B1_uc011kxq.1_3'UTR|FAM86B1_uc010lsf.2_3'UTR|FAM86B1_uc003wvj.3_3'UTR|FAM86B1_uc003wvk.3_3'UTR|FAM86B1_uc010lsg.2_RNA|FAM86B1_uc003wvl.3_RNA	NM_001083537	NP_001077006	Q8N7N1	F86B1_HUMAN	hypothetical protein LOC85002												0			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		GCTTGGCTTTCTGAGGAACCG	0.517													3	18	---	---	---	---	PASS
MTFR1	9650	broad.mit.edu	37	8	66605957	66605957	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66605957G>T	uc003xvm.2	+	4	456	c.244G>T	c.(244-246)GTA>TTA	p.V82L	MTFR1_uc011lep.1_Missense_Mutation_p.V82L|MTFR1_uc003xvn.2_Missense_Mutation_p.V49L|MTFR1_uc003xvo.1_Missense_Mutation_p.V72L	NM_014637	NP_055452	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1 isoform 1	82						mitochondrion|plasma membrane				pancreas(1)	1			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			TGTTGGATGGGTAGCCAAAGA	0.403													11	129	---	---	---	---	PASS
UHRF2	115426	broad.mit.edu	37	9	6420988	6420988	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6420988C>G	uc003zjy.2	+	2	570	c.230C>G	c.(229-231)CCT>CGT	p.P77R	UHRF2_uc003zjz.2_RNA	NM_152896	NP_690856	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains	77	Ubiquitin-like.				cell cycle|cell differentiation|cell proliferation|protein autoubiquitination|regulation of cell cycle|ubiquitin-dependent protein catabolic process	nucleus	DNA binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)		CGCCCAGACCCTGATCATCTT	0.398													51	160	---	---	---	---	PASS
PTPRD	5789	broad.mit.edu	37	9	8454590	8454590	+	Intron	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8454590T>C	uc003zkk.2	-						PTPRD_uc003zkp.2_Missense_Mutation_p.K883E|PTPRD_uc003zkq.2_Missense_Mutation_p.K882E|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Missense_Mutation_p.K879E	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CTGTCGGGTTTACTGCTCCAT	0.393										TSP Lung(15;0.13)			5	305	---	---	---	---	PASS
TLN1	7094	broad.mit.edu	37	9	35704041	35704041	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35704041C>T	uc003zxt.2	-	46	6532	c.6178G>A	c.(6178-6180)GAT>AAT	p.D2060N		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	2060					axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTGACCACATCAGCGAGGCGG	0.632													3	15	---	---	---	---	PASS
TMEM2	23670	broad.mit.edu	37	9	74359990	74359990	+	Silent	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74359990G>T	uc011lsa.1	-	4	1518	c.978C>A	c.(976-978)ACC>ACA	p.T326T	TMEM2_uc010mos.2_Silent_p.T326T|TMEM2_uc011lsb.1_RNA	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a	326						integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TCATCTGGATGGTTCCTTGTA	0.522													4	67	---	---	---	---	PASS
NAA35	60560	broad.mit.edu	37	9	88633642	88633642	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88633642C>T	uc004aoi.3	+	21	2080	c.1943C>T	c.(1942-1944)CCT>CTT	p.P648L	NAA35_uc004aoj.3_Missense_Mutation_p.P648L	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN	corneal wound healing-related protein	648					smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3						AAATATAGCCCTCCTCCTCAG	0.368													8	279	---	---	---	---	PASS
ZNF483	158399	broad.mit.edu	37	9	114293241	114293241	+	Missense_Mutation	SNP	T	A	A	rs140422947		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114293241T>A	uc004bff.2	+	3	723	c.499T>A	c.(499-501)TGT>AGT	p.C167S	ZNF483_uc011lwq.1_Missense_Mutation_p.C167S|ZNF483_uc004bfg.2_Missense_Mutation_p.C167S	NM_133464	NP_597721	Q8TF39	ZN483_HUMAN	zinc finger protein 483 isoform a	167					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1						TACTGAGTCCTGTGTAAGTTT	0.343													21	286	---	---	---	---	PASS
DDX50	79009	broad.mit.edu	37	10	70670871	70670871	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70670871C>G	uc001jou.2	+	4	615	c.508C>G	c.(508-510)CCT>GCT	p.P170A	DDX50_uc001jot.2_Missense_Mutation_p.P170A|DDX50_uc010qjc.1_Missense_Mutation_p.P170A	NM_024045	NP_076950	Q9BQ39	DDX50_HUMAN	nucleolar protein GU2	170	Helicase ATP-binding.					nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1						GACCTTTGGTCCTGTATATGA	0.353													46	139	---	---	---	---	PASS
ZMYND17	118490	broad.mit.edu	37	10	75184106	75184106	+	3'UTR	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75184106G>A	uc001jud.2	-	7					ZMYND17_uc001juc.2_3'UTR|ZMYND17_uc009xrh.2_3'UTR|ZMYND17_uc009xrg.2_3'UTR	NM_001024593	NP_001019764	Q4VC12	ZMY17_HUMAN	zinc finger, MYND domain containing 17								zinc ion binding			ovary(1)	1	Prostate(51;0.0119)					ctgcactccagcctgggcaac	0.090													7	12	---	---	---	---	PASS
NKX2-3	159296	broad.mit.edu	37	10	101294877	101294877	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101294877G>A	uc009xwj.2	+	2	693	c.494G>A	c.(493-495)CGC>CAC	p.R165H		NM_145285	NP_660328	Q8TAU0	NKX23_HUMAN	NK2 transcription factor related, locus 3	165	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.45e-08)		GAGCTGGAACGCAGGTTCAAG	0.642													3	5	---	---	---	---	PASS
INPP5F	22876	broad.mit.edu	37	10	121586174	121586174	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121586174G>T	uc001leo.2	+	20	2447	c.2281G>T	c.(2281-2283)GGT>TGT	p.G761C	INPP5F_uc001lep.2_Missense_Mutation_p.G151C	NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F	761							phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		AGACATCATTGGTATCAGGTC	0.358													5	151	---	---	---	---	PASS
WDR11	55717	broad.mit.edu	37	10	122626585	122626585	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122626585G>T	uc010qtf.1	+	9	1436	c.1198G>T	c.(1198-1200)GGT>TGT	p.G400C	WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2	400						integral to membrane					0						CAGTAGTTCTGGTGTGTCACC	0.348													6	270	---	---	---	---	PASS
FZD4	8322	broad.mit.edu	37	11	86662562	86662562	+	Silent	SNP	G	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86662562G>C	uc001pce.2	-	2	1542	c.1236C>G	c.(1234-1236)GCC>GCG	p.A412A	PRSS23_uc001pcc.1_RNA	NM_012193	NP_036325	Q9ULV1	FZD4_HUMAN	frizzled 4 precursor	412	Cytoplasmic (Potential).				canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TTTTGAACAAGGCCACCAAAC	0.448													46	127	---	---	---	---	PASS
NTM	50863	broad.mit.edu	37	11	131781272	131781272	+	5'UTR	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131781272G>T	uc001qgp.2	+	1					NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_5'UTR|NTM_uc001qgq.2_5'UTR	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						CGGGTTCACCGCTCAGTCCCC	0.687											OREG0021537	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	7	---	---	---	---	PASS
CAPRIN2	65981	broad.mit.edu	37	12	30868061	30868061	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30868061C>T	uc001rji.1	-	15	3233	c.2482G>A	c.(2482-2484)GAT>AAT	p.D828N	CAPRIN2_uc001rjf.1_Missense_Mutation_p.D624N|CAPRIN2_uc001rjg.1_Missense_Mutation_p.D495N|CAPRIN2_uc001rjh.1_Missense_Mutation_p.D778N|CAPRIN2_uc001rjj.1_Missense_Mutation_p.D494N|CAPRIN2_uc001rjk.3_Missense_Mutation_p.D827N|CAPRIN2_uc001rjl.3_Intron|CAPRIN2_uc001rjm.1_3'UTR	NM_001002259	NP_001002259	Q6IMN6	CAPR2_HUMAN	C1q domain containing 1 isoform 1	828					negative regulation of cell growth|negative regulation of translation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of dendrite morphogenesis|positive regulation of dendritic spine morphogenesis|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of transcription from RNA polymerase II promoter	mitochondrion|receptor complex	receptor binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					ATAGTTCCATCAGGATGATAA	0.373													23	81	---	---	---	---	PASS
ACVR1B	91	broad.mit.edu	37	12	52374878	52374878	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52374878T>C	uc001rzn.2	+	4	748	c.706T>C	c.(706-708)TTC>CTC	p.F236L	ACVR1B_uc001rzl.2_Missense_Mutation_p.F236L|ACVR1B_uc001rzm.2_Missense_Mutation_p.F236L|ACVR1B_uc010snn.1_Missense_Mutation_p.F236L	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor	236	Protein kinase.|Cytoplasmic (Potential).				G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway	cell surface	activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding			pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1)	9				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	TGTGAAAATATTCTCTTCTCG	0.502											OREG0021829	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	17	72	---	---	---	---	PASS
OR10A7	121364	broad.mit.edu	37	12	55614840	55614840	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55614840A>T	uc010spf.1	+	1	32	c.32A>T	c.(31-33)GAA>GTA	p.E11V		NM_001005280	NP_001005280	Q8NGE5	O10A7_HUMAN	olfactory receptor, family 10, subfamily A,	11	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)	4						AGAGTCACTGAATTTATTCTT	0.343													28	271	---	---	---	---	PASS
R3HDM2	22864	broad.mit.edu	37	12	57648628	57648628	+	Silent	SNP	C	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57648628C>G	uc009zpm.1	-	22	2894	c.2859G>C	c.(2857-2859)GTG>GTC	p.V953V	R3HDM2_uc010srn.1_Intron|R3HDM2_uc001snu.2_Silent_p.V648V|R3HDM2_uc001snr.2_Silent_p.V680V|R3HDM2_uc001sns.2_Silent_p.V953V|R3HDM2_uc001snt.2_Silent_p.V967V|R3HDM2_uc009zpn.1_Intron	NM_014925	NP_055740	Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	953						nucleus	nucleic acid binding			ovary(2)	2						TGAAGCGACTCACGGAGTTGT	0.562													7	40	---	---	---	---	PASS
SLC5A8	160728	broad.mit.edu	37	12	101584327	101584327	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101584327A>G	uc001thz.3	-	6	1142	c.752T>C	c.(751-753)TTC>TCC	p.F251S		NM_145913	NP_666018	Q8N695	SC5A8_HUMAN	solute carrier family 5 (iodide transporter),	251	Helical; (Potential).				apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0						GGTCCATGTGAAGGTCCCTCC	0.398													28	117	---	---	---	---	PASS
B3GALTL	145173	broad.mit.edu	37	13	31789237	31789237	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31789237G>T	uc010aaz.2	+	2	230	c.120G>T	c.(118-120)CAG>CAT	p.Q40H		NM_194318	NP_919299	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	40	Lumenal (Potential).				fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups	p.Q40*(1)		ovary(2)	2		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		AGCAGTCTCAGGTACTAATCC	0.308													7	393	---	---	---	---	PASS
ESD	2098	broad.mit.edu	37	13	47345586	47345586	+	Missense_Mutation	SNP	G	T	T	rs142467108		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47345586G>T	uc001vbn.2	-	10	997	c.814C>A	c.(814-816)CAC>AAC	p.H272N	ESD_uc001vbo.2_3'UTR	NM_001984	NP_001975	P10768	ESTD_HUMAN	esterase D/formylglutathione hydrolase	272						cytoplasmic membrane-bounded vesicle	carboxylesterase activity|S-formylglutathione hydrolase activity			ovary(1)	1		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	TGTCTGATGTGGTCAGTAATA	0.328													6	287	---	---	---	---	PASS
IRS2	8660	broad.mit.edu	37	13	110408476	110408476	+	3'UTR	SNP	T	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110408476T>G	uc001vqv.2	-	2						NM_003749	NP_003740	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2						fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus	cytosol|plasma membrane	insulin receptor binding|signal transducer activity			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1)	8	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			AAGAGGCAGGTGACCTTGCCT	0.418													5	8	---	---	---	---	PASS
TMEM55B	90809	broad.mit.edu	37	14	20927414	20927414	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20927414C>A	uc001vxl.2	-	6	794	c.641G>T	c.(640-642)TGC>TTC	p.C214F	TMEM55B_uc001vxk.2_Missense_Mutation_p.C221F	NM_144568	NP_653169	Q86T03	TM55B_HUMAN	transmembrane protein 55B isoform 2	214	Helical; (Potential).					integral to membrane|late endosome membrane|lysosomal membrane	hydrolase activity				0	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)		CAAGAAGCAGCAGATACATCT	0.498													10	93	---	---	---	---	PASS
PPIL5	122769	broad.mit.edu	37	14	50074209	50074209	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50074209C>A	uc001wwn.2	+	3	698	c.374C>A	c.(373-375)CCA>CAA	p.P125Q	SDCCAG1_uc010anj.1_Intron|PPIL5_uc001wwo.2_Intron|PPIL5_uc010ank.2_Missense_Mutation_p.P66Q|PPIL5_uc001wwp.2_RNA	NM_152329	NP_689542	Q96L50	LLR1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 5	125											0	all_epithelial(31;0.0021)|Breast(41;0.0124)					ACGCTCACACCAGTGAAGACT	0.358													4	73	---	---	---	---	PASS
C14orf182	283551	broad.mit.edu	37	14	50459020	50459020	+	3'UTR	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50459020T>C	uc001wxi.1	-	3						NM_001012706	NP_001012724	A1A4T8	CN182_HUMAN	hypothetical protein LOC283551												0						GCTGGTTATGTGTCATACACT	0.448													6	306	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105413709	105413709	+	Silent	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105413709G>T	uc010axc.1	-	7	8199	c.8079C>A	c.(8077-8079)ACC>ACA	p.T2693T	AHNAK2_uc001ypx.2_Silent_p.T2593T	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2693						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGATGTCAGTGGTCTTAAGGT	0.632													4	40	---	---	---	---	PASS
CTDSPL2	51496	broad.mit.edu	37	15	44776439	44776439	+	Silent	SNP	T	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44776439T>G	uc001ztr.2	+	3	620	c.204T>G	c.(202-204)CCT>CCG	p.P68P	CTDSPL2_uc001zts.2_Silent_p.P68P|CTDSPL2_uc001ztt.2_Silent_p.P68P|CTDSPL2_uc010bdv.2_Silent_p.P68P	NM_016396	NP_057480	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	68							phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		GAGAAAATCCTTCAAAACGGA	0.333													25	199	---	---	---	---	PASS
GTF2A2	2958	broad.mit.edu	37	15	59944421	59944421	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59944421A>G	uc002agg.2	-	2	238	c.56T>C	c.(55-57)CTA>CCA	p.L19P		NM_004492	NP_004483	P52657	T2AG_HUMAN	general transcription factor IIA, 2, 12kDa	19					interspecies interaction between organisms|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIA complex	protein heterodimerization activity|protein homodimerization activity|TBP-class protein binding|transcription coactivator activity			central_nervous_system(2)	2						GAGCTCATCTAGGCTCTCCTG	0.353													25	323	---	---	---	---	PASS
RORA	6095	broad.mit.edu	37	15	60789657	60789657	+	Silent	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60789657C>A	uc002agv.2	-	12	1824	c.1668G>T	c.(1666-1668)GGG>GGT	p.G556G	uc002ags.1_Intron|RORA_uc002agt.3_Silent_p.G468G|RORA_uc002agw.2_Silent_p.G548G|RORA_uc002agx.2_Silent_p.G523G	NM_134260	NP_599022	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform b	556	Ligand-binding.				positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						ATAACATTTACCCATCAATTT	0.368													10	140	---	---	---	---	PASS
GOLGA6L10	647042	broad.mit.edu	37	15	82635163	82635163	+	RNA	SNP	C	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82635163C>G	uc002bgx.2	-	5		c.417G>C						A6NI86	GG6LA_HUMAN	Homo sapiens cDNA FLJ40113 fis, clone TESTI2008621.												0						CCCTGTTCTCCGCAGCCCGAA	0.478													10	23	---	---	---	---	PASS
AKAP13	11214	broad.mit.edu	37	15	86279333	86279333	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86279333A>T	uc002blv.1	+	33	7695	c.7525A>T	c.(7525-7527)AAC>TAC	p.N2509Y	AKAP13_uc002blu.1_Missense_Mutation_p.N2513Y|AKAP13_uc002blw.1_Missense_Mutation_p.N974Y|AKAP13_uc002blx.1_Missense_Mutation_p.N754Y	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	2509	Interaction with ESR1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						TGGAAATGCTAACCTGGTATT	0.299													47	476	---	---	---	---	PASS
PAQR4	124222	broad.mit.edu	37	16	3021699	3021699	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3021699G>T	uc002csj.3	+	3	906	c.572G>T	c.(571-573)CGG>CTG	p.R191L	PAQR4_uc002csk.3_Missense_Mutation_p.R152L|PAQR4_uc002csl.3_Missense_Mutation_p.R117L|PAQR4_uc010uwm.1_Missense_Mutation_p.R122L	NM_152341	NP_689554	Q8N4S7	PAQR4_HUMAN	progestin and adipoQ receptor family member IV	191	Helical; (Potential).					integral to membrane	receptor activity				0						TTTGGGGCCCGGGGAGTGGGT	0.682													3	2	---	---	---	---	PASS
LONP2	83752	broad.mit.edu	37	16	48385641	48385641	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48385641G>T	uc002efi.1	+	15	2576	c.2487G>T	c.(2485-2487)GAG>GAT	p.E829D	LONP2_uc002efj.1_Missense_Mutation_p.E785D	NM_031490	NP_113678	Q86WA8	LONP2_HUMAN	peroxisomal LON protease-like	829					misfolded or incompletely synthesized protein catabolic process|protein targeting to peroxisome|signal peptide processing	nucleoid|peroxisomal matrix	ATP binding|ATP-dependent peptidase activity|enzyme binding|sequence-specific DNA binding|serine-type endopeptidase activity				0						GCCTGGATGAGGTTCTTAATG	0.408													4	77	---	---	---	---	PASS
PMFBP1	83449	broad.mit.edu	37	16	72188251	72188251	+	Silent	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72188251C>A	uc002fcc.3	-	4	445	c.273G>T	c.(271-273)CTG>CTT	p.L91L	PMFBP1_uc002fcd.2_Silent_p.L91L|PMFBP1_uc002fce.2_RNA|PMFBP1_uc002fcf.2_5'UTR	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	91	Potential.									ovary(2)	2		Ovarian(137;0.179)				GTTGAAGGACCAGCAATTTTT	0.468													6	202	---	---	---	---	PASS
SLC7A5	8140	broad.mit.edu	37	16	87874739	87874739	+	Silent	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87874739G>A	uc002fkm.2	-	3	759	c.687C>T	c.(685-687)CCC>CCT	p.P229P		NM_003486	NP_003477	Q01650	LAT1_HUMAN	solute carrier family 7 (cationic amino acid	229					blood coagulation|cell differentiation|cellular amino acid metabolic process|ion transport|leukocyte migration|nervous system development	apical plasma membrane|cytosol|integral to membrane	neutral amino acid transmembrane transporter activity|peptide antigen binding				0				BRCA - Breast invasive adenocarcinoma(80;0.049)		ATGAGAAGTTGGGATCTAGAT	0.493													4	131	---	---	---	---	PASS
CCDC144C	348254	broad.mit.edu	37	17	20269044	20269044	+	RNA	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20269044C>A	uc010cqy.1	+	12		c.3211C>A				NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						ACAAATGTACCAAAGCAAACT	0.403													5	100	---	---	---	---	PASS
AMAC1	146861	broad.mit.edu	37	17	33521356	33521356	+	5'UTR	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33521356G>A	uc002hjd.2	-	1						NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)		TCTCCTCCTGGCTCAGGGAGC	0.607													4	50	---	---	---	---	PASS
KRT9	3857	broad.mit.edu	37	17	39727785	39727785	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39727785T>C	uc002hxe.3	-	1	526	c.460A>G	c.(460-462)AAG>GAG	p.K154E	JUP_uc010wfs.1_Intron	NM_000226	NP_000217	P35527	K1C9_HUMAN	keratin 9	154	Rod.|Coil 1A.				intermediate filament organization|skin development		protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Breast(137;0.000307)				ATGGTGCTCTTCTCATTAGCA	0.294													6	153	---	---	---	---	PASS
C17orf53	78995	broad.mit.edu	37	17	42225574	42225574	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42225574C>T	uc002ifi.1	+	3	588	c.403C>T	c.(403-405)CAC>TAC	p.H135Y	C17orf53_uc010czq.1_Missense_Mutation_p.H135Y|C17orf53_uc002ifj.1_Missense_Mutation_p.H135Y|C17orf53_uc002ifk.1_RNA	NM_024032	NP_076937	Q8N3J3	CQ053_HUMAN	hypothetical protein LOC78995	135											0		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CTCAGCCTTACACCCCCTACT	0.512													9	40	---	---	---	---	PASS
USP32	84669	broad.mit.edu	37	17	58365979	58365979	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58365979A>G	uc002iyo.1	-	5	762	c.476T>C	c.(475-477)TTC>TCC	p.F159S	USP32_uc010wov.1_Missense_Mutation_p.F159S	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	159					protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CCATCGAGAGAAAGTAAAAGC	0.348													6	135	---	---	---	---	PASS
C17orf80	55028	broad.mit.edu	37	17	71232490	71232490	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71232490T>G	uc002jjm.3	+	3	1063	c.869T>G	c.(868-870)ATC>AGC	p.I290S	C17orf80_uc010wqu.1_Missense_Mutation_p.I290S|C17orf80_uc010dfj.2_Missense_Mutation_p.I290S|C17orf80_uc002jjk.1_Missense_Mutation_p.I290S|C17orf80_uc002jjl.3_Missense_Mutation_p.I290S	NM_017941	NP_060411	Q9BSJ5	CQ080_HUMAN	lung cancer-related protein 8 isoform a	290	Extracellular (Potential).					integral to membrane				skin(1)	1			LUSC - Lung squamous cell carcinoma(166;0.197)			TTAGGTAAAATCCAAGTCATG	0.428													18	62	---	---	---	---	PASS
ZNF253	56242	broad.mit.edu	37	19	20002473	20002473	+	Silent	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20002473C>A	uc002noj.2	+	4	509	c.417C>A	c.(415-417)ACC>ACA	p.T139T	ZNF253_uc002nok.2_Silent_p.T63T|ZNF253_uc002nol.2_RNA	NM_021047	NP_066385	O75346	ZN253_HUMAN	zinc finger protein 253	139					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGACAACTACCCAGAAAGAAA	0.318													9	443	---	---	---	---	PASS
ZNF91	7644	broad.mit.edu	37	19	23543539	23543539	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23543539C>A	uc002nre.2	-	4	2355	c.2242G>T	c.(2242-2244)GGC>TGC	p.G748C	ZNF91_uc002nrd.2_5'Flank|ZNF91_uc010xrj.1_Missense_Mutation_p.G716C	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	748	C2H2-type 22.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				AATGCTTTGCCACATTCTTCA	0.333													4	31	---	---	---	---	PASS
GYS1	2997	broad.mit.edu	37	19	49477487	49477487	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49477487G>C	uc002plp.2	-	12	1773	c.1532C>G	c.(1531-1533)CCT>CGT	p.P511R	GYS1_uc010xzy.1_Missense_Mutation_p.P144R|GYS1_uc010emm.2_Missense_Mutation_p.P447R|GYS1_uc010xzz.1_Missense_Mutation_p.P431R	NM_002103	NP_002094	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle) isoform 1	511					glucose metabolic process|glycogen biosynthetic process	cytosol	glycogen (starch) synthase activity|protein binding			ovary(2)	2		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		GTAGCCCCAAGGCTCATAGTA	0.493													4	18	---	---	---	---	PASS
ZNF616	90317	broad.mit.edu	37	19	52619548	52619548	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52619548A>C	uc002pym.2	-	4	1152	c.869T>G	c.(868-870)ATT>AGT	p.I290S	ZNF616_uc002pyn.2_RNA	NM_178523	NP_848618	Q08AN1	ZN616_HUMAN	zinc finger protein 616	290	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		ACCGGTATGAATTCTCTGATG	0.413													6	105	---	---	---	---	PASS
OVOL2	58495	broad.mit.edu	37	20	18005274	18005274	+	3'UTR	SNP	T	C	C			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18005274T>C	uc002wqi.1	-	4						NM_021220	NP_067043	Q9BRP0	OVOL2_HUMAN	zinc finger protein 339						negative regulation of keratinocyte differentiation|negative regulation of Notch signaling pathway|negative regulation of transcription by competitive promoter binding|regulation of cell cycle|regulation of keratinocyte proliferation|transcription, DNA-dependent	nucleus	DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)	1						ctccccttccttctcctcact	0.408													4	62	---	---	---	---	PASS
CBFA2T2	9139	broad.mit.edu	37	20	32198915	32198915	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32198915A>G	uc002wzg.1	+	4	758	c.221A>G	c.(220-222)AAC>AGC	p.N74S	CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Missense_Mutation_p.N65S|CBFA2T2_uc002wzf.1_RNA|CBFA2T2_uc002wzh.1_Missense_Mutation_p.N45S|CBFA2T2_uc002wzi.1_RNA|CBFA2T2_uc002wzj.1_RNA	NM_005093	NP_005084	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit	74	Pro-rich.					nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2						AATGGCATCAACCATTCTCCT	0.428													15	52	---	---	---	---	PASS
IFNAR1	3454	broad.mit.edu	37	21	34726070	34726070	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34726070C>A	uc002yrn.2	+	10	1568	c.1421C>A	c.(1420-1422)CCT>CAT	p.P474H	IFNAR1_uc011adv.1_Missense_Mutation_p.P405H	NM_000629	NP_000620	P17181	INAR1_HUMAN	interferon-alpha receptor 1 precursor	474	Cytoplasmic (Potential).				JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	integral to plasma membrane	type I interferon receptor activity			central_nervous_system(1)|skin(1)	2					Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)	TCACTTAAACCTTCTTCCAGT	0.333													8	456	---	---	---	---	PASS
COL6A1	1291	broad.mit.edu	37	21	47409686	47409686	+	Silent	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47409686G>T	uc002zhu.1	+	11	1026	c.924G>T	c.(922-924)GGG>GGT	p.G308G		NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor	308	Triple-helical region.				axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)	GGAGCCGTGGGGAGAAGGTGA	0.627													3	8	---	---	---	---	PASS
FAM47B	170062	broad.mit.edu	37	X	34961787	34961787	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34961787C>T	uc004ddi.1	+	1	857	c.839C>T	c.(838-840)GCG>GTG	p.A280V		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	280	Pro-rich.									ovary(3)|breast(1)	4						GATACTGGAGCGTCCCATCTC	0.632													7	19	---	---	---	---	PASS
DLG3	1741	broad.mit.edu	37	X	69720757	69720757	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69720757C>A	uc004dyi.1	+	18	2593	c.2265C>A	c.(2263-2265)AAC>AAA	p.N755K	DLG3_uc004dyj.1_Missense_Mutation_p.N450K|DLG3_uc011mpn.1_Missense_Mutation_p.N303K	NM_021120	NP_066943	Q92796	DLG3_HUMAN	synapse-associated protein 102 isoform a	755	Guanylate kinase-like.				axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)					GGGAAATGAACCGAAGGCAGA	0.398													9	249	---	---	---	---	PASS
ACRC	93953	broad.mit.edu	37	X	70824526	70824526	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70824526G>T	uc004eae.2	+	8	1900	c.1399G>T	c.(1399-1401)GGA>TGA	p.G467*	BCYRN1_uc011mpt.1_Intron	NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	467	Arg/Lys/Pro-rich.					nucleus				ovary(3)	3	Renal(35;0.156)					TGTGACACCTGGTAAGCCAGT	0.488													4	52	---	---	---	---	PASS
COL4A6	1288	broad.mit.edu	37	X	107457373	107457373	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107457373G>A	uc004enw.3	-	6	516	c.413C>T	c.(412-414)CCT>CTT	p.P138L	COL4A6_uc004env.3_Missense_Mutation_p.P137L|COL4A6_uc011msn.1_Missense_Mutation_p.P137L|COL4A6_uc010npk.2_Missense_Mutation_p.P137L	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	138	Triple-helical region.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						ATAGCCATCAGGGCCTGGAAA	0.522									Alport_syndrome_with_Diffuse_Leiomyomatosis				9	40	---	---	---	---	PASS
AMOT	154796	broad.mit.edu	37	X	112024143	112024143	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:112024143C>A	uc004epr.2	-	9	2444	c.2444G>T	c.(2443-2445)CGA>CTA	p.R815L	AMOT_uc004eps.2_Missense_Mutation_p.R406L|AMOT_uc011mtc.1_Missense_Mutation_p.R55L|hsa-mir-4329|MI0015901_5'Flank	NM_001113490	NP_001106962	Q4VCS5	AMOT_HUMAN	angiomotin isoform 1	815					actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction	angiostatin binding|protein binding|receptor activity			ovary(1)	1						CTTGTCGTCTCGCTTTTCTTC	0.502													4	80	---	---	---	---	PASS
PHF6	84295	broad.mit.edu	37	X	133527646	133527646	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133527646C>A	uc004exj.2	+	4	558	c.356C>A	c.(355-357)CCT>CAT	p.P119H	PHF6_uc004exk.2_Missense_Mutation_p.P119H|PHF6_uc011mvk.1_Missense_Mutation_p.P85H|PHF6_uc004exh.2_Missense_Mutation_p.P119H|PHF6_uc010nrr.2_Missense_Mutation_p.P119H|PHF6_uc004exi.2_Missense_Mutation_p.P119H	NM_001015877	NP_001015877	Q8IWS0	PHF6_HUMAN	PHD finger protein 6 isoform 1	119	PHD-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					CGAGAGAAACCTTCACAAGGA	0.323													7	239	---	---	---	---	PASS
CDK11B	984	broad.mit.edu	37	1	1652737	1652738	+	Intron	INS	-	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1652737_1652738insA	uc001agv.1	-						CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc009vkr.2_Intron|CDK11A_uc009vks.2_Intron|CDK11A_uc010nys.1_Intron|CDK11A_uc010nyt.1_Intron|CDK11A_uc010nyu.1_Intron|CDK11A_uc009vkt.1_Intron|CDK11A_uc009vku.1_Intron|CDK11A_uc009vkv.1_Intron|CDK11A_uc001aht.1_Intron|CDK11B_uc001ahu.1_Intron|CDK11B_uc001ahv.1_Intron|CDK11B_uc001ahw.1_Intron	NM_033486	NP_277021	P21127	CD11B_HUMAN	cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1						CAATAGCACACCCCGTCACGTA	0.406													4	2	---	---	---	---	
PRAMEF4	400735	broad.mit.edu	37	1	12942419	12942419	+	Intron	DEL	G	-	-	rs2185333		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12942419delG	uc001aun.2	-							NM_001009611	NP_001009611	O60810	PRAM4_HUMAN	PRAME family member 4											ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ACAttgttttgtttttttttt	0.244													3	3	---	---	---	---	
PRDM2	7799	broad.mit.edu	37	1	14069454	14069456	+	Intron	DEL	AAG	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14069454_14069456delAAG	uc001avi.2	+						PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Intron|PRDM2_uc001avj.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger							Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AATTGTTGAAAAGAAGAAGAAAG	0.350													4	2	---	---	---	---	
NECAP2	55707	broad.mit.edu	37	1	16782519	16782519	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16782519delC	uc001ayo.2	+						NECAP2_uc001ayp.3_Intron|NECAP2_uc010ocd.1_Intron|NECAP2_uc001ayq.2_Intron	NM_018090	NP_060560	Q9NVZ3	NECP2_HUMAN	NECAP endocytosis associated 2 isoform 1						endocytosis|protein transport	clathrin vesicle coat|coated pit|plasma membrane					0		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|Kidney(64;0.000181)|KIRC - Kidney renal clear cell carcinoma(64;0.00268)|STAD - Stomach adenocarcinoma(196;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		Gttttcttttctttttttttt	0.219													5	3	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17242139	17242139	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17242139delA	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		tgtctcaaagaaaaaaaaaaa	0.164													5	3	---	---	---	---	
ZMYM6	9204	broad.mit.edu	37	1	35470913	35470913	+	Intron	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35470913delG	uc001byh.2	-						ZMYM6_uc001byf.1_Intron|ZMYM6_uc010oht.1_Intron|ZMYM6_uc009vup.2_Intron|ZMYM6_uc009vuq.1_Intron|ZMYM6_uc009vur.1_Intron	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258						multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				ATAAGCAAAAGGGTCTCTCTC	0.358													70	31	---	---	---	---	
EIF2C3	192669	broad.mit.edu	37	1	36507533	36507533	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36507533delA	uc001bzp.2	+						EIF2C3_uc001bzq.2_Intron	NM_024852	NP_079128	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TGATGAGAACaaaaaaaaatt	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	43184864	43184864	+	IGR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43184864delA								YBX1 (16847 upstream) : CLDN19 (13900 downstream)																							ACACCTAATTAAAAAaaaagg	0.214													4	2	---	---	---	---	
LEPR	3953	broad.mit.edu	37	1	66064181	66064181	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66064181delT	uc001dci.2	+						LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Intron|LEPR_uc001dck.2_Intron	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1						energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		atgtgcaaactttttttttgg	0.000													7	4	---	---	---	---	
ACADM	34	broad.mit.edu	37	1	76199550	76199551	+	Intron	DEL	TC	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76199550_76199551delTC	uc001dgw.3	+						ACADM_uc010orc.1_Intron|ACADM_uc010ord.1_Intron|ACADM_uc009wbp.2_Intron|ACADM_uc009wbr.2_Intron|ACADM_uc010ore.1_Intron|ACADM_uc010orf.1_Intron|ACADM_uc001dgx.3_Intron|ACADM_uc010org.1_Intron	NM_000016	NP_000007	P11310	ACADM_HUMAN	medium-chain acyl-CoA dehydrogenase isoform a						carnitine biosynthetic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|medium-chain fatty acid catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|identical protein binding|medium-chain-acyl-CoA dehydrogenase activity			breast(2)|ovary(1)|skin(1)	4						GTTCTGACTGTCCTTTGGAGGA	0.450													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88702905	88702908	+	IGR	DEL	CTCC	-	-	rs142556581		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88702905_88702908delCTCC								LMO4 (888302 upstream) : PKN2 (447014 downstream)																							TCGCCCACAGCTCCCTTCTCAAAG	0.495													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	97410430	97410430	+	IGR	DEL	A	-	-	rs35323397		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97410430delA								PTBP2 (129831 upstream) : DPYD (132872 downstream)																							AGTGGTTGACAAAAAAAAGCT	0.393													4	2	---	---	---	---	
ADORA3	140	broad.mit.edu	37	1	112028674	112028674	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112028674delC	uc001ebf.2	-						ADORA3_uc001ebg.3_Intron	NM_020683	NP_065734	P33765	AA3R_HUMAN	adenosine A3 receptor isoform 1						activation of adenylate cyclase activity|inflammatory response|regulation of heart contraction	integral to plasma membrane	adenosine receptor activity, G-protein coupled			ovary(2)|large_intestine(1)|skin(1)	4		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)	GGCCAATGAACCCCTTCCTCA	0.478													4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145352463	145352464	+	Intron	INS	-	GC	GC	rs1973810		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145352463_145352464insGC	uc001end.3	+						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_uc010oyq.1_Intron|NBPF10_uc010oyr.1_Intron|NBPF10_uc010oyn.1_Intron|NBPF10_uc010oyp.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		tgtgtgtgtgtgtgtgtgtgtg	0.243													9	4	---	---	---	---	
GON4L	54856	broad.mit.edu	37	1	155720106	155720106	+	3'UTR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155720106delA	uc001flz.2	-	32					MSTO2P_uc010pgp.1_RNA|GON4L_uc001flx.1_3'UTR|GON4L_uc009wrg.1_RNA|GON4L_uc001fly.1_3'UTR|GON4L_uc009wrh.1_3'UTR|GON4L_uc001fma.1_3'UTR	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					CCATCAGACCAAAAAAAAGTA	0.403													4	2	---	---	---	---	
NCSTN	23385	broad.mit.edu	37	1	160323547	160323547	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160323547delT	uc001fvx.2	+						NCSTN_uc001fvy.2_Intron|NCSTN_uc010pjf.1_Intron|NCSTN_uc001fvz.2_Intron|NCSTN_uc010pjg.1_Intron	NM_015331	NP_056146	Q92542	NICA_HUMAN	nicastrin precursor						amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane|melanosome	protein binding			ovary(1)|lung(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGGTTATCTGTTTGGCATTCA	0.413													4	2	---	---	---	---	
F5	2153	broad.mit.edu	37	1	169529137	169529138	+	Intron	DEL	GC	-	-	rs10560418		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169529137_169529138delGC	uc001ggg.1	-						F5_uc010plr.1_Intron	NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	TATGGCCTGAGCGTGTATGTAT	0.396													3	3	---	---	---	---	
SLC9A11	284525	broad.mit.edu	37	1	173523646	173523646	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173523646delA	uc001giz.2	-						SLC9A11_uc009wwe.2_Intron|SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2						tggtggagggaaaaaaaaacc	0.020													4	2	---	---	---	---	
NPHS2	7827	broad.mit.edu	37	1	179542353	179542353	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179542353delC	uc001gmq.3	-						NPHS2_uc009wxi.2_Intron	NM_014625	NP_055440	Q9NP85	PODO_HUMAN	podocin						excretion	integral to plasma membrane	protein binding				0						AGAAAGGTCACCACCAAATTG	0.348													4	2	---	---	---	---	
SMG7	9887	broad.mit.edu	37	1	183519210	183519210	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183519210delA	uc001gqg.2	+						SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Intron	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						AAGGAAATAGAAAAAAAAAAA	0.299													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	205917450	205917450	+	IGR	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205917450delC								SLC26A9 (4862 upstream) : FAM72A (221461 downstream)																							GAGGTGAGTTCCAGGTGGTTA	0.547													4	2	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207097551	207097552	+	5'Flank	DEL	GT	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207097551_207097552delGT	uc001hey.2	-						FAIM3_uc010prz.1_5'Flank|FAIM3_uc010psa.1_5'Flank|FAIM3_uc010psb.1_5'Flank	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					gtgtccatgagtgtgtgtgtgc	0.000													6	3	---	---	---	---	
PTPN14	5784	broad.mit.edu	37	1	214581343	214581344	+	Intron	DEL	TC	-	-	rs72066875		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214581343_214581344delTC	uc001hkk.1	-						PTPN14_uc010pty.1_Intron	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		CTCTGCTCCTTCTCTCTCTGTC	0.505													4	2	---	---	---	---	
PTPN14	5784	broad.mit.edu	37	1	214626918	214626919	+	Intron	INS	-	CATGG	CATGG	rs146570036	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214626918_214626919insCATGG	uc001hkk.1	-						PTPN14_uc010pty.1_Intron	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		taactacatcataagtggtacc	0.104													4	3	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236707828	236707829	+	Intron	INS	-	G	G	rs144740089	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236707828_236707829insG	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			CTGATTTTAAAGGGTTTTTTTT	0.411													9	5	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	245970654	245970654	+	Intron	DEL	A	-	-	rs111653396		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245970654delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		ACCaacaaagaaaaaaaaaag	0.368													1	5	---	---	---	---	
AHCTF1	25909	broad.mit.edu	37	1	247063196	247063197	+	Intron	DEL	AT	-	-	rs148637144		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247063196_247063197delAT	uc001ibu.1	-						AHCTF1_uc001ibv.1_Intron|AHCTF1_uc009xgs.1_5'Flank	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS						cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TTTATAAAACATATAAATACTA	0.233													3	4	---	---	---	---	
GRHL1	29841	broad.mit.edu	37	2	10138988	10138989	+	Intron	INS	-	TG	TG	rs113984108		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10138988_10138989insTG	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron	NM_198182	NP_937825	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		acacatatatatacgtatatat	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45180422	45180422	+	IGR	DEL	C	-	-	rs11355585		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45180422delC								SIX3 (8032 upstream) : SIX2 (51903 downstream)																							TCCCAGTGGGCCTGGGAATCG	0.532													1	5	---	---	---	---	
SPTBN1	6711	broad.mit.edu	37	2	54848970	54848970	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54848970delC	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron|SPTBN1_uc002rxx.2_Intron	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			GTTGAAAAGGCCCCAGCATCG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	56386062	56386062	+	Intron	DEL	A	-	-	rs111318970		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56386062delA	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																		cagcttggggaaaaaaaaaaa	0.000													11	5	---	---	---	---	
AAK1	22848	broad.mit.edu	37	2	69848612	69848612	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69848612delA	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron|AAK1_uc010fdm.1_Intron	NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						aaactccaccaaaaaaaaaaa	0.035													5	3	---	---	---	---	
GMCL1	64395	broad.mit.edu	37	2	70092373	70092374	+	Intron	DEL	AG	-	-	rs78263806	byFrequency	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70092373_70092374delAG	uc002sfu.2	+							NM_178439	NP_848526	Q96IK5	GMCL1_HUMAN	germ cell-less						cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3						CCAGAAATTAAGATAAAGAAGA	0.342													6	3	---	---	---	---	
TET3	200424	broad.mit.edu	37	2	74319875	74319875	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74319875delC	uc002skb.3	+							NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3								metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						GGACACAGCACCACAGCCCTC	0.572													4	2	---	---	---	---	
USP39	10713	broad.mit.edu	37	2	85871847	85871847	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85871847delT	uc002sqe.2	+						USP39_uc002sqb.2_Intron|USP39_uc010ysu.1_Intron|USP39_uc010ysv.1_Intron|USP39_uc010fgn.1_Intron|USP39_uc002sqf.2_Intron|USP39_uc002sqg.2_Intron|USP39_uc010fgo.2_Intron	NM_006590	NP_006581	Q53GS9	SNUT2_HUMAN	ubiquitin specific protease 39						spliceosome assembly|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)	1						cCTGTCATTCTTTTTTTTTTT	0.199													5	6	---	---	---	---	
THNSL2	55258	broad.mit.edu	37	2	88473897	88473898	+	Intron	INS	-	A	A	rs138356060	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88473897_88473898insA	uc002ssz.3	+						THNSL2_uc002ssv.2_Intron|THNSL2_uc002ssw.3_Intron|THNSL2_uc002ssx.3_Intron|THNSL2_uc002sta.3_Intron|THNSL2_uc002ssy.3_Intron|THNSL2_uc010fhe.2_5'Flank	NM_018271	NP_060741	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2						threonine biosynthetic process		threonine synthase activity			ovary(1)	1						TGAAGAAGTATAAAAAATGAAA	0.356													4	3	---	---	---	---	
GGT8P	645367	broad.mit.edu	37	2	91968430	91968430	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91968430delC	uc010fho.1	+							NR_003503				Homo sapiens cDNA FLJ31276 fis, clone KIDNE2006376, weakly similar to GAMMA-GLUTAMYLTRANSPEPTIDASE 1 PRECURSOR (EC 2.3.2.2).												0						GGCTCTCTCTCCCCAGGAGGG	0.632													4	2	---	---	---	---	
TMEM131	23505	broad.mit.edu	37	2	98374010	98374010	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98374010delT	uc002syh.3	-						TMEM131_uc002syg.2_Intron	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6						ATGTTTCTGAtttttttgaga	0.184													4	2	---	---	---	---	
LONRF2	164832	broad.mit.edu	37	2	100906570	100906571	+	Intron	INS	-	AAAT	AAAT	rs139366121	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100906570_100906571insAAAT	uc002tal.3	-						LONRF2_uc010yvs.1_Intron	NM_198461	NP_940863	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2						ccttgactcaaaaataaacaaa	0.124													5	7	---	---	---	---	
LIMS1	3987	broad.mit.edu	37	2	109297390	109297393	+	Intron	DEL	TTCT	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109297390_109297393delTTCT	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.2_Intron|LIMS1_uc002tei.2_Intron|LIMS1_uc002tej.2_Intron|LIMS1_uc002tek.3_Intron	NM_004987	NP_004978	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0						CTGTTCCCTGTTCTTTCTTCTATT	0.338													7	5	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	125622653	125622654	+	Intron	DEL	CA	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125622653_125622654delCA	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		GTGATAACACCACACACACACA	0.267													6	3	---	---	---	---	
WDR33	55339	broad.mit.edu	37	2	128568364	128568364	+	Intron	DEL	A	-	-	rs35127400		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128568364delA	uc002tpg.1	-						WDR33_uc002tph.1_Intron|WDR33_uc002tpi.1_Intron	NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1						postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CCTTAGTTCTAACCATGGCCG	0.567													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131465789	131465790	+	IGR	INS	-	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131465789_131465790insA								C2orf14 (16527 upstream) : GPR148 (20933 downstream)																							caaaaaaaaagaaaaaaaaaga	0.054													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	144675106	144675106	+	IGR	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144675106delC								ARHGAP15 (149186 upstream) : GTDC1 (28477 downstream)																							atgcaatcaacccCACTTTAT	0.239													4	2	---	---	---	---	
PLA2R1	22925	broad.mit.edu	37	2	160840719	160840719	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160840719delT	uc002ube.1	-						PLA2R1_uc010zcp.1_Intron|PLA2R1_uc002ubf.2_Intron	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor						endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3						TGGGAGGAAGTAATATTTACT	0.199													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	165827404	165827405	+	IGR	DEL	CA	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165827404_165827405delCA								SLC38A11 (15369 upstream) : SCN3A (116627 downstream)																							CGCATATGTGCACACACACACA	0.426													4	2	---	---	---	---	
SCN1A	6323	broad.mit.edu	37	2	166868923	166868923	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166868923delT	uc010zcz.1	-						SCN1A_uc002udo.3_Intron|SCN1A_uc010fpk.2_Intron	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	TTACTGTTACTTTTTTTTTTT	0.284													4	3	---	---	---	---	
SCN9A	6335	broad.mit.edu	37	2	167138537	167138537	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167138537delC	uc010fpl.2	-						uc002udp.2_Intron|SCN9A_uc002udr.1_Intron|SCN9A_uc002uds.1_Intron|SCN9A_uc002udt.1_Intron	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)	atagtgcttgcttcatattct	0.104													4	2	---	---	---	---	
ABCB11	8647	broad.mit.edu	37	2	169803859	169803859	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169803859delT	uc002ueo.1	-						ABCB11_uc010zda.1_Intron|ABCB11_uc010zdb.1_Intron	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),						bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)	ctcacatccattttttttttt	0.164													5	3	---	---	---	---	
GORASP2	26003	broad.mit.edu	37	2	171812743	171812744	+	Intron	DEL	GA	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171812743_171812744delGA	uc002ugk.2	+						GORASP2_uc002ugj.2_Intron|GORASP2_uc010zdl.1_Intron|GORASP2_uc010zdm.1_Intron|GORASP2_uc002ugl.2_Intron|GORASP2_uc002ugm.2_Intron	NM_015530	NP_056345	Q9H8Y8	GORS2_HUMAN	golgi reassembly stacking protein 2							Golgi membrane				breast(1)|central_nervous_system(1)	2						GAAGTGACAGGAGAGAGAGATG	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173566360	173566360	+	IGR	DEL	T	-	-	rs11350083		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173566360delT								PDK1 (76537 upstream) : LOC91149 (21560 downstream)																							GTTTATCCTGttttttttttt	0.249													6	6	---	---	---	---	
SAG	6295	broad.mit.edu	37	2	234215898	234215899	+	5'Flank	INS	-	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234215898_234215899insA	uc002vuh.2	+						SAG_uc002vug.2_5'Flank|SAG_uc010zmq.1_5'Flank	NM_000541	NP_000532	P10523	ARRS_HUMAN	S-arrestin						rhodopsin mediated phototransduction|rhodopsin mediated signaling pathway		protein phosphatase inhibitor activity			ovary(1)	1		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		aaaaacaaaacaaaaaaaagaa	0.238													4	2	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240082222	240082223	+	Intron	DEL	CA	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240082222_240082223delCA	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron|HDAC4_uc010fyy.2_Intron|HDAC4_uc010znz.1_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		tgctttctctcacagtcgattc	0.248													8	7	---	---	---	---	
RFTN1	23180	broad.mit.edu	37	3	16365611	16365612	+	Intron	INS	-	G	G	rs140244689	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16365611_16365612insG	uc003cay.2	-						RFTN1_uc010hes.2_Intron|OXNAD1_uc003cax.2_Intron|OXNAD1_uc011awb.1_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4						AGAAGATCACTGTTTTTTTTTT	0.302													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34154781	34154781	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34154781delT								PDCD6IP (243587 upstream) : None (None downstream)																							AAGGTGTTTGTTTTTTTTTTC	0.229													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	38192405	38192405	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38192405delT								MYD88 (7895 upstream) : OXSR1 (14621 downstream)																							AGCACCTCTCTTTTTTTTTGA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	39746932	39746932	+	IGR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39746932delA								MOBP (179077 upstream) : MYRIP (104371 downstream)																							GAGCCCCCACAAAAAAGCTGA	0.418													4	2	---	---	---	---	
RAD54L2	23132	broad.mit.edu	37	3	51694294	51694294	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51694294delT	uc011bdt.1	+						RAD54L2_uc003dbh.2_Intron|RAD54L2_uc011bdu.1_Intron|RAD54L2_uc003dbj.2_Intron	NM_015106	NP_055921	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2							nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		TTTTGTGTGGTTTTTTTTTTT	0.159													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	53234960	53234961	+	IGR	INS	-	G	G	rs144113410	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53234960_53234961insG								PRKCD (8229 upstream) : TKT (23763 downstream)																							GATGGCATGTTGGGGGCTCTGC	0.505													5	3	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54872311	54872311	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54872311delA	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		ATCAGTGTTTAATTTTCAAGA	0.398													6	5	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	55002146	55002146	+	Intron	DEL	T	-	-	rs112483531		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55002146delT	uc003dhf.2	+						CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		ATCTTTTGAATTTTTTTTTTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	98891693	98891694	+	IGR	INS	-	C	C	rs145792381	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98891693_98891694insC								DCBLD2 (271160 upstream) : COL8A1 (465760 downstream)																							cccacactctgctgtttctcac	0.000													4	6	---	---	---	---	
ZDHHC23	254887	broad.mit.edu	37	3	113673485	113673485	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113673485delT	uc003eau.2	+						ZDHHC23_uc003eav.2_Intron|ZDHHC23_uc003eaw.1_5'Flank	NM_173570	NP_775841	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC domain containing 23							integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2						ACTTGTGGGGTTTTTTTTTTC	0.303													8	4	---	---	---	---	
ZBTB20	26137	broad.mit.edu	37	3	114103000	114103001	+	5'Flank	DEL	TC	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114103000_114103001delTC	uc003ebi.2	-						ZBTB20_uc003ebj.2_Intron|ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron|uc003ebo.1_Intron	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		tctctcattttctctctctctc	0.292											OREG0015721	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126820990	126820991	+	IGR	DEL	CT	-	-	rs11924383	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126820990_126820991delCT								PLXNA1 (64762 upstream) : TPRA1 (470917 downstream)																							GTTTcacacactcacacacaca	0.272													4	2	---	---	---	---	
EEFSEC	60678	broad.mit.edu	37	3	127965305	127965305	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127965305delT	uc003eki.2	+						EEFSEC_uc003ekj.2_Intron	NM_021937	NP_068756	P57772	SELB_HUMAN	eukaryotic elongation factor,							cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1						AGTACGAAACTTTTTTTTTTC	0.353													4	3	---	---	---	---	
IFT122	55764	broad.mit.edu	37	3	129183763	129183764	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129183763_129183764insT	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc003emr.2_Intron|IFT122_uc011bla.1_Intron|IFT122_uc011bkx.1_Intron|IFT122_uc011bkz.1_Intron	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2						ATTTGTATGGATTTTTTTTTTA	0.391													8	4	---	---	---	---	
NEK11	79858	broad.mit.edu	37	3	130871047	130871047	+	Intron	DEL	T	-	-	rs150507740	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130871047delT	uc003eny.2	+						NEK11_uc003enx.2_Intron|NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.1_Intron|NEK11_uc011blm.1_Intron|NEK11_uc010hto.1_Intron	NM_024800	NP_079076	Q8NG66	NEK11_HUMAN	NIMA-related kinase 11 isoform 1						cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6						ACTTTTTTGGTTTTTTTTTTG	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139550401	139550401	+	IGR	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139550401delG								NMNAT3 (153561 upstream) : CLSTN2 (103626 downstream)																							ttggtgttctgggggtgatgc	0.085													6	4	---	---	---	---	
XRN1	54464	broad.mit.edu	37	3	142143963	142143963	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142143963delA	uc003eus.2	-						XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron|XRN1_uc003euv.1_Intron|XRN1_uc003euw.2_Intron|XRN1_uc011bnh.1_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						TTGTGTCTCCAATATTTGTTG	0.284													19	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168417516	168417516	+	IGR	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168417516delG								MIR551B (147779 upstream) : C3orf50 (110068 downstream)																							GAGTCAGTTAGAAGGAGTAAG	0.413													4	2	---	---	---	---	
LYAR	55646	broad.mit.edu	37	4	4283955	4283955	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4283955delT	uc011bvy.1	-						LYAR_uc011bvx.1_5'Flank|LYAR_uc003ght.2_Intron	NM_001145725	NP_001139197	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive homolog							nucleolus	metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AATAGGGTAGTTTTTTTAAAT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6678589	6678589	+	IGR	DEL	G	-	-	rs35072066		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6678589delG								LOC93622 (815 upstream) : S100P (16977 downstream)																							ttctaggcacggggaacaagt	0.204													4	5	---	---	---	---	
NCAPG	64151	broad.mit.edu	37	4	17814927	17814927	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17814927delA	uc003gpp.2	+						NCAPG_uc011bxj.1_Intron|DCAF16_uc003gpn.2_5'Flank	NM_022346	NP_071741	Q9BPX3	CND3_HUMAN	chromosome condensation protein G						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	protein binding			large_intestine(1)	1				STAD - Stomach adenocarcinoma(129;0.18)		cacccagcttaaaaaaaaaag	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25056418	25056419	+	IGR	INS	-	AG	AG	rs147732376	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25056418_25056419insAG								LGI2 (24004 upstream) : SEPSECS (65209 downstream)																							ctgaggtggccagagagagaga	0.000													5	4	---	---	---	---	
CLOCK	9575	broad.mit.edu	37	4	56315294	56315295	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56315294_56315295insT	uc003haz.1	-						CLOCK_uc003hba.1_Intron|CLOCK_uc010igu.1_Intron	NM_004898	NP_004889	O15516	CLOCK_HUMAN	clock						circadian rhythm|photoperiodism|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|transcription factor complex	DNA binding|histone acetyltransferase activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			ATTGGTATTTGAACTTAGACAT	0.307													8	4	---	---	---	---	
DCK	1633	broad.mit.edu	37	4	71857841	71857841	+	5'Flank	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71857841delA	uc003hfx.2	+						DCK_uc011cbb.1_5'Flank	NM_000788	NP_000779	P27707	DCK_HUMAN	deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	GATGCATTTCAGGTCTGATGA	0.393													4	2	---	---	---	---	
LIN54	132660	broad.mit.edu	37	4	83862868	83862868	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83862868delC	uc003hnx.3	-						LIN54_uc003hnz.3_Intron|LIN54_uc003hny.3_Intron|LIN54_uc010ijt.2_Intron|LIN54_uc010iju.2_Intron|LIN54_uc010ijv.2_Intron	NM_194282	NP_919258	Q6MZP7	LIN54_HUMAN	lin-54 homolog isoform a						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Hepatocellular(203;0.114)				GGTGAAAGGACCATGACTTAC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	138321176	138321180	+	IGR	DEL	CACAT	-	-	rs144384378		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138321176_138321180delCACAT								None (None upstream) : PCDH18 (118896 downstream)																							AGTCTCCAAGCACATCATGGAGTGG	0.390													2	6	---	---	---	---	
ETFDH	2110	broad.mit.edu	37	4	159593988	159593988	+	Intron	DEL	A	-	-	rs111870477		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159593988delA	uc003iqb.2	+						C4orf46_uc003iqa.2_5'Flank|C4orf46_uc010iqp.1_5'Flank|ETFDH_uc010iqq.2_Intron|ETFDH_uc011cjg.1_Intron|ETFDH_uc010iqr.2_Intron	NM_004453	NP_004444	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase						fatty acid beta-oxidation using acyl-CoA dehydrogenase|respiratory electron transport chain|response to oxidative stress|transport	integral to mitochondrial inner membrane|mitochondrial matrix	4 iron, 4 sulfur cluster binding|electron carrier activity|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding|metal ion binding|oxidoreductase activity, oxidizing metal ions with flavin as acceptor|ubiquinone binding			large_intestine(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		TTGGAAATGGAAAAAAAAAAA	0.453											OREG0016379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190545398	190545399	+	IGR	INS	-	ATT	ATT	rs35790619		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190545398_190545399insATT								None (None upstream) : FRG1 (316575 downstream)																							ttgtggaagacgttgtgatcac	0.119													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6557700	6557700	+	IGR	DEL	T	-	-	rs11298047		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6557700delT								UBE2QL1 (64995 upstream) : LOC255167 (24587 downstream)																							aaattccaaattccttgaccg	0.000													3	4	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10430398	10430398	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10430398delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						gagagggaggttttttttttt	0.000													6	3	---	---	---	---	
FAM134B	54463	broad.mit.edu	37	5	16574312	16574313	+	Intron	INS	-	T	T	rs35799955		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16574312_16574313insT	uc003jfs.2	-							NM_001034850	NP_001030022	Q9H6L5	F134B_HUMAN	hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3						AATCTGGGGTGCCTCAGCAGGA	0.475													4	2	---	---	---	---	
MIER3	166968	broad.mit.edu	37	5	56260617	56260618	+	Intron	INS	-	C	C	rs146798367	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56260617_56260618insC	uc003jre.2	-						MIER3_uc003jrf.2_Intron|MIER3_uc003jrg.2_Intron			Q7Z3K6	MIER3_HUMAN	Homo sapiens cDNA FLJ61352 complete cds, weakly similar to Mesoderm induction early response protein 1.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		GATGAAGACCACTGCCCCCACT	0.510													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	61549034	61549035	+	IGR	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61549034_61549035insT								FLJ37543 (546672 upstream) : KIF2A (52954 downstream)																							agatcttatggtttataagggg	0.000													4	2	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80733496	80733496	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80733496delT	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		TTCCCAATCGTTTTTTTTTTA	0.289													4	2	---	---	---	---	
CHD1	1105	broad.mit.edu	37	5	98232687	98232687	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98232687delA	uc003knf.2	-							NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	AACATATTTTAAAAAGGCAAC	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	106571947	106571947	+	IGR	DEL	C	-	-	rs147010693		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106571947delC								None (None upstream) : EFNA5 (140644 downstream)																							ttaccctcttcttgctctata	0.000													2	4	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156742324	156742324	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156742324delA	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	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)			attccactggaaaaaaaaacg	0.100													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163008304	163008304	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163008304delT								MAT2B (61971 upstream) : None (None downstream)																							TCTATTATGATTTTTCAGTTT	0.308													4	2	---	---	---	---	
FAM153C	653316	broad.mit.edu	37	5	177457851	177457851	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177457851delT	uc011dge.1	+						FAM153C_uc003mig.1_Intron	NM_001079527	NP_001072995			hypothetical protein LOC653316												0	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCAATGCCAAttttttttttt	0.139													14	8	---	---	---	---	
RREB1	6239	broad.mit.edu	37	6	7240518	7240518	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7240518delT	uc003mxc.2	+						RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				TCATTGATGGTTTTTTTTTTT	0.318													5	4	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38825011	38825011	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38825011delC	uc003ooe.1	+							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						atggaagtatccaatagtctc	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	40219254	40219255	+	IGR	DEL	GA	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40219254_40219255delGA								MOCS1 (317000 upstream) : TDRG1 (126908 downstream)																							AGAGGTGAAGGATGTATGCTTT	0.371													4	2	---	---	---	---	
CENPQ	55166	broad.mit.edu	37	6	49437668	49437669	+	Intron	DEL	AA	-	-	rs143266771		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49437668_49437669delAA	uc003ozh.1	+							NM_018132	NP_060602	Q7L2Z9	CENPQ_HUMAN	centromere protein Q						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)					TTATTCTGATAAGAGTGAAAAT	0.208													5	4	---	---	---	---	
DST	667	broad.mit.edu	37	6	56392018	56392019	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56392018_56392019insT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GATCATTTTCCTTTTTTTTTTC	0.312													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57514537	57514538	+	IGR	INS	-	TCA	TCA	rs142174162		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57514537_57514538insTCA								PRIM2 (1162 upstream) : GUSBL2 (731621 downstream)																							TGCTACTCCCTTCATCATTTGT	0.342													3	3	---	---	---	---	
SNAP91	9892	broad.mit.edu	37	6	84303845	84303845	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84303845delA	uc011dze.1	-						SNAP91_uc011dzd.1_Intron|SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		ATAGCATTAGAAAAAAAAACA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	94502515	94502517	+	IGR	DEL	AGA	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94502515_94502517delAGA								TSG1 (16316 upstream) : None (None downstream)																							acgttgtattagaagaagaagaa	0.133													4	2	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112462354	112462354	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112462354delT	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TAGAAATGACTTTTTTTTTTC	0.313													4	3	---	---	---	---	
C6orf170	221322	broad.mit.edu	37	6	121452506	121452506	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121452506delA	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron|C6orf170_uc010kej.1_Intron|C6orf170_uc003pyp.1_Intron	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)		ACTGAATATGAAAAAAAAAAC	0.259													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	131702648	131702649	+	IGR	DEL	GT	-	-	rs144730495		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131702648_131702649delGT								AKAP7 (97975 upstream) : ARG1 (191716 downstream)																							gtgtgcgtgagtgtgtgtgtgt	0.376													3	3	---	---	---	---	
AHI1	54806	broad.mit.edu	37	6	135726363	135726364	+	Intron	INS	-	GG	GG			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135726363_135726364insGG	uc003qgi.2	-						AHI1_uc003qgf.2_Intron|AHI1_uc003qgg.2_Intron|AHI1_uc003qgh.2_Intron|AHI1_uc003qgj.2_Intron|AHI1_uc003qgk.3_Intron|AHI1_uc003qgl.3_Intron	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a							adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		GTTATCTGCCTCAAGAAAAACT	0.351													4	4	---	---	---	---	
MAP3K5	4217	broad.mit.edu	37	6	136960507	136960507	+	Intron	DEL	C	-	-	rs113792582		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136960507delC	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron|MAP3K5_uc011edk.1_Intron	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TTAAAGAAAACCCCCCCCCAA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	159576923	159576923	+	IGR	DEL	G	-	-	rs5881314		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159576923delG								TAGAP (110739 upstream) : FNDC1 (13506 downstream)																							tattttctctgggaagtatga	0.000													3	4	---	---	---	---	
PACRG	135138	broad.mit.edu	37	6	163283275	163283275	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163283275delC	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623	Q96M98	PACRG_HUMAN	parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		CCTTGTACCACCTTTCACGAG	0.488													4	2	---	---	---	---	
GARS	2617	broad.mit.edu	37	7	30665558	30665558	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30665558delT	uc003tbm.2	+							NM_002047	NP_002038	P41250	SYG_HUMAN	glycyl-tRNA synthetase						cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)	TTGTTTTTGGTTTTACCTTGA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41976468	41976468	+	IGR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41976468delA								LOC285954 (157494 upstream) : GLI3 (24082 downstream)																							tttactcgataaatattttgc	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68376707	68376707	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68376707delT								None (None upstream) : AUTS2 (687198 downstream)																							ATTATTTTTGTTTTTTTTTCT	0.229													4	2	---	---	---	---	
COG5	10466	broad.mit.edu	37	7	106921567	106921567	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106921567delT	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						AGGAGGGCCATTTTTTTGTTA	0.289													5	3	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127700754	127700755	+	Intron	INS	-	GG	GG			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127700754_127700755insGG	uc003vmi.2	+						SND1_uc010lle.2_Intron|uc010llg.1_RNA	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						TGGTAGTGGCAGGAGTCTCAAA	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	141486063	141486063	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141486063delT								TAS2R4 (6875 upstream) : TAS2R5 (3954 downstream)																							GACAGGGTGATTTTTTGGGGG	0.393													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157710340	157710341	+	Intron	INS	-	T	T	rs143693345	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157710340_157710341insT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCAGTTTTCAATTGTTCAAATG	0.297													5	6	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3314701	3314701	+	Intron	DEL	C	-	-	rs146368819		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3314701delC	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TTCCTGGACTCCTCATCGTGG	0.592													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	5821956	5821957	+	IGR	DEL	AC	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5821956_5821957delAC								CSMD1 (969628 upstream) : MCPH1 (442164 downstream)																							ttcatcctctacacacacaccg	0.139													4	2	---	---	---	---	
DPYSL2	1808	broad.mit.edu	37	8	26439768	26439769	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26439768_26439769insT	uc003xfb.1	+						DPYSL2_uc003xfa.2_Intron|DPYSL2_uc011lag.1_Intron|DPYSL2_uc010luk.1_Intron|DPYSL2_uc011lah.1_Intron	NM_001386	NP_001377	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		CAAAGCAACAATTAATGTACAC	0.317													6	3	---	---	---	---	
PPP2CB	5516	broad.mit.edu	37	8	30643538	30643539	+	3'UTR	INS	-	CTAT	CTAT	rs3832549		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30643538_30643539insCTAT	uc003xik.2	-	8						NM_004156	NP_004147	P62714	PP2AB_HUMAN	protein phosphatase 2, catalytic subunit, beta						protein dephosphorylation	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex|spindle pole	metal ion binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)	GTTAGACTGACCTAGAACATAG	0.371													5	6	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32613674	32613675	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32613674_32613675insT	uc003xiv.2	+						NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc011lbg.1_Intron|NRG1_uc011lbh.1_Intron|NRG1_uc003xja.2_Intron	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		GTGTTATCCTATTTTTTTCTTG	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33840739	33840740	+	IGR	INS	-	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33840739_33840740insA								DUSP26 (383300 upstream) : None (None downstream)																							ttttattatttaaaaaaaaaGA	0.228													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37347317	37347317	+	IGR	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37347317delG								KCNU1 (553676 upstream) : ZNF703 (205984 downstream)																							AAGAAAATGAGGCCACTGTCT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	42899748	42899748	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42899748delT								HOOK3 (14067 upstream) : FNTA (11694 downstream)																							cacttttgccttttttttttt	0.000													4	3	---	---	---	---	
PXDNL	137902	broad.mit.edu	37	8	52366468	52366469	+	Intron	INS	-	ATATAT	ATATAT	rs143004029	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52366468_52366469insATATAT	uc003xqu.3	-							NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				AAATATTACACATATATATATA	0.252													3	3	---	---	---	---	
ARFGEF1	10565	broad.mit.edu	37	8	68172424	68172424	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68172424delT	uc003xxo.1	-						ARFGEF1_uc003xxl.1_Intron	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GTATGAAGTATTTTTTTATCC	0.294													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	69002479	69002480	+	Intron	INS	-	TTA	TTA			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69002479_69002480insTTA	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						TATGTTTCTGGTCTTCTCATTT	0.287													6	3	---	---	---	---	
PRDM14	63978	broad.mit.edu	37	8	70979903	70979904	+	Intron	DEL	TA	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70979903_70979904delTA	uc003xym.2	-							NM_024504	NP_078780	Q9GZV8	PRD14_HUMAN	PR domain containing 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			tttcctgtactatattcctaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72103465	72103465	+	IGR	DEL	A	-	-	rs113731029		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72103465delA								XKR9 (455289 upstream) : EYA1 (6205 downstream)																							aaatgtggggaaaaaaccagc	0.000													4	2	---	---	---	---	
CNBD1	168975	broad.mit.edu	37	8	88261728	88261728	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88261728delA	uc003ydy.2	+							NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1											ovary(3)	3						acatttccacaaaatgcacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102271638	102271638	+	IGR	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102271638delC								ZNF706 (53678 upstream) : NACAP1 (102384 downstream)																							gccaagttttcccaagcagcc	0.139													4	2	---	---	---	---	
GRHL2	79977	broad.mit.edu	37	8	102589410	102589410	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102589410delT	uc010mbu.2	+							NM_024915	NP_079191	Q6ISB3	GRHL2_HUMAN	transcription factor CP2-like 3							cytoplasm|nucleus	DNA binding			ovary(2)|skin(1)	3	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			TGTAGGACTCTTTTTTTTTTC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	112587110	112587111	+	IGR	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112587110_112587111insT								None (None upstream) : CSMD3 (648050 downstream)																							tacacagaatatttccttcagc	0.000													4	2	---	---	---	---	
FBXO32	114907	broad.mit.edu	37	8	124525887	124525887	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124525887delC	uc003yqr.2	-						FBXO32_uc003yqq.2_Intron|FBXO32_uc010mdk.2_Intron	NM_058229	NP_478136	Q969P5	FBX32_HUMAN	F-box only protein 32 isoform 1											skin(3)|breast(2)|lung(1)	6	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			TCATTGTTCTCCCAGCAGCCA	0.383													4	2	---	---	---	---	
ANXA13	312	broad.mit.edu	37	8	124706232	124706232	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124706232delT	uc003yqu.2	-						ANXA13_uc003yqt.2_Intron	NM_004306	NP_004297	P27216	ANX13_HUMAN	annexin A13 isoform a						cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			TGGTTTTGCCTTTTTTTTTTT	0.483													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138873158	138873159	+	IGR	INS	-	C	C	rs151139614	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138873158_138873159insC								None (None upstream) : FAM135B (269109 downstream)																							cacacaaaagacaaggtaaggg	0.094													2	4	---	---	---	---	
HAUS6	54801	broad.mit.edu	37	9	19056596	19056596	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19056596delT	uc003znk.2	-						HAUS6_uc011lmz.1_Intron	NM_017645	NP_060115	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2						CCCAGAGTACttttttttttt	0.169													7	5	---	---	---	---	
ELAVL2	1993	broad.mit.edu	37	9	23693124	23693124	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23693124delA	uc003zpu.2	-						ELAVL2_uc003zps.2_Intron|ELAVL2_uc003zpt.2_Intron|ELAVL2_uc003zpv.2_Intron|ELAVL2_uc003zpw.2_Intron	NM_004432	NP_004423	Q12926	ELAV2_HUMAN	ELAV (embryonic lethal, abnormal vision,						regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		AATATCATCCACAATAGCAAA	0.383													5	3	---	---	---	---	
PAX5	5079	broad.mit.edu	37	9	36962223	36962224	+	Intron	INS	-	A	A	rs151228835	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36962223_36962224insA	uc003zzo.1	-						PAX5_uc011lpt.1_Intron|PAX5_uc011lpu.1_Intron|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Intron|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Intron|PAX5_uc011lqa.1_Intron|PAX5_uc010mlq.1_Intron|PAX5_uc011lqb.1_Intron|PAX5_uc010mlo.1_Intron|PAX5_uc010mlp.1_Intron|PAX5_uc011lqc.1_Intron|PAX5_uc010mlr.1_Intron	NM_016734	NP_057953	Q02548	PAX5_HUMAN	paired box 5						cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(19)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2)	147		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		GAGAGTTCTGGATGACAGGCAG	0.564			T|Mis|D|F|S	IGH@|ETV6|PML|FOXP1|ZNF521|ELN	NHL|ALL|B-ALL								3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	43006985	43006985	+	IGR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43006985delA								AQP7P3 (113850 upstream) : LOC642929 (133554 downstream)																							CCTCTTCAGGAAAAAAAAAAT	0.333													22	12	---	---	---	---	
LOC642929	642929	broad.mit.edu	37	9	43140883	43140883	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43140883delC	uc004acy.3	-							NR_027472				Homo sapiens clone HLS_IMAGE_1031047 mRNA sequence.												0						GCTGTGAGAGCTTTTCCACCG	0.418													4	2	---	---	---	---	
AQP7P1	375719	broad.mit.edu	37	9	67265170	67265171	+	Intron	DEL	AC	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67265170_67265171delAC	uc004aem.1	-						AQP7P1_uc004aen.1_Intron					Homo sapiens aquaporin 7 pseudogene 1, mRNA (cDNA clone IMAGE:6191443).												0						acaaaaaaaaacaaaaGTGCAG	0.119													4	4	---	---	---	---	
GDA	9615	broad.mit.edu	37	9	74774426	74774427	+	Intron	INS	-	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74774426_74774427insA	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_Intron	NM_004293	NP_004284	Q9Y2T3	GUAD_HUMAN	guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		ATTCATGAATTAAAAAAAAATT	0.277													4	2	---	---	---	---	
RASEF	158158	broad.mit.edu	37	9	85635027	85635027	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85635027delA	uc004amo.1	-							NM_152573	NP_689786	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing						protein transport|small GTPase mediated signal transduction	perinuclear region of cytoplasm	calcium ion binding|GTP binding			upper_aerodigestive_tract(1)|lung(1)|breast(1)	3						tgttacagttaaaaaaaAATA	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	104610341	104610341	+	IGR	DEL	C	-	-	rs111800241		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104610341delC								GRIN3A (109479 upstream) : None (None downstream)																							cattatctgaccccctcgcat	0.000													7	4	---	---	---	---	
NUP188	23511	broad.mit.edu	37	9	131718396	131718396	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131718396delT	uc004bws.1	+						NUP188_uc004bwq.1_Intron	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7						aTTTAACCACTTTTTTTTTGT	0.124													6	3	---	---	---	---	
EXOSC2	23404	broad.mit.edu	37	9	133577856	133577857	+	Intron	INS	-	TC	TC	rs141015079	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133577856_133577857insTC	uc004bzu.2	+						EXOSC2_uc011mbz.1_Intron|EXOSC2_uc011mca.1_Intron	NM_014285	NP_055100	Q13868	EXOS2_HUMAN	exosome component 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|positive regulation of cell growth|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|7S RNA binding|protein binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		CCATATTATCTTCTCTTCTAAG	0.426													6	7	---	---	---	---	
RALGDS	5900	broad.mit.edu	37	9	135974871	135974872	+	Intron	INS	-	A	A	rs144977251	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135974871_135974872insA	uc004cco.2	-						RALGDS_uc004cct.1_RNA|RALGDS_uc004ccn.2_Intron|RALGDS_uc004ccp.2_Intron|RALGDS_uc004ccq.2_Intron|RALGDS_uc004ccr.2_Intron|RALGDS_uc011mcv.1_Intron|RALGDS_uc004ccs.2_Intron|RALGDS_uc011mcw.1_Intron	NM_006266	NP_006257	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator						nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	Ral guanyl-nucleotide exchange factor activity			large_intestine(1)|lung(1)|ovary(1)	3				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		CTAATGGTGGGAGGTGGTGTTC	0.322			T	CIITA	PMBL|Hodgkin Lymphona|								2	4	---	---	---	---	
C1QL3	389941	broad.mit.edu	37	10	16563566	16563567	+	5'UTR	INS	-	CCT	CCT			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16563566_16563567insCCT	uc001ioj.1	-	1						NM_001010908	NP_001010908	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3							collagen				ovary(1)	1						GCCTTTTTCTGCCTCCTCCTCC	0.535													3	3	---	---	---	---	
ARHGAP21	57584	broad.mit.edu	37	10	24886005	24886008	+	Intron	DEL	TTTC	-	-	rs148465240		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24886005_24886008delTTTC	uc001isb.2	-						ARHGAP21_uc010qdb.1_Intron|ARHGAP21_uc009xkl.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						GTGCTATAATTTTCTTTAAAACAG	0.250													5	3	---	---	---	---	
LOC387646	387646	broad.mit.edu	37	10	27537037	27537042	+	3'UTR	DEL	TAACTT	-	-	rs71487472		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27537037_27537042delTAACTT	uc001its.2	-	1						NR_003525				SubName: Full=cDNA FLJ44924 fis, clone BRAMY3014555;												0						AAGCAAGATGTAACTTAGTGCACTGA	0.437													48	22	---	---	---	---	
AGAP6	414189	broad.mit.edu	37	10	51768242	51768242	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51768242delT	uc001jix.3	+							NM_001077665	NP_001071133	Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			skin(1)	1						tttttttttcttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	70839591	70839591	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70839591delT								KIAA1279 (62857 upstream) : SRGN (8237 downstream)																							GTAGATACTATTTTTTTGGAT	0.284													4	2	---	---	---	---	
BTAF1	9044	broad.mit.edu	37	10	93741188	93741188	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93741188delA	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				TTCTTTTTTTAAAAAAAAACT	0.244													6	3	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106750939	106750939	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106750939delA	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TTGCGGGTGGAAAAAAAAATG	0.269													4	3	---	---	---	---	
SEC23IP	11196	broad.mit.edu	37	10	121662074	121662076	+	Intron	DEL	ATC	-	-	rs72318530		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121662074_121662076delATC	uc001leu.1	+						SEC23IP_uc010qtc.1_Intron	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125						Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		gcaatgtgtaatcatcacatcag	0.054													0	6	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126731459	126731460	+	Intron	INS	-	AAG	AAG	rs142497254	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126731459_126731460insAAG	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		CCAAACCGCACAAGAAACACTA	0.446													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130262667	130262667	+	IGR	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130262667delC								MKI67 (338199 upstream) : None (None downstream)																							tcctcctcctccaccatcctc	0.119													4	3	---	---	---	---	
NUP98	4928	broad.mit.edu	37	11	3794619	3794621	+	Intron	DEL	AAA	-	-	rs112070730		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3794619_3794621delAAA	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyj.1_Intron|NUP98_uc001lyk.1_Intron|NUP98_uc010qxv.1_Intron	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1						carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		agcccatctcaaaaaaaaaaaaa	0.153			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								3	3	---	---	---	---	
TRIM21	6737	broad.mit.edu	37	11	4410120	4410120	+	Intron	DEL	A	-	-	rs74679028		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4410120delA	uc001lyy.1	-							NM_003141	NP_003132	P19474	RO52_HUMAN	tripartite motif protein 21						cell cycle|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein deubiquitination|positive regulation of cell cycle|protein autoubiquitination|protein destabilization|protein monoubiquitination|protein polyubiquitination|protein trimerization	cytoplasmic mRNA processing body|nucleus	DNA binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		AGTTACTGAGAAAAAAATCAC	0.502													6	3	---	---	---	---	
HPS5	11234	broad.mit.edu	37	11	18306706	18306706	+	Intron	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18306706delG	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3						aaaaaaaaaagaaaaaaGCAA	0.294									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
ZDHHC13	54503	broad.mit.edu	37	11	19172490	19172491	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19172490_19172491insT	uc001mpi.2	+						ZDHHC13_uc001mpj.2_Intron	NM_019028	NP_061901	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC domain containing 13 isoform						positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|palmitoyltransferase activity|signal transducer activity|zinc ion binding				0						TGACTTTTAAGGTAGTTATAGT	0.292													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33508295	33508295	+	IGR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33508295delA								HIPK3 (132356 upstream) : C11orf41 (55582 downstream)																							TTTCCAGATTAAAAAAAAAAT	0.353													4	2	---	---	---	---	
LDLRAD3	143458	broad.mit.edu	37	11	36127912	36127912	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36127912delT	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.1_Intron|LDLRAD3_uc010rfa.1_Intron	NM_174902	NP_777562	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain							integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				TCTAAGGACCTTGGACAGTTG	0.458													4	2	---	---	---	---	
HSD17B12	51144	broad.mit.edu	37	11	43852234	43852234	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43852234delA	uc001mxq.3	+						uc001mxr.1_RNA	NM_016142	NP_057226	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12						long-chain fatty-acyl-CoA biosynthetic process|steroid biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	estradiol 17-beta-dehydrogenase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity				0						TTTTCACTGTAAATCCTTCAT	0.348													4	2	---	---	---	---	
CKAP5	9793	broad.mit.edu	37	11	46822532	46822535	+	Intron	DEL	CTGA	-	-	rs149313518		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46822532_46822535delCTGA	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2						GGCCTAGTGCCTGACTTTCTACAT	0.279													4	6	---	---	---	---	
CPSF7	79869	broad.mit.edu	37	11	61189320	61189320	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61189320delC	uc001nrq.2	-						CPSF7_uc001nro.2_Intron|CPSF7_uc001nrp.2_Intron|CPSF7_uc001nrr.2_Intron|CPSF7_uc001nrs.1_Intron|CPSF7_uc009ynp.2_Intron	NM_001136040	NP_001129512	Q8N684	CPSF7_HUMAN	pre-mRNA cleavage factor I, 59 kDa subunit						mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1						CTGGCTTTAGCCAACGGCAAG	0.358													4	2	---	---	---	---	
MARK2	2011	broad.mit.edu	37	11	63630339	63630340	+	Intron	INS	-	A	A	rs141380077	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63630339_63630340insA	uc001nxw.2	+						MARK2_uc001nxx.2_Intron|MARK2_uc001nxy.2_Intron|MARK2_uc001nxv.3_Intron	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2						cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3						CACTCCCCACCAAAAAAAACCC	0.411													6	3	---	---	---	---	
INTS4	92105	broad.mit.edu	37	11	77702604	77702604	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77702604delT	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron|INTS4_uc001oyv.1_Intron	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4						snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			ataggtatacttttttttttt	0.000													4	2	---	---	---	---	
GUCY1A2	2977	broad.mit.edu	37	11	106860456	106860456	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106860456delA	uc001pjg.1	-						GUCY1A2_uc010rvo.1_Intron|GUCY1A2_uc009yxn.1_Intron	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2						intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)		GAAAATTCAGAAAAATGGCAG	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107129198	107129199	+	IGR	INS	-	C	C	rs141843494	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107129198_107129199insC								GUCY1A2 (240027 upstream) : CWF19L2 (67875 downstream)																							gcccatcatgaccctcagatcg	0.040													4	2	---	---	---	---	
KDELC2	143888	broad.mit.edu	37	11	108351623	108351623	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108351623delA	uc001pkj.2	-						KDELC2_uc001pki.2_Intron	NM_153705	NP_714916	Q7Z4H8	KDEL2_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 2 precursor							endoplasmic reticulum lumen				ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;6.93e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;0.00016)|OV - Ovarian serous cystadenocarcinoma(223;0.132)|Colorectal(284;0.14)		AAGCAAATACAAAAAAAAAAA	0.249													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116506034	116506035	+	IGR	INS	-	G	G			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116506034_116506035insG								None (None upstream) : BUD13 (112853 downstream)																							CTCATCTCCATTTTTGGAATCC	0.510													4	2	---	---	---	---	
ARHGEF12	23365	broad.mit.edu	37	11	120335713	120335713	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120335713delA	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		acactgtctcaaaaaaaagaa	0.124			T	MLL	AML								4	2	---	---	---	---	
TMEM218	219854	broad.mit.edu	37	11	124975663	124975663	+	5'Flank	DEL	A	-	-	rs67302846		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124975663delA	uc001qbs.2	-						TMEM218_uc001qbr.2_5'Flank|TMEM218_uc010saw.1_Intron|TMEM218_uc010sax.1_Intron|TMEM218_uc001qbt.2_Intron|TMEM218_uc010say.1_Intron	NM_001080546	NP_001074015	A2RU14	TM218_HUMAN	transmembrane protein 218							integral to membrane					0						tagtaaagtgaaaaaaaaata	0.000													5	3	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126377910	126377910	+	Intron	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126377910delG	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AGGGAGCAGTGGGATTGGGGG	0.537													4	2	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126690213	126690214	+	Intron	INS	-	G	G	rs11463822		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126690213_126690214insG	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		CCTTTAAAAAAAAAGTAACCAA	0.455													3	4	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126811190	126811190	+	Intron	DEL	T	-	-	rs11315647		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126811190delT	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron|uc001qee.1_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		TTTATTTAACTGGCCAAAATT	0.398													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130694194	130694194	+	IGR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130694194delA								ADAMTS15 (350479 upstream) : SNX19 (51573 downstream)																							TCAAGTGATTAAAAATTAATC	0.438													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2797329	2797329	+	Intron	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2797329delG	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron|CACNA1C_uc010sea.1_Intron|uc001qkx.1_Intron|CACNA1C_uc001qky.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	GACCAGGCCAGGGCTAAAAGC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4810513	4810513	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4810513delT								NDUFA9 (14116 upstream) : GALNT8 (19239 downstream)																							caataagggattttttttcCC	0.204													4	2	---	---	---	---	
OLR1	4973	broad.mit.edu	37	12	10321446	10321446	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10321446delA	uc001qxo.1	-						OLR1_uc010sgz.1_5'Flank|OLR1_uc010sha.1_Intron	NM_002543	NP_002534	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like)						blood circulation|blood coagulation|inflammatory response|leukocyte migration|proteolysis	extracellular region|integral to plasma membrane|membrane fraction	sugar binding			ovary(1)	1						acaaacaaacaaaaAAATGCC	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	11596746	11596746	+	IGR	DEL	A	-	-	rs35092836		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11596746delA								PRB2 (48248 upstream) : ETV6 (206042 downstream)																							CACAGGTGGCAAAAAAAAAAG	0.393													4	3	---	---	---	---	
HTR7P1	93164	broad.mit.edu	37	12	13157843	13157843	+	Intron	DEL	A	-	-	rs35516160		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13157843delA	uc001rbh.2	+											Homo sapiens cDNA FLJ43688 fis, clone TBAES2003492.												0						cagcgtccataatgctttgta	0.169													5	5	---	---	---	---	
LRMP	4033	broad.mit.edu	37	12	25250172	25250173	+	Intron	INS	-	AAC	AAC	rs147884989	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25250172_25250173insAAC	uc001rgh.2	+						LRMP_uc010sja.1_Intron|LRMP_uc010sjb.1_Intron|LRMP_uc001rgi.2_Intron|LRMP_uc010sjc.1_Intron|LRMP_uc010sjd.1_Intron	NM_006152	NP_006143	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein						vesicle fusion|vesicle targeting	endoplasmic reticulum membrane|integral to plasma membrane				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					aaaaatataataCGATCCAGTG	0.183													4	2	---	---	---	---	
PDZRN4	29951	broad.mit.edu	37	12	41961421	41961422	+	Intron	DEL	TA	-	-	rs143990010		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41961421_41961422delTA	uc010skn.1	+						PDZRN4_uc001rmq.3_Intron|PDZRN4_uc009zjz.2_Intron|PDZRN4_uc001rmr.2_Intron	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TTTTTTTTTTTATCACCTTTTC	0.376													4	2	---	---	---	---	
YAF2	10138	broad.mit.edu	37	12	42624673	42624673	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42624673delA	uc001rmv.2	-						YAF2_uc001rmw.2_Intron|YAF2_uc010sko.1_Intron|YAF2_uc010skp.1_Intron	NM_005748	NP_005739	Q8IY57	YAF2_HUMAN	YY1 associated factor 2						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|zinc ion binding				0	all_cancers(12;0.000425)	Lung NSC(34;0.0402)|all_lung(34;0.057)		GBM - Glioblastoma multiforme(48;0.0514)		GTTTCAATTTAAAAAGGGCCA	0.398													4	2	---	---	---	---	
DCD	117159	broad.mit.edu	37	12	55044087	55044087	+	5'Flank	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55044087delT	uc001sgj.2	-						DCD_uc009znt.2_5'Flank|DCD_uc009znu.2_5'Flank	NM_053283	NP_444513	P81605	DCD_HUMAN	dermcidin preproprotein						defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			ovary(1)	1		Myeloproliferative disorder(1001;0.0255)				aacaactccattttttttttg	0.000													5	3	---	---	---	---	
IKZF4	64375	broad.mit.edu	37	12	56423140	56423141	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56423140_56423141insT	uc001sjb.1	+						IKZF4_uc010sqa.1_Intron|IKZF4_uc001sjc.1_Intron|IKZF4_uc001sjd.1_Intron|IKZF4_uc009zoi.1_Intron|IKZF4_uc001sje.1_Intron	NM_022465	NP_071910	Q9H2S9	IKZF4_HUMAN	zinc finger protein, subfamily 1A, 4						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (6;0.025)|OV - Ovarian serous cystadenocarcinoma(18;0.123)			AAGCTTTAGGCTTTTGGCTTGG	0.455													4	2	---	---	---	---	
CNOT2	4848	broad.mit.edu	37	12	70747896	70747896	+	3'UTR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70747896delT	uc001svv.2	+	16					CNOT2_uc009zro.2_3'UTR|CNOT2_uc009zrp.2_3'UTR|CNOT2_uc009zrq.2_3'UTR	NM_014515	NP_055330	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	protein binding|RNA polymerase II transcription cofactor activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			ACTAAATTTGTAATTTGTTTT	0.378													8	4	---	---	---	---	
E2F7	144455	broad.mit.edu	37	12	77458037	77458040	+	Intron	DEL	ACTG	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77458037_77458040delACTG	uc001sym.3	-						E2F7_uc001syn.2_Intron	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7						cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3						ACCCTTGACAACTGTATTATAAAC	0.377													6	3	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78570013	78570013	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78570013delA	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron|NAV3_uc009zsf.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						TTTTAATACCAAAAAAAAAAT	0.279										HNSCC(70;0.22)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80690470	80690471	+	IGR	DEL	AC	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80690470_80690471delAC								PPP1R12A (361235 upstream) : PTPRQ (147655 downstream)																							GTTAAAAATGACTTTTTATTTT	0.213													4	3	---	---	---	---	
BTG1	694	broad.mit.edu	37	12	92495218	92495219	+	Intron	INS	-	A	A			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92495218_92495219insA	uc001tbv.1	-						BTG1_uc001tbw.1_Intron|BTG1_uc001tbx.1_Intron|BTG1_uc009zss.1_Intron			P62324	BTG1_HUMAN	Homo sapiens full length insert cDNA clone YW25A12.						cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|transcription cofactor activity				0		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				aagaaagaaagaaagaaagaaa	0.059			T	MYC	BCLL								4	3	---	---	---	---	
ANO4	121601	broad.mit.edu	37	12	101279909	101279909	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101279909delC	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						ctgctctgatccaggcttcta	0.164										HNSCC(74;0.22)			4	2	---	---	---	---	
PAH	5053	broad.mit.edu	37	12	103248608	103248608	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103248608delA	uc001tjq.1	-						PAH_uc010swc.1_3'UTR	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase						catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	aaaacaaaacaaaaaaaaacC	0.388													4	3	---	---	---	---	
MYO1H	283446	broad.mit.edu	37	12	109873145	109873146	+	Intron	INS	-	CAGTTCTC	CAGTTCTC	rs142728604	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109873145_109873146insCAGTTCTC	uc010sxn.1	+							NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H							myosin complex	motor activity				0						TTCCGCCGTTTCAGTTCTCGTT	0.411													10	7	---	---	---	---	
PITPNM2	57605	broad.mit.edu	37	12	123497471	123497471	+	Intron	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123497471delG	uc001uej.1	-						PITPNM2_uc001uek.1_Intron|PITPNM2_uc009zxu.1_Intron|hsa-mir-4304|MI0015832_5'Flank	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,						metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CAGCCAGGATGGGGGCAGGGA	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	124599937	124599938	+	IGR	INS	-	A	A	rs149355690	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124599937_124599938insA								ZNF664 (99970 upstream) : FAM101A (173772 downstream)																							GGAGGCTGAAGAAAAAAAAAAG	0.376													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128884538	128884538	+	IGR	DEL	A	-	-	rs55939312		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128884538delA								None (None upstream) : TMEM132C (14753 downstream)																							aggctgaactatctactgcct	0.114													8	6	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	129098664	129098664	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129098664delT	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						GCGTGATGCCTTCCATGCTCT	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132104101	132104102	+	IGR	DEL	AC	-	-	rs150488331		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132104101_132104102delAC								LOC116437 (406626 upstream) : SFRS8 (91533 downstream)																							atgcacacagacacacacacac	0.168													6	4	---	---	---	---	
CHFR	55743	broad.mit.edu	37	12	133435943	133435944	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133435943_133435944insT	uc001ulf.2	-						CHFR_uc001ulc.1_Intron|CHFR_uc001ule.2_Intron|CHFR_uc010tbs.1_Intron|CHFR_uc001uld.2_Intron|CHFR_uc010tbt.1_Intron	NM_001161344	NP_001154816	Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains						cell division|mitosis|mitotic cell cycle checkpoint|modification-dependent protein catabolic process|protein polyubiquitination	PML body	nucleotide binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		TACATGCAGtcttttttttttc	0.238													4	2	---	---	---	---	
MTMR6	9107	broad.mit.edu	37	13	25856566	25856566	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25856566delT	uc001uqf.3	-						MTMR6_uc001uqe.1_Intron	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6							cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		agggcaggagtttttgtctga	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	57036888	57036888	+	IGR	DEL	G	-	-	rs35210855		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57036888delG								None (None upstream) : PRR20C (678164 downstream)																							aggcataagagggctggctcc	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73943066	73943066	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73943066delT								KLF5 (291391 upstream) : KLF12 (317084 downstream)																							TTCAGATGCATTCAGCTCTTT	0.403													4	2	---	---	---	---	
KLF12	11278	broad.mit.edu	37	13	74347933	74347934	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74347933_74347934insT	uc001vjf.2	-						KLF12_uc010aeq.2_Intron	NM_007249	NP_009180	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		ATGCTACAACATCCCCTTCTGT	0.277													4	2	---	---	---	---	
TMTC4	84899	broad.mit.edu	37	13	101310530	101310530	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101310530delA	uc001vou.2	-						TMTC4_uc001vot.2_Intron|TMTC4_uc010tja.1_Intron	NM_001079669	NP_001073137	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding			ovary(2)|breast(1)	3	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GGAGTAGCAGAAAGGCAAAGG	0.572													4	2	---	---	---	---	
NPAS3	64067	broad.mit.edu	37	14	34145188	34145188	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34145188delA	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GTGTGTGAGGAAAAAAAAAAA	0.338													3	5	---	---	---	---	
ERO1L	30001	broad.mit.edu	37	14	53150337	53150337	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53150337delC	uc001wzv.2	-						ERO1L_uc001wzw.2_Intron|ERO1L_uc010aof.2_Intron	NM_014584	NP_055399	Q96HE7	ERO1A_HUMAN	ERO1-like precursor						chaperone mediated protein folding requiring cofactor|electron transport chain|protein thiol-disulfide exchange|response to temperature stimulus|transport	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome	disulfide oxidoreductase activity|flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor				0	Breast(41;0.226)					TTAAAATTATCCAATGGATGG	0.269													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	61622531	61622532	+	IGR	INS	-	A	A	rs150250509	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61622531_61622532insA								SLC38A6 (72081 upstream) : PRKCH (31755 downstream)																							GACTCCGTGGTAAAAAAAAATC	0.272													6	5	---	---	---	---	
RAD51L1	5890	broad.mit.edu	37	14	68783174	68783175	+	Intron	INS	-	C	C	rs141482428	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68783174_68783175insC	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193	O15315	RA51B_HUMAN	RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)		CCCATGGCAGGCCAGGGAGAGG	0.455			T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					5	3	---	---	---	---	
SMOC1	64093	broad.mit.edu	37	14	70419200	70419200	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70419200delT	uc001xls.1	+						SMOC1_uc001xlt.1_Intron	NM_022137	NP_071420	Q9H4F8	SMOC1_HUMAN	secreted modular calcium-binding protein 1						cell differentiation|eye development|limb development|regulation of osteoblast differentiation|signal transduction	basement membrane	calcium ion binding			upper_aerodigestive_tract(1)|pancreas(1)	2				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GGAATGAGCATTTTTCTATCT	0.473													4	2	---	---	---	---	
RBM25	58517	broad.mit.edu	37	14	73581247	73581248	+	Intron	INS	-	T	T			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73581247_73581248insT	uc001xno.2	+						RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		CACtattattaatattttaatt	0.158													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95337429	95337431	+	IGR	DEL	ACA	-	-	rs143251802		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95337429_95337431delACA								GSC (100930 upstream) : DICER1 (215134 downstream)																							aactttgtttacaacattagttg	0.000													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98362474	98362475	+	IGR	DEL	CT	-	-	rs113710635		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98362474_98362475delCT								None (None upstream) : C14orf64 (29472 downstream)																							cactcatacactcacacacaga	0.104													3	5	---	---	---	---	
CDC42BPB	9578	broad.mit.edu	37	14	103474403	103474404	+	Intron	INS	-	T	T	rs150105545	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103474403_103474404insT	uc001ymi.1	-							NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta						actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		CAGTGGTCCACTTCATTTCTAA	0.485													4	3	---	---	---	---	
GOLGA8DP	100132979	broad.mit.edu	37	15	22710758	22710758	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22710758delC	uc010axw.2	-						GOLGA8DP_uc010axx.2_Intron|uc010tzw.1_5'Flank|uc001yum.2_5'Flank	NM_001012423	NP_001012423			golgi autoantigen, golgin subfamily a, 8E												0						TTCACATAGTCCCAGACTCAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26409745	26409745	+	IGR	DEL	G	-	-	rs111294484		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26409745delG								ATP10A (299428 upstream) : GABRB3 (378950 downstream)																							GCACCACACAGGTTGAAAGCA	0.527													4	4	---	---	---	---	
ZNF609	23060	broad.mit.edu	37	15	64753662	64753662	+	Intron	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64753662delG	uc010bgy.2	+									O15014	ZN609_HUMAN	SubName: Full=ZNF609 protein;							nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						TATCCTGTTTGGAAAACCCAT	0.507													4	2	---	---	---	---	
MTFMT	123263	broad.mit.edu	37	15	65317032	65317032	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65317032delA	uc002aof.3	-							NM_139242	NP_640335	Q96DP5	FMT_HUMAN	mitochondrial methionyl-tRNA formyltransferase							mitochondrion	methionyl-tRNA formyltransferase activity|methyltransferase activity			ovary(2)	2					Tetrahydrofolic acid(DB00116)	aaccagacagaaaaaaaaaat	0.030													4	2	---	---	---	---	
PIAS1	8554	broad.mit.edu	37	15	68480402	68480403	+	3'UTR	INS	-	A	A	rs71666595		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68480402_68480403insA	uc002aqz.2	+	14					PIAS1_uc002ara.2_3'UTR	NM_016166	NP_057250	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1						androgen receptor signaling pathway|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|positive regulation of protein sumoylation|positive regulation of transcription, DNA-dependent|regulation of interferon-gamma-mediated signaling pathway|transcription, DNA-dependent	nuclear speck	androgen receptor binding|DNA binding|enzyme binding|SUMO ligase activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2						AACACTTGTTTaaaaaaaaaaa	0.248													4	2	---	---	---	---	
ARIH1	25820	broad.mit.edu	37	15	72810113	72810113	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72810113delT	uc002aut.3	+							NM_005744	NP_005735	Q9Y4X5	ARI1_HUMAN	ariadne ubiquitin-conjugating enzyme E2 binding						ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0						GCTGAAATTATTTTTTTTTTG	0.224													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92888983	92888983	+	IGR	DEL	A	-	-	rs113075057		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92888983delA								SLCO3A1 (173318 upstream) : ST8SIA2 (48157 downstream)																							CCAGCCAAGCAAAAAAAAAAA	0.498													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97817284	97817285	+	IGR	DEL	AG	-	-	rs34390958		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97817284_97817285delAG								SPATA8 (488440 upstream) : LOC91948 (468561 downstream)																							gtccaaaatcagtaccagtggg	0.000													2	4	---	---	---	---	
CLEC16A	23274	broad.mit.edu	37	16	11238825	11238825	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11238825delA	uc002dao.2	+						CLEC16A_uc002dap.2_Intron	NM_015226	NP_056041	Q2KHT3	CL16A_HUMAN	C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2						TACCAGACCTAGAGCAGGGAA	0.557													4	2	---	---	---	---	
PARN	5073	broad.mit.edu	37	16	14686993	14686993	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14686993delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573	O95453	PARN_HUMAN	poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2						catctcaaggaaaaaaaaaTG	0.199													9	4	---	---	---	---	
NOMO1	23420	broad.mit.edu	37	16	14978640	14978641	+	Intron	DEL	GA	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14978640_14978641delGA	uc002dcv.2	+							NM_014287	NP_055102	Q15155	NOMO1_HUMAN	nodal modulator 1 precursor							integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			ovary(1)	1						ATACAATATGGAATCTAACGTG	0.317													4	2	---	---	---	---	
RRN3	54700	broad.mit.edu	37	16	15178315	15178316	+	Intron	DEL	AA	-	-	rs140423586		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15178315_15178316delAA	uc002dde.2	-						PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Intron|RRN3_uc010uzq.1_Intron|RRN3_uc002ddf.1_Intron	NM_018427	NP_060897	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor						regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1						AAAAACAATTAAAGAGAATAAA	0.302													11	5	---	---	---	---	
SMG1	23049	broad.mit.edu	37	16	18844063	18844064	+	Intron	INS	-	T	T	rs146644880	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18844063_18844064insT	uc002dfm.2	-						SMG1_uc010bwb.2_Intron|SMG1_uc010bwa.2_Intron	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						cctgcctgcactttttttttaa	0.064													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25617519	25617519	+	IGR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25617519delA								ZKSCAN2 (348664 upstream) : HS3ST4 (85828 downstream)																							cggcaaacagaaaaaaaaaaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73569622	73569622	+	IGR	DEL	T	-	-	rs142236447		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73569622delT								HTA (441952 upstream) : PSMD7 (761059 downstream)																							GCCCCCTATCttttttttttt	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84303533	84303533	+	IGR	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84303533delC								KCNG4 (30177 upstream) : WFDC1 (24868 downstream)																							TCTGGCCTCACCCCACAGGCA	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84366015	84366015	+	IGR	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84366015delG								WFDC1 (2569 upstream) : ATP2C2 (36118 downstream)																							gaaacttccagaaacaacaga	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85913106	85913106	+	IGR	DEL	A	-	-	rs5818561		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85913106delA								COX4I1 (72501 upstream) : IRF8 (19668 downstream)																							gcagccagagaaaaccttata	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88182733	88182734	+	IGR	DEL	CA	-	-	rs113262865		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88182733_88182734delCA								BANP (71810 upstream) : ZNF469 (311145 downstream)																							AAGCTGAGCTCACAGTCTTTCC	0.515													3	4	---	---	---	---	
RPA1	6117	broad.mit.edu	37	17	1798642	1798643	+	Intron	INS	-	T	T	rs139754576	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1798642_1798643insT	uc002fto.2	+							NM_002945	NP_002936	P27694	RFA1_HUMAN	replication protein A1						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding				0						tattttttttatttttattttt	0.223								NER					3	3	---	---	---	---	
TEKT3	64518	broad.mit.edu	37	17	15234151	15234151	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15234151delA	uc002gon.2	-							NM_031898	NP_114104	Q9BXF9	TEKT3_HUMAN	tektin 3						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		TAATGCATTTAAAAAAAAAAT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21218954	21218954	+	IGR	DEL	C	-	-	rs5819751		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21218954delC								MAP2K3 (405 upstream) : KCNJ12 (60745 downstream)																							cagatgggaacaacagaccca	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21966646	21966650	+	IGR	DEL	TAACT	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21966646_21966650delTAACT								FLJ36000 (53576 upstream) : None (None downstream)																							AGAAAATTAATAACTTAAAGGCAAA	0.415													6	3	---	---	---	---	
ZNHIT3	9326	broad.mit.edu	37	17	34839662	34839663	+	5'Flank	INS	-	G	G	rs35342470		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34839662_34839663insG	uc002hms.1	+						ZNHIT3_uc010cus.1_5'Flank|ZNHIT3_uc002hmt.1_5'Flank|ZNHIT3_uc010cut.1_5'Flank	NM_004773	NP_004764	Q15649	ZNHI3_HUMAN	thyroid hormone receptor interactor 3						regulation of transcription, DNA-dependent	intracellular	metal ion binding|thyroid hormone receptor binding				0		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0188)		ttagtagagacggggtttcacc	0.000													13	9	---	---	---	---	
TEX14	56155	broad.mit.edu	37	17	56677118	56677118	+	Intron	DEL	A	-	-	rs111881602		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56677118delA	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAAGACTGTCAAAAAAAAAAA	0.413													5	3	---	---	---	---	
LPIN2	9663	broad.mit.edu	37	18	2960970	2960975	+	Intron	DEL	TATTAA	-	-	rs17881253		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2960970_2960975delTATTAA	uc002klo.2	-							NM_014646	NP_055461	Q92539	LPIN2_HUMAN	lipin 2						fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		TCATTAGCCTTATTAATTTTCAACCT	0.388													5	4	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3596703	3596703	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3596703delA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|FLJ35776_uc010wza.1_RNA|FLJ35776_uc010wzb.1_RNA	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				ttgttacatgaaGGCGTGAAC	0.259													5	3	---	---	---	---	
RALBP1	10928	broad.mit.edu	37	18	9535419	9535420	+	Intron	INS	-	T	T	rs146999452	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9535419_9535420insT	uc002kob.2	+						RALBP1_uc002koc.2_Intron	NM_006788	NP_006779	Q15311	RBP1_HUMAN	ralA binding protein 1						chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1						TAAAATAACGGTTTCTGTTGGC	0.401													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10342606	10342607	+	IGR	INS	-	T	T	rs142605826	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10342606_10342607insT								VAPA (382589 upstream) : APCDD1 (112018 downstream)																							tggagtcgtccttctggtgtct	0.238													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11952493	11952495	+	IGR	DEL	TTC	-	-	rs111334421		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11952493_11952495delTTC								MPPE1 (43852 upstream) : IMPA2 (28562 downstream)																							tttcttttttttcttttttttgt	0.000													4	4	---	---	---	---	
CEP192	55125	broad.mit.edu	37	18	13038237	13038237	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13038237delT	uc010xac.1	+						CEP192_uc010dlf.1_Intron|CEP192_uc010xad.1_Intron|CEP192_uc002kru.2_Intron|CEP192_uc002krs.1_Intron	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa											ovary(4)|pancreas(1)	5						GTTTGTCCAATTTTTTTTTTG	0.303													6	4	---	---	---	---	
CHST9	83539	broad.mit.edu	37	18	24524596	24524596	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24524596delC	uc002kwd.2	-						C18orf16_uc010xbm.1_Intron|CHST9_uc002kwc.2_Intron|CHST9_uc002kwe.2_Intron	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)					ATTAAACTTTCACAGATAAAT	0.328													4	2	---	---	---	---	
MAPK4	5596	broad.mit.edu	37	18	48250389	48250389	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48250389delT	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)		GGTACTCGACtttttttcttt	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52801054	52801055	+	IGR	DEL	AG	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52801054_52801055delAG								CCDC68 (174315 upstream) : TCF4 (88507 downstream)																							aatgtgtgacagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53877903	53877903	+	IGR	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53877903delC								TCF4 (574718 upstream) : TXNL1 (392152 downstream)																							GTCCACAGCACCTGCATCCCC	0.502													6	3	---	---	---	---	
CCBE1	147372	broad.mit.edu	37	18	57332413	57332414	+	Intron	INS	-	T	T	rs150497924	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57332413_57332414insT	uc002lib.2	-							NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)				AGAGTCCCCCCGAGACAAAAGC	0.470													7	7	---	---	---	---	
ZNF763	284390	broad.mit.edu	37	19	12088593	12088593	+	Intron	DEL	C	-	-	rs79770930		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12088593delC	uc002msw.2	+						ZNF763_uc010xmf.1_Intron|ZNF763_uc002msv.2_Intron|ZNF763_uc010xmg.1_Intron	NM_001012753	NP_001012771	Q0D2J5	ZN763_HUMAN	zinc finger protein 763						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1						atcactcaagcccccaggagt	0.025													4	2	---	---	---	---	
EMR3	84658	broad.mit.edu	37	19	14773131	14773132	+	Intron	INS	-	TATAAG	TATAAG	rs150464360	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14773131_14773132insTATAAG	uc002mzi.3	-						EMR3_uc010dzp.2_Intron|EMR3_uc010xnv.1_Intron	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor						neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						tgagacgagaatataagtactt	0.104													11	5	---	---	---	---	
EPS15L1	58513	broad.mit.edu	37	19	16489026	16489027	+	Intron	INS	-	AGGC	AGGC			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16489026_16489027insAGGC	uc002ndz.1	-						EPS15L1_uc002ndx.2_Intron|EPS15L1_uc002ndy.2_Intron|EPS15L1_uc010xpe.1_Intron|EPS15L1_uc010xpf.1_Intron|EPS15L1_uc002nea.1_Intron|EPS15L1_uc010eah.1_Intron	NM_021235	NP_067058	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway						endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|nucleus|plasma membrane	calcium ion binding			ovary(3)|skin(2)	5						ggtaggtaggtaggcaCTTCCT	0.252													12	7	---	---	---	---	
ATRN	8455	broad.mit.edu	37	20	3629805	3629805	+	3'UTR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3629805delA	uc002wim.2	+	29						NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2						CTCAGGGCAGAAAAAGGGAAT	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4300671	4300672	+	IGR	INS	-	T	T	rs151292041	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4300671_4300672insT								ADRA1D (71012 upstream) : PRNP (366125 downstream)																							TATTTTTTAAGTTTTTTTTTCT	0.139													1	5	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19700703	19700704	+	Intron	INS	-	AAGAC	AAGAC	rs141396382	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19700703_19700704insAAGAC	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						gacactaagataagacagatgc	0.015													2	4	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25829628	25829629	+	Intron	INS	-	AA	AA	rs141949476	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25829628_25829629insAA	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						ctgcaattgacagaggtagtgg	0.000													3	3	---	---	---	---	
TOX2	84969	broad.mit.edu	37	20	42571943	42571943	+	5'Flank	DEL	T	-	-	rs35344264		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42571943delT	uc002xlf.3	+						TOX2_uc010ggo.2_Intron|TOX2_uc002xle.3_Intron|TOX2_uc010ggp.2_Intron	NM_001098798	NP_001092268	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			ATAAACTCCCTCTCCTACAGA	0.448													3	4	---	---	---	---	
ZFP64	55734	broad.mit.edu	37	20	50777673	50777674	+	Intron	DEL	GC	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50777673_50777674delGC	uc002xwl.2	-						ZFP64_uc002xwk.2_Intron|ZFP64_uc002xwm.2_Intron|ZFP64_uc002xwn.2_Intron	NM_018197	NP_060667	Q9NPA5	ZF64A_HUMAN	zinc finger protein 64 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2						gtcctagcctgcctgctcacct	0.129													4	2	---	---	---	---	
BCAS1	8537	broad.mit.edu	37	20	52668111	52668111	+	Intron	DEL	C	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52668111delC	uc002xws.2	-						BCAS1_uc002xwt.2_Intron|BCAS1_uc010gil.1_Intron|BCAS1_uc010zzc.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)			ACTCCTCCTGCCCCCAGTGAT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54699174	54699174	+	IGR	DEL	T	-	-	rs71898533		TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54699174delT								CBLN4 (119162 upstream) : MC3R (124614 downstream)																							aacttcatgatttttttttta	0.199													10	5	---	---	---	---	
UMODL1	89766	broad.mit.edu	37	21	43551344	43551344	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43551344delT	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc002zal.1_Intron|UMODL1_uc010gpa.1_Intron	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3						TTTTTTGTTGTTTTTTTCCCT	0.254													4	2	---	---	---	---	
A4GALT	53947	broad.mit.edu	37	22	43091196	43091197	+	Intron	INS	-	AG	AG	rs138354849	by1000genomes	TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43091196_43091197insAG	uc003bdb.2	-						A4GALT_uc010gzd.2_Intron	NM_017436	NP_059132	Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase						glycosphingolipid biosynthetic process|plasma membrane organization	Golgi stack|integral to Golgi membrane|membrane fraction	lactosylceramide 4-alpha-galactosyltransferase activity			central_nervous_system(2)	2						ACCATCGACTCTGACTTCTACG	0.540													6	4	---	---	---	---	
ACE2	59272	broad.mit.edu	37	X	15588098	15588098	+	Intron	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15588098delT	uc004cxa.1	-						ACE2_uc004cxb.2_Intron	NM_021804	NP_068576	Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2 precursor						angiotensin-mediated drinking behavior|proteolysis|receptor biosynthetic process|regulation of cell proliferation|virion attachment, binding of host cell surface receptor	cell surface|extracellular space|integral to membrane|membrane raft|plasma membrane	carboxypeptidase activity|glycoprotein binding|metallopeptidase activity|peptidyl-dipeptidase activity|viral receptor activity|zinc ion binding			ovary(3)	3	Hepatocellular(33;0.183)				Moexipril(DB00691)	AATATAACCATATTCTCTTTC	0.274													5	4	---	---	---	---	
RPGR	6103	broad.mit.edu	37	X	38136289	38136289	+	Intron	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38136289delA	uc004deb.2	-						RPGR_uc004dea.2_Intron|RPGR_uc004dec.2_Intron	NM_000328	NP_000319	Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator isoform A						intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						GTTACAATGGAAAAAAAAAAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	45661862	45661862	+	IGR	DEL	A	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45661862delA								MIR222 (55332 upstream) : ZNF673 (644762 downstream)																							CTCTCTGCTGAAAAGCTCCAA	0.333													4	2	---	---	---	---	
MAGT1	84061	broad.mit.edu	37	X	77113317	77113319	+	Intron	DEL	GAG	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77113317_77113319delGAG	uc004fof.2	-						MAGT1_uc004fog.3_Intron	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1						protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				upper_aerodigestive_tract(1)	1						ATACATTTATGAGCACTAAAATA	0.320													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	94487169	94487169	+	IGR	DEL	T	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:94487169delT								MIR548M (168944 upstream) : None (None downstream)																							ATGAACTTGATTTTTTTTTTT	0.398													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	137164182	137164182	+	IGR	DEL	G	-	-			TCGA-A3-3362-01A-02D-1386-10	TCGA-A3-3362-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137164182delG								ZIC3 (509925 upstream) : LOC158696 (532710 downstream)																							gtaagtacttggctcagAAAG	0.214													4	2	---	---	---	---	
