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
CLCN6	1185	broad.mit.edu	37	1	11894362	11894362	+	Silent	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11894362G>T	uc001ate.3	+	16	1709	c.1596G>T	c.(1594-1596)GGG>GGT	p.G532G	CLCN6_uc010oat.1_Silent_p.G248G|CLCN6_uc010oau.1_Silent_p.G510G	NM_001286	NP_001277	P51797	CLCN6_HUMAN	chloride channel 6 isoform ClC-6a	532					cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TCTTGGGCGGGGTGGTCCGCA	0.552													29	117	---	---	---	---	PASS
C1orf94	84970	broad.mit.edu	37	1	34677961	34677961	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34677961C>G	uc001bxs.3	+	6	1504	c.1105C>G	c.(1105-1107)CTA>GTA	p.L369V	C1orf94_uc001bxt.2_Missense_Mutation_p.L559V	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b	369							protein binding				0		Myeloproliferative disorder(586;0.0393)				AGACCCTCCCCTAATGGCAGG	0.567													13	150	---	---	---	---	PASS
FAF1	11124	broad.mit.edu	37	1	50956260	50956260	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50956260C>T	uc009vyx.1	-	18	1716	c.1653G>A	c.(1651-1653)GAG>GAA	p.E551E	FAF1_uc009vyw.1_RNA|FAF1_uc001cse.1_Silent_p.E551E|FAF1_uc010onc.1_Silent_p.E309E	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1	551					apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		TATGCCCCACCTCACGTTCCT	0.328													84	157	---	---	---	---	PASS
USP33	23032	broad.mit.edu	37	1	78189031	78189031	+	Silent	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78189031A>G	uc001dht.2	-	13	1814	c.1467T>C	c.(1465-1467)TGT>TGC	p.C489C	USP33_uc001dhs.2_Silent_p.C210C|USP33_uc001dhu.2_Silent_p.C458C|USP33_uc001dhv.2_Silent_p.C294C|USP33_uc001dhw.2_Silent_p.C489C	NM_015017	NP_055832	Q8TEY7	UBP33_HUMAN	ubiquitin specific protease 33 isoform 1	489					axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3						CACAAGTCAGACACTGCACTG	0.338													7	604	---	---	---	---	PASS
SLC44A3	126969	broad.mit.edu	37	1	95360437	95360437	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95360437A>G	uc001dqv.3	+	15	2028	c.1921A>G	c.(1921-1923)AGG>GGG	p.R641G	SLC44A3_uc001dqx.3_Missense_Mutation_p.R640G|SLC44A3_uc010otq.1_Missense_Mutation_p.R573G|SLC44A3_uc010otr.1_Missense_Mutation_p.R605G|SLC44A3_uc001dqw.3_Missense_Mutation_p.R593G|SLC44A3_uc010ots.1_Missense_Mutation_p.R561G|SLC44A3_uc009wds.2_Missense_Mutation_p.R544G|SLC44A3_uc010ott.1_Missense_Mutation_p.R560G	NM_001114106	NP_001107578	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3 isoform 1	641						integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	GCACTCATTAAGGAATGAGGA	0.378													41	230	---	---	---	---	PASS
ALG14	199857	broad.mit.edu	37	1	95448591	95448591	+	3'UTR	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95448591A>G	uc001dra.2	-	4						NM_144988	NP_659425	Q96F25	ALG14_HUMAN	asparagine-linked glycosylation 14 homolog						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity				0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		AGTACATACTACTGTTAACTG	0.393													4	119	---	---	---	---	PASS
AMY2B	280	broad.mit.edu	37	1	104116348	104116348	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104116348G>A	uc001duq.2	+	6	1148	c.532G>A	c.(532-534)GTT>ATT	p.V178I	AMY2B_uc010ouo.1_RNA|LOC648740_uc001dur.2_Missense_Mutation_p.V178I|AMY2B_uc001dus.1_5'Flank	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor	178					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		TTGTCGTCTGGTTGGTCTTCT	0.363													146	583	---	---	---	---	PASS
HMGCS2	3158	broad.mit.edu	37	1	120307055	120307055	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120307055T>A	uc001eid.2	-	2	350	c.299A>T	c.(298-300)GAG>GTG	p.E100V	HMGCS2_uc010oxj.1_Missense_Mutation_p.E100V|HMGCS2_uc001eie.2_Missense_Mutation_p.E8V	NM_005518	NP_005509	P54868	HMCS2_HUMAN	hydroxymethylglutaryl-CoA synthase 2 isoform 1	100					acetoacetic acid biosynthetic process|cholesterol biosynthetic process|isoprenoid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA synthase activity			ovary(2)	2	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		GTTGATGTCCTCTTGGACTGA	0.552													48	85	---	---	---	---	PASS
LOC200030	200030	broad.mit.edu	37	1	148025821	148025821	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148025821T>C	uc001eqf.2	-	7	1066	c.1031A>G	c.(1030-1032)AAT>AGT	p.N344S	LOC200030_uc001eqe.2_5'UTR|LOC200030_uc001eqg.2_5'UTR|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc009wkf.1_RNA|NBPF14_uc001eqq.2_Missense_Mutation_p.N4S|NBPF14_uc001eqs.1_5'Flank	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672	344	Potential.					cytoplasm					0						CTGTCGCTCATTCCTCAGCAT	0.537													4	84	---	---	---	---	PASS
FCGR3B	2215	broad.mit.edu	37	1	161599827	161599827	+	Splice_Site	SNP	T	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161599827T>G	uc009wul.2	-	3	336	c.62_splice	c.e3-1	p.E21_splice		NM_000570	NP_000561	O75015	FCG3B_HUMAN	low affinity immunoglobulin gamma Fc region						immune response	anchored to membrane|extracellular region|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GGAGATCTTCTGAGGAGCCAA	0.557													32	77	---	---	---	---	PASS
RCSD1	92241	broad.mit.edu	37	1	167663406	167663406	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167663406T>A	uc001gem.2	+	5	528	c.341T>A	c.(340-342)ATG>AAG	p.M114K	RCSD1_uc010pli.1_Missense_Mutation_p.M84K	NM_052862	NP_443094	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	114										ovary(2)|central_nervous_system(2)|skin(1)	5	all_hematologic(923;0.215)					CTCAAGGCTATGGTGTCGCCA	0.557													15	29	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186310211	186310211	+	Silent	SNP	T	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186310211T>G	uc001grv.2	-	29	4266	c.3969A>C	c.(3967-3969)GCA>GCC	p.A1323A		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	1323	Potential.				carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		GCTTCTTCTCTGCCTGCAACA	0.393			T	NTRK1	papillary thyroid								94	457	---	---	---	---	PASS
GREB1	9687	broad.mit.edu	37	2	11706655	11706655	+	Silent	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11706655G>A	uc002rbk.1	+	4	627	c.327G>A	c.(325-327)GAG>GAA	p.E109E	GREB1_uc002rbl.2_Silent_p.E109E|GREB1_uc002rbm.2_5'UTR|GREB1_uc002rbn.1_Silent_p.E109E	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	109						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TTTCCAACGAGCCCATGGATG	0.637													11	29	---	---	---	---	PASS
SDC1	6382	broad.mit.edu	37	2	20403727	20403727	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20403727C>T	uc002rdo.1	-	3	773	c.474G>A	c.(472-474)CAG>CAA	p.Q158Q	SDC1_uc002rdp.1_Silent_p.Q158Q|SDC1_uc010exv.2_Silent_p.Q158Q|SDC1_uc010exw.1_RNA	NM_002997	NP_002988	P18827	SDC1_HUMAN	syndecan 1 precursor	158	Extracellular (Potential).				lipid metabolic process|lipoprotein metabolic process|myoblast development|striated muscle cell development	cytoplasm|extracellular region|focal adhesion|integral to plasma membrane	cytoskeletal protein binding|protein C-terminus binding			ovary(4)|skin(1)	5	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)		GGTGGCCAGGCTGCATGTCCC	0.657													51	107	---	---	---	---	PASS
TMEM17	200728	broad.mit.edu	37	2	62729497	62729497	+	Intron	SNP	C	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62729497C>G	uc002sbt.2	-						TMEM17_uc002sbu.2_3'UTR|TMEM17_uc002sbv.1_3'UTR	NM_198276	NP_938017	Q86X19	TMM17_HUMAN	transmembrane protein 17							integral to membrane					0	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			tctgccacacctcactgcctt	0.159													12	87	---	---	---	---	PASS
ANAPC1	64682	broad.mit.edu	37	2	112630631	112630631	+	Intron	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112630631A>G	uc002thi.2	-						ANAPC1_uc002thj.2_3'UTR	NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						ATATAACCAAAAGTTCTTAGG	0.299													6	8	---	---	---	---	PASS
UGGT1	56886	broad.mit.edu	37	2	128928844	128928844	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128928844C>A	uc002tps.2	+	28	3268	c.3090C>A	c.(3088-3090)GAC>GAA	p.D1030E	UGGT1_uc010fme.1_Missense_Mutation_p.D905E|UGGT1_uc002tpr.2_Missense_Mutation_p.D1006E	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	1030					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						AACTTTCTGACATGCCTTTAA	0.338													147	443	---	---	---	---	PASS
POTEF	728378	broad.mit.edu	37	2	130878125	130878125	+	5'UTR	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130878125A>G	uc010fmh.2	-	3						NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5						GTAGTAGCCAACAGATCGCGT	0.498													4	73	---	---	---	---	PASS
C2orf77	129881	broad.mit.edu	37	2	170531470	170531470	+	Silent	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170531470T>C	uc002ufe.2	-	3	469	c.375A>G	c.(373-375)GAA>GAG	p.E125E		NM_001085447	NP_001078916	Q0VFZ6	CB077_HUMAN	hypothetical protein LOC129881	125	Potential.										0						ATATTTCTTCTTCCAGATCAA	0.333													7	479	---	---	---	---	PASS
DYNC1I2	1781	broad.mit.edu	37	2	172583232	172583232	+	Intron	SNP	A	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172583232A>C	uc002uha.1	+						DYNC1I2_uc002uhc.2_Intron|DYNC1I2_uc002uhb.1_Intron|DYNC1I2_uc010zds.1_Intron|DYNC1I2_uc002uhd.1_Intron|DYNC1I2_uc002uhe.1_Intron|DYNC1I2_uc002uhf.1_Intron|DYNC1I2_uc010zdt.1_Intron|DYNC1I2_uc002uhg.1_Intron|DYNC1I2_uc010zdu.1_5'UTR	NM_001378	NP_001369	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)			GATAAAGACAAATAACTAGGA	0.323													31	167	---	---	---	---	PASS
DFNB59	494513	broad.mit.edu	37	2	179325760	179325760	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179325760T>C	uc002umi.3	+	7	1174	c.818T>C	c.(817-819)CTT>CCT	p.L273P	DFNB59_uc002umj.3_Missense_Mutation_p.L273P	NM_001042702	NP_001036167	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	273					sensory perception of sound						0			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			TTGGATGATCTTTTTTCTGAC	0.348													8	758	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	179444587	179444587	+	Intron	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179444587G>A	uc002umo.2	+						uc002ump.1_Intron|TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|uc002umv.1_3'UTR					Homo sapiens cDNA FLJ36414 fis, clone THYMU2010848.																		TAAAGCAAAGGAGAAATGATA	0.428													4	172	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179446298	179446298	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179446298A>G	uc010zfg.1	-	265	59217	c.58993T>C	c.(58993-58995)TAT>CAT	p.Y19665H	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.Y13360H|TTN_uc010zfi.1_Missense_Mutation_p.Y13293H|TTN_uc010zfj.1_Missense_Mutation_p.Y13168H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20592							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)			TTAACGGCATACACACGGAAT	0.443													6	313	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179483337	179483337	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179483337T>C	uc010zfg.1	-	200	39460	c.39236A>G	c.(39235-39237)GAA>GGA	p.E13079G	TTN_uc010zfh.1_Missense_Mutation_p.E6774G|TTN_uc010zfi.1_Missense_Mutation_p.E6707G|TTN_uc010zfj.1_Missense_Mutation_p.E6582G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	14006							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)			GATGAATCCTTCTGCTTTTCC	0.363													7	689	---	---	---	---	PASS
NCKAP1	10787	broad.mit.edu	37	2	183866762	183866762	+	Silent	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183866762T>C	uc002upc.2	-	6	924	c.522A>G	c.(520-522)GAA>GAG	p.E174E	NCKAP1_uc002upb.2_Silent_p.E180E	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1	174					apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			GGCGTGGGTATTCTCTGTCAC	0.373													7	725	---	---	---	---	PASS
FAM126B	285172	broad.mit.edu	37	2	201862153	201862153	+	Intron	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201862153A>G	uc002uws.3	-						FAM126B_uc002uwu.2_Intron|FAM126B_uc002uwv.2_Intron|FAM126B_uc002uww.1_3'UTR	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN	hypothetical protein LOC285172							intracellular				ovary(1)	1						GATTAGTAATAATCACTCTTC	0.219													53	110	---	---	---	---	PASS
ALS2	57679	broad.mit.edu	37	2	202622211	202622211	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202622211T>C	uc002uyo.2	-	5	1741	c.1385A>G	c.(1384-1386)AAG>AGG	p.K462R	ALS2_uc002uyp.3_Missense_Mutation_p.K462R|ALS2_uc002uyq.2_Missense_Mutation_p.K462R	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	462					cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						TGAACTTTTCTTTCCTTGCAT	0.463													8	756	---	---	---	---	PASS
COL4A4	1286	broad.mit.edu	37	2	227964335	227964335	+	Splice_Site	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227964335C>T	uc010zlt.1	-	18	1753	c.1099_splice	c.e18+1	p.G367_splice		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GGAACACAAACCTTTGAGTGG	0.453													4	178	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191488	10191488	+	Nonsense_Mutation	SNP	C	T	T	rs5030818		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191488C>T	uc003bvc.2	+	3	694	c.481C>T	c.(481-483)CGA>TGA	p.R161*	VHL_uc003bvd.2_Nonsense_Mutation_p.R120*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	161	Interaction with Elongin BC complex.		R -> P (in pheochromocytoma and VHLD; type I).|R -> Q (in pheochromocytoma and VHLD; type II).		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.R161*(10)|p.R161P(3)|p.R161del(1)|p.R161fs*13(1)|p.R161fs*12(1)|p.E160fs*9(1)|p.?fs(1)|p.L158fs*6(1)|p.E160fs*13(1)|p.R161Q(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TCTGAAAGAGCGATGCCTCCA	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				52	88	---	---	---	---	PASS
ZNF620	253639	broad.mit.edu	37	3	40558394	40558394	+	3'UTR	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40558394C>T	uc003ckk.2	+	5					ZNF620_uc003ckl.2_3'UTR	NM_175888	NP_787084	Q6ZNG0	ZN620_HUMAN	zinc finger protein 620						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CTCCTTTTTTCTCTTTATTTT	0.418													3	43	---	---	---	---	PASS
ULK4	54986	broad.mit.edu	37	3	41504634	41504634	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41504634C>G	uc003ckv.3	-	33	3538	c.3337G>C	c.(3337-3339)GAT>CAT	p.D1113H		NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	1113							ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGCAAAATATCAAGCAGGGAA	0.473													27	195	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47127736	47127736	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47127736C>T	uc003cqs.2	-	11	5399	c.5346G>A	c.(5344-5346)TGG>TGA	p.W1782*	SETD2_uc003cqv.2_Nonsense_Mutation_p.W1849*|SETD2_uc003cqt.1_5'Flank	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1782					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GCTCTGCCATCCAGATCCACA	0.478			N|F|S|Mis		clear cell renal carcinoma								65	107	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52597493	52597493	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52597493G>A	uc003des.2	-	24	3904	c.3892C>T	c.(3892-3894)CAG>TAG	p.Q1298*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.Q1298*|PBRM1_uc003der.2_Nonsense_Mutation_p.Q1266*|PBRM1_uc003det.2_Nonsense_Mutation_p.Q1313*|PBRM1_uc003deu.2_Nonsense_Mutation_p.Q1313*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.Q1298*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.Q1273*|PBRM1_uc003dey.2_Nonsense_Mutation_p.Q1273*|PBRM1_uc003dez.1_Nonsense_Mutation_p.Q1297*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1298					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding	p.Q1298*(3)		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)		GGCTCCTTCTGAGGAACAATT	0.408			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								64	110	---	---	---	---	PASS
TNIK	23043	broad.mit.edu	37	3	170802027	170802027	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170802027T>A	uc003fhh.2	-	26	3431	c.3086A>T	c.(3085-3087)AAC>ATC	p.N1029I	TNIK_uc003fhi.2_Missense_Mutation_p.N974I|TNIK_uc003fhj.2_Missense_Mutation_p.N1000I|TNIK_uc003fhk.2_Missense_Mutation_p.N1021I|TNIK_uc003fhl.2_Missense_Mutation_p.N945I|TNIK_uc003fhm.2_Missense_Mutation_p.N966I|TNIK_uc003fhn.2_Missense_Mutation_p.N992I|TNIK_uc003fho.2_Missense_Mutation_p.N937I|TNIK_uc003fhg.2_Missense_Mutation_p.N207I|TNIK_uc003fhp.2_5'Flank	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1	1029	Mediates interaction with NEDD4.				actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			AGGCCGAATGTTGGTTGGGTT	0.408													37	369	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62800598	62800598	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62800598C>A	uc010ihh.2	+	11	2122	c.1949C>A	c.(1948-1950)GCT>GAT	p.A650D	LPHN3_uc003hcq.3_Missense_Mutation_p.A650D|LPHN3_uc003hct.2_Missense_Mutation_p.A43D|LPHN3_uc003hcs.1_Missense_Mutation_p.A466D	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	637	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						CAGCCACAAGCTTTGAATGCA	0.478													37	107	---	---	---	---	PASS
LEF1	51176	broad.mit.edu	37	4	108999469	108999469	+	Silent	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108999469A>G	uc003hyt.1	-	8	1570	c.915T>C	c.(913-915)GCT>GCC	p.A305A	LEF1_uc011cfj.1_Silent_p.A162A|LEF1_uc011cfk.1_Silent_p.A209A|LEF1_uc003hyu.1_Silent_p.A277A|LEF1_uc003hyv.1_Silent_p.A277A|LEF1_uc010imb.1_RNA|LEF1_uc010ima.1_5'UTR|LEF1_uc003hyw.1_RNA	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	305	HMG box.				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		ATAACATAAAAGCATTCAGAG	0.438													7	425	---	---	---	---	PASS
CLGN	1047	broad.mit.edu	37	4	141321553	141321553	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141321553T>C	uc011chi.1	-	8	870	c.652A>G	c.(652-654)AAA>GAA	p.K218E	CLGN_uc003iii.2_Missense_Mutation_p.K218E	NM_001130675	NP_001124147	O14967	CLGN_HUMAN	calmegin precursor	218	Lumenal (Potential).				protein folding	endoplasmic reticulum membrane|integral to membrane	calcium ion binding|unfolded protein binding			ovary(2)|skin(1)	3	all_hematologic(180;0.162)					AAGAACTTTTTAAGGTCTACA	0.279													137	332	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16818168	16818168	+	Missense_Mutation	SNP	C	T	T	rs35214419		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16818168C>T	uc003jft.3	-	3	697	c.229G>A	c.(229-231)GGC>AGC	p.G77S	MYO10_uc003jfu.2_Missense_Mutation_p.G44S|MYO10_uc003jfv.2_Missense_Mutation_p.G77S	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	77	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						ATGATGGAGCCGCCATGGAGC	0.448													21	218	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33588814	33588814	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33588814G>T	uc003jia.1	-	18	2918	c.2755C>A	c.(2755-2757)CAG>AAG	p.Q919K	ADAMTS12_uc010iuq.1_Missense_Mutation_p.Q834K	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	919	TSP type-1 3.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						GGGAGAGCCTGCTCGTCAGAG	0.637										HNSCC(64;0.19)			7	70	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35644519	35644519	+	Silent	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35644519T>C	uc003jjo.2	+	4	588	c.477T>C	c.(475-477)TTT>TTC	p.F159F	SPEF2_uc003jjn.1_Silent_p.F159F|SPEF2_uc003jjq.3_Silent_p.F159F	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	159					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CATACAGGTTTCAAGAAAAAT	0.313													5	230	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469440	75469440	+	Intron	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469440A>G	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CAGAGCTACAATGCATTTAGT	0.418													9	266	---	---	---	---	PASS
F2RL2	2151	broad.mit.edu	37	5	75914170	75914170	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75914170A>C	uc003kem.2	-	2	547	c.362T>G	c.(361-363)TTC>TGC	p.F121C	IQGAP2_uc003kek.2_Intron|IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron|F2RL2_uc011csw.1_Missense_Mutation_p.F99C	NM_004101	NP_004092	O00254	PAR3_HUMAN	coagulation factor II (thrombin) receptor-like 2	121	Cytoplasmic (Potential).				platelet activation	extracellular region|integral to plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|thrombin receptor activity			skin(2)|ovary(1)	3		all_lung(232;0.000462)|Lung NSC(167;0.00124)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)		TCTGGTCCTGAAGAAAAGCAT	0.453													47	82	---	---	---	---	PASS
PAPD4	167153	broad.mit.edu	37	5	78919207	78919207	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78919207G>T	uc010jae.1	+	5	778	c.360G>T	c.(358-360)TTG>TTT	p.L120F	PAPD4_uc003kgb.2_Missense_Mutation_p.L120F|PAPD4_uc010jaf.1_Missense_Mutation_p.L120F|PAPD4_uc003kga.2_Missense_Mutation_p.L120F|PAPD4_uc003kfz.2_Missense_Mutation_p.L120F	NM_001114393	NP_001107865	Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	120					histone mRNA catabolic process|mRNA processing|RNA polyadenylation	cytoplasm	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity			ovary(1)	1		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		TGCCACCATTGTTTCATACAC	0.423													19	252	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90074272	90074272	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90074272A>C	uc003kju.2	+	63	12791	c.12695A>C	c.(12694-12696)AAA>ACA	p.K4232T	GPR98_uc003kjt.2_Missense_Mutation_p.K1938T|GPR98_uc003kjw.2_5'Flank	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4232	Extracellular (Potential).|Calx-beta 28.				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCCGAGGAAAAAAGCTTCTAT	0.453													36	84	---	---	---	---	PASS
SRP19	6728	broad.mit.edu	37	5	112228273	112228273	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112228273A>G	uc011cvv.1	+	4	1267	c.1012A>G	c.(1012-1014)AAA>GAA	p.K338E	SRP19_uc011cvu.1_Missense_Mutation_p.K323E|REEP5_uc011cvw.1_Intron|REEP5_uc003kqe.1_Intron|REEP5_uc011cvx.1_RNA|REEP5_uc011cvy.1_Intron|REEP5_uc011cvz.1_Intron			P09132	SRP19_HUMAN	SubName: Full=Zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2;	Error:Variant_position_missing_in_P09132_after_alignment					response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|mitochondrion|nucleolus|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding				0		all_cancers(142;0.00328)|all_epithelial(76;6.39e-05)|Prostate(80;0.00174)|Colorectal(10;0.00372)|Ovarian(225;0.156)		Epithelial(69;1.7e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.17e-08)|all cancers(49;3.96e-07)|Colorectal(14;0.0056)|COAD - Colon adenocarcinoma(37;0.0104)		GACCCGGTGGAAAATGGCGAT	0.448													114	207	---	---	---	---	PASS
DMXL1	1657	broad.mit.edu	37	5	118502399	118502399	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118502399T>G	uc003ksd.2	+	22	5240	c.5059T>G	c.(5059-5061)TCT>GCT	p.S1687A	DMXL1_uc010jcl.1_Missense_Mutation_p.S1687A	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1687										ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GAATGCTTTTTCTTTGCTAGG	0.358													73	428	---	---	---	---	PASS
PAIP2	51247	broad.mit.edu	37	5	138699475	138699475	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138699475T>C	uc003led.2	+	2	179	c.2T>C	c.(1-3)ATG>ACG	p.M1T	PAIP2_uc003lee.2_Missense_Mutation_p.M1T|PAIP2_uc003lef.2_Missense_Mutation_p.M1T	NM_016480	NP_057564	Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	1					negative regulation of translational initiation	cytoplasm	protein binding|translation repressor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			ACATCAGCCATGAAAGATCCA	0.333													103	167	---	---	---	---	PASS
PCDHAC2	56134	broad.mit.edu	37	5	140348756	140348756	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140348756G>A	uc003lii.2	+	1	2645	c.2405G>A	c.(2404-2406)GGG>GAG	p.G802E	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron|PCDHAC2_uc011dag.1_Missense_Mutation_p.G802E	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1	802	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGGCTCAGGGAGTGACACT	0.557													4	115	---	---	---	---	PASS
ZNF300	91975	broad.mit.edu	37	5	150276423	150276423	+	Silent	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150276423T>C	uc003lsy.1	-	6	645	c.378A>G	c.(376-378)AAA>AAG	p.K126K	IRGM_uc011dcl.1_Intron	NM_052860	NP_443092	Q96RE9	ZN300_HUMAN	zinc finger protein 300	126					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTTGACAGACTTTTAAAATGG	0.423													95	167	---	---	---	---	PASS
ZNF300	91975	broad.mit.edu	37	5	150276453	150276453	+	Silent	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150276453T>C	uc003lsy.1	-	6	615	c.348A>G	c.(346-348)ACA>ACG	p.T116T	IRGM_uc011dcl.1_Intron	NM_052860	NP_443092	Q96RE9	ZN300_HUMAN	zinc finger protein 300	116					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AACCATCCCTTGTGACTCCTT	0.408													83	139	---	---	---	---	PASS
GEMIN5	25929	broad.mit.edu	37	5	154270986	154270986	+	Silent	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154270986G>A	uc003lvx.3	-	26	4160	c.4077C>T	c.(4075-4077)CTC>CTT	p.L1359L	GEMIN5_uc011ddk.1_Silent_p.L1358L	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	1359					ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTTCTGAAAAGAGCTCCTTAA	0.468													85	286	---	---	---	---	PASS
ZNF165	7718	broad.mit.edu	37	6	28054028	28054028	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28054028C>G	uc003nkg.2	+	4	1574	c.490C>G	c.(490-492)CAG>GAG	p.Q164E	ZNF165_uc003nkh.2_Missense_Mutation_p.Q164E|ZNF165_uc003nki.3_Missense_Mutation_p.Q164E	NM_003447	NP_003438	P49910	ZN165_HUMAN	zinc finger protein 165	164					viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TGTCAAGTTACAGCCAGTGGA	0.438													40	117	---	---	---	---	PASS
ABCF1	23	broad.mit.edu	37	6	30551602	30551602	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30551602T>C	uc003nql.2	+	12	1132	c.1037T>C	c.(1036-1038)CTC>CCC	p.L346P	ABCF1_uc003nqk.2_Missense_Mutation_p.L347P|ABCF1_uc003nqm.2_Missense_Mutation_p.L308P|ABCF1_uc010jsb.2_Intron|MIR877_hsa-mir-877|MI0005561_5'Flank	NM_001025091	NP_001020262	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F, member 1	346	ABC transporter 1.				inflammatory response|translational initiation	nuclear envelope|nuclear envelope|nucleoplasm|nucleoplasm|polysomal ribosome	ATP binding|ATP binding|ATPase activity|protein binding|ribosome binding|translation activator activity|translation factor activity, nucleic acid binding			ovary(2)	2						ACCACACTCCTCAAGCACATT	0.547													3	13	---	---	---	---	PASS
XPO5	57510	broad.mit.edu	37	6	43517659	43517659	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43517659C>T	uc003ovp.2	-	16	1952	c.1741G>A	c.(1741-1743)GTC>ATC	p.V581I		NM_020750	NP_065801	Q9HAV4	XPO5_HUMAN	exportin 5	581	Necessary for interaction with ILF3.				gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			TCAAAAGTGACAGATGAAAAT	0.244													6	692	---	---	---	---	PASS
XPO5	57510	broad.mit.edu	37	6	43528033	43528033	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43528033C>T	uc003ovp.2	-	11	1314	c.1103G>A	c.(1102-1104)CGC>CAC	p.R368H		NM_020750	NP_065801	Q9HAV4	XPO5_HUMAN	exportin 5	368					gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			AGTTGAAGAGCGTAGAAACTA	0.363													38	114	---	---	---	---	PASS
GPR116	221395	broad.mit.edu	37	6	46826546	46826546	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46826546C>T	uc003oyo.3	-	17	3383	c.3094G>A	c.(3094-3096)GTT>ATT	p.V1032I	GPR116_uc011dwj.1_Missense_Mutation_p.V587I|GPR116_uc011dwk.1_Missense_Mutation_p.V461I|GPR116_uc003oyp.3_Missense_Mutation_p.V890I|GPR116_uc003oyq.3_Missense_Mutation_p.V1032I|GPR116_uc010jzi.1_Missense_Mutation_p.V704I	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor	1032	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			GCTTCCACAACTAGACAGGCT	0.507													18	46	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51612746	51612746	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51612746G>T	uc003pah.1	-	58	9944	c.9668C>A	c.(9667-9669)TCA>TAA	p.S3223*	PKHD1_uc010jzn.1_Nonsense_Mutation_p.S1206*|PKHD1_uc003pai.2_Nonsense_Mutation_p.S3223*	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3223	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					CAAGTTGGCTGAGTGCGGCTT	0.463													47	106	---	---	---	---	PASS
LMBRD1	55788	broad.mit.edu	37	6	70459302	70459302	+	Splice_Site	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70459302T>C	uc003pfa.2	-	5	521	c.406_splice	c.e5-1	p.Q136_splice	LMBRD1_uc003pez.2_Splice_Site_p.Q63_splice|LMBRD1_uc010kal.2_Splice_Site_p.Q63_splice|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838	Q9NUN5	LMBD1_HUMAN	liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1						TTTAATTTGCTAGATGCCAAG	0.318													5	283	---	---	---	---	PASS
HBS1L	10767	broad.mit.edu	37	6	135303606	135303606	+	Silent	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135303606A>G	uc003qez.2	-	13	1794	c.1587T>C	c.(1585-1587)TGT>TGC	p.C529C	HBS1L_uc003qey.2_Silent_p.C365C|HBS1L_uc011ecy.1_Silent_p.C253C|HBS1L_uc011ecz.1_Silent_p.C365C|HBS1L_uc011eda.1_Silent_p.C487C	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	Hsp70 subfamily B suppressor 1-like protein	529					signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CTTTCACGGTACAAGTTTCAT	0.378													5	331	---	---	---	---	PASS
UTRN	7402	broad.mit.edu	37	6	144811221	144811221	+	Silent	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144811221G>A	uc003qkt.2	+	30	4241	c.4149G>A	c.(4147-4149)GAG>GAA	p.E1383E		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	1383	Interaction with SYNM.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TCCAAGCAGAGATCTCAGCCC	0.423													39	126	---	---	---	---	PASS
H2AFV	94239	broad.mit.edu	37	7	44874056	44874056	+	3'UTR	SNP	A	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44874056A>C	uc003tma.2	-	5					H2AFV_uc003tlz.2_Intron|H2AFV_uc011kca.1_5'Flank|H2AFV_uc003tmb.2_3'UTR|H2AFV_uc003tmc.2_3'UTR|H2AFV_uc003tmd.2_3'UTR	NM_012412	NP_036544	Q71UI9	H2AV_HUMAN	H2A histone family, member V isoform 1						nucleosome assembly	nucleosome|nucleus	DNA binding				0						TGTCCCAGTTACAGTACAATG	0.388													11	242	---	---	---	---	PASS
CDK14	5218	broad.mit.edu	37	7	90356089	90356089	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90356089A>T	uc003uky.2	+	3	554	c.332A>T	c.(331-333)GAG>GTG	p.E111V	CDK14_uc003ukt.1_Missense_Mutation_p.E65V|CDK14_uc003ukv.1_Missense_Mutation_p.E65V|CDK14_uc003uku.1_Missense_Mutation_p.E65V|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Missense_Mutation_p.E93V|CDK14_uc010les.1_Missense_Mutation_p.E65V|CDK14_uc011khl.1_Missense_Mutation_p.S14C	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1	111					cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						ACTGGCAAAGAGTCACCTAAA	0.438													17	80	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100677624	100677624	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100677624C>T	uc003uxp.1	+	3	2980	c.2927C>T	c.(2926-2928)TCG>TTG	p.S976L	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	976	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|14.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					ATACCAACCTCGACTCCTAGT	0.507													12	232	---	---	---	---	PASS
UBR5	51366	broad.mit.edu	37	8	103288055	103288055	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103288055G>T	uc003ykr.1	-	46	6544	c.6511C>A	c.(6511-6513)CCA>ACA	p.P2171T	UBR5_uc003yks.1_Missense_Mutation_p.P2171T	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	2171					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			CTACACTGTGGCCTGTAAGAA	0.408													5	98	---	---	---	---	PASS
JAK2	3717	broad.mit.edu	37	9	5126444	5126444	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5126444G>T	uc010mhm.2	+	23	3402	c.3289G>T	c.(3289-3291)GAG>TAG	p.E1097*	JAK2_uc003ziw.2_Nonsense_Mutation_p.E1097*	NM_004972	NP_004963	O60674	JAK2_HUMAN	Janus kinase 2	1097	Protein kinase 2.				actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)		ATGCCCAGATGAGGTAACAAT	0.363		1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				103	239	---	---	---	---	PASS
C9orf128	392307	broad.mit.edu	37	9	35826098	35826098	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35826098G>C	uc010mlc.2	-	2	346	c.61C>G	c.(61-63)CCT>GCT	p.P21A	C9orf128_uc003zyj.2_RNA|C9orf128_uc011lpg.1_Missense_Mutation_p.P21A	NM_001012446	NP_001012448	A6H8Z2	CI128_HUMAN	hypothetical protein LOC392307	21											0	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)			TCCTTTGAAGGGGGGTGCTTC	0.498											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	30	63	---	---	---	---	PASS
ZFAND5	7763	broad.mit.edu	37	9	74971941	74971941	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74971941C>T	uc004aiv.2	-	5	677	c.399G>A	c.(397-399)CAG>CAA	p.Q133Q	ZFAND5_uc010mox.1_Silent_p.Q30Q|ZFAND5_uc010moy.1_Silent_p.Q133Q|ZFAND5_uc004aix.2_Silent_p.Q133Q|ZFAND5_uc004aiw.2_Silent_p.Q133Q|ZFAND5_uc004aiy.2_Silent_p.Q133Q	NM_006007	NP_005998	O76080	ZFAN5_HUMAN	zinc finger, AN1-type domain 5	133							DNA binding|zinc ion binding				0						AAGTACTGGGCTGAGAAACTG	0.383													5	603	---	---	---	---	PASS
ZER1	10444	broad.mit.edu	37	9	131495800	131495800	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131495800C>T	uc004bwa.1	-	15	2581	c.2148G>A	c.(2146-2148)AAG>AAA	p.K716K		NM_006336	NP_006327	Q7Z7L7	ZER1_HUMAN	zyg-11 homolog B (C. elegans)-like	716	ARM 5.				ATP hydrolysis coupled proton transport|regulation of ubiquitin-protein ligase activity	Cul2-RING ubiquitin ligase complex|vacuolar proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism|ubiquitin-protein ligase activity			ovary(1)	1						GAGGGCAGTACTTGTCCGCTG	0.567											OREG0019523	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	69	---	---	---	---	PASS
C9orf114	51490	broad.mit.edu	37	9	131587284	131587284	+	Silent	SNP	A	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131587284A>T	uc004bwd.2	-	8	710	c.684T>A	c.(682-684)ACT>ACA	p.T228T	C9orf114_uc004bwe.2_Silent_p.T228T|C9orf114_uc010mym.2_Intron	NM_016390	NP_057474	Q5T280	CI114_HUMAN	hypothetical protein LOC51490	228											0						TCAGTCGCACAGTCACCCGAA	0.592													7	55	---	---	---	---	PASS
OGDHL	55753	broad.mit.edu	37	10	50960187	50960187	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50960187G>A	uc001jie.2	-	5	728	c.586C>T	c.(586-588)CGC>TGC	p.R196C	OGDHL_uc009xog.2_Missense_Mutation_p.R223C|OGDHL_uc010qgt.1_Missense_Mutation_p.R139C|OGDHL_uc010qgu.1_5'UTR|OGDHL_uc009xoh.2_5'UTR	NM_018245	NP_060715	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like isoform a	196					glycolysis	mitochondrial matrix	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			pancreas(1)	1						ACCTCCAGGCGCCGAATGATC	0.567													6	29	---	---	---	---	PASS
SUPV3L1	6832	broad.mit.edu	37	10	70958902	70958902	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70958902A>G	uc001jpe.1	+	10	1302	c.1247A>G	c.(1246-1248)GAC>GGC	p.D416G	SUPV3L1_uc010qjd.1_Missense_Mutation_p.D285G	NM_003171	NP_003162	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 precursor	416	Helicase C-terminal.				DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2						GATCCCAATGACCCATGCAAA	0.323													6	411	---	---	---	---	PASS
RPP30	10556	broad.mit.edu	37	10	92660488	92660488	+	3'UTR	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92660488T>C	uc009xtx.2	+	11					RPP30_uc001khd.2_Intron	NM_006413	NP_006404	P78346	RPP30_HUMAN	ribonuclease P/MRP 30kDa subunit isoform b						tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0						TTATAGTTCATCAGCCACAAC	0.373													7	47	---	---	---	---	PASS
TRIM6-TRIM34	445372	broad.mit.edu	37	11	5655129	5655129	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5655129G>C	uc001mbf.2	+	9	1825	c.1581G>C	c.(1579-1581)AAG>AAC	p.K527N	HBG2_uc001mak.1_Intron|TRIM34_uc001mbh.2_Missense_Mutation_p.K173N|TRIM34_uc009yeq.2_5'UTR|TRIM34_uc001mbi.2_Missense_Mutation_p.K173N|TRIM34_uc001mbj.2_Missense_Mutation_p.K173N	NM_001003819	NP_001003819	B2RNG4	B2RNG4_HUMAN	tripartite motif-containing 6 and tripartite	527						intracellular	zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)		CTTCCTGGAAGGCAAGAGGAG	0.473													60	137	---	---	---	---	PASS
HSD17B12	51144	broad.mit.edu	37	11	43852783	43852783	+	Intron	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43852783T>C	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						AGGGTTGTAGTGGTTCCTTTA	0.483													4	12	---	---	---	---	PASS
FOLH1	2346	broad.mit.edu	37	11	49168304	49168304	+	3'UTR	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49168304C>T	uc001ngy.2	-	19					FOLH1_uc001ngx.2_3'UTR|FOLH1_uc001ngz.2_3'UTR|FOLH1_uc009yly.2_3'UTR|FOLH1_uc009ylz.2_3'UTR|FOLH1_uc009yma.2_3'UTR	NM_004476	NP_004467	Q04609	FOLH1_HUMAN	folate hydrolase 1 isoform 1						proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)|ovary(1)|skin(1)	3					Capromab(DB00089)|L-Glutamic Acid(DB00142)	TCTAAAGAATCCTCTTAGGCT	0.393													34	251	---	---	---	---	PASS
OR5J2	282775	broad.mit.edu	37	11	55944981	55944981	+	Silent	SNP	C	T	T	rs142214796	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55944981C>T	uc010rjb.1	+	1	888	c.888C>T	c.(886-888)GAC>GAT	p.D296D		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	296	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)					GAAACAAGGACGTAAAGGAGG	0.383													4	218	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62290074	62290074	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62290074T>A	uc001ntl.2	-	5	12115	c.11815A>T	c.(11815-11817)AAG>TAG	p.K3939*	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	3939					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				ATGCTGATCTTGGGCATTTTT	0.502													36	83	---	---	---	---	PASS
SLC29A2	3177	broad.mit.edu	37	11	66130881	66130881	+	3'UTR	SNP	C	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66130881C>A	uc001oht.2	-	12					SLC29A2_uc001ohs.2_3'UTR|SLC29A2_uc010rpb.1_RNA|SLC29A2_uc009yrf.2_3'UTR|SLC29A2_uc001ohu.2_3'UTR|SLC29A2_uc001ohv.2_3'UTR	NM_001532	NP_001523	Q14542	S29A2_HUMAN	solute carrier family 29 (nucleoside						cell proliferation|nucleobase, nucleoside and nucleotide metabolic process	basolateral plasma membrane|integral to plasma membrane|nuclear membrane|nucleolus	nucleoside transmembrane transporter activity			ovary(1)	1						CGAGAAGAGGCTGCCAAAGAG	0.642													7	34	---	---	---	---	PASS
YAP1	10413	broad.mit.edu	37	11	101984953	101984953	+	Silent	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101984953T>C	uc001pgt.2	+	2	770	c.400T>C	c.(400-402)TTG>CTG	p.L134L	YAP1_uc001pgs.2_Silent_p.L134L|YAP1_uc001pgu.2_Silent_p.L134L|YAP1_uc001pgv.2_Silent_p.L134L|YAP1_uc010ruo.1_5'UTR|YAP1_uc001pgw.2_5'UTR	NM_001130145	NP_001123617	P46937	YAP1_HUMAN	Yes-associated protein 1, 65kDa isoform 1	134					cell proliferation|cellular response to gamma radiation|contact inhibition|hippo signaling cascade|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		TTCTCTGCAGTTGGGAGCTGT	0.527													5	48	---	---	---	---	PASS
EXPH5	23086	broad.mit.edu	37	11	108382795	108382795	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108382795T>A	uc001pkk.2	-	6	3550	c.3439A>T	c.(3439-3441)ATG>TTG	p.M1147L	EXPH5_uc010rvy.1_Missense_Mutation_p.M959L|EXPH5_uc010rvz.1_Missense_Mutation_p.M991L|EXPH5_uc010rwa.1_Missense_Mutation_p.M1071L	NM_015065	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5 isoform a	1147					intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		GAAGCATCCATGCCTGAGGTC	0.468													28	149	---	---	---	---	PASS
NCAM1	4684	broad.mit.edu	37	11	113078566	113078566	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113078566A>T	uc009yyq.1	+	7	1098	c.404A>T	c.(403-405)CAG>CTG	p.Q135L	NCAM1_uc001pno.2_Missense_Mutation_p.Q135L	NM_001076682	NP_001070150	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1 isoform 3	253	Ig-like C2-type 3.|Extracellular (Potential).				axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GATGGGGAACAGATAGAGCAA	0.423													5	116	---	---	---	---	PASS
C12orf53	196500	broad.mit.edu	37	12	6806817	6806817	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6806817C>T	uc001qqf.1	-	3	235	c.159G>A	c.(157-159)TCG>TCA	p.S53S	C12orf53_uc001qqg.1_Silent_p.S53S	NM_153685	NP_710152	Q8IYJ0	CL053_HUMAN	hypothetical protein LOC196500 precursor	53	Extracellular (Potential).					integral to membrane					0						GACGTGGGGCCGAGGGGCCTC	0.697													4	6	---	---	---	---	PASS
SUOX	6821	broad.mit.edu	37	12	56395974	56395974	+	Intron	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56395974T>C	uc001six.2	+						SUOX_uc009zoh.2_Intron|SUOX_uc001siy.2_Intron|SUOX_uc001siz.2_Intron|SUOX_uc001sja.2_5'UTR	NM_000456	NP_000447	P51687	SUOX_HUMAN	sulfite oxidase precursor							mitochondrial intermembrane space	electron carrier activity|molybdenum ion binding|sulfite oxidase activity				0			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			CCTATCTTGATCCCAGAATCT	0.562													43	161	---	---	---	---	PASS
GLI1	2735	broad.mit.edu	37	12	57861144	57861144	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57861144G>T	uc001snx.2	+	9	1019	c.941G>T	c.(940-942)CGC>CTC	p.R314L	GLI1_uc009zpq.2_Missense_Mutation_p.R186L	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	314	C2H2-type 3.				epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	15			GBM - Glioblastoma multiforme(3;3.99e-32)			TCATACTCACGCCTCGAAAAC	0.542													15	66	---	---	---	---	PASS
LLPH	84298	broad.mit.edu	37	12	66517664	66517664	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66517664T>C	uc010ssw.1	-	3	402	c.346A>G	c.(346-348)AGC>GGC	p.S116G	LLPH_uc010ssx.1_RNA	NM_032338	NP_115714	Q9BRT6	LLPH_HUMAN	LLP homolog	116	Lys-rich.										0						TTTGCTTTGCTTTTCCCCTTT	0.428													8	694	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78401106	78401106	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78401106C>T	uc001syp.2	+	8	1961	c.1788C>T	c.(1786-1788)TCC>TCT	p.S596S	NAV3_uc001syo.2_Silent_p.S596S	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	596						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						CTTCTGGTTCCTGTACCATGA	0.522										HNSCC(70;0.22)			22	70	---	---	---	---	PASS
SSH1	54434	broad.mit.edu	37	12	109210974	109210974	+	Intron	SNP	G	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109210974G>C	uc001tnm.2	-						SSH1_uc010sxg.1_Intron|SSH1_uc001tnn.3_Intron|SSH1_uc001tno.1_Missense_Mutation_p.Q8E	NM_018984	NP_061857	Q8WYL5	SSH1_HUMAN	slingshot 1 isoform 1						actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4						ACCTGCCTTTGGAGGTGGTGC	0.522													9	29	---	---	---	---	PASS
PIWIL1	9271	broad.mit.edu	37	12	130839159	130839159	+	Silent	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130839159G>T	uc001uik.2	+	10	1212	c.1122G>T	c.(1120-1122)GGG>GGT	p.G374G	PIWIL1_uc001uij.1_Silent_p.G374G	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	374	PAZ.				gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		GCCCTGGGGGGACACTGCCAG	0.542													7	15	---	---	---	---	PASS
C13orf26	122046	broad.mit.edu	37	13	31549022	31549022	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31549022A>G	uc001uti.2	+	7	867	c.848A>G	c.(847-849)GAC>GGC	p.D283G		NM_152325	NP_689538	Q8N6G2	CM026_HUMAN	hypothetical protein LOC122046	283										ovary(2)|skin(1)	3		Lung SC(185;0.0281)		all cancers(112;0.0176)|Epithelial(112;0.0768)|OV - Ovarian serous cystadenocarcinoma(117;0.0852)		ACTCACTGTGACACTAACAAA	0.294													8	594	---	---	---	---	PASS
TRPC4	7223	broad.mit.edu	37	13	38211534	38211534	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38211534T>C	uc001uws.2	-	11	2675	c.2440A>G	c.(2440-2442)AGA>GGA	p.R814G	TRPC4_uc010abv.2_Missense_Mutation_p.R394G|TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Missense_Mutation_p.R641G|TRPC4_uc010abx.2_Missense_Mutation_p.R819G|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	814	Binds to ITPR1, ITPR2 and ITPR3.|Cytoplasmic (Potential).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		ATGTTATGTCTTTCAGAGGCA	0.438													7	251	---	---	---	---	PASS
DGKH	160851	broad.mit.edu	37	13	42795441	42795441	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42795441C>G	uc001uyl.1	+	29	3505	c.3484C>G	c.(3484-3486)CTG>GTG	p.L1162V	DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron|DGKH_uc010tfi.1_Intron|DGKH_uc010tfj.1_Missense_Mutation_p.L1017V|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.L1017V|DGKH_uc001uyp.2_Intron	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	1162	SAM.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TTGGCTGGATCTGCTCAATTT	0.428													9	557	---	---	---	---	PASS
TPP2	7174	broad.mit.edu	37	13	103275383	103275383	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103275383C>T	uc001vpi.3	+	6	880	c.777C>T	c.(775-777)ACC>ACT	p.T259T		NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II	259					proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CCATTGTGACCAGTGGAGGTA	0.403													100	242	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33292794	33292794	+	Silent	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33292794A>G	uc001wrq.2	+	13	5945	c.5775A>G	c.(5773-5775)AAA>AAG	p.K1925K		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1925					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		CACATGGGAAAGAGATTTCAG	0.378													5	152	---	---	---	---	PASS
INO80	54617	broad.mit.edu	37	15	41279359	41279359	+	Silent	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41279359G>A	uc001zni.2	-	31	3975	c.3762C>T	c.(3760-3762)TTC>TTT	p.F1254F	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	1254	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.|Helicase C-terminal.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						TATCTGGTTTGAAGTTCCCAC	0.438													51	116	---	---	---	---	PASS
TMEM87A	25963	broad.mit.edu	37	15	42531886	42531886	+	Silent	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42531886T>C	uc010udd.1	-	8	825	c.666A>G	c.(664-666)GAA>GAG	p.E222E	TMEM87A_uc001zpf.3_Silent_p.E161E|TMEM87A_uc010bcu.1_Silent_p.E161E	NM_015497	NP_056312	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A isoform 1	222						integral to membrane				ovary(1)	1		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		AGGGATAGTCTTCAAGTGTGA	0.358													6	307	---	---	---	---	PASS
ELL3	80237	broad.mit.edu	37	15	44066816	44066816	+	Silent	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44066816T>C	uc001zsw.1	-	7	1204	c.801A>G	c.(799-801)GAA>GAG	p.E267E	ELL3_uc001zsv.1_Silent_p.E221E|ELL3_uc001zsx.1_Silent_p.E152E|uc001zsy.2_5'Flank	NM_025165	NP_079441	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	267					positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				ovary(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		AGGAACTGTGTTCTAATCTGG	0.448													8	613	---	---	---	---	PASS
MYO5C	55930	broad.mit.edu	37	15	52517293	52517293	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52517293T>C	uc010bff.2	-	27	3481	c.3344A>G	c.(3343-3345)GAC>GGC	p.D1115G	MYO5C_uc010uga.1_RNA	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	1115	Potential.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)		ATCTTCAATGTCATAGCTTTC	0.323													7	587	---	---	---	---	PASS
DAPK2	23604	broad.mit.edu	37	15	64200798	64200798	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64200798C>A	uc002amr.2	-	12	1065	c.1034G>T	c.(1033-1035)AGG>ATG	p.R345M	DAPK2_uc010uim.1_RNA	NM_014326	NP_055141	Q9UIK4	DAPK2_HUMAN	death-associated kinase 2	345					apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)		CTCACAGTTCCTCTGGAGAAA	0.587													11	17	---	---	---	---	PASS
LOC390595	390595	broad.mit.edu	37	15	65386873	65386873	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65386873C>A	uc010uit.1	-	4	1095	c.951G>T	c.(949-951)CAG>CAT	p.Q317H	LOC390595_uc002aok.2_Missense_Mutation_p.Q317H|LOC390595_uc010bhe.2_RNA	NM_001163692	NP_001157164	F5GYI3	F5GYI3_HUMAN	hypothetical protein LOC390595	317											0						CCTCATATCCCTGACGTAACA	0.632													20	50	---	---	---	---	PASS
PAQR5	54852	broad.mit.edu	37	15	69677202	69677202	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69677202C>T	uc002arz.2	+	5	744	c.366C>T	c.(364-366)GCC>GCT	p.A122A	PAQR5_uc002asa.2_Silent_p.A122A	NM_017705	NP_060175	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	122	Helical; Name=3; (Potential).				cell differentiation|multicellular organismal development|oogenesis	integral to membrane	receptor activity|steroid binding			ovary(2)	2						ACTATGGTGCCGTCAACCTCT	0.562													4	191	---	---	---	---	PASS
GOLGA6L10	647042	broad.mit.edu	37	15	83014132	83014132	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83014132C>G	uc010uny.1	-	6	513	c.415G>C	c.(415-417)GAG>CAG	p.E139Q	GOLGA6L10_uc010unt.1_RNA|uc002bhl.2_Intron|uc002bhm.2_Intron|GOLGA6L10_uc002bia.1_5'Flank	NM_198181	NP_937824	A6NI86	GG6LA_HUMAN	golgi autoantigen, golgin subfamily a, 6D-like	151											0						GCTGGGGGCTCTGGGGCCAGG	0.522													3	23	---	---	---	---	PASS
BTBD12	84464	broad.mit.edu	37	16	3641170	3641170	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3641170C>T	uc002cvp.2	-	12	3096	c.2469G>A	c.(2467-2469)TGG>TGA	p.W823*		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	823	Potential.|Interaction with PLK1 and TERF2-TERF2IP.|Glu-rich.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0						CTTCATCTGCCCACATTGACC	0.458								Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				34	302	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													5	32	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268081	70268081	+	RNA	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268081G>A	uc010cfp.1	-	3		c.334C>T								Homo sapiens cDNA, FLJ98908.																		TCTTACTGTTGGCTAAAAGGC	0.373													4	33	---	---	---	---	PASS
VAC14	55697	broad.mit.edu	37	16	70834811	70834811	+	Translation_Start_Site	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70834811G>T	uc002ezm.2	-	1	251	c.-7C>A	c.(-9--5)AGCTG>AGATG		VAC14_uc010cfw.2_Translation_Start_Site|VAC14_uc002ezn.2_Translation_Start_Site	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog						interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				CATGGTGGCAGCTGGGGGAAC	0.557													6	11	---	---	---	---	PASS
GLG1	2734	broad.mit.edu	37	16	74503886	74503886	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74503886T>C	uc002fcy.3	-	16	2365	c.2315A>G	c.(2314-2316)AAG>AGG	p.K772R	GLG1_uc002fcx.2_Missense_Mutation_p.K772R|GLG1_uc002fcw.3_Missense_Mutation_p.K761R|GLG1_uc002fcz.3_Missense_Mutation_p.K189R	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	772	Cys-rich GLG1 11.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						TACATACTTCTTTTTTATGTT	0.443													8	263	---	---	---	---	PASS
ADAD2	161931	broad.mit.edu	37	16	84229248	84229248	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84229248G>T	uc002fhr.2	+	6	1111	c.997G>T	c.(997-999)GTC>TTC	p.V333F	ADAD2_uc002fhq.2_Missense_Mutation_p.V415F|uc002fhs.1_Intron	NM_001145400	NP_001138872	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2 isoform	333	A to I editase.				RNA processing	intracellular	adenosine deaminase activity|double-stranded RNA binding				0						CAAGCCCCGCGTCTTCCTGCA	0.711													8	21	---	---	---	---	PASS
ITGAE	3682	broad.mit.edu	37	17	3659186	3659186	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3659186C>T	uc002fwo.3	-	11	1276	c.1177G>A	c.(1177-1179)GTT>ATT	p.V393I		NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	393	FG-GAP 3.|Extracellular (Potential).				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GCGTCTCCAACCGTGCCTGCA	0.572													3	43	---	---	---	---	PASS
CCDC144A	9720	broad.mit.edu	37	17	16631046	16631046	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16631046C>T	uc002gqk.1	+	9	2173	c.2097C>T	c.(2095-2097)TAC>TAT	p.Y699Y	CCDC144A_uc002gql.1_Silent_p.Y169Y|LOC162632_uc010cpj.1_RNA	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	699	Potential.										0						AAGAGCTGTACGATTTGAGGT	0.313													18	328	---	---	---	---	PASS
TMIGD1	388364	broad.mit.edu	37	17	28659164	28659164	+	5'UTR	SNP	A	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28659164A>C	uc002hfa.1	-	2					TMIGD1_uc010csh.1_5'UTR	NM_206832	NP_996663	Q6UXZ0	TMIG1_HUMAN	transmembrane and immunoglobulin domain							integral to membrane					0						TTAATGAGTTAAACTCAGATC	0.363													5	259	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29562634	29562634	+	Silent	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29562634A>G	uc002hgg.2	+	28	4047	c.3714A>G	c.(3712-3714)GAA>GAG	p.E1238E	NF1_uc002hgh.2_Silent_p.E1238E|NF1_uc010csn.1_Silent_p.E1098E|NF1_uc002hgi.1_Silent_p.E271E	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1238	Ras-GAP.				actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CTCAGGATGAACTAGCTCGAG	0.383			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			6	390	---	---	---	---	PASS
DHX40P1	653645	broad.mit.edu	37	17	58091725	58091725	+	5'UTR	SNP	T	C	C			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58091725T>C	uc002iyf.2	-	3					uc010wor.1_5'Flank	NR_002924				Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 40 pseudogene, mRNA (cDNA clone IMAGE:5170263).												0						TCCAGGTCCATCTGCTGGATG	0.522													16	107	---	---	---	---	PASS
TBX4	9496	broad.mit.edu	37	17	59557596	59557596	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59557596C>A	uc002izi.2	+	7	982	c.937C>A	c.(937-939)CTC>ATC	p.L313I	TBX4_uc010ddo.2_Missense_Mutation_p.L313I|TBX4_uc010woy.1_Missense_Mutation_p.L313I	NM_018488	NP_060958	P57082	TBX4_HUMAN	T-box 4	313					leg morphogenesis|skeletal system morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2						ACACTCACAGCTCGCGGAGCC	0.647													8	13	---	---	---	---	PASS
TEX2	55852	broad.mit.edu	37	17	62228234	62228234	+	Silent	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62228234G>A	uc002jec.2	-	11	3401	c.3228C>T	c.(3226-3228)GAC>GAT	p.D1076D	TEX2_uc002jed.2_Silent_p.D1083D|TEX2_uc002jee.2_Silent_p.D1076D	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2	1076					signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		TCTCTATCCAGTCTGTCACAT	0.418													64	381	---	---	---	---	PASS
ST6GALNAC2	10610	broad.mit.edu	37	17	74563616	74563616	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74563616C>G	uc002jsg.3	-	8	1131	c.876G>C	c.(874-876)TTG>TTC	p.L292F		NM_006456	NP_006447	Q9UJ37	SIA7B_HUMAN	sialyltransferase 7B	292	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	sialyltransferase activity				0						GTGTGTTAATCAACTTTGATT	0.438													82	204	---	---	---	---	PASS
DSG1	1828	broad.mit.edu	37	18	28934934	28934934	+	Silent	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28934934A>G	uc002kwp.2	+	15	2987	c.2775A>G	c.(2773-2775)AGA>AGG	p.R925R	DSG1_uc010xbp.1_Silent_p.R284R	NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	925	Cytoplasmic (Potential).|Desmoglein repeat 4.				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			TGACAGAAAGAGTAATCCAAC	0.458													5	187	---	---	---	---	PASS
DEFB129	140881	broad.mit.edu	37	20	207960	207960	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:207960C>T	uc002wda.2	+	1	36	c.31C>T	c.(31-33)CTC>TTC	p.L11F		NM_080831	NP_543021	Q9H1M3	DB129_HUMAN	beta defensin 129 precursor	11					defense response to bacterium	extracellular region				ovary(1)	1		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CTTTGCCAGCCTCATGCTACA	0.483													55	157	---	---	---	---	PASS
TH1L	51497	broad.mit.edu	37	20	57561823	57561823	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57561823G>A	uc002yag.2	+	3	245	c.218G>A	c.(217-219)GGA>GAA	p.G73E	TH1L_uc010zzu.1_Missense_Mutation_p.G73E|TH1L_uc002yaf.1_RNA|TH1L_uc002yah.2_Missense_Mutation_p.G73E	NM_198976	NP_945327	Q8IXH7	NELFD_HUMAN	TH1-like protein	73					negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	all_lung(29;0.00711)		Colorectal(105;0.109)			TTTCAGGCAGGAGGGTCTCCA	0.483													120	403	---	---	---	---	PASS
IFNAR2	3455	broad.mit.edu	37	21	34632973	34632973	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34632973A>T	uc002yrd.2	+	8	1109	c.781A>T	c.(781-783)ATA>TTA	p.I261L	IFNAR2_uc002yrb.2_Missense_Mutation_p.I261L|IFNAR2_uc002yrc.2_Missense_Mutation_p.I261L|IFNAR2_uc002yre.2_Missense_Mutation_p.I261L|IFNAR2_uc002yrf.2_Intron|IFNAR2_uc002yrg.2_Missense_Mutation_p.I130L|IL10RB_uc002yrh.1_Intron|IL10RB_uc002yri.1_Intron	NM_207585	NP_997468	P48551	INAR2_HUMAN	interferon alpha/beta receptor 2 isoform a	261	Helical; (Potential).				JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to interferon-alpha|response to virus|type I interferon-mediated signaling pathway	extracellular region|extracellular space|integral to plasma membrane	protein kinase binding|type I interferon binding|type I interferon receptor activity				0					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)	GACAAGCACCATAGTGACACT	0.294													5	443	---	---	---	---	PASS
HSF2BP	11077	broad.mit.edu	37	21	45053264	45053264	+	Silent	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45053264C>T	uc002zdi.2	-	5	662	c.330G>A	c.(328-330)AAG>AAA	p.K110K	HSF2BP_uc011aey.1_Silent_p.K35K	NM_007031	NP_008962	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding	110					spermatogenesis|transcription from RNA polymerase II promoter	cytosol	binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.18)		GGAGTTGCTGCTTCGCTTCAT	0.438													4	189	---	---	---	---	PASS
C21orf67	84536	broad.mit.edu	37	21	46353962	46353962	+	3'UTR	SNP	G	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46353962G>T	uc011afm.1	-	4						NR_027128				RecName: Full=Uncharacterized protein C21orf67;												0						gtctgggtggggccggagact	0.214													3	25	---	---	---	---	PASS
POFUT2	23275	broad.mit.edu	37	21	46689908	46689908	+	Silent	SNP	G	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46689908G>A	uc002zhc.2	-	7	883	c.858C>T	c.(856-858)GGC>GGT	p.G286G	POFUT2_uc002zha.2_RNA|POFUT2_uc002zhb.2_RNA|POFUT2_uc002zhd.2_Silent_p.G286G	NM_133635	NP_598368	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2 isoform C	286					fucose metabolic process	endoplasmic reticulum	peptide-O-fucosyltransferase activity				0				Colorectal(79;0.243)		CCAGGTAGGGGCCCCCTAGCG	0.602													29	57	---	---	---	---	PASS
SMARCB1	6598	broad.mit.edu	37	22	24175884	24175884	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24175884A>G	uc002zyb.2	+	8	1319	c.1112A>G	c.(1111-1113)AAC>AGC	p.N371S	SMARCB1_uc002zya.2_Intron|SMARCB1_uc002zyc.2_Missense_Mutation_p.N362S|SMARCB1_uc002zyd.2_Missense_Mutation_p.N380S	NM_003073	NP_003064	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin	371					cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex	p53 binding	p.?(2)|p.L266_*386del(1)		soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1)	407		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				CAGGACAGGAACACGAGGTAC	0.622			D|N|F|S		malignant rhabdoid 	malignant rhabdoid			Rhabdoid_Predisposition_syndrome|Schwannomatosis				4	68	---	---	---	---	PASS
UPB1	51733	broad.mit.edu	37	22	24906778	24906778	+	Silent	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24906778A>G	uc003aaf.2	+	4	547	c.426A>G	c.(424-426)GCA>GCG	p.A142A	UPB1_uc003aae.2_Silent_p.A74A|UPB1_uc011ajt.1_Silent_p.A142A	NM_016327	NP_057411	Q9UBR1	BUP1_HUMAN	beta-ureidopropionase	142	CN hydrolase.				pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)					CTGAGTCAGCAGAGGATGGGC	0.488													12	139	---	---	---	---	PASS
C22orf13	83606	broad.mit.edu	37	22	24938958	24938958	+	3'UTR	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24938958C>T	uc003aah.2	-	6					C22orf13_uc003aal.2_3'UTR|C22orf13_uc003aai.3_3'UTR|C22orf13_uc003aaj.3_3'UTR|C22orf13_uc003aak.3_3'UTR	NM_031444	NP_113632	Q96NT3	CV013_HUMAN	chromosome 22 open reading frame 13												0						GGCCTAGGCGCACCAGGCTCC	0.627													23	55	---	---	---	---	PASS
POLR2F	5435	broad.mit.edu	37	22	38349736	38349736	+	Translation_Start_Site	SNP	C	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38349736C>A	uc003aul.2	+	1	63	c.-58C>A	c.(-60--56)CGCTG>CGATG		C22orf23_uc003auj.1_5'Flank|C22orf23_uc003auk.1_5'Flank|POLR2F_uc010gxi.2_Translation_Start_Site|POLR2F_uc003aum.2_RNA	NM_021974	NP_068809	P61218	RPAB2_HUMAN	DNA directed RNA polymerase II polypeptide F						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex|nucleolus	DNA binding|DNA-directed RNA polymerase activity			breast(1)	1	Melanoma(58;0.045)					CGTAGTGTCGCTGTTTGCGGG	0.657													10	17	---	---	---	---	PASS
TBL1X	6907	broad.mit.edu	37	X	9621602	9621602	+	5'UTR	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9621602C>T	uc010ndq.2	+	4					TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_5'UTR	NM_001139466	NP_001132938	O60907	TBL1X_HUMAN	transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)				GGCCTCCTTGCAGAAACATCG	0.582													9	13	---	---	---	---	PASS
KIF4A	24137	broad.mit.edu	37	X	69622483	69622483	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69622483C>T	uc004dyg.2	+	23	2684	c.2557C>T	c.(2557-2559)CGC>TGC	p.R853C	KIF4A_uc010nkw.2_Missense_Mutation_p.R853C	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	853	Potential.|Interaction with PRC1.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4						ACCAAAACAACGCTGGGAGAA	0.468													26	132	---	---	---	---	PASS
RBM41	55285	broad.mit.edu	37	X	106310800	106310800	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106310800A>G	uc004emz.2	-	7	1230	c.1199T>C	c.(1198-1200)ATA>ACA	p.I400T	RBM41_uc004emy.1_Missense_Mutation_p.I400T	NM_018301	NP_060771	Q96IZ5	RBM41_HUMAN	RNA binding motif protein 41	400							nucleotide binding|RNA binding			ovary(1)	1						AGCACATGATATGAGAGAAGT	0.368													5	381	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	1318117	1318117	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1318117delC								AURKAIP1 (7299 upstream) : CCNL2 (2974 downstream)																							ATCCAGAGGTCACCACCCCTT	0.488													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	16841472	16841472	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16841472delT								CROCCL2 (22276 upstream) : NBPF1 (48940 downstream)																							ATCTTGTAGGTTTTTTTTTTT	0.378													4	2	---	---	---	---	
WNT4	54361	broad.mit.edu	37	1	22461334	22461335	+	Intron	INS	-	TG	TG			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22461334_22461335insTG	uc001bfs.3	-						WNT4_uc010odt.1_Intron	NM_030761	NP_110388	P56705	WNT4_HUMAN	wingless-type MMTV integration site family,						adrenal gland development|androgen biosynthetic process|anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cellular response to transforming growth factor beta stimulus|dermatome development|endoderm development|epithelial to mesenchymal transition|establishment of protein localization in plasma membrane|female gonad development|female sex determination|liver development|male gonad development|mesonephric tubule development|metanephric mesenchymal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of male gonad development|negative regulation of testicular blood vessel morphogenesis|negative regulation of testosterone biosynthetic process|negative regulation of transcription, DNA-dependent|oocyte development|paramesonephric duct development|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of collagen biosynthetic process|positive regulation of cortisol biosynthetic process|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|protein palmitoylation|renal vesicle formation|smooth muscle cell differentiation|somatotropin secreting cell differentiation|tertiary branching involved in mammary gland duct morphogenesis|thyroid-stimulating hormone-secreting cell differentiation|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|extracellular space|Golgi apparatus|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|signal transducer activity|transcription corepressor activity			ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		TTCTGCTCATTTGTGTGTGTGT	0.574													4	2	---	---	---	---	
FCN3	8547	broad.mit.edu	37	1	27697630	27697630	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27697630delT	uc001boa.2	-						FCN3_uc001bob.2_Intron	NM_003665	NP_003656	O75636	FCN3_HUMAN	ficolin 3 isoform 1 precursor						complement activation, lectin pathway|signal transduction	collagen|extracellular space	receptor binding|sugar binding				0		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GAACTCTACATTCCCTTGTTA	0.463													4	2	---	---	---	---	
TRIT1	54802	broad.mit.edu	37	1	40307167	40307167	+	3'UTR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40307167delA	uc010oiz.1	-	11					TRIT1_uc001cec.3_RNA|TRIT1_uc001ced.3_3'UTR|TRIT1_uc001cee.3_RNA|TRIT1_uc001cef.3_RNA|TRIT1_uc001ceg.3_3'UTR|TRIT1_uc001ceh.3_3'UTR|TRIT1_uc009vvv.2_3'UTR|TRIT1_uc001cei.3_3'UTR|TRIT1_uc001ceq.2_3'UTR|TRIT1_uc001cek.2_3'UTR|TRIT1_uc009vvx.2_RNA|TRIT1_uc001cel.2_RNA|TRIT1_uc001cem.2_3'UTR|TRIT1_uc001cen.2_3'UTR|TRIT1_uc001ceo.2_3'UTR|TRIT1_uc001cep.2_3'UTR	NM_017646	NP_060116	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1 precursor						tRNA processing	mitochondrion	ATP binding|metal ion binding|tRNA dimethylallyltransferase activity			ovary(1)	1	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGGTTCAAAGAAAAAAAAAAT	0.378													4	2	---	---	---	---	
ZNF643	65243	broad.mit.edu	37	1	40920061	40920061	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40920061delT	uc001cfn.1	+						ZNF643_uc001cfl.1_Intron|ZNF643_uc001cfm.1_Intron	NM_023070	NP_075558	Q9UJL9	ZN643_HUMAN	zinc finger protein 643						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.25e-18)			TTGGCTtttctttttttttct	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	63468613	63468614	+	IGR	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63468613_63468614insT								ATG4C (138564 upstream) : FOXD3 (320116 downstream)																							TCATTGGAGGGTTTTTTTTTTC	0.366													4	2	---	---	---	---	
NEGR1	257194	broad.mit.edu	37	1	72011242	72011243	+	Intron	DEL	TT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72011242_72011243delTT	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		TGTCTCTCTCTTTCTGTCCCCT	0.356													4	2	---	---	---	---	
AK5	26289	broad.mit.edu	37	1	78004550	78004550	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78004550delG	uc001dhn.2	+						AK5_uc001dho.2_Intron	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1						ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1						TCTGATTTCTGGAATCTTCCT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88613016	88613017	+	IGR	INS	-	A	A	rs142394454	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88613016_88613017insA								LMO4 (798413 upstream) : PKN2 (536905 downstream)																							atacaaagtgcaaaaaaaagat	0.000													3	7	---	---	---	---	
PKN2	5586	broad.mit.edu	37	1	89255932	89255932	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89255932delT	uc001dmn.2	+						PKN2_uc001dmm.1_Intron|PKN2_uc010osp.1_Intron|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Intron|PKN2_uc010osr.1_Intron	NM_006256	NP_006247	Q16513	PKN2_HUMAN	protein kinase N2						signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		ttgctttacctcctcatgctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	107623489	107623490	+	IGR	INS	-	C	C	rs72502343	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107623489_107623490insC								PRMT6 (21582 upstream) : NTNG1 (59139 downstream)																							AAAAACACAAATTTTTTGTCAT	0.351													1	6	---	---	---	---	
NTNG1	22854	broad.mit.edu	37	1	107736797	107736797	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107736797delC	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697	Q9Y2I2	NTNG1_HUMAN	netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		agcctgtcctccctctaCCTC	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	114836757	114836757	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114836757delT								SYT6 (140285 upstream) : TRIM33 (98644 downstream)																							CCTGAGAACATGGAGATGAGC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142540540	142540544	+	IGR	DEL	TGGAG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142540540_142540544delTGGAG								None (None upstream) : None (None downstream)																							aggaatgggatggagtggagtggag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142649812	142649812	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142649812delG	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		ttcttgagcagtaggtgtcaa	0.000													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145002425	145002426	+	Intron	INS	-	A	A	rs147987741		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145002425_145002426insA	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron|uc001emi.3_5'Flank	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ATTATACAAATAAAAGTTTAAT	0.272			T	PDGFRB	MPD								2	5	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145054413	145054413	+	Intron	DEL	C	-	-	rs146644913		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145054413delC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						AAGTGCTACACCAAGCAGAAC	0.289													4	2	---	---	---	---	
ITGA10	8515	broad.mit.edu	37	1	145530534	145530534	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145530534delA	uc001eoa.2	+						NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Intron|ITGA10_uc009wiw.2_Intron|ITGA10_uc010oyw.1_Intron	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor						cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					aatatgaaagaaaaaaaaaat	0.025													5	4	---	---	---	---	
TMOD4	29765	broad.mit.edu	37	1	151147849	151147849	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151147849delA	uc001exc.3	-						TMOD4_uc001exd.2_Intron|TMOD4_uc010pct.1_Intron	NM_013353	NP_037485	Q9NZQ9	TMOD4_HUMAN	tropomodulin 4 (muscle)						muscle contraction	cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TAAACCGGATAAAAAAACCAA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159564701	159564702	+	IGR	INS	-	A	A	rs140197770	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159564701_159564702insA								APCS (6041 upstream) : CRP (117378 downstream)																							GCAACCAGTAGAAAAAAAagag	0.401													4	7	---	---	---	---	
GAS5	60674	broad.mit.edu	37	1	173834333	173834333	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173834333delA	uc001gji.2	-						GAS5_uc001gjj.2_Intron|GAS5_uc001gjk.2_RNA|SNORD81_uc009wwi.1_5'Flank|SNORD47_uc001gjl.2_5'Flank|SNORD80_uc009wwj.1_5'Flank|ZBTB37_uc001gjp.1_5'Flank					Homo sapiens mRNA; cDNA DKFZp564D0164 (from clone DKFZp564D0164).												0						actcttgtctaaaaaaaaaaa	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177361796	177361796	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177361796delA								FAM5B (110239 upstream) : SEC16B (535693 downstream)																							TGGCAACAACAACAAAATGCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	188040128	188040129	+	IGR	INS	-	T	T	rs149794004	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188040128_188040129insT								None (None upstream) : None (None downstream)																							ttgctgggaagtaaaatgctat	0.000													3	5	---	---	---	---	
TMEM9	252839	broad.mit.edu	37	1	201112088	201112088	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201112088delC	uc001gvw.2	-						TMEM9_uc001gvx.2_Intron|TMEM9_uc001gvy.2_Intron|TMEM9_uc010ppo.1_Intron|TMEM9_uc001gvz.2_Intron|TMEM9_uc001gwa.2_Intron	NM_016456	NP_057540	Q9P0T7	TMEM9_HUMAN	transmembrane protein 9 precursor						transport	integral to membrane|late endosome membrane|lysosomal membrane					0		Breast(1374;0.000301)				ACGTCTCACTCCCACGAAGAG	0.572													4	2	---	---	---	---	
ZC3H11A	9877	broad.mit.edu	37	1	203816133	203816133	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203816133delA	uc001hac.2	+						ZC3H11A_uc001had.2_Intron|ZC3H11A_uc001hae.2_Intron|ZC3H11A_uc001haf.2_Intron|ZC3H11A_uc010pqm.1_Intron|ZC3H11A_uc001hag.1_Intron	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A								nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			actctgtcttaaaaaaaaaaa	0.070													4	2	---	---	---	---	
CR2	1380	broad.mit.edu	37	1	207648021	207648022	+	Intron	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207648021_207648022insA	uc001hfw.2	+						CR2_uc001hfv.2_Intron|CR2_uc009xch.2_Intron	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)						complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						AAGCTGTTTTTAAAAAAAGCAT	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	221965538	221965539	+	IGR	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221965538_221965539insT								DUSP10 (50077 upstream) : HHIPL2 (730063 downstream)																							ACCTATAAGTCTTTTTTTTTTT	0.248													4	2	---	---	---	---	
TRIM58	25893	broad.mit.edu	37	1	248023727	248023728	+	Intron	INS	-	ACA	ACA	rs142315385	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248023727_248023728insACA	uc001ido.2	+							NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58							intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			cgcaacactgcacaacctgagt	0.094													4	3	---	---	---	---	
TRIB2	28951	broad.mit.edu	37	2	12861055	12861055	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12861055delT	uc002rbv.3	+						TRIB2_uc010yjp.1_Intron	NM_021643	NP_067675	Q92519	TRIB2_HUMAN	tribbles homolog 2						negative regulation of fat cell differentiation|negative regulation of interleukin-10 biosynthetic process|negative regulation of protein kinase activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity	cytoplasm|cytoskeleton|nucleus	ATP binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			stomach(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GAATGGGTACTTTTTTTTTGC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23533266	23533266	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23533266delC								None (None upstream) : KLHL29 (222189 downstream)																							TTCCTGTTCTCCCTCTCAGCC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23579337	23579337	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23579337delA								None (None upstream) : KLHL29 (176118 downstream)																							AAACCTGGGTAAAAAATAAAA	0.388													4	2	---	---	---	---	
DTNB	1838	broad.mit.edu	37	2	25678013	25678013	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25678013delG	uc002rgh.2	-						DTNB_uc002rgg.2_Intron|DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707	O60941	DTNB_HUMAN	dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATATTTTTTGAGTGTAAGCT	0.428													4	2	---	---	---	---	
CIB4	130106	broad.mit.edu	37	2	26836503	26836503	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26836503delG	uc002rhm.2	-							NM_001029881	NP_001025052	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tttttcagatggggaaagctg	0.244													4	2	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29456183	29456184	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29456183_29456184insT	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	taatttttaaattttttttggt	0.000			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	30235400	30235400	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30235400delT								ALK (90968 upstream) : YPEL5 (134350 downstream)																							ttgacattagtttttttaaag	0.000													4	2	---	---	---	---	
LBH	81606	broad.mit.edu	37	2	30480654	30480656	+	3'UTR	DEL	GCC	-	-	rs113721073		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30480654_30480656delGCC	uc002rne.2	+	3						NM_030915	NP_112177	Q53QV2	LBH_HUMAN	limb bud and heart development homolog						multicellular organismal development|transcription, DNA-dependent	cytoplasm|nucleolus					0	Acute lymphoblastic leukemia(172;0.155)					ttcttttcttgcctttttttttt	0.429													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35772028	35772028	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35772028delA								None (None upstream) : CRIM1 (811369 downstream)																							ctgagtgagcaaaaaaaaaaa	0.000													3	4	---	---	---	---	
EIF2AK2	5610	broad.mit.edu	37	2	37368086	37368087	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37368086_37368087insT	uc010ynh.1	-						EIF2AK2_uc010fab.1_Intron|EIF2AK2_uc010yng.1_Intron|EIF2AK2_uc010fac.2_Intron|EIF2AK2_uc010fad.2_Intron	NM_002759	NP_002750	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha						evasion by virus of host immune response|modulation by virus of host cellular process|negative regulation of osteoblast proliferation|protein autophosphorylation|response to virus|viral infectious cycle	cytosol	ATP binding|double-stranded RNA binding|eukaryotic translation initiation factor 2alpha kinase activity|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|lung(2)|pancreas(1)	5		all_hematologic(82;0.248)				TTGATTTCTGCTTTTTTCAGTT	0.332													4	2	---	---	---	---	
STON1	11037	broad.mit.edu	37	2	48755411	48755413	+	5'Flank	DEL	TCC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48755411_48755413delTCC	uc002rwo.3	+						STON1_uc010fbm.2_5'Flank	NM_006873	NP_006864	Q9Y6Q2	STON1_HUMAN	stonin 1						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex				skin(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTTCTTCCGTTCCTCCTCCTCCT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67481818	67481824	+	Intron	DEL	AGAATAC	-	-	rs11277709		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67481818_67481824delAGAATAC	uc002sdx.2	+											Homo sapiens, clone IMAGE:5541055, mRNA.																		cccaatagctagaatacacagggccat	0.000													3	4	---	---	---	---	
ARHGAP25	9938	broad.mit.edu	37	2	68961908	68961909	+	5'Flank	INS	-	AC	AC	rs141359242	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68961908_68961909insAC	uc002seu.2	+						ARHGAP25_uc010yqk.1_Intron|ARHGAP25_uc010fdg.2_5'Flank|ARHGAP25_uc010yql.1_5'Flank	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4						TTAAAAAAGAAACACACACACA	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91791556	91791557	+	IGR	DEL	TT	-	-	rs10569836		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91791556_91791557delTT								None (None upstream) : LOC654342 (13635 downstream)																							GATTAAAGTCTTTTAGAAATGT	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92194836	92194837	+	IGR	INS	-	T	T	rs145003390		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92194836_92194837insT								FKSG73 (64342 upstream) : None (None downstream)																							AGAGCAGGCTCTTGCCCACATC	0.495													5	3	---	---	---	---	
CHST10	9486	broad.mit.edu	37	2	101025637	101025637	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101025637delC	uc002tam.2	-							NM_004854	NP_004845	O43529	CHSTA_HUMAN	HNK-1 sulfotransferase						carbohydrate biosynthetic process|cell adhesion	Golgi membrane|integral to membrane|membrane fraction				ovary(1)	1						CCCCTGATCACCCTCGCCCGG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105591261	105591261	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105591261delA								POU3F3 (117791 upstream) : MRPS9 (63222 downstream)																							tgaggcttttaagtaggagat	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118271797	118271797	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118271797delC								None (None upstream) : DDX18 (300458 downstream)																							TTGAGTTGGTCCCCATTGAAC	0.433													4	2	---	---	---	---	
DDX18	8886	broad.mit.edu	37	2	118581453	118581454	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118581453_118581454insT	uc002tlh.1	+							NM_006773	NP_006764	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18								ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|ovary(1)|lung(1)	4						atggtcaaatgttttttttctg	0.000													4	2	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121529114	121529115	+	Intron	DEL	AA	-	-	rs72502183		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121529114_121529115delAA	uc010yyu.1	+						GLI2_uc002tmp.1_Intron			P10070	GLI2_HUMAN	SubName: Full=cDNA FLJ60878, highly similar to Homo sapiens GLI-Kruppel family member GLI2, mRNA;						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				GTGAAGACAGAAGATGTTTCTG	0.411													3	6	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121529120	121529121	+	Intron	INS	-	A	A	rs2311403		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121529120_121529121insA	uc010yyu.1	+						GLI2_uc002tmp.1_Intron			P10070	GLI2_HUMAN	SubName: Full=cDNA FLJ60878, highly similar to Homo sapiens GLI-Kruppel family member GLI2, mRNA;						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				ACAGAAGATGTTTCTGTTGAAA	0.431													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121858051	121858052	+	IGR	DEL	TC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121858051_121858052delTC								GLI2 (107823 upstream) : TFCP2L1 (116114 downstream)																							GGctctcctttctctctctctc	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133096858	133096858	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133096858delA								NCRNA00164 (81316 upstream) : GPR39 (77289 downstream)																							caacaacaataaaaaaaacaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133118606	133118606	+	IGR	DEL	C	-	-	rs151129987	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133118606delC								NCRNA00164 (103064 upstream) : GPR39 (55541 downstream)																							AATCTTAACTCCATCGCCTAC	0.488													4	2	---	---	---	---	
MGAT5	4249	broad.mit.edu	37	2	135168946	135168947	+	Intron	INS	-	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135168946_135168947insG	uc002ttv.1	+							NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)		AGCCAGCATTAGGGGCTCTGCT	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	136843298	136843298	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136843298delA								DARS (100076 upstream) : CXCR4 (28622 downstream)																							atgaggatttaaaaaaaaaat	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139227459	139227459	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139227459delA	uc002tvg.2	-											full-length cDNA clone CS0DL004YM17 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																		aatatttaacaaaaaaaaaag	0.144													4	3	---	---	---	---	
UPP2	151531	broad.mit.edu	37	2	158992099	158992100	+	3'UTR	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158992099_158992100insT	uc002tzp.2	+	7					UPP2_uc002tzo.2_3'UTR	NM_173355	NP_775491	O95045	UPP2_HUMAN	uridine phosphorylase 2 isoform a						nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0						CCTTCTAGCCATTTTTTCTTGT	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176096713	176096713	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176096713delT								ATP5G3 (50223 upstream) : KIAA1715 (693697 downstream)																							GTCTAGAAACTTTTTTTTTTG	0.328													4	4	---	---	---	---	
NFE2L2	4780	broad.mit.edu	37	2	178127028	178127028	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178127028delG	uc002ulh.3	-						NFE2L2_uc002ulg.3_Intron|NFE2L2_uc010zfa.1_Intron|NFE2L2_uc002uli.3_Intron|NFE2L2_uc010fra.2_Intron|NFE2L2_uc010frb.2_Intron	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			CCCTCATCTAGGAAAGTGCTT	0.393			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			4	2	---	---	---	---	
PDE11A	50940	broad.mit.edu	37	2	178906802	178906803	+	Intron	INS	-	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178906802_178906803insG	uc002ulq.2	-						PDE11A_uc002ulr.2_Intron|PDE11A_uc002ult.1_Intron	NM_016953	NP_058649	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)			TTCTTGTGTGAGGAAAGAGGAC	0.332									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				4	2	---	---	---	---	
PLEKHA3	65977	broad.mit.edu	37	2	179351321	179351322	+	Intron	INS	-	CTTA	CTTA	rs145560289	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179351321_179351322insCTTA	uc002umn.2	+							NM_019091	NP_061964	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A							cytoplasm|membrane				ovary(1)|kidney(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			ataagtgttgtcttttaatgtt	0.109													0	6	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179633980	179633980	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179633980delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002unb.2_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAATTAACAAttttttttctt	0.184													4	2	---	---	---	---	
PPP1R1C	151242	broad.mit.edu	37	2	182906593	182906593	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182906593delT	uc002uoo.2	+						PPP1R1C_uc002uon.2_Intron|PPP1R1C_uc002uop.1_Intron|PPP1R1C_uc010frm.1_Intron|PPP1R1C_uc010frn.1_Intron	NM_001080545	NP_001074014	Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor)						signal transduction	cytoplasm	protein phosphatase inhibitor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0628)			TTTATTCTGCTTTTGGCAGCT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	204762304	204762304	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204762304delT								CTLA4 (23621 upstream) : ICOS (39167 downstream)																							AATAATTATGTTTTTTCCCCT	0.353													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	205325897	205325897	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205325897delT								ICOS (499601 upstream) : PARD3B (84619 downstream)																							TAGTCCCTTCTTTTTTTTTAT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206785006	206785007	+	IGR	INS	-	AAA	AAA	rs67779539	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206785006_206785007insAAA								NRP2 (122150 upstream) : INO80D (73439 downstream)																							aagaaagaaaggagaaagaaag	0.173													5	3	---	---	---	---	
CRYGB	1419	broad.mit.edu	37	2	209011954	209011954	+	5'Flank	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209011954delT	uc002vcp.3	-							NM_005210	NP_005201	P07316	CRGB_HUMAN	crystallin, gamma B						visual perception		structural constituent of eye lens				0				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		CTGCCTGCTGTTTGGTGTTCC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	237868395	237868395	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237868395delA								CXCR7 (377403 upstream) : COPS8 (125689 downstream)																							TTTAAAAACTAAAAAGCAGAA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240426921	240426922	+	IGR	DEL	GA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240426921_240426922delGA								HDAC4 (103575 upstream) : NDUFA10 (473236 downstream)																							gtgtgtgtgtgagagagagaga	0.347													3	3	---	---	---	---	
ATG4B	23192	broad.mit.edu	37	2	242610453	242610453	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242610453delG	uc002wbv.2	+						ATG4B_uc002wbu.2_Intron|ATG4B_uc002wbw.2_Intron|ATG4B_uc010zox.1_Intron|ATG4B_uc010zoy.1_Intron|ATG4B_uc010fzp.2_Intron|ATG4B_uc010zoz.1_Intron|ATG4B_uc002wby.2_Intron	NM_013325	NP_037457	Q9Y4P1	ATG4B_HUMAN	APG4 autophagy 4 homolog B isoform a						autophagic vacuole assembly|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		GTCCTCATCCGTCTCCTGTTG	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	41232047	41232047	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41232047delT								ZNF621 (651004 upstream) : CTNNB1 (4354 downstream)																							ATAAAGTTGCTTTCAAGATCA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	46554990	46554990	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46554990delA								RTP3 (12551 upstream) : LRRC2 (1890 downstream)																							GAGATACTAGAAAAAAATGTC	0.318													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52581862	52581862	+	3'UTR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52581862delA	uc003des.2	-	30					PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_3'UTR|PBRM1_uc003der.2_3'UTR|PBRM1_uc003det.2_3'UTR|PBRM1_uc003deu.2_3'UTR|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_3'UTR|PBRM1_uc010hmk.1_3'UTR|PBRM1_uc003dey.2_3'UTR	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						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)		AAACATATGCAAAAAAATCTT	0.289			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								4	2	---	---	---	---	
ITIH1	3697	broad.mit.edu	37	3	52815594	52815594	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52815594delA	uc003dfs.2	+						ITIH1_uc010hmn.1_Intron|ITIH1_uc003dft.2_5'Flank|ITIH1_uc010hmo.1_5'Flank	NM_002215	NP_002206	P19827	ITIH1_HUMAN	inter-alpha (globulin) inhibitor H1						hyaluronan metabolic process|leukocyte activation	extracellular region	calcium ion binding|serine-type endopeptidase inhibitor activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		GTTCTTTGTCAACCTGGGCAG	0.408													4	2	---	---	---	---	
UBA3	9039	broad.mit.edu	37	3	69112881	69112881	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69112881delT	uc003dno.2	-						UBA3_uc003dnq.2_Intron|UBA3_uc011bfy.1_Intron|UBA3_uc011bfz.1_Intron	NM_003968	NP_003959	Q8TBC4	UBA3_HUMAN	ubiquitin-activating enzyme 3 isoform 1						protein neddylation|proteolysis	nucleus	acid-amino acid ligase activity|ATP binding|protein heterodimerization activity			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)		taaagtttactaattaaaaaA	0.159													5	3	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	85149962	85149963	+	Intron	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85149962_85149963insA	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		GCATGTAATTCAAAAATTACTT	0.282													4	2	---	---	---	---	
NSUN3	63899	broad.mit.edu	37	3	93845542	93845542	+	3'UTR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93845542delG	uc003drl.1	+	6						NM_022072	NP_071355	Q9H649	NSUN3_HUMAN	NOL1/NOP2/Sun domain family, member 3								methyltransferase activity			skin(1)	1						GATTTAAGGTGGTGCAGATGG	0.289													4	2	---	---	---	---	
LOC152225	152225	broad.mit.edu	37	3	101658010	101658010	+	5'Flank	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101658010delA	uc003dvr.1	+							NR_026934				Homo sapiens cDNA FLJ33269 fis, clone ASTRO2007578.												0						cagtgtatctaaaatgaagcc	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	118318573	118318573	+	Intron	DEL	A	-	-	rs113545673		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118318573delA	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																		tctaccccccaccccacacac	0.000													2	4	---	---	---	---	
NPHP3	27031	broad.mit.edu	37	3	132417745	132417745	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132417745delT	uc003epe.1	-						NPHP3_uc003epd.1_Intron	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						cccaaatccctttttttttgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137045115	137045116	+	IGR	DEL	GA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137045115_137045116delGA								IL20RB (315195 upstream) : SOX14 (438463 downstream)																							ATCAGGTAAGGAGAGAGAGATT	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	143881434	143881434	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143881434delT								C3orf58 (170225 upstream) : None (None downstream)																							AAGGAGAAGCTTTTAGCTCTT	0.179													4	2	---	---	---	---	
TM4SF4	7104	broad.mit.edu	37	3	149216352	149216353	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149216352_149216353insT	uc003exd.1	+							NM_004617	NP_004608	P48230	T4S4_HUMAN	transmembrane 4 superfamily member 4							integral to membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			aaAACTGTACATTTTGTGGTAT	0.183													10	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162744147	162744148	+	Intron	DEL	CT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162744147_162744148delCT	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																		ATATGACAGCctctctctctct	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189265763	189265763	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189265763delT								TPRG1 (224493 upstream) : TP63 (83453 downstream)																							CTTTGAAAAATTTTTCTCAGT	0.189													4	2	---	---	---	---	
STX18	53407	broad.mit.edu	37	4	4451412	4451412	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4451412delC	uc003gic.2	-							NM_016930	NP_058626	Q9P2W9	STX18_HUMAN	syntaxin 18						ER to Golgi vesicle-mediated transport|intracellular protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	SNAP receptor activity				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		tgctaggcttccccactgtca	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	15328814	15328814	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15328814delT								CPEB2 (257040 upstream) : C1QTNF7 (12746 downstream)																							ATTAAGCACATTTTTACCGAA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	29063891	29063891	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29063891delA								None (None upstream) : None (None downstream)																							taggattgctaaatcatatgg	0.000													4	2	---	---	---	---	
KIAA1239	57495	broad.mit.edu	37	4	37389821	37389821	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37389821delT	uc011bxz.1	+							NM_001144990	NP_001138462	Q9ULI1	K1239_HUMAN	hypothetical protein LOC57495												0						ttttgttttgtttttttaaga	0.060													4	2	---	---	---	---	
RUFY3	22902	broad.mit.edu	37	4	71641155	71641156	+	Intron	DEL	TT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71641155_71641156delTT	uc003hfq.2	+						RUFY3_uc003hfp.3_Intron|RUFY3_uc011cax.1_Intron|RUFY3_uc003hfr.2_Intron|RUFY3_uc011cay.1_Intron	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			Gtatataatgttatatataata	0.149													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	83403557	83403557	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83403557delA								ENOPH1 (21314 upstream) : TMEM150C (2047 downstream)																							cagaacttctaaaaccgttga	0.000													4	2	---	---	---	---	
CDS1	1040	broad.mit.edu	37	4	85561782	85561782	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85561782delT	uc011ccv.1	+						CDS1_uc010ike.1_Intron	NM_001263	NP_001254	Q92903	CDS1_HUMAN	CDP-diacylglycerol synthase 1						signal transduction|visual perception	endoplasmic reticulum membrane|integral to membrane	diacylglycerol cholinephosphotransferase activity|phosphatidate cytidylyltransferase activity			large_intestine(2)|ovary(1)|breast(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		TCAAAAAAACTTTTTTTTTCT	0.269													4	2	---	---	---	---	
UNC5C	8633	broad.mit.edu	37	4	96388460	96388460	+	Intron	DEL	T	-	-	rs35044968		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96388460delT	uc003htp.1	-						UNC5C_uc010ilc.1_Intron|UNC5C_uc003htq.2_Intron	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		atgcaATCACTTTTTTTGGAA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	115174250	115174251	+	IGR	DEL	AA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115174250_115174251delAA								ARSJ (273372 upstream) : UGT8 (345360 downstream)																							aaaaaataacaaaaaaaaaagt	0.000													3	3	---	---	---	---	
PDE5A	8654	broad.mit.edu	37	4	120514165	120514165	+	Intron	DEL	A	-	-	rs34873286		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120514165delA	uc003idh.2	-						PDE5A_uc003idf.2_Intron|PDE5A_uc003idg.2_Intron	NM_001083	NP_001074	O76074	PDE5A_HUMAN	phosphodiesterase 5A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)	GTGGGGTTACATATTCATGTA	0.279													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120844650	120844651	+	IGR	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120844650_120844651insA								PDE5A (294669 upstream) : MAD2L1 (135928 downstream)																							TGGAAAAAATGTTAATAGCCTG	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	126146537	126146537	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126146537delC								ANKRD50 (512650 upstream) : FAT4 (91030 downstream)																							gtacttctgaccaaAAGTGTG	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	160428017	160428017	+	IGR	DEL	T	-	-	rs71798752		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160428017delT								RAPGEF2 (146718 upstream) : None (None downstream)																							ATTCAAACTCTTTTTTTTTTC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	166664003	166664003	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166664003delA								CPE (244522 upstream) : TLL1 (130407 downstream)																							ACCCAATTCTAATCATGAGCC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188284171	188284172	+	IGR	DEL	CA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188284171_188284172delCA								FAT1 (636321 upstream) : ZFP42 (632753 downstream)																							gacacccaggcacacacacaca	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190545398	190545399	+	IGR	INS	-	ATT	ATT	rs35790619		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190545398_190545399insATT								None (None upstream) : FRG1 (316575 downstream)																							ttgtggaagacgttgtgatcac	0.119													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190845829	190845830	+	Intron	INS	-	A	A	rs148088473		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190845829_190845830insA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		atccaaattggaaaaaaaagtc	0.000													4	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	11724	11724	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11724delT								None (None upstream) : PLEKHG4B (128649 downstream)																							accctaaccctaaccctaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3323011	3323012	+	IGR	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3323011_3323012insA								C5orf38 (567499 upstream) : IRX1 (273156 downstream)																							catgtggtgtgtgatgtgCCTG	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3871547	3871548	+	IGR	INS	-	T	T	rs112758937		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3871547_3871548insT								IRX1 (270031 upstream) : None (None downstream)																							ggaggtggttattttttttctt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	4266146	4266146	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4266146delT								IRX1 (664630 upstream) : LOC340094 (768326 downstream)																							CTCTAAAATCTTGCATGAAAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8565062	8565062	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8565062delA								MTRR (663829 upstream) : SEMA5A (470076 downstream)																							cataaaatgtatggcagcttc	0.055													4	2	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16775092	16775093	+	Intron	INS	-	G	G	rs149924246	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16775092_16775093insG	uc003jft.3	-							NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						ACCCCAGCCCTGCTCAGTGCCA	0.446													5	3	---	---	---	---	
CDH9	1007	broad.mit.edu	37	5	26904147	26904147	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26904147delA	uc003jgs.1	-						CDH9_uc010iug.2_Intron	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9						taagtcccagaaaaaaaaatt	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	30589309	30589309	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30589309delT								None (None upstream) : CDH6 (604487 downstream)																							taaagattgcttttgggactg	0.000													4	2	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	32100649	32100649	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32100649delG	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc003jhn.2_RNA	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						GCCATAGCCAGGGGCAGGGTT	0.572													4	2	---	---	---	---	
AMACR	23600	broad.mit.edu	37	5	34007609	34007609	+	Intron	DEL	A	-	-	rs138553455		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34007609delA	uc003jig.2	-						AMACR_uc003jih.2_Intron|AMACR_uc003jii.2_Intron|AMACR_uc003jij.2_Intron|AMACR_uc003jil.1_Intron|AMACR_uc003jik.1_Intron	NM_014324	NP_055139	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase isoform 1						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	mitochondrion|peroxisomal matrix	alpha-methylacyl-CoA racemase activity				0						CGTTTCTTAGAAAAAAAAGGA	0.274													4	2	---	---	---	---	
PRLR	5618	broad.mit.edu	37	5	35066375	35066375	+	Intron	DEL	T	-	-	rs77557478		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35066375delT	uc003jjm.2	-						PRLR_uc003jjg.1_Intron|PRLR_uc003jjh.1_Intron|PRLR_uc003jji.1_Intron|PRLR_uc003jjj.1_Intron|PRLR_uc003jjk.1_Intron|PRLR_uc003jjl.3_Intron	NM_000949	NP_000940	P16471	PRLR_HUMAN	prolactin receptor precursor						activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	attcagcagattttttttttt	0.109													3	3	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59763965	59763965	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59763965delT	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron	NM_006203	NP_006194	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	ttcttttttcttttttttttg	0.209													4	2	---	---	---	---	
LOC100170939	100170939	broad.mit.edu	37	5	69515692	69515693	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69515692_69515693insT	uc003jyp.1	-						GUSBP3_uc003jxm.2_Intron|uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|LOC100170939_uc003jyl.2_Intron|LOC100170939_uc003jyo.1_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000370107;												0						GGGGAGGCAAGTGGCATCTCTG	0.446													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	77649803	77649803	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77649803delC								AP3B1 (59275 upstream) : SCAMP1 (6536 downstream)																							CAGAACCCTACCCCAGAGATG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	88991893	88991893	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88991893delT								MEF2C (792024 upstream) : CETN3 (697638 downstream)																							TCATGGTTGCTTTTTGTTAGG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	89466053	89466054	+	IGR	DEL	AC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89466053_89466054delAC								None (None upstream) : CETN3 (223477 downstream)																							AAGTGTGTATACACACACACAC	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96199715	96199716	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96199715_96199716insT	uc003kmo.1	-											Homo sapiens cDNA FLJ37666 fis, clone BRHIP2011576.																		TAAATTCTTGATTTTTTTTTAC	0.322													4	2	---	---	---	---	
NUDT12	83594	broad.mit.edu	37	5	102891991	102891992	+	Intron	DEL	TG	-	-	rs143398928	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102891991_102891992delTG	uc003koi.2	-						NUDT12_uc011cvb.1_Intron	NM_031438	NP_113626	Q9BQG2	NUD12_HUMAN	nudix-type motif 12							nucleus|peroxisome	metal ion binding|NAD+ diphosphatase activity				0		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		TAGATTTTTTTGTTTGAATAAA	0.252													4	2	---	---	---	---	
CAMK4	814	broad.mit.edu	37	5	110655716	110655716	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110655716delA	uc011cvj.1	+						CAMK4_uc003kpf.2_Intron|CAMK4_uc010jbv.2_Intron	NM_001744	NP_001735	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		AGGATGGAATAAAAAAGAATG	0.353													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111625555	111625555	+	Intron	DEL	C	-	-	rs75249306		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111625555delC	uc003kpv.1	-						EPB41L4A_uc003kpw.1_Intron	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		taatttaaagcccctacattt	0.005													3	5	---	---	---	---	
COMMD10	51397	broad.mit.edu	37	5	115498579	115498580	+	Intron	INS	-	T	T	rs144772973	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115498579_115498580insT	uc003krt.1	+							NM_016144	NP_057228	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		TTTTTAAAAAATTATCAGATAT	0.386													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115919754	115919754	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115919754delT								SEMA6A (9203 upstream) : None (None downstream)																							tgactcctccttttttcccat	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116542912	116542912	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116542912delA								SEMA6A (632361 upstream) : None (None downstream)																							ggcagacattaacacttgaat	0.000													4	2	---	---	---	---	
ADAMTS19	171019	broad.mit.edu	37	5	128844467	128844467	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128844467delG	uc003kvb.1	+						ADAMTS19_uc003kvc.1_Intron	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GTGACCCCATGGGTCTCCCAA	0.383													4	2	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	131008745	131008745	+	Intron	DEL	T	-	-	rs12513562		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131008745delT	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron|FNIP1_uc010jdm.1_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		CGtttttttgttttttttttt	0.149													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144908463	144908463	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144908463delA								None (None upstream) : PRELID2 (230119 downstream)																							GTTTAATGGGAAAAAAGAGTA	0.353													4	2	---	---	---	---	
FABP6	2172	broad.mit.edu	37	5	159662781	159662782	+	Intron	DEL	TC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159662781_159662782delTC	uc003lya.1	+						FABP6_uc003lxx.1_Intron|FABP6_uc003lxz.1_Intron	NM_001445	NP_001436	P51161	FABP6_HUMAN	gastrotropin isoform 2						bile acid and bile salt transport|bile acid metabolic process|negative regulation of cell proliferation	cytosol	transporter activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ctttgatccttctctctctctc	0.416													5	3	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168103731	168103732	+	Intron	INS	-	AG	AG	rs138343014	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168103731_168103732insAG	uc003mab.2	-						SLIT3_uc010jjg.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ggtgtgtcaacatgctggacag	0.208													3	4	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168713235	168713238	+	Intron	DEL	AAGC	-	-	rs72277881		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168713235_168713238delAAGC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACTATAGAGGAAGCAAAATTATGT	0.343													5	4	---	---	---	---	
F12	2161	broad.mit.edu	37	5	176831178	176831178	+	Intron	DEL	C	-	-	rs67902409		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176831178delC	uc003mgo.3	-						F12_uc011dfy.1_Intron|F12_uc003mgn.3_5'UTR|F12_uc010jkl.2_Intron	NM_000505	NP_000496	P00748	FA12_HUMAN	coagulation factor XII precursor						Factor XII activation|fibrinolysis|innate immune response|positive regulation of blood coagulation|positive regulation of fibrinolysis|positive regulation of plasminogen activation|protein autoprocessing|response to misfolded protein|zymogen activation	extracellular space|plasma membrane	serine-type endopeptidase activity				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)			GCTCCTCCTTCCCCCCCCCAC	0.736									Hereditary_Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	177411316	177411316	+	IGR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177411316delG								LOC728554 (100049 upstream) : PROP1 (7920 downstream)																							AACCAAAGCTGGACTGGGAAG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	827122	827122	+	IGR	DEL	A	-	-	rs111473937		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:827122delA								EXOC2 (134013 upstream) : LOC285768 (134120 downstream)																							TGGCACTGAgaaaaaaaaaag	0.104													3	3	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5327044	5327045	+	Intron	INS	-	T	T	rs149288618	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5327044_5327045insT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	TGTGCTGTGGATTTTTTTTTCT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	5898052	5898052	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5898052delA								FARS2 (126236 upstream) : NRN1 (100183 downstream)																							ttttaagtataaaaaagatga	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	12585257	12585258	+	IGR	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12585257_12585258insA								EDN1 (287831 upstream) : PHACTR1 (131630 downstream)																							AGGCTTGTCTTAAAAAAAAAGC	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16785747	16785748	+	IGR	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16785747_16785748insA								ATXN1 (24026 upstream) : RBM24 (496061 downstream)																							aaataaaagttaaaaaataaTA	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27731170	27731170	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27731170delT								ZNF184 (290273 upstream) : HIST1H2BL (44088 downstream)																							TTCTGTTGTGTTTTTTAgtta	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29447225	29447226	+	IGR	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29447225_29447226insA								OR2H1 (15128 upstream) : MAS1L (7319 downstream)																							CCTTCCTCAGTAAAAAAAAAAT	0.371													4	2	---	---	---	---	
NUDT3	11165	broad.mit.edu	37	6	34304899	34304902	+	Intron	DEL	TTGT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34304899_34304902delTTGT	uc003ojl.2	-							NM_006703	NP_006694	O95989	NUDT3_HUMAN	nudix-type motif 3						cell-cell signaling|diadenosine polyphosphate catabolic process|diphosphoinositol polyphosphate catabolic process	cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|magnesium ion binding				0						CTTATTTTTATTGTTTGTACATTT	0.299													1	5	---	---	---	---	
TCP11	6954	broad.mit.edu	37	6	35107857	35107857	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35107857delA	uc003okd.2	-						TCP11_uc003ojz.1_5'UTR|TCP11_uc003oka.2_5'UTR|TCP11_uc003okb.2_5'UTR|TCP11_uc003okc.2_5'UTR|TCP11_uc011dsu.1_Intron|TCP11_uc011dsv.1_Intron|TCP11_uc011dsw.1_Intron	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5						TCAGTTAACCAGCAGCGACCT	0.388											OREG0017369	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	179	82	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38743907	38743908	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38743907_38743908insT	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						CCACTAAAGGATTTTTTTTTGA	0.292													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57440798	57440799	+	Intron	INS	-	A	A	rs146617443		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57440798_57440799insA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ctgaacaactcacgatcagaac	0.079													5	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57452326	57452326	+	Intron	DEL	A	-	-	rs67590913		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57452326delA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CCTACAACAGAACCTATGATG	0.378													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57527818	57527818	+	IGR	DEL	G	-	-	rs67858073		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57527818delG								PRIM2 (14443 upstream) : GUSBL2 (718341 downstream)																							AACCAGAACTGGGGGCTGACA	0.348													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57551058	57551058	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57551058delT								PRIM2 (37683 upstream) : GUSBL2 (695101 downstream)																							aaggacctcatccaggagaac	0.000													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	64650210	64650210	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64650210delA	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						aaccattgttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	94149567	94149572	+	IGR	DEL	ACACAC	-	-	rs113978522		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:94149567_94149572delACACAC								EPHA7 (20267 upstream) : TSG1 (267229 downstream)																							CAAATCTTCTacacacacacacacac	0.112													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	97212073	97212073	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97212073delA								FHL5 (147561 upstream) : GPR63 (33816 downstream)																							TGCTGCCTCTAAAAAGGATAT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	115487802	115487802	+	IGR	DEL	T	-	-	rs67332920		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115487802delT								HS3ST5 (824262 upstream) : FRK (774891 downstream)																							AAAGATGCAATTTTTTTGTGC	0.259													4	2	---	---	---	---	
UST	10090	broad.mit.edu	37	6	149207402	149207402	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149207402delA	uc003qmg.2	+							NM_005715	NP_005706	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		ctcctctgttaaaaggggaca	0.065													4	2	---	---	---	---	
PCMT1	5110	broad.mit.edu	37	6	150123757	150123759	+	Intron	DEL	TTG	-	-	rs59621324		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150123757_150123759delTTG	uc003qne.2	+						PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)		TTTTGTTTGTTTGTTTGTTTTTT	0.315													4	2	---	---	---	---	
SNX9	51429	broad.mit.edu	37	6	158290884	158290885	+	Intron	DEL	CA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158290884_158290885delCA	uc003qqv.1	+							NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9						cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		tgcatacccccacacacactcg	0.149													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170728960	170728961	+	IGR	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170728960_170728961insA								FAM120B (14724 upstream) : PSMB1 (51146 downstream)																							CAAATCAAGACAAAAAAAAGTC	0.421													4	2	---	---	---	---	
COL28A1	340267	broad.mit.edu	37	7	7441240	7441241	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7441240_7441241insT	uc003src.1	-						COL28A1_uc011jxe.1_Intron	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor						cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		tgtctatattataccccatatt	0.000													4	2	---	---	---	---	
TMEM195	392636	broad.mit.edu	37	7	15556604	15556604	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15556604delT	uc003stb.1	-							NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0						CACAAGAGTCTTTTTTTTTTG	0.323													4	2	---	---	---	---	
GPNMB	10457	broad.mit.edu	37	7	23312939	23312940	+	Intron	DEL	CA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23312939_23312940delCA	uc003swc.2	+						GPNMB_uc003swb.2_Intron|GPNMB_uc011jyy.1_Intron|GPNMB_uc011jyz.1_Intron	NM_001005340	NP_001005340	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb isoform a						negative regulation of cell proliferation	melanosome				ovary(3)|breast(2)	5			GBM - Glioblastoma multiforme(13;0.154)			CACAGTGTTCCAGACATGCTGA	0.500											OREG0017893	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SKAP2	8935	broad.mit.edu	37	7	26898308	26898309	+	Intron	DEL	AC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26898308_26898309delAC	uc003syc.2	-						SKAP2_uc011jzi.1_5'Flank|SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1						CAAGTATCTAACACACACACAC	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	27459158	27459159	+	IGR	DEL	TG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27459158_27459159delTG								EVX1 (172966 upstream) : HIBADH (105904 downstream)																							CAGCTCACTCTGTGTGTAGGTC	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	38281641	38281641	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38281641delC	uc003tfu.3	-						uc003tfv.2_Intron					SubName: Full=TARP protein;																		CCTGAtttttctttttttttt	0.179													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	47312203	47312203	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47312203delT								None (None upstream) : TNS3 (2550 downstream)																							gttctttttcttttttttagt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56699457	56699457	+	IGR	DEL	A	-	-	rs78077053		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56699457delA								DKFZp434L192 (134480 upstream) : ZNF479 (487871 downstream)																							TTCATAGTCCAAAAAAAAAAT	0.294													8	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64961238	64961238	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64961238delA								ZNF92 (95241 upstream) : INTS4L2 (151539 downstream)																							ACGACATTTTAAAATCTAGAT	0.289													4	2	---	---	---	---	
TYW1B	441250	broad.mit.edu	37	7	72085782	72085782	+	Intron	DEL	C	-	-	rs35569946		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72085782delC	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kei.1_Intron	NM_001145440	NP_001138912	Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0						AAGTTCTTCACCCAAAACTCT	0.368													4	3	---	---	---	---	
SEMA3E	9723	broad.mit.edu	37	7	83153027	83153028	+	Intron	DEL	TT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83153027_83153028delTT	uc003uhy.1	-							NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				ATAAATATTGTTAAGGCCTTTT	0.238													6	3	---	---	---	---	
C7orf63	79846	broad.mit.edu	37	7	89938873	89938873	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89938873delA	uc010lep.2	+						C7orf63_uc011khj.1_Intron|C7orf63_uc011khk.1_Intron	NM_001039706	NP_001034795	A5D8W1	CG063_HUMAN	hypothetical protein LOC79846 isoform 1								binding			ovary(1)	1						aaaaattaataaaaaaaaaaC	0.139													6	3	---	---	---	---	
AKAP9	10142	broad.mit.edu	37	7	91706403	91706403	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91706403delT	uc003ulg.2	+						AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron|AKAP9_uc003ulj.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			attattattattTCtttcttt	0.100			T	BRAF	papillary thyroid								6	4	---	---	---	---	
CFTR	1080	broad.mit.edu	37	7	117270586	117270586	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117270586delT	uc003vjd.2	+						CFTR_uc011knq.1_Intron	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)	caggattttattgggcaaaaa	0.000									Cystic_Fibrosis				4	2	---	---	---	---	
CTTNBP2	83992	broad.mit.edu	37	7	117356191	117356191	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117356191delT	uc003vjf.2	-							NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2											ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		AATAACATAGTTTTTTTTTCT	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	126033242	126033245	+	IGR	DEL	TCTC	-	-	rs138149422		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126033242_126033245delTCTC								None (None upstream) : GRM8 (45407 downstream)																							TCACTACACTtctctctctgtgtg	0.127													2	4	---	---	---	---	
MKLN1	4289	broad.mit.edu	37	7	130905833	130905833	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130905833delG	uc011kpl.1	+							NM_001145354	NP_001138826	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)					cagtgattttgcagcaaacct	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131451303	131451303	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131451303delA								PODXL (209927 upstream) : PLXNA4 (356789 downstream)																							CACTGACAACAAATGAGATGA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131519933	131519933	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131519933delC								PODXL (278557 upstream) : PLXNA4 (288159 downstream)																							AAGAGCTTTACCATCCTACCC	0.473													4	2	---	---	---	---	
PTN	5764	broad.mit.edu	37	7	136981934	136981935	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136981934_136981935insT	uc003vtq.2	-						PTN_uc010lmx.2_Intron|PTN_uc003vtr.1_Intron	NM_002825	NP_002816	P21246	PTN_HUMAN	pleiotrophin						nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			upper_aerodigestive_tract(1)|pancreas(1)	2						GTACATGATCATTTTTTTTCCA	0.307													4	2	---	---	---	---	
PRSS1	5644	broad.mit.edu	37	7	142459337	142459337	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142459337delT	uc003wak.2	+						uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_Intron|PRSS1_uc011ksm.1_3'UTR|PRSS1_uc003wam.2_5'UTR	NM_002769	NP_002760	P07477	TRY1_HUMAN	protease, serine, 1 preproprotein						digestion|proteolysis	extracellular space	metal ion binding|protein binding|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)			TGCTAGTGACTGTGGAGATTG	0.572									Hereditary_Pancreatitis				4	2	---	---	---	---	
TPK1	27010	broad.mit.edu	37	7	144255998	144255998	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144255998delA	uc003weq.2	-						TPK1_uc003weo.2_Intron|TPK1_uc003wep.2_Intron|TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)	gtctgttcccaaaccagcagt	0.154													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146741293	146741294	+	Intron	INS	-	AT	AT	rs148378854	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146741293_146741294insAT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			tgcatagatacatatatatata	0.198										HNSCC(39;0.1)			9	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152106898	152106898	+	Intron	DEL	A	-	-	rs10707629		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152106898delA	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		GTTTTTTTTTAAATCATCATG	0.254			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152965997	152965997	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152965997delT								ACTR3B (413534 upstream) : DPP6 (618422 downstream)																							TGAGGAAGGATTTTTTTTTAA	0.184													4	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158123999	158124003	+	Intron	DEL	ACCAT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158123999_158124003delACCAT	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)		CCACACTCTCACCATAAGAGCTGAG	0.551													2	4	---	---	---	---	
FAM66D	100132923	broad.mit.edu	37	8	12055185	12055189	+	Intron	DEL	CTTTC	-	-	rs138083611		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12055185_12055189delCTTTC	uc011kxp.1	+						uc003wvm.1_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						AAAATTTCCACTTTCCTTAGGCTGT	0.366													3	3	---	---	---	---	
CNOT7	29883	broad.mit.edu	37	8	17102865	17102866	+	Intron	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17102865_17102866insA	uc003wxf.1	-						CNOT7_uc003wxg.1_Intron|CNOT7_uc003wxh.1_Intron|CNOT7_uc003wxi.1_5'Flank|VPS37A_uc003wxj.2_5'Flank|VPS37A_uc003wxk.2_5'Flank	NM_013354	NP_037486	Q9UIV1	CNOT7_HUMAN	CCR4-NOT transcription complex, subunit 7						carbohydrate metabolic process|nuclear-transcribed mRNA poly(A) tail shortening	CCR4-NOT complex|cytoplasmic mRNA processing body|cytosol	nucleic acid binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1				Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209)		tcttgactcataaaaaaaaaaa	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20478373	20478373	+	IGR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20478373delG								LZTS1 (365570 upstream) : None (None downstream)																							CCATGTTGGTGGTGGGTGGTT	0.448													5	10	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27766955	27766955	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27766955delT	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		TGCAGGCCTGTCCTGTACCTT	0.542													4	2	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27766959	27766959	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27766959delG	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		GGCCTGTCCTGTACCTTTTCC	0.542													4	2	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27766961	27766961	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27766961delA	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		CCTGTCCTGTACCTTTTCCTT	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29125587	29125587	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29125587delT								KIF13B (4977 upstream) : DUSP4 (68030 downstream)																							TTGTCCTATCTTTTTTTTTTT	0.388													3	3	---	---	---	---	
FGFR1	2260	broad.mit.edu	37	8	38313243	38313244	+	Intron	DEL	GA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38313243_38313244delGA	uc003xlp.2	-						FGFR1_uc011lbo.1_Intron|FGFR1_uc011lbp.1_Intron|FGFR1_uc011lbq.1_Intron|FGFR1_uc010lwk.2_Intron|FGFR1_uc011lbs.1_Intron|FGFR1_uc011lbt.1_Intron|FGFR1_uc011lbu.1_Intron|FGFR1_uc011lbv.1_Intron|FGFR1_uc011lbw.1_Intron|FGFR1_uc011lbx.1_Intron|FGFR1_uc003xlv.2_Intron|FGFR1_uc003xlu.2_Intron|FGFR1_uc003xlw.1_Intron	NM_023110	NP_075598	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1 isoform 1						axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)	TGCTGTCTCTGAACACTCATGC	0.480		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	39722073	39722073	+	IGR	DEL	A	-	-	rs67729232		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39722073delA								ADAM2 (26294 upstream) : IDO1 (49255 downstream)																							CTGCAAAAAGAAAAAAAAATC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64680647	64680647	+	5'Flank	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64680647delT	uc003xvc.2	+											Homo sapiens hypothetical protein LOC286184, mRNA (cDNA clone IMAGE:5265748).																		gcagtgggggttttggaccat	0.000													4	2	---	---	---	---	
ZFAND1	79752	broad.mit.edu	37	8	82625928	82625928	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82625928delA	uc003ycj.1	-						ZFAND1_uc010lzx.1_Intron|ZFAND1_uc003yck.1_Intron	NM_024699	NP_078975	Q8TCF1	ZFAN1_HUMAN	zinc finger, AN1-type domain 1								zinc ion binding			ovary(1)	1						cccaagtgggaaaaaaaaaga	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	91064321	91064321	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91064321delA								DECR1 (94 upstream) : CALB1 (6517 downstream)																							tCAAAACATTAAAAAAAAAAA	0.199													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	92818970	92818970	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92818970delC								SLC26A7 (408590 upstream) : RUNX1T1 (152182 downstream)																							ggctaatcttcccaccctaca	0.144													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96505389	96505390	+	IGR	DEL	AC	-	-	rs5893337		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96505389_96505390delAC								C8orf37 (223952 upstream) : GDF6 (649170 downstream)																							GGTGGCCTGTacacacacacac	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102177676	102177676	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102177676delT								YWHAZ (212053 upstream) : ZNF706 (31592 downstream)																							ttcctcattcttagggtgttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	113220297	113220298	+	IGR	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113220297_113220298insA								None (None upstream) : CSMD3 (14863 downstream)																							AACAAAATCTCAAAAAAAAATC	0.302													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124772003	124772004	+	IGR	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124772003_124772004insT								ANXA13 (22356 upstream) : FAM91A1 (8878 downstream)																							CACATTTGGAATTTTTTTTCGT	0.337													4	2	---	---	---	---	
MTSS1	9788	broad.mit.edu	37	8	125587214	125587214	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125587214delT	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			aatcggtaggttttttttttc	0.020													3	3	---	---	---	---	
NSMCE2	286053	broad.mit.edu	37	8	126202564	126202564	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126202564delC	uc003yrw.2	+							NM_173685	NP_775956	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			AAGAGGttatccccatcttca	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127894903	127894903	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127894903delC								FAM84B (324437 upstream) : LOC727677 (407159 downstream)																							agctccattgcccacactggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134317562	134317563	+	IGR	DEL	AG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134317562_134317563delAG								NDRG1 (8015 upstream) : ST3GAL1 (149528 downstream)																							gggaagaagaagagagagagag	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139948101	139948102	+	IGR	INS	-	CA	CA	rs141517449	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139948101_139948102insCA								COL22A1 (21865 upstream) : KCNK9 (664980 downstream)																							CATCATTAATTCAGTGTTTGTT	0.322													4	2	---	---	---	---	
SMARCA2	6595	broad.mit.edu	37	9	2127964	2127965	+	Intron	INS	-	T	T	rs141570888	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2127964_2127965insT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		ACACAGTTCAGTTTTTTTTTTA	0.312													5	3	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	10611906	10611906	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10611906delC	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	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)		CCCTTTTCCGCCCCCCCCCCC	0.413										TSP Lung(15;0.13)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16039795	16039795	+	IGR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16039795delG								C9orf93 (67900 upstream) : BNC2 (369707 downstream)																							tgagctacgtgggtgtctggg	0.139													4	2	---	---	---	---	
CNTLN	54875	broad.mit.edu	37	9	17143630	17143631	+	Intron	DEL	TG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17143630_17143631delTG	uc003zmz.2	+						CNTLN_uc003zmx.3_Intron|CNTLN_uc003zmy.2_Intron|CNTLN_uc003zmw.1_Intron	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)		TCTTAAATACTGTGTGTGTGTG	0.416													4	2	---	---	---	---	
VCP	7415	broad.mit.edu	37	9	35065040	35065040	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35065040delT	uc003zvy.2	-						VCP_uc003zvz.2_Intron|VCP_uc010mkh.1_Intron|VCP_uc010mki.1_Intron	NM_007126	NP_009057	P55072	TERA_HUMAN	valosin-containing protein						activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol	cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex	ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding			upper_aerodigestive_tract(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			aatttttgtatttttagtaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66461540	66461540	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66461540delC	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		tgtttatcagcttaaggagtt	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68330460	68330460	+	IGR	DEL	G	-	-	rs75982239		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68330460delG								FAM27B (536271 upstream) : MIR1299 (671779 downstream)																							tctcaaaaaagaatgccaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68407437	68407438	+	5'Flank	INS	-	A	A	rs146708055		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68407437_68407438insA	uc004aew.1	+											Homo sapiens cDNA, FLJ98602.																		tagctgtatttaaaaaaaaact	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68420783	68420783	+	IGR	DEL	C	-	-	rs67820203		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68420783delC								FAM27B (626594 upstream) : MIR1299 (581456 downstream)																							CACACACACACAAACTTGTAT	0.383													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98799718	98799718	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98799718delG	uc011lun.1	+											Homo sapiens cDNA, FLJ97452.																		tcccatgtatgGCCTCTGCCT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98893036	98893036	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98893036delT								NCRNA00092 (108999 upstream) : HSD17B3 (104553 downstream)																							ACAGGATGCCTTGGAAGACCA	0.527													4	2	---	---	---	---	
SMC2	10592	broad.mit.edu	37	9	106900093	106900095	+	Intron	DEL	GAG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106900093_106900095delGAG	uc004bbv.2	+						SMC2_uc004bbw.2_Intron|SMC2_uc011lvl.1_Intron|SMC2_uc004bbx.2_Intron|SMC2_uc004bby.2_Intron	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2						cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						CTTCCGAAAAGAGGAGAAATGGA	0.256													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	108812965	108812966	+	IGR	DEL	TG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108812965_108812966delTG								TMEM38B (275521 upstream) : ZNF462 (812412 downstream)																							CTGTGGGATAtgtgtgtgtgtg	0.262													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	112321642	112321642	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112321642delT								PTPN3 (61049 upstream) : PALM2 (81430 downstream)																							CTTCCCTTCCTTGGACTTCTT	0.423													4	2	---	---	---	---	
LPAR1	1902	broad.mit.edu	37	9	113687093	113687093	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113687093delC	uc004bfa.2	-						LPAR1_uc011lwm.1_Intron|LPAR1_uc004bfb.2_Intron|LPAR1_uc004bfc.2_Intron|LPAR1_uc011lwn.1_Intron|LPAR1_uc011lwo.1_Intron|LPAR1_uc010mub.2_Intron	NM_057159	NP_476500	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2						ataaagctttcctgattttac	0.144													4	2	---	---	---	---	
GOLGA2	2801	broad.mit.edu	37	9	131019150	131019151	+	3'UTR	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131019150_131019151insT	uc011maw.1	-	26					GOLGA2_uc010mxw.2_3'UTR|uc004bui.2_5'Flank	NM_004486	NP_004477	Q08379	GOGA2_HUMAN	Golgi autoantigen, golgin subfamily a, 2							Golgi cisterna membrane	protein binding			ovary(1)	1						ATAACttttaatttttttttaa	0.302													6	3	---	---	---	---	
LCN1	3933	broad.mit.edu	37	9	138415348	138415349	+	Intron	INS	-	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138415348_138415349insG	uc004cfz.1	+						LCN1_uc004cga.1_Intron	NM_002297	NP_002288	P31025	LCN1_HUMAN	lipocalin 1 precursor						proteolysis|response to stimulus|sensory perception of taste	extracellular region	cysteine-type endopeptidase inhibitor activity|transporter activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.54e-08)|Epithelial(140;5.25e-08)|all cancers(34;9.27e-07)|READ - Rectum adenocarcinoma(205;0.155)		CAGGTGTGGCAGGTTTGTCCCG	0.589													4	3	---	---	---	---	
PARD3	56288	broad.mit.edu	37	10	34669489	34669490	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34669489_34669490insT	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixo.1_Intron|PARD3_uc001ixp.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron|PARD3_uc001ixs.1_Intron	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)				CATTATTTTCCTTTTTTTGGAG	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42648209	42648209	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42648209delC								None (None upstream) : LOC441666 (179106 downstream)																							TGAAGAAATGCCCCTTGCCTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42660137	42660137	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42660137delA								None (None upstream) : LOC441666 (167178 downstream)																							gtagaatcacaaaaaaattca	0.144													4	4	---	---	---	---	
WDFY4	57705	broad.mit.edu	37	10	50177984	50177985	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50177984_50177985insT	uc001jha.3	+						WDFY4_uc009xob.2_Intron|WDFY4_uc010qgn.1_Intron	NM_020945	NP_065996	Q6ZS81	WDFY4_HUMAN	WDFY family member 4							integral to membrane	binding				0						TTCTTCCCACCTGCTGGAGGAG	0.594													4	2	---	---	---	---	
ASCC1	51008	broad.mit.edu	37	10	73975366	73975366	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73975366delA	uc001jst.1	-						ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron|ANAPC16_uc001jsv.2_5'Flank|ANAPC16_uc001jsw.2_5'Flank			Q8N9N2	ASCC1_HUMAN	RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0						GGAAAAGCTTAAAAAAAAAAT	0.463													4	2	---	---	---	---	
KCNMA1	3778	broad.mit.edu	37	10	79395889	79395889	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79395889delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)	CCTTCCCTCCAAAACGGTTCG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86930714	86930717	+	IGR	DEL	CATT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86930714_86930717delCATT								FAM190B (652438 upstream) : GRID1 (428595 downstream)																							ACATTATACACATTCATAAAGAGC	0.373													4	2	---	---	---	---	
GRID1	2894	broad.mit.edu	37	10	87905203	87905203	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87905203delG	uc001kdl.1	-						GRID1_uc009xsu.1_Intron	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	TTTTCTATTTGTTTTTACATT	0.269										Multiple Myeloma(13;0.14)			4	2	---	---	---	---	
RNLS	55328	broad.mit.edu	37	10	89990263	89990263	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89990263delC	uc010qms.1	-									Q5VYX0	RNLS_HUMAN	SubName: Full=cDNA FLJ55083, highly similar to Renalase (EC 1.4.-.-);							extracellular region	oxidoreductase activity			ovary(1)	1						GTGCCTTCTTCCCCCTCCAAT	0.512													4	2	---	---	---	---	
LOC100188947	100188947	broad.mit.edu	37	10	93311855	93311855	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93311855delC	uc010qnl.1	-							NR_024467				Homo sapiens, clone IMAGE:6063621, mRNA.												0						TCTCTAGGAACCCCCAACCCT	0.552											OREG0020365	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
FBXW4	6468	broad.mit.edu	37	10	103409759	103409759	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103409759delC	uc001kto.2	-							NM_022039	NP_071322	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4						ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	ubiquitin ligase complex				skin(1)	1		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)		GCAGACCACACCCAGGCTGAG	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107444486	107444486	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107444486delC								SORCS3 (419493 upstream) : SORCS1 (888936 downstream)																							TCTGGCTTCTCCATCCTTCTG	0.393													4	2	---	---	---	---	
C10orf96	374355	broad.mit.edu	37	10	118126194	118126194	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118126194delC	uc001lck.2	+							NM_198515	NP_940917	P0C7W6	CJ096_HUMAN	hypothetical protein LOC374355											ovary(2)	2		Lung NSC(174;0.204)|all_lung(145;0.248)		all cancers(201;0.014)		aggatagatgcctgttggaat	0.000													4	2	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127605306	127605306	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127605306delT	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				agaacaagtattttatgTGAT	0.030													4	2	---	---	---	---	
BRSK2	9024	broad.mit.edu	37	11	1440751	1440751	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1440751delT	uc001lti.2	+						BRSK2_uc009ycv.1_Intron|BRSK2_uc001lth.1_Intron|BRSK2_uc001ltj.2_Intron|BRSK2_uc001ltk.2_Intron|BRSK2_uc001ltl.2_Intron|BRSK2_uc001ltm.2_Intron	NM_003957	NP_003948	Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2						establishment of cell polarity|neuron differentiation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		gtcttagagcttttttttgtt	0.104													4	2	---	---	---	---	
STIM1	6786	broad.mit.edu	37	11	3987498	3987498	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3987498delA	uc001lyv.2	+						STIM1_uc009yef.2_Intron	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor						activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		ttcaatgttcAACATACTTCT	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	13778206	13778206	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13778206delA								FAR1 (24315 upstream) : SPON1 (205708 downstream)																							actccatctcaaaaaaaaaaa	0.149													4	3	---	---	---	---	
LDHC	3948	broad.mit.edu	37	11	18436474	18436474	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18436474delA	uc001mon.3	+						LDHC_uc001mom.3_Intron|LDHC_uc009yhp.2_Intron|LDHC_uc001moo.3_Intron|LDHC_uc009yhq.2_Intron|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144	P07864	LDHC_HUMAN	L-lactate dehydrogenase C						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)	TCTGAATGGCAAAAAAAAACA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	25332250	25332250	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25332250delA								LUZP2 (228068 upstream) : ANO3 (878579 downstream)																							atggagatttaaaaaaaaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59723683	59723684	+	Intron	INS	-	CTG	CTG			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59723683_59723684insCTG	uc001nok.1	+											Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit01-13-09-F.																		ctttttttttttAAAGTAATTC	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59723685	59723685	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59723685delA	uc001nok.1	+											Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit01-13-09-F.																		ttttttttttAAAGTAATTCA	0.269													4	2	---	---	---	---	
TBX10	347853	broad.mit.edu	37	11	67408753	67408754	+	5'Flank	DEL	CA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67408753_67408754delCA	uc001omp.2	-							NM_005995	NP_005986	O75333	TBX10_HUMAN	T-box 10						anatomical structure morphogenesis|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0						ACCCCCCTCCCACACACACACA	0.579													3	4	---	---	---	---	
P2RY6	5031	broad.mit.edu	37	11	72999916	72999916	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72999916delC	uc001otm.2	+						P2RY6_uc001otn.2_Intron|P2RY6_uc001oto.2_Intron|P2RY6_uc001otp.2_Intron|P2RY6_uc001otq.2_Intron|P2RY6_uc001otr.2_Intron|P2RY6_uc001ots.2_Intron	NM_176796	NP_789766	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y6						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1						CCCCTGACATCCTGTGCCCTT	0.393													4	2	---	---	---	---	
SLCO2B1	11309	broad.mit.edu	37	11	74853965	74853966	+	Intron	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74853965_74853966insA	uc010rrp.1	+									O94956	SO2B1_HUMAN	Homo sapiens mRNA for KIAA0880 protein, partial cds.						sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)	ACCTAGGGGACAAAAAAAAGAC	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	87224014	87224015	+	IGR	DEL	TC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87224014_87224015delTC								TMEM135 (189446 upstream) : RAB38 (622416 downstream)																							cttgtgcctatctctctctctc	0.267													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95976200	95976201	+	Intron	DEL	AC	-	-	rs34648958		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95976200_95976201delAC	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CAGTTCAGGGacacacacacac	0.327			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
TMEM123	114908	broad.mit.edu	37	11	102269328	102269328	+	3'UTR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102269328delA	uc001pha.2	-	5					TMEM123_uc009yxc.2_3'UTR	NM_052932	NP_443164	Q8N131	PORIM_HUMAN	transmembrane protein 123 precursor						oncosis	external side of plasma membrane|integral to membrane	receptor activity			breast(2)	2	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		CACCCCAGCCAAAAAAAAAAA	0.388													4	2	---	---	---	---	
MMP20	9313	broad.mit.edu	37	11	102496262	102496262	+	5'Flank	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102496262delT	uc001phc.2	-							NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein						proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)		AAGCTTCATATTTTTTTTGTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	105348988	105348988	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105348988delA								CARD18 (339182 upstream) : GRIA4 (131812 downstream)																							tctagggcagaaggtgactct	0.070													4	2	---	---	---	---	
GUCY1A2	2977	broad.mit.edu	37	11	106803118	106803118	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106803118delA	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)		TGGTTCATTTAAAAAAAATAC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107365636	107365640	+	IGR	DEL	GCCTC	-	-	rs67219576	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107365636_107365640delGCCTC								CWF19L2 (37064 upstream) : ALKBH8 (7814 downstream)																							agccacactggcctcctgcggttct	0.000													4	2	---	---	---	---	
C11orf57	55216	broad.mit.edu	37	11	111948563	111948563	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111948563delT	uc001pmr.3	+						C11orf57_uc001pmu.2_Intron|C11orf57_uc001pmw.3_Intron|C11orf57_uc001pmt.3_Intron|C11orf57_uc001pmv.3_Intron|C11orf57_uc001pms.3_Intron	NM_001082970	NP_001076439	Q6ZUT1	CK057_HUMAN	hypothetical protein LOC55216 isoform b											breast(2)|ovary(1)	3		all_cancers(61;9.8e-15)|all_epithelial(67;6.57e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.6e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;7.01e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0521)		AGTTAGTTGCttttttttttt	0.194													2	4	---	---	---	---	
RNF214	257160	broad.mit.edu	37	11	117134501	117134501	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117134501delA	uc001pqt.2	+						RNF214_uc001pqu.2_Intron|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226	Q8ND24	RN214_HUMAN	ring finger protein 214								zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		ttatgtaggtaaaaatctctG	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124718582	124718582	+	IGR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124718582delG								C11orf61 (48283 upstream) : ROBO3 (16700 downstream)																							GTGAGGCAGTGGAGGCTAAAG	0.473													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2166044	2166045	+	Intron	DEL	GT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2166044_2166045delGT	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CAGTATTTAAGTGTGTGTGTGT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	4470761	4470762	+	IGR	INS	-	T	T	rs138219343	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4470761_4470762insT								C12orf5 (1573 upstream) : FGF23 (6631 downstream)																							gactttctttgtttttttttta	0.000													4	2	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11273805	11273808	+	Intron	DEL	AGAA	-	-	rs138238074		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11273805_11273808delAGAA	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						AAATAAAAATAGAAAGAGATGCCT	0.387										HNSCC(22;0.051)			4	4	---	---	---	---	
EPS8	2059	broad.mit.edu	37	12	15815859	15815859	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15815859delA	uc009zif.2	-						EPS8_uc001rdb.2_Intron|EPS8_uc009zig.2_Intron|EPS8_uc010shv.1_5'Flank	NM_004447	NP_004438	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway						cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		AGAGAACTGCAAAAAAAAATT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16346538	16346538	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16346538delA								DERA (156224 upstream) : MGST1 (153538 downstream)																							GGAAGTGAGGAAaatgaaaat	0.169													4	2	---	---	---	---	
PKP2	5318	broad.mit.edu	37	12	33029469	33029470	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33029469_33029470insT	uc001rlj.3	-						PKP2_uc001rlk.3_Intron|PKP2_uc010skj.1_Intron	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b						cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					TACACtttctcttttttttttt	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	42303585	42303585	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42303585delA								PDZRN4 (335201 upstream) : GXYLT1 (172065 downstream)																							ACCCCATACCAAATGTCCTCT	0.458													4	2	---	---	---	---	
FLJ12825	440101	broad.mit.edu	37	12	54497545	54497546	+	Intron	INS	-	T	T	rs144888465	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54497545_54497546insT	uc001sey.2	+							NR_026655				Homo sapiens cDNA FLJ12825 fis, clone NT2RP2002800.												0						ctgttctcttctgaatgccctt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54566849	54566850	+	IGR	DEL	AC	-	-	rs145812469		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54566849_54566850delAC								LOC400043 (40230 upstream) : SMUG1 (6933 downstream)																							AAGGCCAGAGACAAGAAGACGG	0.559													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69440987	69440987	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69440987delA								CPM (83967 upstream) : CPSF6 (192330 downstream)																							TGGGATCTGTAAAGCATGGTG	0.463													4	2	---	---	---	---	
TBC1D15	64786	broad.mit.edu	37	12	72274071	72274072	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72274071_72274072insT	uc001swu.2	+						TBC1D15_uc009zrv.2_Intron|TBC1D15_uc010stt.1_Intron|TBC1D15_uc001swv.2_Intron|TBC1D15_uc001sww.2_Intron	NM_022771	NP_073608	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15 isoform 1								protein binding|Rab GTPase activator activity				0						GCTTCTCTTCCTTTTTTTTTTT	0.386													2	4	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78334655	78334655	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78334655delT	uc001syp.2	+						NAV3_uc001syo.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						TTCTCACTCATTTTTTTTTTT	0.398										HNSCC(70;0.22)			7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	78932420	78932420	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78932420delT								NAV3 (325632 upstream) : SYT1 (325353 downstream)																							tcagaatcactttttatcttt	0.000													4	2	---	---	---	---	
ACSS3	79611	broad.mit.edu	37	12	81624457	81624457	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81624457delA	uc001szl.1	+						ACSS3_uc001szm.1_Intron|ACSS3_uc001szn.1_Intron	NM_024560	NP_078836	Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3							mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4						TTAGTACTTCAAAAAATAAAT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	88690390	88690391	+	IGR	DEL	TG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88690390_88690391delTG								TMTC3 (96727 upstream) : KITLG (196178 downstream)																							tttgtgtgtttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
BTG1	694	broad.mit.edu	37	12	92495240	92495241	+	Intron	DEL	AA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92495240_92495241delAA	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)				ggaaagaaagaaagaaagaaag	0.099			T	MYC	BCLL								4	3	---	---	---	---	
BTG1	694	broad.mit.edu	37	12	92495246	92495247	+	Intron	INS	-	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92495246_92495247insG	uc001tbv.1	-						BTG1_uc001tbw.1_Intron|BTG1_uc001tbx.1_Intron|BTG1_uc009zss.1_Intron			P62324	BTG1_HUMAN	Homo sapiens full length insert cDNA clone YW25A12.						cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|transcription cofactor activity				0		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				aaagaaagaaagaaagaaagaa	0.114			T	MYC	BCLL								4	3	---	---	---	---	
ACTR6	64431	broad.mit.edu	37	12	100612541	100612541	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100612541delT	uc001thb.1	+						ACTR6_uc001thc.1_Intron|ACTR6_uc001thd.1_Intron|ACTR6_uc009ztu.1_Intron|ACTR6_uc001the.1_Intron|ACTR6_uc001thf.1_Intron|uc001thg.1_Intron	NM_022496	NP_071941	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog							cytoplasm|cytoskeleton				ovary(1)	1						TGATTATAAGTTTTTTTTTGT	0.279													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106452029	106452029	+	IGR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106452029delG								C12orf75 (686734 upstream) : NUAK1 (5096 downstream)																							TCTCTAAAATGGGAGGCAACT	0.448													4	2	---	---	---	---	
PTPN11	5781	broad.mit.edu	37	12	112876130	112876131	+	Intron	DEL	TG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112876130_112876131delTG	uc001ttx.2	+						PTPN11_uc001ttw.1_Intron	NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type						axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						attgttttcttgtgtgtgtttc	0.000			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				4	2	---	---	---	---	
MSI1	4440	broad.mit.edu	37	12	120809496	120809497	+	5'Flank	INS	-	A	A	rs112962110		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120809496_120809497insA	uc001tye.1	-							NM_002442	NP_002433	O43347	MSI1H_HUMAN	musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CATTTTGGATTAAAAAAAAAAA	0.396													3	3	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124952858	124952859	+	Intron	INS	-	TCC	TCC			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124952858_124952859insTCC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		caccctcatcatcctcatcacc	0.000													5	4	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124952877	124952879	+	Intron	DEL	TCC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124952877_124952879delTCC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		accctcatcatcctcatcctcct	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127271462	127271462	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127271462delT								LOC100128554 (314132 upstream) : None (None downstream)																							TATTGGTCCCTTGGCCACAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22716669	22716670	+	Intron	DEL	AC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22716669_22716670delAC	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																		CCTTTTCTAAACACACACACAC	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	27526061	27526061	+	IGR	DEL	A	-	-	rs71188762		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27526061delA								GPR12 (191139 upstream) : USP12 (116377 downstream)																							CAATAAAAAGAAAAAAAAGTG	0.418													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31394954	31394956	+	IGR	DEL	TCC	-	-	rs113575593		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31394954_31394956delTCC								ALOX5AP (56398 upstream) : C13orf33 (85356 downstream)																							gctgaagcaatcctcctgcttca	0.000													2	4	---	---	---	---	
TRPC4	7223	broad.mit.edu	37	13	38255593	38255593	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38255593delT	uc001uws.2	-						TRPC4_uc010abv.2_Intron|TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Intron|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,						axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TGTTGGTATCTTTTTTTTTTG	0.323													4	2	---	---	---	---	
MTRF1	9617	broad.mit.edu	37	13	41828987	41828987	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41828987delT	uc001uxx.2	-						MTRF1_uc001uxy.2_Intron|MTRF1_uc001uxz.2_Intron|MTRF1_uc010tff.1_Intron|MTRF1_uc001uyc.1_Intron	NM_004294	NP_004285	O75570	RF1M_HUMAN	mitochondrial translational release factor 1						regulation of translational termination	mitochondrion	translation release factor activity, codon specific				0		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)		AAACCTTGTGTTTTTTTTTTT	0.264													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	43343357	43343374	+	IGR	DEL	CTTAGATATGGGCTGTGC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43343357_43343374delCTTAGATATGGGCTGTGC								TNFSF11 (161208 upstream) : C13orf30 (12312 downstream)																							ttcccaactgcttagatatgggctgtgccttagctggg	0.060													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68286898	68286899	+	IGR	INS	-	GAT	GAT	rs148493690	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68286898_68286899insGAT								PCDH9 (482430 upstream) : None (None downstream)																							TCAGATTTGTAgatgatgatga	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73145749	73145750	+	IGR	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73145749_73145750insT								DACH1 (704419 upstream) : C13orf37 (136745 downstream)																							AAACTGATGTGTTTTTTTTTCA	0.327													4	2	---	---	---	---	
PIBF1	10464	broad.mit.edu	37	13	73534776	73534777	+	Intron	INS	-	CA	CA			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73534776_73534777insCA	uc001vjc.2	+						PIBF1_uc001vjb.2_Intron|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337	Q8WXW3	PIBF1_HUMAN	progesterone-induced blocking factor 1							centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		CACCCTTTCCCCACACACACAC	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	80899532	80899532	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80899532delA								NDFIP2 (769327 upstream) : SPRY2 (10582 downstream)																							actccatctcaaaaaaaaaaa	0.124													3	3	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102590624	102590626	+	Intron	DEL	ACA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102590624_102590626delACA	uc001vpf.2	-							NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGCTTCATACACAACAACAACAA	0.345													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107103285	107103285	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107103285delT								DAOA (959903 upstream) : EFNB2 (38813 downstream)																							ctTTCTCAGATTTTTTTTTAA	0.179													4	2	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109608869	109608870	+	Intron	INS	-	T	T	rs141011584	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109608869_109608870insT	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			atgacaaactctttttttttcc	0.099													4	2	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109859345	109859354	+	3'UTR	DEL	TGTGTGTGTT	-	-	rs71670580		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109859345_109859354delTGTGTGTGTT	uc001vqt.1	+	35					MYO16_uc010agk.1_3'UTR	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			Cgtgtgtgtgtgtgtgtgtttgtgtgtgtg	0.390													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19830111	19830112	+	IGR	INS	-	CCT	CCT	rs142159711		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19830111_19830112insCCT								POTEG (245169 upstream) : P704P (153842 downstream)																							tgccacagatgcctcacctctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22968406	22968407	+	Intron	DEL	CA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22968406_22968407delCA	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc010tmt.1_Intron|uc010ajv.1_Intron|uc001weg.2_Intron|uc001weh.1_Intron|uc001wei.2_Intron|uc001wej.2_Intron|uc001wek.2_Intron|uc001wel.2_Intron|uc001wem.3_Intron|uc001wen.1_Intron|uc001weo.2_Intron|uc001wep.2_Intron|uc001weq.2_Intron|uc001wer.2_Intron|uc001wes.1_5'Flank|uc001wet.2_Intron|uc001weu.2_5'Flank|uc001wev.2_5'Flank|uc001wew.2_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																		CTCATATGTTCACTAAATCAGA	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	25761122	25761122	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25761122delA								STXBP6 (241951 upstream) : None (None downstream)																							CAAAATCTTGATTACATTCAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	44398778	44398778	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44398778delA								None (None upstream) : FSCB (574577 downstream)																							acaagcactgaaaaaaaaacc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51825124	51825124	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51825124delT								TMX1 (100754 upstream) : FRMD6 (130731 downstream)																							AATGACTTTATTTTTTCCCTA	0.368													4	2	---	---	---	---	
RTN1	6252	broad.mit.edu	37	14	60194207	60194207	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60194207delG	uc001xen.1	-	3	1404	c.1195delC	c.(1195-1197)CTGfs	p.L399fs	RTN1_uc001xem.1_5'UTR	NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	399					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		TCGTGGTCCAGGGGGCTGGGG	0.687													4	2	---	---	---	---	
HIF1A	3091	broad.mit.edu	37	14	62195274	62195274	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62195274delA	uc001xfq.2	+						HIF1A_uc001xfr.2_Intron|HIF1A_uc001xfs.2_Intron	NM_001530	NP_001521	Q16665	HIF1A_HUMAN	hypoxia-inducible factor 1, alpha subunit						cellular response to hypoxia|collagen metabolic process|connective tissue replacement involved in inflammatory response wound healing|elastin metabolic process|epithelial to mesenchymal transition|oxygen homeostasis|positive regulation of chemokine production|positive regulation of epithelial cell migration|positive regulation of hormone biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|regulation of transforming growth factor-beta2 production	cytoplasm|nucleolus|transcription factor complex	histone acetyltransferase binding|Hsp90 protein binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			kidney(3)|lung(1)	4				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)		ttaatacaccaccatacacac	0.000													4	2	---	---	---	---	
PPP2R5E	5529	broad.mit.edu	37	14	63949193	63949193	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63949193delA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237	Q16537	2A5E_HUMAN	epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		caacaacaacaaaaaaaaaCT	0.159													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95846460	95846460	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95846460delT								CLMN (60215 upstream) : C14orf139 (27146 downstream)																							TTAGCTTTTCTTTTTTTAATA	0.239													4	2	---	---	---	---	
MARK3	4140	broad.mit.edu	37	14	103849097	103849098	+	5'Flank	INS	-	CCC	CCC	rs74519455		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103849097_103849098insCCC	uc001ymz.3	+						MARK3_uc001ymx.3_5'Flank|MARK3_uc001ymw.3_5'Flank|MARK3_uc001yna.3_5'Flank|MARK3_uc001ymy.3_5'Flank|MARK3_uc010awp.2_5'Flank	NM_001128918	NP_001122390	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)			TCCGGCCTTCTGCAGTCTCACT	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20867625	20867628	+	IGR	DEL	GAGT	-	-	rs61049442		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20867625_20867628delGAGT								GOLGA8C (86599 upstream) : BCL8 (2428 downstream)																							AAGAAAATAAGAGTAAGTTTAATG	0.157													14	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23577687	23577687	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23577687delA								GOLGA8E (129264 upstream) : MKRN3 (232767 downstream)																							ACCATGGCTGAAAAAAAAGGC	0.418													4	2	---	---	---	---	
MTMR15	22909	broad.mit.edu	37	15	31199993	31199994	+	Intron	DEL	GG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31199993_31199994delGG	uc001zff.2	+						MTMR15_uc001zfc.3_Intron|MTMR15_uc010azw.2_Intron|MTMR15_uc001zfd.3_Intron|MTMR15_uc001zfe.2_Intron	NM_014967	NP_055782	Q9Y2M0	FAN1_HUMAN	myotubularin related protein 15 isoform a						double-strand break repair via homologous recombination|nucleotide-excision repair, DNA incision	nucleus	5'-3' exonuclease activity|5'-flap endonuclease activity|DNA binding|magnesium ion binding|phosphodiesterase I activity|ubiquitin binding				0		all_lung(180;2.23e-09)		all cancers(64;4.72e-15)|Epithelial(43;5.4e-11)|GBM - Glioblastoma multiforme(186;0.000136)|BRCA - Breast invasive adenocarcinoma(123;0.00402)|Lung(196;0.168)		CATTTTTTTTGGAAAATTATTT	0.366								Direct_reversal_of_damage|Editing_and_processing_nucleases					4	2	---	---	---	---	
PATL2	197135	broad.mit.edu	37	15	44966687	44966687	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44966687delT	uc010uej.1	-						PATL2_uc001zub.3_Intron	NM_001145112	NP_001138584	C9JE40	PATL2_HUMAN	protein associated with topoisomerase II homolog						negative regulation of translation	cytoplasm|nucleus	protein binding|RNA binding				0						aagggatgcctagaactggat	0.129													4	2	---	---	---	---	
ATP8B4	79895	broad.mit.edu	37	15	50367974	50367974	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50367974delC	uc001zxu.2	-						ATP8B4_uc010ber.2_Intron|ATP8B4_uc010ufd.1_Intron|ATP8B4_uc010ufe.1_Intron	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		CTTGCTGATGCCCCAACAAAG	0.423													4	2	---	---	---	---	
AP4E1	23431	broad.mit.edu	37	15	51260736	51260736	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51260736delA	uc001zyx.1	+							NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		TATCCAGAGGAAAAAAAAAAG	0.284													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	54951668	54951669	+	IGR	DEL	CA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54951668_54951669delCA								UNC13C (30863 upstream) : RSL24D1 (521852 downstream)																							ACCCTACCCTCACACAGAGATG	0.441													3	3	---	---	---	---	
RNF111	54778	broad.mit.edu	37	15	59358809	59358809	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59358809delA	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron|RNF111_uc002afw.2_Intron|RNF111_uc002afx.2_5'Flank	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		actccatctcaaaaaaaaaag	0.119													4	2	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62172995	62172996	+	Intron	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62172995_62172996insA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						GAGGCTGATTTAAATTTTGTTA	0.272													188	105	---	---	---	---	
TLN2	83660	broad.mit.edu	37	15	63020098	63020098	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63020098delG	uc002alb.3	+							NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2						cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						AGGGTGAAGAGGGGAGGAGTG	0.209													2	4	---	---	---	---	
ITGA11	22801	broad.mit.edu	37	15	68672249	68672249	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68672249delA	uc002ari.2	-						ITGA11_uc010bib.2_Intron	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)	GCATGGTAGGAAGGAAAGGGG	0.453													4	2	---	---	---	---	
THSD4	79875	broad.mit.edu	37	15	71535608	71535608	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71535608delT	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2						CATAGTTTTCTTTTTTTTTTT	0.323													6	3	---	---	---	---	
SLC28A1	9154	broad.mit.edu	37	15	85501550	85501550	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85501550delG	uc010upf.1	+						SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)			ctgtcaccctgggacttgctt	0.000													4	2	---	---	---	---	
IQGAP1	8826	broad.mit.edu	37	15	91022457	91022458	+	Intron	INS	-	T	T			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91022457_91022458insT	uc002bpl.1	+							NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ttaactgatactttttttttca	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95220887	95220887	+	IGR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95220887delG								MCTP2 (193707 upstream) : LOC145820 (755435 downstream)																							cttatgatctggaggagacag	0.025													4	2	---	---	---	---	
SELS	55829	broad.mit.edu	37	15	101813214	101813214	+	Intron	DEL	A	-	-	rs55877664	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101813214delA	uc010use.1	-						SELS_uc010usf.1_Intron	NM_203472	NP_982298	Q9BQE4	SELS_HUMAN	selenoprotein S						anti-apoptosis|cell redox homeostasis|cellular response to insulin stimulus|cellular response to lipopolysaccharide|cellular response to oxidative stress|endoplasmic reticulum unfolded protein response|ER overload response|ER-associated protein catabolic process|negative regulation of acute inflammatory response to antigenic stimulus|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of interleukin-6 production|negative regulation of nitric-oxide synthase biosynthetic process|negative regulation of tumor necrosis factor production|regulation of gluconeogenesis|regulation of nitric oxide metabolic process|response to glucose stimulus|response to redox state|retrograde protein transport, ER to cytosol	integral to endoplasmic reticulum membrane|low-density lipoprotein particle|microsome|plasma membrane|very-low-density lipoprotein particle	antioxidant activity|enzyme binding|receptor activity|selenium binding				0	Lung NSC(78;0.00156)|all_lung(78;0.00195)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00113)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TAGCTATGTGAAAAAAAAAAA	0.358													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	1985703	1985703	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1985703delC								HS3ST6 (17472 upstream) : SEPX1 (2532 downstream)																							gaggagtgttcccctcacaaa	0.000													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7188503	7188503	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7188503delC	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		CACATCTCTGCCCACAAACTC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8509652	8509652	+	IGR	DEL	T	-	-	rs111744116		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8509652delT								A2BP1 (746312 upstream) : TMEM114 (109851 downstream)																							AACCATTTGCTTTTTTTTTTT	0.388													2	4	---	---	---	---	
RUNDC2A	84127	broad.mit.edu	37	16	12080242	12080243	+	Intron	INS	-	G	G	rs72556582		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12080242_12080243insG	uc002dbw.1	+							NM_032167	NP_115543	Q9HA26	RUN2A_HUMAN	RUN domain containing 2A											ovary(1)	1						AAAAAAAAAAAAAAAAAGCGAA	0.332			T	CIITA	PMBL|Hodgkin Lymphona|								2	4	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12340757	12340757	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12340757delC	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						GGTGTCCCCTCCCCTCGGCAG	0.542													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12415861	12415861	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12415861delG	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						GTCCAGGTAAGGGGGGATTCC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	12949507	12949508	+	IGR	INS	-	A	A	rs77967297		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12949507_12949508insA								CPPED1 (51763 upstream) : SHISA9 (45969 downstream)																							CACAACACAACAAAAAAAAAAC	0.193													4	2	---	---	---	---	
C16orf62	57020	broad.mit.edu	37	16	19629581	19629581	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19629581delG	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020							integral to membrane				ovary(1)	1						GTACAGAAAAGAAAAAAAAAG	0.214													4	2	---	---	---	---	
IQCK	124152	broad.mit.edu	37	16	19733272	19733273	+	Intron	INS	-	AATC	AATC	rs144947614	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19733272_19733273insAATC	uc002dgr.2	+						IQCK_uc002dgs.2_Intron|IQCK_uc010vat.1_Intron|IQCK_uc010bwc.2_Intron|IQCK_uc010vau.1_Intron	NM_153208	NP_694940	Q8N0W5	IQCK_HUMAN	IQ motif containing K											skin(1)	1						GTTCATCACTTAATCAAGCACT	0.347													4	2	---	---	---	---	
IQCK	124152	broad.mit.edu	37	16	19742080	19742080	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19742080delT	uc002dgr.2	+						IQCK_uc002dgs.2_Intron|IQCK_uc010vat.1_Intron|IQCK_uc010bwc.2_Intron|IQCK_uc010vau.1_Intron	NM_153208	NP_694940	Q8N0W5	IQCK_HUMAN	IQ motif containing K											skin(1)	1						tctatctatcttatcttatct	0.000													4	2	---	---	---	---	
VWA3A	146177	broad.mit.edu	37	16	22151203	22151204	+	Intron	DEL	CA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22151203_22151204delCA	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		ACTCTCATCTcacacacacaca	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32437422	32437422	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32437422delA								HERC2P4 (273548 upstream) : TP53TG3B (247419 downstream)																							AAGGAATGTCAAAAAATATAC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32531514	32531514	+	IGR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32531514delG								HERC2P4 (367640 upstream) : TP53TG3B (153327 downstream)																							tgagatgaatggaagcatcac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32819123	32819125	+	IGR	DEL	TCA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32819123_32819125delTCA								TP53TG3B (130245 upstream) : SLC6A10P (69672 downstream)																							tcatttcatctcatcatttcatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33535748	33535748	+	IGR	DEL	C	-	-	rs143157205		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33535748delC								SLC6A10P (639285 upstream) : MIR1826 (429760 downstream)																							GAAAAAAAAACACAATAGAAT	0.219													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34481062	34481062	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34481062delA								UBE2MP1 (76300 upstream) : LOC283914 (116725 downstream)																							CCTTTGGGGCAAAAAAAAAAA	0.438													6	5	---	---	---	---	
ZNF423	23090	broad.mit.edu	37	16	49674329	49674330	+	Intron	DEL	AC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49674329_49674330delAC	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)				tcacctgcagacacacacacac	0.223													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	63071954	63071954	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63071954delT								None (None upstream) : None (None downstream)																							CCCAGAAGGCTTTTTTTTCCC	0.328													4	2	---	---	---	---	
LOC283867	283867	broad.mit.edu	37	16	65373662	65373662	+	Intron	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65373662delG	uc010cdo.1	-						LOC283867_uc010cdp.1_Intron|LOC283867_uc002eol.1_Intron					Homo sapiens cDNA clone IMAGE:5276218.												0				OV - Ovarian serous cystadenocarcinoma(108;0.17)		AACCTTCAGTGGGGGGGATGG	0.398													4	2	---	---	---	---	
CENPT	80152	broad.mit.edu	37	16	67866689	67866690	+	Intron	INS	-	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67866689_67866690insG	uc002eun.3	-						CENPT_uc002eum.3_Intron|CENPT_uc010vkc.1_Intron|CENPT_uc010vkd.1_Intron|CENPT_uc010vke.1_Intron	NM_025082	NP_079358	Q96BT3	CENPT_HUMAN	centromere protein T						mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleus	DNA binding				0		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		caggaggggctgggaaaggctt	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73650502	73650503	+	IGR	DEL	TG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73650502_73650503delTG								HTA (522832 upstream) : PSMD7 (680178 downstream)																							CAAAATTCAATGTGTGTGTGTA	0.366													4	2	---	---	---	---	
CMIP	80790	broad.mit.edu	37	16	81712859	81712860	+	Intron	DEL	TG	-	-	rs71701140		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81712859_81712860delTG	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron|CMIP_uc002fgr.1_Intron	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0						TCTGTAGGGAtgtgtgtgtgtg	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	1946801	1946801	+	IGR	DEL	G	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1946801delG								DPH1 (77 upstream) : MIR132 (6401 downstream)																							ATAGTTTTCTGGGCAGCGCCA	0.448													4	2	---	---	---	---	
MYBBP1A	10514	broad.mit.edu	37	17	4455005	4455005	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4455005delA	uc002fyb.3	-						MYBBP1A_uc002fxz.3_Intron	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2						nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2						acttcatctcaaaaaaaaaaa	0.279													3	3	---	---	---	---	
MED11	400569	broad.mit.edu	37	17	4634664	4634669	+	5'Flank	DEL	TCCTGG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4634664_4634669delTCCTGG	uc002fyp.2	+							NM_001001683	NP_001001683	Q9P086	MED11_HUMAN	mediator complex subunit 11						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	protein binding				0						GCGCTGAGCATCCTGGGAATCGTAGT	0.626													13	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5749823	5749823	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5749823delT	uc002gcm.2	+											Homo sapiens hypothetical protein LOC339166, mRNA (cDNA clone IMAGE:5163423), partial cds.																		atatttaccattttttttaat	0.000													4	2	---	---	---	---	
PIK3R5	23533	broad.mit.edu	37	17	8812614	8812614	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8812614delT	uc002glt.2	-						PIK3R5_uc010vuz.1_Intron|PIK3R5_uc002glu.3_Intron|PIK3R5_uc010coa.1_Intron|PIK3R5_uc010cob.1_Intron	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5						platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						TGGAACACTCttttttttttt	0.249													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21336734	21336734	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21336734delA								KCNJ12 (13555 upstream) : C17orf51 (94838 downstream)																							CACAATTTAGAAATCCATGTA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21345392	21345392	+	IGR	DEL	G	-	-	rs112741354		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21345392delG								KCNJ12 (22213 upstream) : C17orf51 (86180 downstream)																							GGGGAGGGCTGGGGGGGCAAG	0.502													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21559647	21559655	+	IGR	DEL	GGCCCAGAT	-	-	rs112293315		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21559647_21559655delGGCCCAGAT								C17orf51 (81916 upstream) : FAM27L (265715 downstream)																							TGACACCTAGGGCCCAGATGGACATGTGG	0.560													4	2	---	---	---	---	
CPD	1362	broad.mit.edu	37	17	28792067	28792072	+	3'UTR	DEL	CTTTTT	-	-	rs72148018		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28792067_28792072delCTTTTT	uc002hfb.1	+	21					CPD_uc010wbo.1_3'UTR|CPD_uc010wbp.1_RNA	NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor						proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2						GGGACAGCCACTTTTTCTTTTTAATT	0.345													4	4	---	---	---	---	
MYO1D	4642	broad.mit.edu	37	17	30845786	30845786	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30845786delC	uc002hho.1	-							NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)			GTGGCCAAATCCCCAGCACTC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32862435	32862435	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32862435delT								CCL1 (172183 upstream) : C17orf102 (38707 downstream)																							cttcttggcattagggttaca	0.025													4	2	---	---	---	---	
SOCS7	30837	broad.mit.edu	37	17	36512702	36512703	+	Intron	DEL	TC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36512702_36512703delTC	uc002hqa.2	+						SOCS7_uc010cvl.2_Intron|SOCS7_uc002hqb.2_Intron	NM_014598	NP_055413	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7						intracellular signal transduction|negative regulation of signal transduction|regulation of growth	cytoplasm|nucleus|plasma membrane	protein binding|SH3 domain binding			skin(1)	1	Breast(7;3.47e-17)					CTCAGTGTAATCTAGCATTGCT	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	41761702	41761702	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41761702delA								MEOX1 (22440 upstream) : SOST (69397 downstream)																							GGATCTGGGGAAGGGAAGGGT	0.542													4	2	---	---	---	---	
ITGA3	3675	broad.mit.edu	37	17	48157869	48157870	+	Intron	INS	-	GTGA	GTGA	rs2018134	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48157869_48157870insGTGA	uc010dbl.2	+						ITGA3_uc010dbm.2_Intron	NM_002204	NP_002195	P26006	ITA3_HUMAN	integrin alpha 3 isoform a precursor						blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3						tgtgtgtgtgtgatttgcgtgt	0.282													8	4	---	---	---	---	
ABCA6	23460	broad.mit.edu	37	17	67109140	67109140	+	Intron	DEL	A	-	-	rs34141662		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67109140delA	uc002jhw.1	-						ABCA6_uc002jhx.1_Intron	NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6						transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)					CAGCTGATCTAAAAAAAAAAG	0.284													4	2	---	---	---	---	
ABCA10	10349	broad.mit.edu	37	17	67171329	67171329	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67171329delT	uc010dfa.1	-						ABCA10_uc010wqs.1_Intron|ABCA10_uc010wqt.1_Intron	NM_080282	NP_525021	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A, member 10						transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)					TTTAGCATGATTTCCCTTACA	0.323													4	2	---	---	---	---	
TMEM105	284186	broad.mit.edu	37	17	79289123	79289123	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79289123delC	uc002kad.1	-							NM_178520	NP_848615	Q8N8V8	TM105_HUMAN	transmembrane protein 105							integral to membrane				ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.0892)			TCCCCTCCATCCCCTCCTGAA	0.642													4	2	---	---	---	---	
TGIF1	7050	broad.mit.edu	37	18	3424245	3424246	+	Intron	INS	-	T	T	rs143813178	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3424245_3424246insT	uc002klu.2	+							NM_174886	NP_777480	Q15583	TGIF1_HUMAN	TG-interacting factor isoform d						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				TTTTTTTGTTGTTTTTTTTTAa	0.109													4	2	---	---	---	---	
L3MBTL4	91133	broad.mit.edu	37	18	6051773	6051773	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6051773delA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				TCCTCCTCGGAGTGGTGAGCT	0.542													4	2	---	---	---	---	
CHST9	83539	broad.mit.edu	37	18	24717644	24717644	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24717644delT	uc002kwd.2	-						C18orf16_uc010xbm.1_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)					CCAATTTGTATTTTTAAAAAA	0.383													4	2	---	---	---	---	
DSC2	1824	broad.mit.edu	37	18	28662008	28662008	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28662008delA	uc002kwl.3	-						DSC2_uc002kwk.3_Intron	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			TGGACTTTTTAAAAAAAAAAA	0.274													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35372934	35372935	+	IGR	DEL	TT	-	-	rs33948900		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35372934_35372935delTT								CELF4 (226934 upstream) : None (None downstream)																							TCTTGTCCTCTTTGCACCCATA	0.455													4	2	---	---	---	---	
HDHD2	84064	broad.mit.edu	37	18	44663014	44663014	+	Intron	DEL	T	-	-	rs144963110		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44663014delT	uc002lcs.2	-						HDHD2_uc002lct.2_Intron	NM_032124	NP_115500	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain								hydrolase activity				0						AATACTTAGGtttttttttaa	0.284													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50242144	50242144	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50242144delC	uc002lfe.1	+							NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CATCAATCTACCATCCTCTTC	0.453													4	2	---	---	---	---	
ZCCHC2	54877	broad.mit.edu	37	18	60244189	60244189	+	3'UTR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60244189delA	uc002lip.3	+	14					ZCCHC2_uc002lio.2_Intron|ZCCHC2_uc002liq.2_3'UTR	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2						cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding			lung(1)|prostate(1)	2						TATGGTTTTGAAAAAAAAAAG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63329071	63329072	+	IGR	DEL	AA	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63329071_63329072delAA								None (None upstream) : CDH7 (88416 downstream)																							TTTCCCAGTTAAAAGAGCAAAA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	63845337	63845337	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63845337delA								CDH7 (297163 upstream) : CDH19 (325984 downstream)																							ggtgcaaaagaaaaaaaaagt	0.000													4	2	---	---	---	---	
TMEM146	257062	broad.mit.edu	37	19	5772666	5772667	+	Intron	INS	-	G	G			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5772666_5772667insG	uc002mda.2	+							NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3						TGGGAGCGGCAGGCGTCCTTTG	0.649													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	6517621	6517622	+	IGR	DEL	TT	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6517621_6517622delTT								TUBB4 (15291 upstream) : TNFSF9 (13388 downstream)																							TGTTGCTAGCtttttttttttt	0.158											OREG0025201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	4	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7153189	7153190	+	Intron	DEL	AC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153189_7153190delAC	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	cacaccacaaacacacaaccac	0.000													4	3	---	---	---	---	
JAK3	3718	broad.mit.edu	37	19	17947088	17947088	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17947088delT	uc002nhn.3	-						JAK3_uc010ebh.2_Intron|JAK3_uc002nho.2_Intron	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3						B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56						TGTATCTCACttttttttttc	0.244		2	Mis		acute megakaryocytic leukemia|								6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	23030331	23030331	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23030331delA								ZNF99 (77547 upstream) : ZNF91 (491088 downstream)																							gatgttctggaaaaaaaaaaa	0.100													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24065805	24065805	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24065805delT								RPSAP58 (54888 upstream) : ZNF254 (150442 downstream)																							ccattttctgttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	40650015	40650015	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40650015delA								ZNF780A (53170 upstream) : MAP3K10 (47636 downstream)																							TCTTCAGGGGAAAAAAAAAAT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6824397	6824397	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6824397delA								BMP2 (63487 upstream) : None (None downstream)																							TTGGCCTCCTAAAGTGATGGG	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12484518	12484519	+	IGR	INS	-	T	T	rs147222516	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12484518_12484519insT								BTBD3 (577276 upstream) : SPTLC3 (505108 downstream)																							TTTGTGTTCTCTTTTTTTTTCT	0.322													4	2	---	---	---	---	
DTD1	92675	broad.mit.edu	37	20	18652929	18652930	+	Intron	INS	-	A	A			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18652929_18652930insA	uc002wrf.3	+							NM_080820	NP_543010	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1						D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2						CAAAGAAAATTAAAAAAAAAAT	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19854706	19854707	+	IGR	DEL	GT	-	-	rs143702549		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19854706_19854707delGT								SLC24A3 (151166 upstream) : RIN2 (15503 downstream)																							tcacattttggtgtgtgtgtgt	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25903695	25903695	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25903695delA								FAM182B (54909 upstream) : LOC100134868 (86740 downstream)																							TTAAGATGACAAAAAAACACC	0.428													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26074256	26074257	+	IGR	INS	-	TC	TC	rs141028126	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26074256_26074257insTC								FAM182A (6704 upstream) : C20orf191 (9796 downstream)																							GCACATGTGGTCCCCCAAAGAA	0.243													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26077447	26077448	+	IGR	INS	-	C	C	rs144886402	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26077447_26077448insC								FAM182A (9895 upstream) : C20orf191 (6605 downstream)																							GCTGCAAGAGTCCCCCCTCCCT	0.589													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29601621	29601621	+	IGR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29601621delC								None (None upstream) : FRG1B (10258 downstream)																							cactgagaatcagaaatagta	0.000													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29616935	29616936	+	Intron	INS	-	T	T	rs141973478	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29616935_29616936insT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0						gagaattaagattttttaagag	0.000													3	4	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29628987	29628988	+	Intron	INS	-	C	C	rs138771657		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29628987_29628988insC	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						tctctctctcttttttaacagc	0.119													3	6	---	---	---	---	
GDF5	8200	broad.mit.edu	37	20	33943596	33943597	+	Intron	DEL	AC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33943596_33943597delAC	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548	P43026	GDF5_HUMAN	growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			TATAACCTATACACACACAAGT	0.381													4	2	---	---	---	---	
DLGAP4	22839	broad.mit.edu	37	20	34961734	34961734	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34961734delT	uc002xff.2	+							NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				TAATAGAGGGTTTTTTTTTct	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36750495	36750496	+	IGR	DEL	TG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36750495_36750496delTG								RPRD1B (29731 upstream) : TGM2 (6370 downstream)																							actgacaccttgtgtgtgtgtg	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42532692	42532693	+	IGR	INS	-	C	C	rs142500291	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42532692_42532693insC								GTSF1L (177050 upstream) : TOX2 (10799 downstream)																							AATTTGAAGAACCATCTGCTTA	0.510													3	3	---	---	---	---	
ZNF335	63925	broad.mit.edu	37	20	44594117	44594117	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44594117delT	uc002xqw.2	-						ZNF335_uc010zxk.1_Intron	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)				CTTTGAGGGCTTTCCCCTTTC	0.507													4	2	---	---	---	---	
CBLN4	140689	broad.mit.edu	37	20	54574000	54574001	+	Intron	INS	-	T	T	rs11367988		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54574000_54574001insT	uc002xxa.2	-							NM_080617	NP_542184	Q9NTU7	CBLN4_HUMAN	cerebellin 4 precursor							cell junction|extracellular region|synapse				ovary(3)|pancreas(1)	4			Colorectal(105;0.202)			GATTTTTTTAATTTTTTTTTTC	0.356													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60329958	60329961	+	Intron	DEL	ACAG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60329958_60329961delACAG	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			cataccacacacaGAGTGCGTGCC	0.039													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10583485	10583485	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10583485delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		atcttcttagttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10745454	10745454	+	IGR	DEL	G	-	-	rs71182420		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10745454delG								None (None upstream) : TPTE (161289 downstream)																							ctctctttttgtagaatctgc	0.000													3	5	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10918246	10918246	+	Intron	DEL	G	-	-	rs113499448		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10918246delG	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCCATAGGCTGGGAAAGAGCA	0.478													2	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11037537	11037537	+	Intron	DEL	T	-	-	rs57142183		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037537delT	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AAACAAAAAATACTTACTGGA	0.274													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11048067	11048070	+	Intron	DEL	CTCT	-	-	rs140519785		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11048067_11048070delCTCT	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tagactaaagctctctgagtttca	0.020													3	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11062343	11062344	+	Intron	INS	-	AG	AG	rs148978863		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11062343_11062344insAG	uc002yit.1	-						BAGE_uc002yiw.1_5'Flank|BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TAGTAAAAGACAGCAACTTTCA	0.208													12	6	---	---	---	---	
APP	351	broad.mit.edu	37	21	27256759	27256759	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27256759delT	uc002ylz.2	-						APP_uc011acg.1_Intron|APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron	NM_000484	NP_000475	P05067	A4_HUMAN	amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)				TCCTCTCCTCTTTCCTTTGCT	0.433													4	2	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45391036	45391036	+	Intron	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45391036delC	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron|AGPAT3_uc002zdx.2_Intron|AGPAT3_uc002zdy.2_Intron	NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		AGCGTCAGTACCCATGGGAAA	0.318													4	2	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45839640	45839641	+	Intron	INS	-	GTG	GTG	rs140387137		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45839640_45839641insGTG	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron|uc011afe.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						tgatgatggcagtggtggtggt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17234958	17234964	+	IGR	DEL	CTGCAAC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17234958_17234964delCTGCAAC								psiTPTE22 (55437 upstream) : XKR3 (29349 downstream)																							ccgtggctcactgcaacctccacctcc	0.000													6	4	---	---	---	---	
CECR2	27443	broad.mit.edu	37	22	18022833	18022833	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18022833delT	uc010gqw.1	+						CECR2_uc010gqv.1_Intron|CECR2_uc002zml.2_Intron	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		ttctgttttgtttttttgaga	0.139													4	2	---	---	---	---	
BID	637	broad.mit.edu	37	22	18221943	18221945	+	Intron	DEL	TCT	-	-	rs145054162		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18221943_18221945delTCT	uc002znd.1	-						BID_uc002znc.1_Intron|BID_uc002zne.1_Intron|BID_uc010gra.1_Intron|BID_uc002znf.1_Intron|BID_uc010grb.1_Intron|BID_uc010grc.1_Intron	NM_001196	NP_001187	P55957	BID_HUMAN	BH3 interacting domain death agonist isoform 2						activation of pro-apoptotic gene products|establishment of protein localization in membrane|induction of apoptosis by intracellular signals|induction of apoptosis via death domain receptors|neuron apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|release of cytochrome c from mitochondria	cytosol|membrane fraction|mitochondrial outer membrane	death receptor binding				0		all_epithelial(15;0.198)		Lung(27;0.0419)		CCAGCTGAAATCTTCTGCAAGGC	0.478													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20207082	20207082	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20207082delA								LOC150197 (11022 upstream) : RTN4R (21858 downstream)																							ATCACCCAATAAAAAAGGTAA	0.483													4	2	---	---	---	---	
UPB1	51733	broad.mit.edu	37	22	24919297	24919298	+	Intron	DEL	AC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24919297_24919298delAC	uc003aaf.2	+						UPB1_uc003aae.2_Intron|UPB1_uc011ajt.1_Intron	NM_016327	NP_057411	Q9UBR1	BUP1_HUMAN	beta-ureidopropionase						pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)					CCAGAGTGTGACTTTCTGTTTT	0.564													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27439971	27439972	+	IGR	INS	-	CCAT	CCAT	rs145278778	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27439971_27439972insCCAT								MIAT (325022 upstream) : MN1 (704294 downstream)																							CGtccacccacccatccatcca	0.050													4	2	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	28693360	28693360	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28693360delT	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						cacccagctattttttttttt	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	29805057	29805057	+	IGR	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29805057delT								AP1B1 (20488 upstream) : RFPL1S (27949 downstream)																							GTACATATACTTTTTttttta	0.124													6	3	---	---	---	---	
NF2	4771	broad.mit.edu	37	22	30093987	30093987	+	3'UTR	DEL	C	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30093987delC	uc003age.3	+	16					NF2_uc003agf.3_3'UTR|NF2_uc003agb.3_3'UTR|NF2_uc003agc.3_3'UTR|NF2_uc003agd.3_RNA|NF2_uc003agg.3_3'UTR|NF2_uc003aga.3_3'UTR|NF2_uc003agh.3_3'UTR|NF2_uc003agi.3_3'UTR|NF2_uc003agj.3_3'UTR|NF2_uc003agk.3_3'UTR|NF2_uc011akq.1_3'UTR	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding			meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						CAGGCAGAAGCCCCACAGCAC	0.567			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				4	2	---	---	---	---	
TBC1D10A	83874	broad.mit.edu	37	22	30719960	30719960	+	Intron	DEL	A	-	-	rs34782876		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30719960delA	uc011akt.1	-						TBC1D10A_uc010gvu.2_Intron|TBC1D10A_uc003ahk.3_Intron	NM_031937	NP_114143	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A							intracellular|microvillus	guanyl-nucleotide exchange factor activity|PDZ domain binding|Rab GTPase activator activity			ovary(1)	1						actccgtctcaaaaaaaaaag	0.129													6	3	---	---	---	---	
MYH9	4627	broad.mit.edu	37	22	36708400	36708401	+	Intron	INS	-	A	A	rs143290016	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36708400_36708401insA	uc003apg.2	-						MYH9_uc003aph.1_Intron	NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11						CCAGGAGAAGCAAAGCACTGTT	0.574			T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				5	3	---	---	---	---	
TNRC6B	23112	broad.mit.edu	37	22	40589970	40589970	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40589970delT	uc011aor.1	+						TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Intron	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						TGTGCAGGGGTTTTTTTTCCC	0.483													5	3	---	---	---	---	
KIAA1644	85352	broad.mit.edu	37	22	44665472	44665473	+	Intron	DEL	AC	-	-	rs150753842		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44665472_44665473delAC	uc003bet.2	-							NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor							integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				ACcacaccatacacacacacac	0.010													2	4	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47300233	47300234	+	Intron	INS	-	CTG	CTG	rs139436143	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47300233_47300234insCTG	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		TTCAGTGATGTCTATGTGGCGA	0.490													3	5	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47314726	47314726	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47314726delT	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron|uc003big.3_5'Flank	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		ttttaaataattttttatGAT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48029120	48029120	+	Intron	DEL	G	-	-	rs36094688		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48029120delG	uc003bik.1	+						uc003bij.2_Intron					Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																		TTGGCCGTGAGTGGGTCTGCA	0.587													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48656977	48656979	+	IGR	DEL	CAT	-	-	rs111747572		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48656977_48656979delCAT								None (None upstream) : FAM19A5 (228309 downstream)																							tcatcgccaacatcatcatcttc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	50162155	50162156	+	IGR	INS	-	AC	AC	rs145585991	by1000genomes	TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50162155_50162156insAC								C22orf34 (110965 upstream) : BRD1 (4782 downstream)																							CAACGGGAGAAACTGTAATGAG	0.485													1	5	---	---	---	---	
ATP7A	538	broad.mit.edu	37	X	77276190	77276190	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77276190delT	uc004ecx.3	+							NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0						attaaaaaaatttttttttat	0.000													4	2	---	---	---	---	
TMEM164	84187	broad.mit.edu	37	X	109388299	109388299	+	Intron	DEL	T	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109388299delT	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron	NM_032227	NP_115603	Q5U3C3	TM164_HUMAN	transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3						GTCTGGGGACTTTTTAGACCC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	115003424	115003425	+	IGR	DEL	AG	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115003424_115003425delAG								PLS3 (118434 upstream) : AGTR2 (298533 downstream)																							TGAGATTGACagagagagagag	0.356													4	2	---	---	---	---	
RHOXF2B	727940	broad.mit.edu	37	X	119297128	119297128	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119297128delA	uc004esl.3	+							NM_001099685	NP_001093155	P0C7M4	RHF2B_HUMAN	Rhox homeobox family, member 2B							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TATTACAGATAAAAGGAGAGA	0.458													4	2	---	---	---	---	
RHOXF2B	727940	broad.mit.edu	37	X	119297134	119297134	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119297134delA	uc004esl.3	+							NM_001099685	NP_001093155	P0C7M4	RHF2B_HUMAN	Rhox homeobox family, member 2B							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						AGATAAAAGGAGAGAGACAAA	0.453													4	2	---	---	---	---	
CUL4B	8450	broad.mit.edu	37	X	119668062	119668062	+	Intron	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119668062delA	uc004esw.2	-						CUL4B_uc010nqq.2_Intron|CUL4B_uc004esv.2_Intron	NM_003588	NP_003579	Q13620	CUL4B_HUMAN	cullin 4B isoform 1						cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3						ctgtctctacaaaaaaaaatt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	133571348	133571348	+	IGR	DEL	A	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133571348delA								PHF6 (8527 upstream) : HPRT1 (22827 downstream)																							cttctactgcaacatttctag	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	3660444	3660445	+	IGR	DEL	AC	-	-			TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:3660444_3660445delAC								TGIF2LY (212364 upstream) : None (None downstream)																							ttaaagaaagacacacacacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59006024	59006028	+	IGR	DEL	TTATA	-	-	rs111313709		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59006024_59006028delTTATA								None (None upstream) : None (None downstream)																							ttggatttctttatattatttctta	0.015													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59010488	59010491	+	IGR	DEL	AAAC	-	-	rs113406480		TCGA-CJ-5676-01A-11D-1534-10	TCGA-CJ-5676-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59010488_59010491delAAAC								None (None upstream) : None (None downstream)																							tacaaaaacaaaacaaacaactat	0.000													5	3	---	---	---	---	
