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
C1orf86	199990	broad.mit.edu	37	1	2116266	2116266	+	3'UTR	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2116266C>T	uc001aix.1	-	8					PRKCZ_uc001aiq.2_Intron|PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron|PRKCZ_uc009vla.2_Intron|PRKCZ_uc010nyx.1_Intron|PRKCZ_uc001ait.2_Intron|uc009vlc.1_5'Flank|C1orf86_uc001aiv.1_RNA|C1orf86_uc001aiw.1_RNA			Q6NZ36	CA086_HUMAN	SubName: Full=cDNA FLJ46112 fis, clone TESTI2035962;												0	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		CTCCAGTGGGCGTTGGGGGAG	0.662													6	26	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17083652	17083652	+	3'UTR	SNP	C	T	T	rs113710576	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17083652C>T	uc010ock.1	-	15					CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_3'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						aaatctcaaccttgagtacaa	0.209													8	19	---	---	---	---	PASS
KIAA1522	57648	broad.mit.edu	37	1	33238488	33238488	+	Nonstop_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33238488A>G	uc001bvv.2	+	7	3244	c.3108A>G	c.(3106-3108)TGA>TGG	p.*1036W	KIAA1522_uc001bvu.1_Nonstop_Mutation_p.*1095W|KIAA1522_uc010ohm.1_Nonstop_Mutation_p.*1047W|KIAA1522_uc010ohn.1_Nonstop_Mutation_p.*144W	NM_020888	NP_065939	Q9P206	K1522_HUMAN	hypothetical protein LOC57648	1036											0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				AGCTGGCCTGACCACCAGGCA	0.547											OREG0013333	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	119	---	---	---	---	PASS
ZMYM1	79830	broad.mit.edu	37	1	35579833	35579833	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35579833A>C	uc001bym.2	+	11	2550	c.2402A>C	c.(2401-2403)AAG>ACG	p.K801T	ZMYM1_uc001byn.2_Missense_Mutation_p.K801T|ZMYM1_uc010ohu.1_Missense_Mutation_p.K782T|ZMYM1_uc001byo.2_Missense_Mutation_p.K441T|ZMYM1_uc009vut.2_Missense_Mutation_p.K726T	NM_024772	NP_079048	Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM domain containing 1	801						nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AAAACATGCAAGAAACATATA	0.338													45	282	---	---	---	---	PASS
SFPQ	6421	broad.mit.edu	37	1	35657016	35657016	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35657016T>C	uc001bys.2	-	2	1036	c.943A>G	c.(943-945)AGA>GGA	p.R315G	SFPQ_uc001byr.2_5'Flank	NM_005066	NP_005057	P23246	SFPQ_HUMAN	splicing factor proline/glutamine rich	315	RRM 1.				alternative nuclear mRNA splicing, via spliceosome|DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix|paraspeckles	DNA binding|nucleotide binding|protein binding|protein binding|RNA binding		SFPQ/TFE3(6)	kidney(4)|soft_tissue(2)|ovary(1)|skin(1)	8		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				GCAAATAGTCTTTTGAATTCA	0.388			T	TFE3	papillary renal cell								8	631	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70518807	70518807	+	Silent	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70518807T>C	uc001dep.2	+	21	4125	c.4095T>C	c.(4093-4095)CCT>CCC	p.P1365P	LRRC7_uc009wbg.2_Silent_p.P649P|LRRC7_uc001deq.2_Silent_p.P559P	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1365						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						GGGATGTACCTCCGGACACCA	0.398													23	92	---	---	---	---	PASS
ODF2L	57489	broad.mit.edu	37	1	86847989	86847989	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86847989T>C	uc001dll.1	-	7	900	c.560A>G	c.(559-561)GAA>GGA	p.E187G	ODF2L_uc001dlm.1_Missense_Mutation_p.E187G|ODF2L_uc001dln.2_Missense_Mutation_p.E187G|ODF2L_uc001dlo.2_Missense_Mutation_p.E56G|ODF2L_uc001dlp.2_Missense_Mutation_p.E187G|ODF2L_uc010osg.1_Missense_Mutation_p.E187G|ODF2L_uc001dlq.1_Intron|ODF2L_uc009wcr.1_Missense_Mutation_p.E56G	NM_020729	NP_065780	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like isoform	187	Potential.					centrosome				ovary(1)	1				all cancers(265;0.0313)|Epithelial(280;0.0611)		CTGTAGTCGTTCATGTACTAC	0.299													7	360	---	---	---	---	PASS
FNDC7	163479	broad.mit.edu	37	1	109280146	109280146	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109280146G>A	uc001dvx.2	+	11	2170	c.2170G>A	c.(2170-2172)GTG>ATG	p.V724M	FNDC7_uc010ova.1_Intron	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	725						extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		ACTTGGAATGGGTAAGTCATT	0.299													158	521	---	---	---	---	PASS
GDAP2	54834	broad.mit.edu	37	1	118426150	118426150	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118426150A>G	uc001ehf.2	-	11	1506	c.1207T>C	c.(1207-1209)TCC>CCC	p.S403P	GDAP2_uc001ehg.2_Missense_Mutation_p.S403P	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated	403	CRAL-TRIO.									ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		AGGAAGTCGGAGTCCAGGTGA	0.358													22	129	---	---	---	---	PASS
PVRL4	81607	broad.mit.edu	37	1	161044038	161044038	+	Silent	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161044038G>T	uc001fxo.2	-	6	1425	c.1126C>A	c.(1126-1128)CGG>AGG	p.R376R	PVRL4_uc010pjy.1_Silent_p.R55R|PVRL4_uc010pjz.1_Silent_p.R110R	NM_030916	NP_112178	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4 precursor	376	Cytoplasmic (Potential).				adherens junction organization|cell adhesion|cell junction assembly	adherens junction|extracellular region|integral to membrane				ovary(2)	2	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			GCCTTGCGCCGATGGTATCGG	0.577													6	171	---	---	---	---	PASS
NUF2	83540	broad.mit.edu	37	1	163315676	163315676	+	Intron	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163315676T>C	uc001gcq.1	+						NUF2_uc001gcp.2_3'UTR|NUF2_uc001gcr.1_Intron|NUF2_uc009wvc.1_Intron	NM_145697	NP_663735	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component						cell division|chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|Ndc80 complex|nucleus	protein binding			ovary(3)|skin(1)	4	all_hematologic(923;0.101)					TGTATTTTGCTTTCACTTTTT	0.289													5	114	---	---	---	---	PASS
RABGAP1L	9910	broad.mit.edu	37	1	174190201	174190201	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174190201G>T	uc001gjx.2	+	3	425	c.230G>T	c.(229-231)TGT>TTT	p.C77F	RABGAP1L_uc009wwq.1_Missense_Mutation_p.C77F|RABGAP1L_uc001gjw.2_Missense_Mutation_p.C40F	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A	77					regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						CTTGTTGATTGTCAAAGTTCC	0.393													9	437	---	---	---	---	PASS
CFH	3075	broad.mit.edu	37	1	196684863	196684863	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196684863G>A	uc001gtj.3	+	11	1900	c.1660G>A	c.(1660-1662)GGT>AGT	p.G554S		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	554	Sushi 9.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6						CATAGTGTGTGGTTACAATGG	0.279													25	161	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235969775	235969775	+	Silent	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235969775C>T	uc001hxj.2	-	6	2836	c.2661G>A	c.(2659-2661)AAG>AAA	p.K887K	LYST_uc009xgb.1_RNA|LYST_uc010pxs.1_RNA|LYST_uc001hxl.1_Silent_p.K887K	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	887					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GGTTAACAGTCTTCCGTCTCT	0.413									Chediak-Higashi_syndrome				48	126	---	---	---	---	PASS
GTF3C2	2976	broad.mit.edu	37	2	27565792	27565792	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27565792G>A	uc002rjv.1	-	4	833	c.470C>T	c.(469-471)TCA>TTA	p.S157L	GTF3C2_uc002rju.1_Missense_Mutation_p.S168L|GTF3C2_uc002rjw.1_Missense_Mutation_p.S157L|GTF3C2_uc010eyz.1_Missense_Mutation_p.S157L	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide	157						transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAGGTCTTTTGACAACTTCAG	0.557													120	161	---	---	---	---	PASS
SRBD1	55133	broad.mit.edu	37	2	45616439	45616439	+	3'UTR	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45616439C>T	uc002rus.2	-	21					SRBD1_uc010yoc.1_3'UTR	NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			GTCTGGCCTTCGTGGGATACT	0.433													26	106	---	---	---	---	PASS
RAB1A	5861	broad.mit.edu	37	2	65316108	65316108	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65316108T>C	uc002sdm.2	-	5	771	c.385A>G	c.(385-387)ACC>GCC	p.T129A	RAB1A_uc002sdn.2_Intron|RAB1A_uc010yqe.1_Missense_Mutation_p.T97A|RAB1A_uc002sdo.2_Missense_Mutation_p.T65A	NM_004161	NP_004152	P62820	RAB1A_HUMAN	RAB1A, member RAS oncogene family isoform 1	129					protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	GTP binding|GTPase activity				0						TTCTTTGTGGTCAGATCACAT	0.358													79	330	---	---	---	---	PASS
GKN2	200504	broad.mit.edu	37	2	69177365	69177365	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69177365C>A	uc002sfa.2	-	3	206	c.97G>T	c.(97-99)GGT>TGT	p.G33C	GKN2_uc002sfb.3_Missense_Mutation_p.G33C	NM_182536	NP_872342	Q86XP6	GKN2_HUMAN	trefoil factor interactions(z) 1 precursor	33						extracellular region					0						ACATTGCCACCATTGTTGCTT	0.343													61	436	---	---	---	---	PASS
RAB11FIP5	26056	broad.mit.edu	37	2	73315745	73315745	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73315745G>A	uc002siu.3	-	3	1242	c.1001C>T	c.(1000-1002)TCT>TTT	p.S334F	RAB11FIP5_uc002sit.3_Missense_Mutation_p.S256F	NM_015470	NP_056285	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	334					protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0						ACAGAGCGAAGAGCGGGAGGC	0.627													4	7	---	---	---	---	PASS
NAT8	9027	broad.mit.edu	37	2	73868603	73868603	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73868603G>A	uc002sji.1	-	2	320	c.153C>T	c.(151-153)CTC>CTT	p.L51L		NM_003960	NP_003951	Q9UHE5	NAT8_HUMAN	N-acetyltransferase 8	51	Helical; (Potential).				gastrulation with mouth forming second|response to drug	integral to membrane	N-acetyltransferase activity			ovary(1)	1						GGAGTAGGGCGAGGGGCCCCC	0.612													9	61	---	---	---	---	PASS
ALMS1P	200420	broad.mit.edu	37	2	73900989	73900989	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73900989G>A	uc010yrl.1	+	5	787	c.266G>A	c.(265-267)CGG>CAG	p.R89Q		NR_003683				RecName: Full=Putative ALMS1-like protein;												0						ATTGGGGAGCGGATAAAGCGT	0.428													19	164	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96521862	96521862	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96521862T>A	uc002suz.1	-	31	2705	c.1228A>T	c.(1228-1230)AGG>TGG	p.R410W						SubName: Full=Putative uncharacterized protein ENSP00000312008; Flags: Fragment;																		AGCCTGAGCCTGGCAATTTCA	0.348													3	62	---	---	---	---	PASS
CNNM4	26504	broad.mit.edu	37	2	97427956	97427956	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97427956G>A	uc002swx.2	+	1	1318	c.1220G>A	c.(1219-1221)CGC>CAC	p.R407H		NM_020184	NP_064569	Q6P4Q7	CNNM4_HUMAN	cyclin M4	407	CBS 1.				biomineral tissue development|ion transport|response to stimulus|visual perception	integral to membrane|plasma membrane				breast(2)|ovary(1)	3						GGCTATACTCGCATCCCGGTG	0.517													80	118	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	142888338	142888338	+	5'UTR	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142888338C>A	uc002tvj.1	-	1					LRP1B_uc010fnl.1_Silent_p.P24P	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GGAGACTGCTCGGCGGCACCT	0.463										TSP Lung(27;0.18)			4	25	---	---	---	---	PASS
ERMN	57471	broad.mit.edu	37	2	158182140	158182140	+	Silent	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158182140C>T	uc002tzh.2	-	1	277	c.15G>A	c.(13-15)CCG>CCA	p.P5P	ERMN_uc010zcj.1_5'Flank|ERMN_uc010zck.1_Silent_p.P5P|ERMN_uc002tzi.2_Silent_p.P18P	NM_020711	NP_065762	Q8TAM6	ERMIN_HUMAN	ermin, ERM-like protein isoform b	5						cytoplasm|cytoskeleton				ovary(1)|skin(1)	2						TAAATGTAGCCGGAACATCTG	0.453													79	288	---	---	---	---	PASS
TANC1	85461	broad.mit.edu	37	2	160080760	160080760	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160080760G>A	uc002uag.2	+	23	3970	c.3696G>A	c.(3694-3696)GAG>GAA	p.E1232E	TANC1_uc010zcm.1_Silent_p.E1224E|TANC1_uc010fom.1_Silent_p.E1038E|TANC1_uc010fon.2_Silent_p.E76E	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1232	ANK 10.					cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						ACCTGGTGGAGAAGGGAGCCG	0.602													18	50	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178095721	178095721	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178095721T>C	uc002ulh.3	-	5	2165	c.1610A>G	c.(1609-1611)GAA>GGA	p.E537G	NFE2L2_uc002ulg.3_Missense_Mutation_p.E521G|NFE2L2_uc010zfa.1_Missense_Mutation_p.E514G|NFE2L2_uc002uli.3_Missense_Mutation_p.E521G	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	537	Leucine-zipper.				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)			GAGCAATTTTTCTTTTTCATC	0.343			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			9	670	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196681492	196681492	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196681492G>A	uc002utj.3	-	51	9722	c.9621C>T	c.(9619-9621)GCC>GCT	p.A3207A		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3207					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						AAGAATGGATGGCAATAGGAC	0.443													6	581	---	---	---	---	PASS
HECW2	57520	broad.mit.edu	37	2	197184391	197184391	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197184391G>A	uc002utm.1	-	9	1406	c.1223C>T	c.(1222-1224)CCT>CTT	p.P408L	HECW2_uc002utl.1_Missense_Mutation_p.P52L	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin	408					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						TCCTCTGGGAGGTGAGGTCCT	0.522													18	121	---	---	---	---	PASS
SF3B1	23451	broad.mit.edu	37	2	198257832	198257832	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198257832G>A	uc002uue.2	-	24	3668	c.3620C>T	c.(3619-3621)TCG>TTG	p.S1207L		NM_012433	NP_036565	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1 isoform 1	1207					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTGATTCAGCGAATCTTCACA	0.458													55	273	---	---	---	---	PASS
SATB2	23314	broad.mit.edu	37	2	200245089	200245089	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200245089G>A	uc002uuy.1	-	5	1412	c.595C>T	c.(595-597)CAG>TAG	p.Q199*	SATB2_uc010fsq.1_Intron|SATB2_uc002uuz.1_Nonsense_Mutation_p.Q199*|SATB2_uc002uva.1_Nonsense_Mutation_p.Q199*	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	199						cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						ATACTGACCTGGGAGAGAGGG	0.507													12	172	---	---	---	---	PASS
NRP2	8828	broad.mit.edu	37	2	206580920	206580920	+	Silent	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206580920T>C	uc002vaw.2	+	3	1046	c.255T>C	c.(253-255)TAT>TAC	p.Y85Y	NRP2_uc002vat.2_Silent_p.Y85Y|NRP2_uc002vau.2_Silent_p.Y85Y|NRP2_uc002vav.2_Silent_p.Y85Y|NRP2_uc002vax.2_Silent_p.Y85Y|NRP2_uc002vay.2_Silent_p.Y85Y|NRP2_uc010fud.2_Silent_p.Y85Y	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	85	Extracellular (Potential).|CUB 1.				angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4						CACCCAGGTATGACTTTATCG	0.532													26	59	---	---	---	---	PASS
CPS1	1373	broad.mit.edu	37	2	211342450	211342450	+	5'UTR	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211342450T>C	uc010fur.2	+	1					LANCL1_uc010zjh.1_5'Flank|LANCL1_uc002ved.2_5'Flank|LANCL1_uc010fuq.2_5'Flank	NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a						carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		AGTTGCTTTCTTAACCTCATC	0.428													8	688	---	---	---	---	PASS
STK36	27148	broad.mit.edu	37	2	219557312	219557312	+	Missense_Mutation	SNP	C	T	T	rs145717046		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219557312C>T	uc002viu.2	+	16	2188	c.1922C>T	c.(1921-1923)CCG>CTG	p.P641L	STK36_uc002viv.2_Missense_Mutation_p.P641L|STK36_uc002viw.2_5'Flank	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36	641					cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		ACAGGAGCCCCGCAAGTGAGC	0.572													5	39	---	---	---	---	PASS
CCDC108	255101	broad.mit.edu	37	2	219888914	219888914	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219888914C>A	uc002vjl.1	-	15	2502	c.2418G>T	c.(2416-2418)AAG>AAT	p.K806N		NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	806						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGTCAGCAGCTTGCAGTCTT	0.642													13	60	---	---	---	---	PASS
ZFAND2B	130617	broad.mit.edu	37	2	220072990	220072990	+	Silent	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220072990C>A	uc002vka.2	+	5	619	c.447C>A	c.(445-447)ATC>ATA	p.I149I	ZFAND2B_uc010zkt.1_Silent_p.I149I|ZFAND2B_uc010fwd.1_Silent_p.I149I|ZFAND2B_uc002vjy.1_Silent_p.I149I|ZFAND2B_uc002vjz.1_Silent_p.I149I|ZFAND2B_uc002vkb.1_Silent_p.I40I	NM_138802	NP_620157	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	149						endoplasmic reticulum	protein binding|zinc ion binding				0		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTGCTGCCATCTCCAGAGCAC	0.532													16	91	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191648	10191648	+	Nonstop_Mutation	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191648G>T	uc003bvc.2	+	3	854	c.641G>T	c.(640-642)TGA>TTA	p.*214L	VHL_uc003bvd.2_Nonstop_Mutation_p.*173L	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	214					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.?(1)|p.*214C(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)		ATGGGAGATTGAAGATTTCTG	0.458		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				16	32	---	---	---	---	PASS
RARB	5915	broad.mit.edu	37	3	25636158	25636158	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25636158T>C	uc011awl.1	+	7	1226	c.1160T>C	c.(1159-1161)ATC>ACC	p.I387T	RARB_uc003cdi.1_Missense_Mutation_p.I268T|RARB_uc003cdh.2_Missense_Mutation_p.I380T	NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2	387	Ligand-binding.				embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	CTCCGTAGCATCAGTGCTAAA	0.413													22	36	---	---	---	---	PASS
PDHB	5162	broad.mit.edu	37	3	58416621	58416621	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58416621G>A	uc003dkf.3	-	6	381	c.352C>T	c.(352-354)CAA>TAA	p.Q118*	PDHB_uc003dke.3_Nonsense_Mutation_p.Q76*|PDHB_uc003dkg.3_Nonsense_Mutation_p.Q100*|PDHB_uc010hnl.2_Nonsense_Mutation_p.Q100*|PDHB_uc011bff.1_Nonsense_Mutation_p.Q118*	NM_000925	NP_000916	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta	118					glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate|tricarboxylic acid cycle	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	NADH(DB00157)|Pyruvic acid(DB00119)	TCAATGGCTTGCATGGAGAAA	0.458													9	35	---	---	---	---	PASS
MINA	84864	broad.mit.edu	37	3	97661535	97661535	+	3'UTR	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97661535A>G	uc003drz.1	-	10					CRYBG3_uc003drx.2_Intron|CRYBG3_uc010hoz.1_Intron|MINA_uc003dry.1_3'UTR|MINA_uc003dsa.1_3'UTR|MINA_uc003dsb.1_3'UTR|MINA_uc003dsc.1_3'UTR	NM_001042533	NP_001035998	Q8IUF8	MINA_HUMAN	MYC induced nuclear antigen isoform a						ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1						TGAACTCAGAACAGTTCTAAA	0.333													2	0	---	---	---	---	PASS
COX17	10063	broad.mit.edu	37	3	119393997	119393997	+	Nonstop_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119393997C>A	uc003ecz.1	-	2	277	c.191G>T	c.(190-192)TGA>TTA	p.*64L	uc003edb.1_5'Flank	NM_005694	NP_005685	Q14061	COX17_HUMAN	COX17 homolog, cytochrome c oxidase assembly	64					copper ion transport|generation of precursor metabolites and energy	mitochondrial intermembrane space	copper chaperone activity				0				GBM - Glioblastoma multiforme(114;0.227)		CTTACCATTTCATATTTTAAA	0.368													105	337	---	---	---	---	PASS
GOLGB1	2804	broad.mit.edu	37	3	121396286	121396286	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121396286C>T	uc003eei.3	-	16	8996	c.8870G>A	c.(8869-8871)AGT>AAT	p.S2957N	GOLGB1_uc010hrc.2_Missense_Mutation_p.S2962N|GOLGB1_uc003eej.3_Missense_Mutation_p.S2923N	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	2957	Cytoplasmic (Potential).|Potential.				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)		TTCCCAGGAACTCTTCTCCAT	0.303													5	552	---	---	---	---	PASS
COL29A1	256076	broad.mit.edu	37	3	130174477	130174477	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130174477C>A	uc010htj.1	+	37	7251	c.6757C>A	c.(6757-6759)CAA>AAA	p.Q2253K	COL29A1_uc010hti.1_RNA|COL29A1_uc010htk.1_Missense_Mutation_p.Q292K	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	2253	Nonhelical region.				axon guidance|cell adhesion	collagen					0						TGAAAAAGATCAAAAATCTGC	0.333													30	86	---	---	---	---	PASS
KCNAB1	7881	broad.mit.edu	37	3	156175241	156175241	+	Splice_Site	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156175241G>T	uc003far.2	+	4	422	c.358_splice	c.e4-1	p.V120_splice	KCNAB1_uc011bon.1_Splice_Site_p.V120_splice|KCNAB1_uc003fas.2_Splice_Site_p.V109_splice|KCNAB1_uc003fat.2_Splice_Site_p.V102_splice|KCNAB1_uc010hvt.1_Splice_Site_p.V102_splice|KCNAB1_uc011boo.1_Splice_Site	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TCCCCTTGCAGGTTGCTGAAC	0.473													58	156	---	---	---	---	PASS
MECOM	2122	broad.mit.edu	37	3	168833688	168833688	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168833688C>A	uc003ffi.3	-	7	1677	c.1408G>T	c.(1408-1410)GTG>TTG	p.V470L	MECOM_uc010hwk.1_Missense_Mutation_p.V493L|MECOM_uc003ffj.3_Missense_Mutation_p.V535L|MECOM_uc011bpi.1_Missense_Mutation_p.V471L|MECOM_uc003ffn.3_Missense_Mutation_p.V470L|MECOM_uc003ffk.2_Missense_Mutation_p.V470L|MECOM_uc003ffl.2_Missense_Mutation_p.V630L|MECOM_uc011bpj.1_Missense_Mutation_p.V658L|MECOM_uc011bpk.1_Missense_Mutation_p.V460L|MECOM_uc010hwn.2_Missense_Mutation_p.V658L	NM_005241	NP_005232	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform b	470					apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						GAATCATTCACAGCTCCTGAC	0.398													206	570	---	---	---	---	PASS
ECT2	1894	broad.mit.edu	37	3	172473334	172473334	+	Intron	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172473334A>G	uc003fii.2	+						ECT2_uc010hwv.1_Missense_Mutation_p.D91G|ECT2_uc003fih.2_Intron|ECT2_uc003fij.1_Intron|ECT2_uc003fik.1_Intron|ECT2_uc003fil.1_Missense_Mutation_p.D91G	NM_018098	NP_060568	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			GGAAAATCGGATGAAAAATTA	0.323													4	57	---	---	---	---	PASS
USO1	8615	broad.mit.edu	37	4	76676621	76676621	+	Intron	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76676621T>C	uc003hiu.2	+							NM_003715	NP_003706	O60763	USO1_HUMAN	USO1 homolog, vesicle docking protein						intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GAAGTTCATGTTTCTCAAACA	0.358													7	584	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79308552	79308552	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79308552A>T	uc003hlb.2	+	29	4112	c.3672A>T	c.(3670-3672)GAA>GAT	p.E1224D	FRAS1_uc003hkw.2_Missense_Mutation_p.E1224D	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	1223	CSPG 2.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						TGAGAAATGAAGTTCTCCACA	0.468													12	57	---	---	---	---	PASS
DAPP1	27071	broad.mit.edu	37	4	100761576	100761576	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100761576A>G	uc003hvf.3	+	3	445	c.355A>G	c.(355-357)ACA>GCA	p.T119A	DAPP1_uc011cek.1_Missense_Mutation_p.T119A|DAPP1_uc010ilh.2_Missense_Mutation_p.T119A	NM_014395	NP_055210	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and	119	SH2.				signal transduction	cytoplasm|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein tyrosine phosphatase activity				0				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		TGGAAGCGAGACAGGTAAGCT	0.343													6	234	---	---	---	---	PASS
BBS7	55212	broad.mit.edu	37	4	122747087	122747087	+	Silent	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122747087T>C	uc003ied.2	-	19	2250	c.2076A>G	c.(2074-2076)AAA>AAG	p.K692K	CCNA2_uc003iec.3_5'Flank	NM_176824	NP_789794	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7 protein isoform a	692					cilium morphogenesis|digestive tract morphogenesis|fat cell differentiation|heart looping|melanosome transport|pigment granule aggregation in cell center|response to stimulus|visual perception	BBSome|centrosome|cilium membrane	protein binding			ovary(1)	1						GAAGGGGTACTTTAGTTTTTA	0.318									Bardet-Biedl_syndrome				7	611	---	---	---	---	PASS
BBS12	166379	broad.mit.edu	37	4	123664977	123664977	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123664977A>C	uc003ieu.2	+	2	2123	c.1930A>C	c.(1930-1932)AAT>CAT	p.N644H		NM_152618	NP_689831	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	644					cellular protein metabolic process	cilium	ATP binding			ovary(2)	2						TAGTAAACTAAATAGTAGAAT	0.378									Bardet-Biedl_syndrome				60	179	---	---	---	---	PASS
SORBS2	8470	broad.mit.edu	37	4	186548090	186548090	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186548090C>T	uc003iyl.2	-	12	1676	c.818G>A	c.(817-819)AGT>AAT	p.S273N	SORBS2_uc003iyh.2_Missense_Mutation_p.S524N|SORBS2_uc011ckw.1_Missense_Mutation_p.S361N|SORBS2_uc003iyi.2_Missense_Mutation_p.S431N|SORBS2_uc011ckx.1_Missense_Mutation_p.S366N|SORBS2_uc003iyk.2_Missense_Mutation_p.S344N|SORBS2_uc003iym.2_Missense_Mutation_p.S373N|SORBS2_uc003iyn.1_Missense_Mutation_p.S391N|SORBS2_uc011cky.1_Missense_Mutation_p.S336N|SORBS2_uc011cku.1_Missense_Mutation_p.S192N|SORBS2_uc011ckv.1_Missense_Mutation_p.S177N|SORBS2_uc003iyd.2_Missense_Mutation_p.S499N|SORBS2_uc003iye.2_Missense_Mutation_p.S373N|SORBS2_uc003iya.2_Missense_Mutation_p.S320N|SORBS2_uc003iyb.2_Missense_Mutation_p.S273N|SORBS2_uc003iyc.2_Missense_Mutation_p.S253N|SORBS2_uc003iyg.2_Missense_Mutation_p.S387N|SORBS2_uc003iyf.2_Missense_Mutation_p.S336N|SORBS2_uc003iyo.1_Missense_Mutation_p.S249N	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	273						actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		CCTGCTCGCACTTTGATCTCC	0.552													49	94	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	5	86534689	86534689	+	Intron	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86534689C>T	uc003kit.2	+						uc003kiu.1_5'UTR|uc003kiv.1_5'UTR					Homo sapiens cDNA clone IMAGE:5444809, **** WARNING: chimeric clone ****.																		TCCCATTTTGCAATCCCGAAC	0.443													2	1	---	---	---	---	PASS
YTHDC2	64848	broad.mit.edu	37	5	112927786	112927786	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112927786C>T	uc003kqn.2	+	28	4306	c.4123C>T	c.(4123-4125)CGA>TGA	p.R1375*		NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1375	YTH.						ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GGAGTGGATACGAAAAGAAAG	0.453													5	273	---	---	---	---	PASS
CTNNA1	1495	broad.mit.edu	37	5	138261073	138261073	+	Silent	SNP	A	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138261073A>C	uc003ldh.2	+	13	1971	c.1876A>C	c.(1876-1878)AGG>CGG	p.R626R	CTNNA1_uc011cyx.1_Silent_p.R523R|CTNNA1_uc011cyy.1_Silent_p.R503R|CTNNA1_uc003ldi.2_Silent_p.R324R|CTNNA1_uc003ldj.2_Silent_p.R626R|CTNNA1_uc003ldl.2_Silent_p.R256R	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1	626					adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CCGGGACATCAGGAAAGCAGT	0.488													13	91	---	---	---	---	PASS
PCDHB3	56132	broad.mit.edu	37	5	140481311	140481311	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140481311T>G	uc003lio.2	+	1	1078	c.1078T>G	c.(1078-1080)TCG>GCG	p.S360A	uc003lin.2_Intron	NM_018937	NP_061760	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3 precursor	360	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCTGAGAACTCGGGAGAGAC	0.478													14	103	---	---	---	---	PASS
SLC36A2	153201	broad.mit.edu	37	5	150701632	150701632	+	Silent	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150701632A>G	uc003lty.2	-	9	1285	c.1155T>C	c.(1153-1155)ATT>ATC	p.I385I	GM2A_uc011dcs.1_Intron|SLC36A2_uc003ltz.2_RNA|SLC36A2_uc003lua.2_Silent_p.I187I|SLC36A2_uc010jhv.2_Silent_p.I385I	NM_181776	NP_861441	Q495M3	S36A2_HUMAN	solute carrier family 36, member 2	385	Helical; (Potential).				cellular nitrogen compound metabolic process	cytoplasm|integral to membrane|plasma membrane	glycine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGACGAGGCGAATGGACAGAT	0.512													46	78	---	---	---	---	PASS
ZNF354B	117608	broad.mit.edu	37	5	178309752	178309752	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178309752A>T	uc003mjl.2	+	5	525	c.299A>T	c.(298-300)CAG>CTG	p.Q100L	ZNF354B_uc003mjm.2_Missense_Mutation_p.Q100L	NM_058230	NP_478137	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	100					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACTCAAACTCAGGATTCATTT	0.358													104	114	---	---	---	---	PASS
TXNDC5	81567	broad.mit.edu	37	6	7883469	7883469	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7883469G>A	uc003mxv.2	-	10	1239	c.1207C>T	c.(1207-1209)CGA>TGA	p.R403*	TXNDC5_uc003mxw.2_Nonsense_Mutation_p.R360*|TXNDC5_uc010jnz.2_Nonsense_Mutation_p.R295*	NM_030810	NP_110437	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 isoform 1	403	Thioredoxin 3.				anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)					TTCCCTCCTCGGAAAAGCAAT	0.453													28	79	---	---	---	---	PASS
VARS	7407	broad.mit.edu	37	6	31752061	31752061	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31752061G>A	uc003nxe.2	-	13	2024	c.1601C>T	c.(1600-1602)GCA>GTA	p.A534V	VARS_uc011doi.1_RNA	NM_006295	NP_006286	P26640	SYVC_HUMAN	valyl-tRNA synthetase	534					translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3					L-Valine(DB00161)	CCGAGTTGTTGCCACCACCAC	0.597													11	75	---	---	---	---	PASS
HS3ST5	222537	broad.mit.edu	37	6	114383925	114383925	+	Missense_Mutation	SNP	C	T	T	rs144143119	byFrequency	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114383925C>T	uc003pwg.3	-	1	117	c.85G>A	c.(85-87)GCC>ACC	p.A29T	uc003pwf.2_Intron|HS3ST5_uc003pwh.3_Missense_Mutation_p.A29T	NM_153612	NP_705840	Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine)	29	Helical; Signal-anchor for type II membrane protein; (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)		CCAACTCTGGCGACTAGATAC	0.483													19	109	---	---	---	---	PASS
EYA4	2070	broad.mit.edu	37	6	133844277	133844277	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133844277C>T	uc003qec.3	+	18	2158	c.1700C>T	c.(1699-1701)GCT>GTT	p.A567V	EYA4_uc011ecq.1_Missense_Mutation_p.A513V|EYA4_uc011ecr.1_Missense_Mutation_p.A519V|EYA4_uc003qed.3_Missense_Mutation_p.A567V|EYA4_uc003qee.3_Missense_Mutation_p.A544V|EYA4_uc011ecs.1_Missense_Mutation_p.A573V|uc003qeg.1_Intron	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a	567					anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		TTAGGAGGTGCTTTCCCCATT	0.388													11	78	---	---	---	---	PASS
MAP3K5	4217	broad.mit.edu	37	6	136923035	136923035	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136923035G>C	uc003qhc.2	-	20	3123	c.2762C>G	c.(2761-2763)CCA>CGA	p.P921R	MAP3K5_uc011edj.1_Missense_Mutation_p.P168R|MAP3K5_uc011edk.1_Missense_Mutation_p.P766R	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase	921	Protein kinase.				activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GTCAGGATCTGGTTCAAAACA	0.398													37	248	---	---	---	---	PASS
MAP3K5	4217	broad.mit.edu	37	6	136934259	136934259	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136934259T>C	uc003qhc.2	-	17	2775	c.2414A>G	c.(2413-2415)AAG>AGG	p.K805R	MAP3K5_uc011edj.1_Missense_Mutation_p.K52R|MAP3K5_uc011edk.1_Missense_Mutation_p.K650R	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase	805	Protein kinase.				activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GTACCTCACCTTTATGTCCCG	0.328													7	401	---	---	---	---	PASS
SP4	6671	broad.mit.edu	37	7	21469813	21469813	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21469813A>G	uc003sva.2	+	3	1211	c.1030A>G	c.(1030-1032)ACT>GCT	p.T344A	SP4_uc003svb.2_Missense_Mutation_p.T31A	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor	344					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5						CTCAGCAGATACTGGCCAGTA	0.502													10	44	---	---	---	---	PASS
OGDH	4967	broad.mit.edu	37	7	44664056	44664056	+	Silent	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44664056G>T	uc003tln.2	+	2	223	c.114G>T	c.(112-114)CGG>CGT	p.R38R	OGDH_uc003tlm.2_Silent_p.R38R|OGDH_uc011kbx.1_Silent_p.R38R|OGDH_uc011kby.1_Silent_p.R38R|OGDH_uc003tlp.2_Silent_p.R38R|OGDH_uc011kbz.1_5'UTR	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	38					glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)	AACAGATTCGGTGCTATTCTG	0.488													27	191	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48427461	48427461	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48427461C>T	uc003toq.2	+	36	11403	c.11378C>T	c.(11377-11379)GCC>GTC	p.A3793V	ABCA13_uc010kys.1_Missense_Mutation_p.A867V|ABCA13_uc003tos.1_Missense_Mutation_p.A619V|ABCA13_uc010kyt.1_RNA	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3793					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						CCCTTTACTGCCTCATATTGG	0.318													6	553	---	---	---	---	PASS
WBSCR22	114049	broad.mit.edu	37	7	73118169	73118169	+	3'UTR	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73118169G>A	uc003tyw.1	+	10					STX1A_uc003tyx.2_Intron|STX1A_uc003tyy.2_Intron|STX1A_uc010lbj.1_Intron			O43709	WBS22_HUMAN	Homo sapiens clone PP3381 unknown mRNA.							nucleus	methyltransferase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)				CTGCAAGCGAGTGGGGTCACA	0.527													7	48	---	---	---	---	PASS
GNGT1	2792	broad.mit.edu	37	7	93535945	93535945	+	5'UTR	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93535945A>G	uc003unc.1	+	1					GNGT1_uc003umx.1_Intron	NM_021955	NP_068774	P63211	GBG1_HUMAN	guanine nucleotide binding protein (G protein),						G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|signal transducer activity				0	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			AAAACAAAGAACAGTTTACTT	0.358													9	51	---	---	---	---	PASS
SGCE	8910	broad.mit.edu	37	7	94228247	94228247	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94228247G>A	uc003unl.2	-	9	1204	c.1093C>T	c.(1093-1095)CAG>TAG	p.Q365*	SGCE_uc003unk.2_Nonsense_Mutation_p.Q188*|SGCE_uc003unm.2_Nonsense_Mutation_p.Q365*|SGCE_uc003unn.2_Nonsense_Mutation_p.Q356*|SGCE_uc011kic.1_Nonsense_Mutation_p.Q324*|SGCE_uc011kid.1_Nonsense_Mutation_p.Q401*	NM_003919	NP_003910	O43556	SGCE_HUMAN	sarcoglycan, epsilon isoform 2	365	Cytoplasmic (Potential).				cell-matrix adhesion|muscle organ development	cytoplasm|cytoskeleton|integral to plasma membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GTAGATTTCTGAATAGCACTG	0.403													6	365	---	---	---	---	PASS
FAM185A	222234	broad.mit.edu	37	7	102392213	102392213	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102392213A>G	uc011klf.1	+	2	782	c.526A>G	c.(526-528)ACA>GCA	p.T176A	FAM185A_uc011klg.1_Intron|FAM185A_uc011klh.1_5'UTR	NM_001145268	NP_001138740	Q8N0U4	F185A_HUMAN	hypothetical protein LOC222234 isoform 1	176											0						CAAAATTGAAACAGAGCATGG	0.313													9	743	---	---	---	---	PASS
CFTR	1080	broad.mit.edu	37	7	117180383	117180383	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117180383G>A	uc003vjd.2	+	8	1231	c.1099G>A	c.(1099-1101)GCA>ACA	p.A367T	CFTR_uc011knq.1_5'UTR	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	367	Cytoplasmic (Potential).				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)	CTCTCTTGGAGCAATAAACAA	0.378									Cystic_Fibrosis				32	94	---	---	---	---	PASS
IQUB	154865	broad.mit.edu	37	7	123152356	123152356	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123152356T>C	uc003vkn.2	-	2	616	c.39A>G	c.(37-39)ATA>ATG	p.I13M	IQUB_uc003vko.2_Missense_Mutation_p.I13M|IQUB_uc010lkt.2_RNA|IQUB_uc003vkp.1_Missense_Mutation_p.I13M|IQUB_uc003vkq.2_Missense_Mutation_p.I13M	NM_178827	NP_849149	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	13										ovary(3)|large_intestine(1)	4						TTGAATTGACTATATTCTGAG	0.343													5	206	---	---	---	---	PASS
MGAM	8972	broad.mit.edu	37	7	141765603	141765603	+	Intron	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141765603C>T	uc003vwy.2	+							NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase						polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TACCCCTTCTCAAGAAACCAC	0.478													4	58	---	---	---	---	PASS
IDO1	3620	broad.mit.edu	37	8	39775487	39775487	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39775487A>G	uc003xnm.2	+	2	295	c.181A>G	c.(181-183)AAG>GAG	p.K61E	IDO1_uc003xnn.2_RNA	NM_002164	NP_002155	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	61					female pregnancy|tryptophan catabolic process	cytosol	electron carrier activity|heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			central_nervous_system(2)	2					L-Tryptophan(DB00150)	AAGAGTTGAGAAGGTTTGACA	0.338													5	166	---	---	---	---	PASS
KIAA1429	25962	broad.mit.edu	37	8	95531232	95531232	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95531232A>G	uc003ygo.1	-	9	2507	c.2494T>C	c.(2494-2496)TAT>CAT	p.Y832H	KIAA1429_uc003ygp.2_Missense_Mutation_p.Y832H|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	832					mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TCTTTGGAATAGTACTCCATT	0.328													49	40	---	---	---	---	PASS
KIAA1429	25962	broad.mit.edu	37	8	95538745	95538745	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95538745T>G	uc003ygo.1	-	8	1740	c.1727A>C	c.(1726-1728)AAG>ACG	p.K576T	KIAA1429_uc003ygp.2_Missense_Mutation_p.K576T|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	576					mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			AGATGAAGTCTTCTCTGCTAA	0.418													111	101	---	---	---	---	PASS
DMRTA1	63951	broad.mit.edu	37	9	22451073	22451073	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22451073G>T	uc003zpp.1	+	2	903	c.678G>T	c.(676-678)GAG>GAT	p.E226D		NM_022160	NP_071443	Q5VZB9	DMRTA_HUMAN	DMRT-like family A1	226					cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|skin(1)	2		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)		AACAAAAAGAGAGTAAATGTG	0.393													24	99	---	---	---	---	PASS
C9orf144B	259308	broad.mit.edu	37	9	34724109	34724109	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34724109A>G	uc011lor.1	-	4	3239	c.3128T>C	c.(3127-3129)ATG>ACG	p.M1043T		NM_001141917	NP_001135389	Q6ZU69	CI14B_HUMAN	hypothetical protein LOC259308	1043						integral to membrane					0						TCCTGCTAGCATGGGGACATG	0.582													21	51	---	---	---	---	PASS
SEMA4D	10507	broad.mit.edu	37	9	91994191	91994191	+	Silent	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91994191A>G	uc004aqo.1	-	18	2589	c.2017T>C	c.(2017-2019)TTG>CTG	p.L673L	SEMA4D_uc011ltm.1_Intron|SEMA4D_uc011ltn.1_Intron|SEMA4D_uc011lto.1_Intron|SEMA4D_uc004aqp.1_Silent_p.L671L	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	673	Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						GATGCCACCAACACTTTGGTG	0.622													4	31	---	---	---	---	PASS
SVEP1	79987	broad.mit.edu	37	9	113312161	113312161	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113312161A>G	uc010mtz.2	-	2	1092	c.755T>C	c.(754-756)TTT>TCT	p.F252S	SVEP1_uc010mua.1_Missense_Mutation_p.F252S|SVEP1_uc004beu.2_Missense_Mutation_p.F252S|SVEP1_uc004bev.2_5'UTR	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	252	VWFA.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						TAAAGCCTCAAATTCTTCAAA	0.458													13	96	---	---	---	---	PASS
GSN	2934	broad.mit.edu	37	9	124072995	124072995	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124072995G>A	uc004blf.1	+	4	599	c.538G>A	c.(538-540)GTA>ATA	p.V180I	GSN_uc004bld.1_Missense_Mutation_p.V129I|GSN_uc010mvq.1_Missense_Mutation_p.V140I|GSN_uc010mvr.1_Missense_Mutation_p.V140I|GSN_uc010mvu.1_Missense_Mutation_p.V129I|GSN_uc010mvt.1_Missense_Mutation_p.V129I|GSN_uc010mvs.1_Missense_Mutation_p.V129I|GSN_uc004ble.1_Missense_Mutation_p.V129I|GSN_uc010mvv.1_Missense_Mutation_p.V129I|GSN_uc011lyh.1_Missense_Mutation_p.V146I|GSN_uc011lyi.1_Missense_Mutation_p.V129I|GSN_uc011lyj.1_Missense_Mutation_p.V153I|GSN_uc004blg.1_5'Flank	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor	180					actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						CAAGCACGTGGTACCCAACGA	0.582													35	121	---	---	---	---	PASS
ITIH5	80760	broad.mit.edu	37	10	7682816	7682816	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7682816A>C	uc001ijq.2	-	4	381	c.302T>G	c.(301-303)CTT>CGT	p.L101R	ITIH5_uc001ijr.1_Missense_Mutation_p.L101R	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	101	VIT.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4						GTCTCCAATAAGCCTGAAATA	0.388													173	443	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	11715686	11715686	+	RNA	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11715686T>C	uc001ikv.1	+	1		c.460T>C								full-length cDNA clone CS0DL010YP06 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																		AATATCCCATTCCAAACCTCT	0.473													4	13	---	---	---	---	PASS
CNGA4	1262	broad.mit.edu	37	11	6263120	6263120	+	Intron	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6263120G>T	uc001mco.2	+						CNGA4_uc010raa.1_3'UTR|CNGA4_uc001mcn.2_3'UTR	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4						response to stimulus|sensory perception of smell		cAMP binding			skin(1)	1		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCTGATTGAGGAAACCTGGCC	0.522													7	40	---	---	---	---	PASS
KCNA4	3739	broad.mit.edu	37	11	30034211	30034211	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30034211C>A	uc001msk.2	-	2	1167	c.15G>T	c.(13-15)ATG>ATT	p.M5I		NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	5						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CCGCACTCACCATTGCAACCT	0.537													4	16	---	---	---	---	PASS
OR4C3	256144	broad.mit.edu	37	11	48346714	48346714	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48346714C>G	uc010rhv.1	+	1	222	c.222C>G	c.(220-222)ATC>ATG	p.I74M		NM_001004702	NP_001004702	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C,	47	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						TGGTCACTATCACCTCCAGCC	0.463													43	189	---	---	---	---	PASS
OR8J3	81168	broad.mit.edu	37	11	55904652	55904652	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55904652A>C	uc010riz.1	-	1	543	c.543T>G	c.(541-543)ATT>ATG	p.I181M		NM_001004064	NP_001004064	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J,	181	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Esophageal squamous(21;0.00693)					ACAGAGGTGCAATATCACAGT	0.333													117	309	---	---	---	---	PASS
BSCL2	26580	broad.mit.edu	37	11	62472858	62472858	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62472858A>T	uc001nuo.1	-	2	551	c.127T>A	c.(127-129)TGG>AGG	p.W43R	BSCL2_uc009yoc.1_Missense_Mutation_p.W43R|BSCL2_uc001nup.2_Missense_Mutation_p.W43R|BSCL2_uc001nuq.1_Missense_Mutation_p.W43R|BSCL2_uc001nur.3_Missense_Mutation_p.W107R|BSCL2_uc009yod.2_Missense_Mutation_p.W107R|BSCL2_uc001nut.3_Missense_Mutation_p.W107R|HNRNPUL2_uc001nuu.1_RNA|GNG3_uc001nuv.2_5'Flank	NM_032667	NP_116056	Q96G97	BSCL2_HUMAN	seipin isoform 2	43	Helical; (Potential).				cell death	integral to endoplasmic reticulum membrane					0						ACAGACACCCAGAGCAAAAGG	0.577													22	72	---	---	---	---	PASS
SPTBN2	6712	broad.mit.edu	37	11	66483388	66483388	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66483388G>A	uc001ojd.2	-	3	294	c.222C>T	c.(220-222)GTC>GTT	p.V74V		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	74	CH 1.|Actin-binding.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						CCCGGCACGTGACCCGGGCCA	0.592													44	113	---	---	---	---	PASS
RNF121	55298	broad.mit.edu	37	11	71707272	71707272	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71707272C>A	uc001ora.2	+	9	1235	c.895C>A	c.(895-897)CTG>ATG	p.L299M	RNF121_uc001ord.2_Missense_Mutation_p.L218M|RNF121_uc001orb.2_Missense_Mutation_p.L267M|RNF121_uc009yst.2_3'UTR|IL18BP_uc001ore.1_5'Flank|IL18BP_uc001orf.1_5'Flank|IL18BP_uc009ysu.1_5'Flank|IL18BP_uc001org.1_5'Flank|IL18BP_uc001orh.1_5'Flank	NM_018320	NP_060790	Q9H920	RN121_HUMAN	ring finger protein 121	299						integral to membrane	zinc ion binding				0						GTATGGGCAACTGCTGGACTG	0.527													49	123	---	---	---	---	PASS
C11orf70	85016	broad.mit.edu	37	11	101946733	101946733	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101946733C>T	uc001pgp.2	+	5	593	c.565C>T	c.(565-567)CCA>TCA	p.P189S	C11orf70_uc001pgo.2_3'UTR|C11orf70_uc001pgq.2_Missense_Mutation_p.P151S	NM_032930	NP_116319	Q9BRQ4	CK070_HUMAN	hypothetical protein LOC85016	189										skin(1)	1	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)		TGTGATTAGCCCATATCTGGA	0.353													10	606	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108235939	108235939	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108235939A>G	uc001pkb.1	+	62	9366	c.8981A>G	c.(8980-8982)AAT>AGT	p.N2994S	ATM_uc009yxr.1_Missense_Mutation_p.N2994S|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.N1646S	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2994					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TGCAAACGAAATCTCAGGTGA	0.408			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			7	444	---	---	---	---	PASS
FXYD2	486	broad.mit.edu	37	11	117691415	117691415	+	Intron	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117691415G>T	uc001prj.2	-						FXYD2_uc001prl.2_3'UTR|FXYD2_uc001prk.1_Intron	NM_001680	NP_001671	P54710	ATNG_HUMAN	FXYD domain-containing ion transport regulator 2							sodium:potassium-exchanging ATPase complex	ion channel activity|sodium:potassium-exchanging ATPase activity				0	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;2.83e-05)|Epithelial(105;0.00114)	Cyclothiazide(DB00606)	GATTTGCCTGGTGGGGGAAGG	0.587													18	59	---	---	---	---	PASS
FXYD2	486	broad.mit.edu	37	11	117691416	117691416	+	Intron	SNP	T	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117691416T>G	uc001prj.2	-						FXYD2_uc001prl.2_3'UTR|FXYD2_uc001prk.1_Intron	NM_001680	NP_001671	P54710	ATNG_HUMAN	FXYD domain-containing ion transport regulator 2							sodium:potassium-exchanging ATPase complex	ion channel activity|sodium:potassium-exchanging ATPase activity				0	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;2.83e-05)|Epithelial(105;0.00114)	Cyclothiazide(DB00606)	ATTTGCCTGGTGGGGGAAGGA	0.592													21	55	---	---	---	---	PASS
MLL	4297	broad.mit.edu	37	11	118379865	118379865	+	Missense_Mutation	SNP	T	C	C	rs146191865	byFrequency	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118379865T>C	uc001pta.2	+	29	10864	c.10841T>C	c.(10840-10842)CTT>CCT	p.L3614P	MLL_uc001ptb.2_Missense_Mutation_p.L3617P	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	3614					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		GTCGCTGTTCTTCCGGAAGTT	0.323			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								8	654	---	---	---	---	PASS
VPS11	55823	broad.mit.edu	37	11	118938631	118938631	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118938631C>G	uc010ryx.1	+	1	139	c.97C>G	c.(97-99)CCT>GCT	p.P33A	VPS11_uc010ryy.1_5'UTR	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11	33					protein transport	endocytic vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		CGGGGCCACACCTGCTTCTGG	0.607													7	37	---	---	---	---	PASS
OR10S1	219873	broad.mit.edu	37	11	123847986	123847986	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123847986A>T	uc001pzm.1	-	1	413	c.413T>A	c.(412-414)CTG>CAG	p.L138Q		NM_001004474	NP_001004474	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S,	138	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		ACAGATAGCCAGATAGCGGTC	0.542													10	93	---	---	---	---	PASS
WNK1	65125	broad.mit.edu	37	12	1018030	1018030	+	3'UTR	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1018030G>T	uc001qio.3	+	28					WNK1_uc001qip.3_3'UTR|WNK1_uc001qir.3_3'UTR	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GGGGTGGGAAGTAGCCTATAT	0.493													5	14	---	---	---	---	PASS
CD163	9332	broad.mit.edu	37	12	7639565	7639565	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7639565G>A	uc001qsz.3	-	9	2196	c.2068C>T	c.(2068-2070)CTG>TTG	p.L690L	CD163_uc001qta.3_Silent_p.L690L|CD163_uc009zfw.2_Silent_p.L723L	NM_004244	NP_004235	Q86VB7	C163A_HUMAN	CD163 antigen isoform a	690	Extracellular (Potential).				acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity			ovary(6)|pancreas(1)|skin(1)	8						CACGAGGACAGTGTTTGGGAC	0.458													9	112	---	---	---	---	PASS
C12orf11	55726	broad.mit.edu	37	12	27064239	27064239	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27064239A>G	uc001rhk.3	-	15	2354	c.1817T>C	c.(1816-1818)ATC>ACC	p.I606T	C12orf11_uc001rhj.3_Missense_Mutation_p.I174T|C12orf11_uc010sjk.1_Missense_Mutation_p.I505T	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	606	Potential.				cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)					ACGCTCTAAGATTCCTTTTAA	0.328													8	489	---	---	---	---	PASS
TM7SF3	51768	broad.mit.edu	37	12	27156169	27156169	+	Silent	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27156169C>T	uc010sjl.1	-	2	484	c.246G>A	c.(244-246)CCG>CCA	p.P82P		NM_016551	NP_057635	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3 precursor	82						integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)					TTGCACTTACCGGAGAAAAGG	0.308													63	212	---	---	---	---	PASS
C12orf10	60314	broad.mit.edu	37	12	53700059	53700059	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53700059G>A	uc001scp.3	+	5	772	c.720G>A	c.(718-720)CTG>CTA	p.L240L	C12orf10_uc009zmx.2_Silent_p.L189L|C12orf10_uc001scq.3_Silent_p.L125L	NM_021640	NP_067653	Q86UA3	Q86UA3_HUMAN	MYG1 protein precursor	240										ovary(2)	2						ACAGCTGGCTGCCAGCCCGGG	0.517													50	123	---	---	---	---	PASS
PLXNC1	10154	broad.mit.edu	37	12	94634271	94634271	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94634271A>G	uc001tdc.2	+	11	2380	c.2131A>G	c.(2131-2133)AGC>GGC	p.S711G		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	711	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						GATACAGGTTAGCCATGTGCT	0.413													4	182	---	---	---	---	PASS
APAF1	317	broad.mit.edu	37	12	99117077	99117077	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99117077A>G	uc001tfz.2	+	23	3768	c.3191A>G	c.(3190-3192)GAT>GGT	p.D1064G	APAF1_uc001tfy.2_Missense_Mutation_p.D1053G|APAF1_uc001tga.2_Missense_Mutation_p.D1010G|APAF1_uc001tgb.2_Missense_Mutation_p.D1021G|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Missense_Mutation_p.D430G	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform	1064	WD 10.				activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)	TGGTCATTTGATGGAACAGTG	0.333													31	447	---	---	---	---	PASS
SCYL2	55681	broad.mit.edu	37	12	100732421	100732421	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100732421T>C	uc001thn.2	+	18	2311	c.2261T>C	c.(2260-2262)ATT>ACT	p.I754T		NM_017988	NP_060458	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 protein	754	Necessary for interaction with AP2 complex and clathrin, interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes.				endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization	clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|protein kinase activity|receptor binding			lung(3)|ovary(2)|skin(1)	6						TCCATGGGCATTGGTATGATG	0.403													48	132	---	---	---	---	PASS
MED13L	23389	broad.mit.edu	37	12	116429263	116429263	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116429263C>A	uc001tvw.2	-	17	3551	c.3496G>T	c.(3496-3498)GCG>TCG	p.A1166S		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1166					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TTCATAATCGCACTAAACCCA	0.473													25	75	---	---	---	---	PASS
GPR81	27198	broad.mit.edu	37	12	123213779	123213779	+	3'UTR	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123213779C>T	uc001ucz.2	-	1					GPR81_uc001ucw.1_RNA	NM_032554	NP_115943	Q9BXC0	HCAR1_HUMAN	G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)		TCAAAGCCCCCGACCCCTTAG	0.473													21	93	---	---	---	---	PASS
DDX55	57696	broad.mit.edu	37	12	124104803	124104803	+	3'UTR	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124104803C>A	uc001ufi.2	+	14					DDX55_uc001ufk.2_3'UTR|DDX55_uc001ufl.2_3'UTR	NM_020936	NP_065987	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		AGAATGATGTCTCTGAAAGCT	0.353													12	30	---	---	---	---	PASS
XPO4	64328	broad.mit.edu	37	13	21371063	21371063	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21371063G>T	uc001unq.3	-	17	2492	c.2456C>A	c.(2455-2457)ACC>AAC	p.T819N		NM_022459	NP_071904	Q9C0E2	XPO4_HUMAN	exportin 4	819					protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		GTCAATCTGGGTAGCCTCAGC	0.438													6	84	---	---	---	---	PASS
FLT1	2321	broad.mit.edu	37	13	28913320	28913320	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28913320C>A	uc001usb.3	-	17	2758	c.2473G>T	c.(2473-2475)GAG>TAG	p.E825*	FLT1_uc001usa.3_Nonsense_Mutation_p.E43*	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	825	Cytoplasmic (Potential).				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	TTAAGTCTCTCCCGGGCAAAC	0.313													36	261	---	---	---	---	PASS
CHD8	57680	broad.mit.edu	37	14	21853805	21853805	+	Silent	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21853805A>G	uc001was.1	-	38	6970	c.6876T>C	c.(6874-6876)GCT>GCC	p.A2292A	CHD8_uc001war.1_Silent_p.A2188A|SUPT16H_uc001wao.2_5'Flank|SUPT16H_uc001wap.2_5'Flank|SUPT16H_uc001waq.1_5'Flank	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	2571	Asp-rich.				ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		AGTCTGAGTTAGCTGGCATCA	0.408													5	123	---	---	---	---	PASS
WDHD1	11169	broad.mit.edu	37	14	55423922	55423922	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55423922C>T	uc001xbm.1	-	23	2824	c.2746G>A	c.(2746-2748)GTA>ATA	p.V916I	WDHD1_uc010aom.1_Missense_Mutation_p.V433I|WDHD1_uc001xbn.1_Missense_Mutation_p.V793I	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	916						cytoplasm|nucleoplasm	DNA binding			skin(1)	1						CTGGCTGATACCTAAAGAGCA	0.343													5	255	---	---	---	---	PASS
KLC1	3831	broad.mit.edu	37	14	104038081	104038081	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104038081A>G	uc010tyd.1	+	2	285	c.245A>G	c.(244-246)AAG>AGG	p.K82R	C14orf153_uc001ynl.3_RNA|C14orf153_uc010tyc.1_Missense_Mutation_p.K95R	NM_005552	NP_005543	Q07866	KLC1_HUMAN	kinesin light chain 1 isoform 1	Error:Variant_position_missing_in_Q07866_after_alignment					blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)				TTGGAACAAAAGCTTAGAAAA	0.348													6	272	---	---	---	---	PASS
INO80	54617	broad.mit.edu	37	15	41341486	41341486	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41341486T>C	uc001zni.2	-	21	2788	c.2575A>G	c.(2575-2577)AGG>GGG	p.R859G	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	859	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				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						CTTCCCTACCTGTCTCGTGAA	0.308													7	348	---	---	---	---	PASS
PDIA3	2923	broad.mit.edu	37	15	44058112	44058112	+	Silent	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44058112A>G	uc001zsu.2	+	7	895	c.747A>G	c.(745-747)GAA>GAG	p.E249E	PDIA3_uc010bdp.2_Silent_p.E229E|PDIA3_uc010ued.1_Silent_p.E23E	NM_005313	NP_005304	P30101	PDIA3_HUMAN	protein disulfide-isomerase A3 precursor	249					cell redox homeostasis|glycerol ether metabolic process|post-translational protein modification|protein folding|protein import into nucleus|protein N-linked glycosylation via asparagine|protein retention in ER lumen|signal transduction	endoplasmic reticulum lumen|melanosome	cysteine-type endopeptidase activity|electron carrier activity|phospholipase C activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)|skin(1)	2		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)		ACATGACAGAAGACAATAAAG	0.358													7	490	---	---	---	---	PASS
TNFAIP8L3	388121	broad.mit.edu	37	15	51350524	51350524	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51350524A>G	uc001zyy.2	-	3	533	c.433T>C	c.(433-435)TTT>CTT	p.F145L		NM_207381	NP_997264	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein	145											0				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)		AGCTCATCAAAGATCTCGCTG	0.443													8	507	---	---	---	---	PASS
DENND4A	10260	broad.mit.edu	37	15	66023980	66023980	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66023980C>T	uc002aph.2	-	9	1544	c.1166G>A	c.(1165-1167)AGT>AAT	p.S389N	DENND4A_uc002api.2_Missense_Mutation_p.S389N|DENND4A_uc002apj.3_Missense_Mutation_p.S389N|DENND4A_uc010ujj.1_Missense_Mutation_p.S389N	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2	389	DENN.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						TTTTACTTGCCTTAGTGGAAG	0.294													95	248	---	---	---	---	PASS
IL16	3603	broad.mit.edu	37	15	81552201	81552201	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81552201G>T	uc002bgh.3	+	3	777	c.401G>T	c.(400-402)AGG>ATG	p.R134M	IL16_uc002bgc.2_RNA|IL16_uc010blq.1_Missense_Mutation_p.R134M|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Missense_Mutation_p.R176M|IL16_uc002bgg.2_Missense_Mutation_p.R134M	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	134					immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4						TGCCACCAAAGGGCACGCAGC	0.483													36	84	---	---	---	---	PASS
BAIAP3	8938	broad.mit.edu	37	16	1399321	1399321	+	3'UTR	SNP	G	A	A	rs149496703	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1399321G>A	uc002clk.1	+	34					BAIAP3_uc002clj.2_3'UTR|BAIAP3_uc010uuz.1_3'UTR|BAIAP3_uc010uva.1_3'UTR|BAIAP3_uc010uvc.1_3'UTR|C16orf42_uc002cll.2_3'UTR|GNPTG_uc002clm.2_5'Flank	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3						G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)				GGGAGAACCCGGACAGCTCAG	0.562													3	31	---	---	---	---	PASS
PDXDC1	23042	broad.mit.edu	37	16	15221657	15221657	+	Intron	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15221657C>T	uc002ddc.2	+						uc010uzs.1_RNA|uc002ddh.2_Silent_p.P416P|uc002ddi.2_Silent_p.P192P|uc010uzt.1_Silent_p.P416P	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	AGCTACGAGGCGGCCGGTCCC	0.632													7	20	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	16465246	16465246	+	5'UTR	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16465246A>G	uc002dey.2	+	1										SubName: Full=cDNA FLJ42525 fis, clone BRACE3001391, highly similar to Polycystin;																		CTCTTTGGCTATATCAGCAAC	0.622													3	1	---	---	---	---	PASS
C16orf62	57020	broad.mit.edu	37	16	19613023	19613023	+	Silent	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19613023G>T	uc002dgn.1	+	9	774	c.762G>T	c.(760-762)GTG>GTT	p.V254V	C16orf62_uc002dgo.1_Silent_p.V254V|C16orf62_uc002dgp.1_Silent_p.V3V|C16orf62_uc010vas.1_Silent_p.V128V|C16orf62_uc002dgm.1_Silent_p.V254V	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020	254						integral to membrane				ovary(1)	1						CCATGTGTGTGGATAGCCGCA	0.478											OREG0023661	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	19	166	---	---	---	---	PASS
GPT2	84706	broad.mit.edu	37	16	46958369	46958369	+	Silent	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46958369C>T	uc002eel.2	+	10	1375	c.1281C>T	c.(1279-1281)GTC>GTT	p.V427V	GPT2_uc002eem.2_Silent_p.V327V|GPT2_uc002een.2_Silent_p.V70V	NM_133443	NP_597700	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase 2 isoform 1	427					2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	TTAACCAAGTCCCAGGAATTC	0.547													16	150	---	---	---	---	PASS
PRSS54	221191	broad.mit.edu	37	16	58320016	58320016	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58320016A>G	uc002enf.2	-	5	742	c.347T>C	c.(346-348)ATC>ACC	p.I116T	PRSS54_uc002eng.2_Missense_Mutation_p.I116T|PRSS54_uc010vie.1_Missense_Mutation_p.I17T	NM_001080492	NP_001073961	Q6PEW0	PRS54_HUMAN	plasma kallikrein-like protein 4 precursor	116	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						CTCATGGATGATGATGGTATT	0.463													6	380	---	---	---	---	PASS
HYDIN	54768	broad.mit.edu	37	16	70841462	70841462	+	3'UTR	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70841462T>C	uc002ezr.2	-	86					HYDIN_uc010cfy.2_RNA	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				TTTTGGTTGATACAGGTAACC	0.398													53	84	---	---	---	---	PASS
ADAMTS18	170692	broad.mit.edu	37	16	77353974	77353974	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77353974G>A	uc002ffc.3	-	16	2723	c.2304C>T	c.(2302-2304)GTC>GTT	p.V768V	ADAMTS18_uc010chc.1_Silent_p.V356V|ADAMTS18_uc002ffe.1_Silent_p.V464V	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	768	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						CTGGAATGAGGACCACCGGAT	0.488													6	38	---	---	---	---	PASS
TMEM102	284114	broad.mit.edu	37	17	7340067	7340067	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7340067G>A	uc002ggx.1	+	3	1042	c.769G>A	c.(769-771)GCG>ACG	p.A257T	FGF11_uc010vtw.1_Intron|TMEM102_uc002ggy.1_Missense_Mutation_p.A257T|FGF11_uc010cmh.1_5'Flank|FGF11_uc010cmi.2_5'Flank|FGF11_uc002ggz.2_5'Flank	NM_178518	NP_848613	Q8N9M5	TM102_HUMAN	transmembrane protein 102	257	Extracellular (Potential).				regulation of apoptosis|response to cytokine stimulus|signal transduction	cell surface|integral to membrane|intracellular	protein binding				0		Prostate(122;0.173)				GGCTCGGGAAGCGTGGCCCAC	0.622													7	21	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7722587	7722587	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7722587T>A	uc002giu.1	+	71	10890	c.10876T>A	c.(10876-10878)TGC>AGC	p.C3626S	DNAH2_uc010cnm.1_Missense_Mutation_p.C564S	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	3626					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGATATGGGCTGCATCGACCC	0.567													28	56	---	---	---	---	PASS
SARM1	23098	broad.mit.edu	37	17	26687838	26687838	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26687838G>A	uc010wah.1	+	5	506	c.499G>A	c.(499-501)GGA>AGA	p.G167R	TMEM199_uc002hba.2_Missense_Mutation_p.G167R	NM_152464	NP_689677	Q6SZW1	SARM1_HUMAN	transmembrane protein 199	Error:Variant_position_missing_in_Q6SZW1_after_alignment					innate immune response	cytoplasm|intrinsic to membrane	binding|transmembrane receptor activity				0	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		CACTTACCTTGGAAGCCAATA	0.532													14	176	---	---	---	---	PASS
GGNBP2	79893	broad.mit.edu	37	17	34937813	34937813	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34937813C>T	uc002hnb.2	+	9	1309	c.1060C>T	c.(1060-1062)CAA>TAA	p.Q354*	GGNBP2_uc002hna.2_Nonsense_Mutation_p.Q354*|GGNBP2_uc002hnc.1_Nonsense_Mutation_p.Q183*	NM_024835	NP_079111	Q9H3C7	GGNB2_HUMAN	zinc finger protein 403	354					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		CAGATTGGAACAACTTTGTGA	0.333													33	421	---	---	---	---	PASS
CDK12	51755	broad.mit.edu	37	17	37657633	37657633	+	Silent	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37657633T>C	uc010cvv.2	+	6	3136	c.2550T>C	c.(2548-2550)TGT>TGC	p.C850C	CDK12_uc010wef.1_Silent_p.C849C|CDK12_uc002hrw.3_Silent_p.C850C	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich	850	Protein kinase.				mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19						TGGAATACTGTCACAAAAAGA	0.373										TCGA Ovarian(9;0.13)			8	704	---	---	---	---	PASS
SC65	10609	broad.mit.edu	37	17	39967279	39967279	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39967279A>T	uc002hxt.2	-	3	907	c.623T>A	c.(622-624)TTC>TAC	p.F208Y	FKBP10_uc002hxv.2_5'Flank|SC65_uc002hxu.2_Missense_Mutation_p.F299Y	NM_006455	NP_006446	Q92791	SC65_HUMAN	synaptonemal complex protein SC65	208					synaptonemal complex assembly	nucleolus|synaptonemal complex	binding				0		Breast(137;0.000162)		BRCA - Breast invasive adenocarcinoma(366;0.149)		AGCCCGGAGGAACACGGCCTG	0.647													8	26	---	---	---	---	PASS
RNF43	54894	broad.mit.edu	37	17	56435542	56435542	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56435542G>A	uc002iwf.2	-	8	3551	c.1595C>T	c.(1594-1596)TCC>TTC	p.S532F	RNF43_uc010wnv.1_Missense_Mutation_p.S491F|RNF43_uc002iwh.3_Missense_Mutation_p.S532F|RNF43_uc002iwg.3_Missense_Mutation_p.S532F|RNF43_uc010dcw.2_Missense_Mutation_p.S405F	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	532	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CGAGTCCAAGGAACGAGGCCG	0.592													12	25	---	---	---	---	PASS
POTEC	388468	broad.mit.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14513764C>T	uc010dln.2	-	10	1884	c.1430G>A	c.(1429-1431)CGG>CAG	p.R477Q	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	477										skin(3)	3						AAGTTGTTTCCGGGTATCATT	0.358													8	426	---	---	---	---	PASS
C18orf22	79863	broad.mit.edu	37	18	77806266	77806266	+	3'UTR	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77806266C>A	uc002lns.2	+	7					C18orf22_uc010drh.2_3'UTR|C18orf22_uc010dri.1_Intron|C18orf22_uc002lnt.2_3'UTR|uc002lnu.2_5'Flank	NM_024805	NP_079081	Q8N0V3	RBFA_HUMAN	hypothetical protein LOC79863 precursor						rRNA processing	mitochondrion					0		all_cancers(4;3.21e-14)|all_epithelial(4;7.11e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0545)|all_hematologic(56;0.15)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;6.46e-08)|BRCA - Breast invasive adenocarcinoma(31;0.00376)		TCTTCTGCTACTTCAACATTT	0.408													4	6	---	---	---	---	PASS
ZNF57	126295	broad.mit.edu	37	19	2917051	2917051	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2917051G>C	uc002lwr.2	+	4	580	c.432G>C	c.(430-432)AAG>AAC	p.K144N	ZNF57_uc010xha.1_Missense_Mutation_p.K112N	NM_173480	NP_775751	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	144	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		AATGCACCAAGTGCAGGACAG	0.448													62	128	---	---	---	---	PASS
ACER1	125981	broad.mit.edu	37	19	6309756	6309756	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6309756T>A	uc002mel.2	-	4	518	c.440A>T	c.(439-441)AAC>ATC	p.N147I		NM_133492	NP_597999	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	147	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane	ceramidase activity				0						GGCAATGCTGTTGAGGGCGTA	0.607													23	60	---	---	---	---	PASS
ZNF426	79088	broad.mit.edu	37	19	9641687	9641687	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9641687C>T	uc002mlq.2	-	7	646	c.382G>A	c.(382-384)GGT>AGT	p.G128S	ZNF426_uc010dws.2_Missense_Mutation_p.G90S	NM_024106	NP_077011	Q9BUY5	ZN426_HUMAN	zinc finger protein 426	128					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GATGTCTGACCCCTCAAAAAG	0.368													5	391	---	---	---	---	PASS
COL5A3	50509	broad.mit.edu	37	19	10084433	10084433	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10084433T>A	uc002mmq.1	-	49	3697	c.3611A>T	c.(3610-3612)AAG>ATG	p.K1204M		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1204	Triple-helical region.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)			CTCACTCACCTTCTCACCCAC	0.607													17	146	---	---	---	---	PASS
ILF3	3609	broad.mit.edu	37	19	10781221	10781221	+	5'UTR	SNP	C	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10781221C>G	uc002mpn.2	+	2					ILF3_uc002mpm.2_5'UTR|ILF3_uc002mpl.2_5'UTR|ILF3_uc002mpk.2_5'UTR|ILF3_uc010xli.1_5'UTR|ILF3_uc002mpo.2_5'UTR	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a						M phase|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleolus|ribonucleoprotein complex	DNA binding|double-stranded RNA binding|protein binding|protein binding			ovary(3)	3			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			CCAAGGAACTCTATCACAATT	0.303													196	507	---	---	---	---	PASS
SIN3B	23309	broad.mit.edu	37	19	16977286	16977286	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16977286G>T	uc002ney.1	+	13	1835	c.1821G>T	c.(1819-1821)CAG>CAT	p.Q607H	SIN3B_uc002nez.1_Missense_Mutation_p.Q575H|SIN3B_uc010xpi.1_Missense_Mutation_p.Q165H	NM_015260	NP_056075	O75182	SIN3B_HUMAN	SIN3 homolog B, transcription regulator	607					cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	protein binding			ovary(2)	2						TTGACCACCAGGCTGTGAACT	0.582													9	57	---	---	---	---	PASS
ZNF780B	163131	broad.mit.edu	37	19	40540306	40540306	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40540306G>A	uc002omu.2	-	5	2525	c.2460C>T	c.(2458-2460)ATC>ATT	p.I820I	ZNF780B_uc002omv.2_Silent_p.I672I	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	820					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AGTTGCTACTGATGTCTGAAG	0.388													37	110	---	---	---	---	PASS
BCL2L12	83596	broad.mit.edu	37	19	50169188	50169188	+	Silent	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50169188G>T	uc002ppa.2	+	1	790	c.108G>T	c.(106-108)CCG>CCT	p.P36P	IRF3_uc002pot.1_5'Flank|IRF3_uc010end.1_5'Flank|IRF3_uc002pox.1_5'Flank|IRF3_uc002poy.1_5'Flank|IRF3_uc002pou.2_5'Flank|IRF3_uc002pov.2_5'Flank|IRF3_uc002pow.2_5'Flank|IRF3_uc002poz.1_5'Flank|IRF3_uc010ene.1_5'Flank|BCL2L12_uc002ppb.2_Silent_p.P36P	NM_138639	NP_619580	Q9HB09	B2L12_HUMAN	BCL2-like 12 isoform 1	36					apoptosis					central_nervous_system(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.000681)|GBM - Glioblastoma multiforme(134;0.0214)		CCAGCGTTCCGCCCTTTCTAC	0.602													10	27	---	---	---	---	PASS
NLRP13	126204	broad.mit.edu	37	19	56443398	56443398	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56443398G>T	uc010ygg.1	-	1	305	c.280C>A	c.(280-282)CTG>ATG	p.L94M		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	94	DAPIN.						ATP binding			skin(4)|ovary(3)|pancreas(1)|lung(1)	9		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		AGTGAGGTCAGATTCATTGTC	0.512													20	55	---	---	---	---	PASS
ESF1	51575	broad.mit.edu	37	20	13750637	13750637	+	Silent	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13750637A>G	uc002woj.2	-	7	1542	c.1434T>C	c.(1432-1434)GAT>GAC	p.D478D	ESF1_uc002wok.1_Silent_p.D478D	NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein	478					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1						CCTTAGGCTCATCATCAAAAG	0.313													106	306	---	---	---	---	PASS
CDK5RAP1	51654	broad.mit.edu	37	20	31958402	31958402	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31958402A>T	uc010gek.2	-	12	1461	c.1337T>A	c.(1336-1338)TTT>TAT	p.F446Y	CDK5RAP1_uc002wyy.2_Missense_Mutation_p.F342Y|CDK5RAP1_uc002wyz.2_Missense_Mutation_p.F432Y|CDK5RAP1_uc002wza.2_Missense_Mutation_p.F432Y|CDK5RAP1_uc010gel.2_Missense_Mutation_p.F341Y|CDK5RAP1_uc010gem.2_Missense_Mutation_p.F355Y|CDK5RAP1_uc002wzc.1_Missense_Mutation_p.F432Y|CDK5RAP1_uc002wzb.1_Missense_Mutation_p.F67Y	NM_016408	NP_057492	Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	446					brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			ovary(2)|skin(2)|lung(1)	5						CTCACCACAAAAGCCAGCAAT	0.517													20	103	---	---	---	---	PASS
PHF20	51230	broad.mit.edu	37	20	34459576	34459576	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34459576G>T	uc002xek.1	+	9	1218	c.1107G>T	c.(1105-1107)CAG>CAT	p.Q369H	PHF20_uc002xei.1_Missense_Mutation_p.Q369H|PHF20_uc010gfo.1_Missense_Mutation_p.Q369H|PHF20_uc002xej.1_Missense_Mutation_p.Q253H	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	369					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					TTCTAGGTCAGTTGAAGTCTG	0.453													19	55	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40710578	40710578	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40710578C>T	uc002xkg.2	-	30	4400	c.4216G>A	c.(4216-4218)GTG>ATG	p.V1406M	PTPRT_uc010ggj.2_Missense_Mutation_p.V1425M|PTPRT_uc010ggi.2_Missense_Mutation_p.V609M	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1406	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity	p.R1406C(1)		skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				ATGTGGAACACGTCAATGATG	0.498													8	298	---	---	---	---	PASS
SS18L1	26039	broad.mit.edu	37	20	60754289	60754289	+	3'UTR	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60754289C>A	uc002ycb.2	+	11					SS18L1_uc002ybz.1_RNA|SS18L1_uc002yca.1_RNA|SS18L1_uc002ycc.1_RNA	NM_198935	NP_945173	O75177	CREST_HUMAN	SS18-like protein 1						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore				ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			GGCTGGAGCCCTTGTGGTAGC	0.517			T	SSX1	synovial sarcoma								92	276	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47850087	47850087	+	Silent	SNP	G	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47850087G>A	uc002zji.3	+	36	7961	c.7854G>A	c.(7852-7854)CAG>CAA	p.Q2618Q	PCNT_uc002zjj.2_Silent_p.Q2500Q	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	2618	Potential.				cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					AGAGCAGGCAGAAGAGCGAAC	0.617													30	66	---	---	---	---	PASS
CCDC117	150275	broad.mit.edu	37	22	29179508	29179508	+	Silent	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29179508A>G	uc003aeb.2	+	4	653	c.477A>G	c.(475-477)GAA>GAG	p.E159E	CCDC117_uc011aki.1_Silent_p.E141E|CCDC117_uc011akj.1_Silent_p.E84E|CCDC117_uc011akk.1_Silent_p.E27E	NM_173510	NP_775781	Q8IWD4	CC117_HUMAN	coiled-coil domain containing 117	159	Potential.									breast(1)	1						TAATTGATGAAGATGAAGAAG	0.303													7	465	---	---	---	---	PASS
VCX	26609	broad.mit.edu	37	X	7812155	7812155	+	3'UTR	SNP	A	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7812155A>T	uc004crz.2	+	3						NM_013452	NP_038480	Q9H320	VCX1_HUMAN	variable charge, X chromosome						chromatin organization|ribosome assembly|spermatogenesis	nucleolus	chromatin binding				0		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GCCATTCTGAAGATAATAAAA	0.398													4	40	---	---	---	---	PASS
SCML2	10389	broad.mit.edu	37	X	18352186	18352186	+	Silent	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18352186T>C	uc004cyl.2	-	2	163	c.6A>G	c.(4-6)GGA>GGG	p.G2G	SCML2_uc004cyk.3_RNA|SCML2_uc010nfd.1_Silent_p.G2G|SCML2_uc011miz.1_5'UTR	NM_006089	NP_006080	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2	2					anatomical structure morphogenesis	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)					TCACTGTTTGTCCCATGGTAT	0.318													7	514	---	---	---	---	PASS
APOO	79135	broad.mit.edu	37	X	23874429	23874429	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23874429T>A	uc004dax.2	-	7	782	c.551A>T	c.(550-552)AAC>ATC	p.N184I	APOO_uc004daw.2_RNA|APOO_uc004day.3_RNA	NM_024122	NP_077027	Q9BUR5	APOO_HUMAN	apolipoprotein O precursor	184					lipid transport	high-density lipoprotein particle|integral to membrane|low-density lipoprotein particle|very-low-density lipoprotein particle					0						CTTTTGAAAGTTCTCCTTCCA	0.289													210	174	---	---	---	---	PASS
USP9X	8239	broad.mit.edu	37	X	41010278	41010278	+	Silent	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41010278T>C	uc004dfb.2	+	13	2364	c.1731T>C	c.(1729-1731)TGT>TGC	p.C577C	USP9X_uc004dfc.2_Silent_p.C577C	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	577					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						GAGAAATTTGTAGTTTGTTTG	0.313													5	227	---	---	---	---	PASS
PAGE3	139793	broad.mit.edu	37	X	55286975	55286975	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55286975G>C	uc004dul.2	-	4	620	c.311C>G	c.(310-312)CCA>CGA	p.P104R	PAGE3_uc011mon.1_RNA	NM_001017931	NP_001017931			P antigen family, member 3 (prostate												0						ACCTGCTTCTGGTATTTTAAC	0.368													65	63	---	---	---	---	PASS
TAF1	6872	broad.mit.edu	37	X	70603945	70603945	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70603945A>G	uc004dzu.3	+	13	2129	c.2078A>G	c.(2077-2079)CAG>CGG	p.Q693R	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.Q714R	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	693					G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)				TTAATGATGCAGGTTGGCATG	0.398													68	64	---	---	---	---	PASS
OCRL	4952	broad.mit.edu	37	X	128709167	128709167	+	Silent	SNP	A	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128709167A>G	uc004euq.2	+	16	1818	c.1653A>G	c.(1651-1653)GTA>GTG	p.V551V	OCRL_uc004eur.2_Silent_p.V551V	NM_000276	NP_000267	Q01968	OCRL_HUMAN	phosphatidylinositol polyphosphate 5-phosphatase	551					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	clathrin-coated vesicle|cytosol|early endosome|Golgi stack|Golgi-associated vesicle	GTPase activator activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			lung(2)|ovary(1)|kidney(1)	4						AAGATAGTGTACGCATCATGG	0.428													6	213	---	---	---	---	PASS
MAGEA11	4110	broad.mit.edu	37	X	148797543	148797543	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148797543C>A	uc004fdq.2	+	5	499	c.397C>A	c.(397-399)CTG>ATG	p.L133M	HSFX2_uc004fdl.2_Intron|HSFX1_uc004fdm.2_Intron|MAGEA11_uc004fdr.2_Missense_Mutation_p.L104M	NM_005366	NP_005357	P43364	MAGAB_HUMAN	melanoma antigen family A, 11 isoform a	133						cytoplasm|nucleus	protein binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					AGAAGAAGACCTGGGCCTGGT	0.572													17	9	---	---	---	---	PASS
HAUS7	55559	broad.mit.edu	37	X	152721103	152721103	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152721103T>C	uc004fho.1	-	8	1415	c.857A>G	c.(856-858)TAC>TGC	p.Y286C	HAUS7_uc004fhl.2_RNA|HAUS7_uc004fhm.2_RNA|HAUS7_uc004fhn.1_Missense_Mutation_p.Y286C|HAUS7_uc004fhp.1_RNA	NM_017518	NP_059988	Q99871	HAUS7_HUMAN	HAUS augmin-like complex subunit 7	286					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleolus|plasma membrane|spindle	thioesterase binding				0						CTCGTCGTCGTAGACTTGGAG	0.632													16	20	---	---	---	---	PASS
USP9Y	8287	broad.mit.edu	37	Y	14850172	14850172	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:14850172A>T	uc004fst.1	+	11	2191	c.1246A>T	c.(1246-1248)AAA>TAA	p.K416*	USP9Y_uc010nwu.1_RNA	NM_004654	NP_004645	O00507	USP9Y_HUMAN	ubiquitin specific protease 9, Y-linked	416					BMP signaling pathway|protein deubiquitination|spermatogenesis|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0						AAAGCTAGAGAAAATTCTTCG	0.328													19	42	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	12015	12015	+	RNA	SNP	T	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:12015T>C	uc004cov.3	+	1		c.1438T>C			uc004cow.1_5'Flank|uc004cox.3_5'Flank|uc004coy.2_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		ATGGGGCTCACTCACCCACCA	0.453													15	45	---	---	---	---	PASS
CAMTA1	23261	broad.mit.edu	37	1	7016605	7016606	+	Intron	DEL	AA	-	-	rs34321205		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7016605_7016606delAA	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		ACAATCTCTTAAAACTGACTCA	0.381													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	10890909	10890914	+	IGR	DEL	AGCAAC	-	-	rs5772431		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10890909_10890914delAGCAAC								CASZ1 (34202 upstream) : C1orf127 (115619 downstream)																							gaataataatagcaacagcaacagct	0.019													4	2	---	---	---	---	
CAP1	10487	broad.mit.edu	37	1	40531607	40531607	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40531607delA	uc001cfa.3	+						CAP1_uc001cey.3_Intron|CAP1_uc001cez.3_Intron|CAP1_uc009vvz.2_Intron|CAP1_uc010oje.1_Intron	NM_006367	NP_006358	Q01518	CAP1_HUMAN	adenylyl cyclase-associated protein						activation of adenylate cyclase activity|axon guidance|establishment or maintenance of cell polarity|platelet activation|platelet degranulation|signal transduction	plasma membrane	actin binding			ovary(1)	1	Lung NSC(20;5.03e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;4.63e-18)|Epithelial(16;1.27e-16)|all cancers(16;2.3e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TGGTCAAAAGAAAAAAAAAAG	0.209													4	3	---	---	---	---	
FOXJ3	22887	broad.mit.edu	37	1	42656715	42656716	+	Intron	INS	-	ATAATT	ATAATT			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42656715_42656716insATAATT	uc001che.2	-						FOXJ3_uc001chf.2_Intron|FOXJ3_uc001chg.2_Intron	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				gataatgtaagataatgtatct	0.099													4	3	---	---	---	---	
CCDC23	374969	broad.mit.edu	37	1	43278232	43278232	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43278232delA	uc001cib.2	-							NM_199342	NP_955374	Q8N300	CCD23_HUMAN	coiled-coil domain containing 23												0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				AATCATCAGTAACATCCTCCC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	44502891	44502891	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44502891delT								SLC6A9 (5757 upstream) : KLF17 (11139 downstream)																							GGGTGTTGGCTTTTTTGTGGC	0.463											OREG0012973	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
HECTD3	79654	broad.mit.edu	37	1	45473573	45473573	+	Intron	DEL	T	-	-	rs35006324		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45473573delT	uc009vxk.2	-						HECTD3_uc001cmx.3_5'Flank|HECTD3_uc001cmy.3_Intron|HECTD3_uc010olh.1_Intron	NM_024602	NP_078878	Q5T447	HECD3_HUMAN	HECT domain containing 3						proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	ubiquitin-protein ligase activity				0	Acute lymphoblastic leukemia(166;0.155)					gcccacatccttccaccctca	0.000													3	3	---	---	---	---	
PIK3R3	8503	broad.mit.edu	37	1	46546081	46546081	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46546081delT	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)					TACAATGCTCtttttttttga	0.060													3	3	---	---	---	---	
FAAH	2166	broad.mit.edu	37	1	46872228	46872228	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46872228delT	uc001cpu.2	+						FAAH_uc001cpv.2_Intron	NM_001441	NP_001432	O00519	FAAH1_HUMAN	fatty acid amide hydrolase						fatty acid catabolic process	cytoplasm|cytoskeleton|endomembrane system|integral to membrane|organelle membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|fatty acid amide hydrolase activity			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	ATCCTCAGGCTTTTTTTTTTT	0.328													4	2	---	---	---	---	
C1orf185	284546	broad.mit.edu	37	1	51577808	51577808	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51577808delA	uc001csh.2	+							NM_001136508	NP_001129980	Q5T7R7	CA185_HUMAN	hypothetical protein LOC284546							integral to membrane					0						ACGGGAGGGGAAAAAAAAAAA	0.373													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	53039570	53039570	+	IGR	DEL	A	-	-	rs113441580		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53039570delA								ZCCHC11 (20440 upstream) : GPX7 (28473 downstream)																							CTGAATATTGAAAAAAAAAAA	0.343													4	3	---	---	---	---	
TNNI3K	51086	broad.mit.edu	37	1	74666674	74666677	+	Intron	DEL	TGTA	-	-	rs149674058		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74666674_74666677delTGTA	uc001dge.1	+						LRRIQ3_uc001dfy.3_5'Flank|LRRIQ3_uc001dfz.3_5'Flank|TNNI3K_uc001dgc.1_Intron|TNNI3K_uc001dgd.2_Intron|FPGT_uc010oqt.1_Intron|FPGT_uc010oqu.1_Intron|FPGT_uc001dgb.1_Intron|FPGT_uc010oqv.1_Intron	NM_001112808	NP_001106279	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform a							cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10						TTTGTAACTCTGTATGAATGTTTA	0.284													3	3	---	---	---	---	
CDC14A	8556	broad.mit.edu	37	1	100938325	100938325	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100938325delT	uc001dtg.3	+						CDC14A_uc009web.2_Intron|CDC14A_uc010oui.1_Intron|CDC14A_uc001dte.3_Intron|CDC14A_uc001dtf.2_Intron|CDC14A_uc009wed.1_Intron|CDC14A_uc009wee.2_Intron	NM_003672	NP_003663	Q9UNH5	CC14A_HUMAN	CDC14 homolog A isoform 1						cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		gtcaagcttctttttttttgg	0.000													3	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145016992	145016992	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145016992delT	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|uc001emj.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GTaacaattataacagccaac	0.124			T	PDGFRB	MPD								4	2	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148001285	148001286	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148001285_148001286insA	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						CATCATTTTTGAAAAGAGTATT	0.277													7	5	---	---	---	---	
GPATCH4	54865	broad.mit.edu	37	1	156571618	156571619	+	5'Flank	INS	-	A	A	rs140650281	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156571618_156571619insA	uc001fpm.2	-						GPATCH4_uc001fpl.2_5'Flank	NM_015590	NP_056405	Q5T3I0	GPTC4_HUMAN	G patch domain containing 4 isoform 1							intracellular	nucleic acid binding			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GAGTAGGTGATAGCTGTGTCCT	0.460													1	5	---	---	---	---	
FCGR2C	9103	broad.mit.edu	37	1	161548680	161548680	+	5'Flank	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161548680delA	uc001gav.2	+						FCGR2C_uc009wuj.2_5'Flank|FCGR2C_uc009wuk.2_5'Flank	NM_201563	NP_963857			Fc fragment of IgG, low affinity IIc, receptor												0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			gttggatcctaagcagatagc	0.000													4	2	---	---	---	---	
GPR161	23432	broad.mit.edu	37	1	168056552	168056553	+	Intron	DEL	TG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168056552_168056553delTG	uc001gfc.2	-						GPR161_uc001gfb.2_Intron|GPR161_uc010pll.1_Intron|GPR161_uc010plm.1_Intron|GPR161_uc009wvo.2_Intron|GPR161_uc001gfd.2_Intron|GPR161_uc010pln.1_Intron	NM_153832	NP_722561	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161 isoform 2						multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)					GGATCTGGGCTGTGTGTGTAAA	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193943724	193943724	+	IGR	DEL	C	-	-	rs72221613		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193943724delC								CDC73 (719784 upstream) : None (None downstream)																							aaagtgtcagccttttttttt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	196837716	196837717	+	IGR	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196837716_196837717insT								CFHR1 (36400 upstream) : CFHR4 (19495 downstream)																							AGCAACAGGAAttttttttttt	0.238													8	5	---	---	---	---	
LOC148709	148709	broad.mit.edu	37	1	202831870	202831871	+	Intron	DEL	TG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202831870_202831871delTG	uc001gyk.1	+						uc001gyi.1_5'Flank|uc001gyj.2_5'Flank	NR_002929				Homo sapiens cDNA FLJ31247 fis, clone KIDNE2005296, weakly similar to ACTIN, CYTOPLASMIC 1.												0						CACTGGCCATTGTGACATCAGA	0.436													4	2	---	---	---	---	
CDK18	5129	broad.mit.edu	37	1	205499086	205499087	+	Intron	INS	-	A	A	rs140236794	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205499086_205499087insA	uc001hcr.2	+						CDK18_uc001hcp.2_Intron|CDK18_uc001hcq.2_Intron|CDK18_uc010prj.1_Intron|CDK18_uc001hcs.2_Intron|CDK18_uc009xbm.1_3'UTR|CDK18_uc001hct.2_Intron	NM_212503	NP_997668	Q07002	CDK18_HUMAN	PCTAIRE protein kinase 3 isoform a								ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity			stomach(2)	2						CGCTTCCTGTTACGGATGTTCT	0.272													5	3	---	---	---	---	
TGFB2	7042	broad.mit.edu	37	1	218579626	218579626	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218579626delG	uc001hlm.2	+						TGFB2_uc001hll.2_3'UTR|TGFB2_uc001hln.2_Intron|TGFB2_uc010pue.1_Intron|TGFB2_uc001hlo.2_Intron	NM_003238	NP_003229	P61812	TGFB2_HUMAN	transforming growth factor, beta 2 isoform 2						activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway	axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen	beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding				0				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		TGGAGTTGGTGGGCAGCTGCG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	227176260	227176261	+	IGR	INS	-	AAG	AAG	rs149824611	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227176260_227176261insAAG								CABC1 (1014 upstream) : CDC42BPA (1306 downstream)																							TTGTGTGTCCTAAGTCTGAGAG	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	231019773	231019774	+	IGR	INS	-	A	A	rs144368302	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231019773_231019774insA								C1orf198 (14438 upstream) : TTC13 (22216 downstream)																							atagtaatTCCAAAAAAAACCA	0.193													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	231256766	231256766	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231256766delA								FAM89A (80771 upstream) : TRIM67 (41908 downstream)																							atagaaaaggaaaaaaaatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238431721	238431722	+	IGR	DEL	TT	-	-	rs35844222		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238431721_238431722delTT								LOC100130331 (340104 upstream) : LOC339535 (211964 downstream)																							AATAATACACTTTAACATATAT	0.218													5	7	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240458490	240458501	+	Intron	DEL	ACACACACACAC	-	-	rs145889361		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240458490_240458501delACACACACACAC	uc010pyd.1	+						FMN2_uc010pye.1_Intron|FMN2_uc010pyf.1_Intron|FMN2_uc010pyg.1_Intron	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TGCACTTcatacacacacacacacacacacac	0.198													3	4	---	---	---	---	
WDR64	128025	broad.mit.edu	37	1	241847167	241847168	+	Intron	DEL	AC	-	-	rs35225606		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241847167_241847168delAC	uc001hze.1	+						WDR64_uc001hzf.1_Intron			B1ANS9	WDR64_HUMAN	RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GTTCATGTATacacacacacac	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244382575	244382575	+	IGR	DEL	A	-	-	rs146125083		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244382575delA								ZNF238 (161799 upstream) : C1orf100 (133362 downstream)																							GTGTTAAATGAAAAAAAAAAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4087628	4087628	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4087628delT								ALLC (337370 upstream) : None (None downstream)																							AGTTACTGCCTTGAAAATGAA	0.423													4	2	---	---	---	---	
SOX11	6664	broad.mit.edu	37	2	5835565	5835565	+	3'UTR	DEL	A	-	-	rs113402297		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5835565delA	uc002qyj.2	+	1						NM_003108	NP_003099	P35716	SOX11_HUMAN	SRY-box 11						cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis	cytoplasm|nucleolus	enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding			central_nervous_system(3)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)		AGCAAAAAAGAAAAAAAAAAG	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6465613	6465613	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6465613delA								LOC400940 (337249 upstream) : CMPK2 (514890 downstream)																							atCCATGTGTAAGAGGAAACC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	10573682	10573683	+	IGR	DEL	TA	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10573682_10573683delTA								HPCAL1 (5940 upstream) : ODC1 (6825 downstream)																							ATGGTGTAACTATGTGTACAtg	0.084													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	14899678	14899678	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14899678delT								FAM84A (108745 upstream) : NBAS (407354 downstream)																							gcaaaCATGATTTTTACAAAG	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16385812	16385812	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16385812delG								MYCN (298684 upstream) : FAM49A (348089 downstream)																							GCATTGAATTGGGAACTCATT	0.443													4	2	---	---	---	---	
SMC6	79677	broad.mit.edu	37	2	17890091	17890092	+	Intron	INS	-	TATA	TATA	rs147636514	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17890091_17890092insTATA	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron|SMC6_uc002rcp.1_Intron|SMC6_uc002rcq.2_Intron	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					tgaaaattgtgtatatatatat	0.198													8	5	---	---	---	---	
KLHL29	114818	broad.mit.edu	37	2	23896734	23896736	+	Intron	DEL	CCA	-	-	rs72289738		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23896734_23896736delCCA	uc002reg.2	+						KLHL29_uc010ykg.1_Intron			Q96CT2	KLH29_HUMAN	RecName: Full=Kelch-like protein 29; AltName: Full=Kelch repeat and BTB domain-containing protein 9;											ovary(1)|lung(1)	2						acccttgtacccaccacatgctc	0.187													3	5	---	---	---	---	
ATAD2B	54454	broad.mit.edu	37	2	24029524	24029524	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24029524delA	uc002rek.3	-						ATAD2B_uc010yki.1_Intron|ATAD2B_uc002rei.3_Intron|ATAD2B_uc002rej.3_Intron	NM_017552	NP_060022	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ttaatttaggaaaaaacctca	0.114													4	2	---	---	---	---	
ATAD2B	54454	broad.mit.edu	37	2	24050192	24050192	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24050192delA	uc002rek.3	-						ATAD2B_uc010yki.1_Intron|ATAD2B_uc002rej.3_Intron	NM_017552	NP_060022	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTAAAAGCTAAAAAAATCAC	0.313													4	2	---	---	---	---	
DNMT3A	1788	broad.mit.edu	37	2	25552827	25552829	+	Intron	DEL	AAC	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25552827_25552829delAAC	uc002rgc.2	-						DNMT3A_uc002rgd.2_Intron|DNMT3A_uc010eyi.2_Intron|DNMT3A_uc002rge.2_Intron|DNMT3A_uc002rgf.2_Intron|MIR1301_hsa-mir-1301|MI0003815_5'Flank	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform						regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					aaccattcataacattgttctga	0.138			Mis|F|N|S		AML								4	2	---	---	---	---	
DTNB	1838	broad.mit.edu	37	2	25769713	25769713	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25769713delT	uc002rgh.2	-						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)					TCTTCTAttcttttttttttt	0.194													6	7	---	---	---	---	
CAPN13	92291	broad.mit.edu	37	2	30954522	30954522	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30954522delT	uc002rnn.2	-						CAPN13_uc002rnm.2_Intron	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					CCCAGCTTCCTTGCACTCCCT	0.607													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	47565393	47565393	+	Intron	DEL	A	-	-	rs35620049		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47565393delA	uc002rvu.1	-											Homo sapiens cDNA FLJ37024 fis, clone BRACE2010837.									p.?(1)									agggaagGCTAAAAAAAAAAA	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	51272287	51272287	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51272287delC								NRXN1 (12613 upstream) : None (None downstream)																							TTGCTGTGCTCCCCAGAGTAA	0.383													4	2	---	---	---	---	
UGP2	7360	broad.mit.edu	37	2	64116952	64116952	+	Intron	DEL	A	-	-	rs72380681		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64116952delA	uc002scm.2	+						UGP2_uc002scl.2_Intron|UGP2_uc010ypx.1_Intron	NM_006759	NP_006750	Q16851	UGPA_HUMAN	UDP-glucose pyrophosphorylase 2 isoform a						glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0						GATTATCTTTAAAAAAAAAAA	0.214													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	73540360	73540361	+	IGR	INS	-	GCCCCCTCGCCA	GCCCCCTCGCCA	rs146590506	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73540360_73540361insGCCCCCTCGCCA								EGR4 (19531 upstream) : ALMS1 (72525 downstream)																							ACTGTCTGCCCGTACTGATTAG	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	76901394	76901394	+	IGR	DEL	A	-	-	rs67691893		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76901394delA								C2orf3 (963283 upstream) : LRRTM4 (73464 downstream)																							GAGTCCTGTTAAAAAATATTT	0.313													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91775272	91775272	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91775272delC								None (None upstream) : LOC654342 (29920 downstream)																							GACTGCCTTTCCAGACCCCTG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96815198	96815198	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96815198delT								DUSP2 (4019 upstream) : STARD7 (35407 downstream)																							gctgacCTCAttgcttcaaca	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108186973	108186973	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108186973delA								ST6GAL2 (683410 upstream) : LOC729121 (252547 downstream)																							GGTCTACTTGATTTCACGTCA	0.299													4	2	---	---	---	---	
CKAP2L	150468	broad.mit.edu	37	2	113518554	113518554	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113518554delT	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron|CKAP2L_uc010yxq.1_Intron	NM_152515	NP_689728	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like							centrosome					0						GCTCCTACTCTTTTTTTTTTT	0.303													15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	116761657	116761657	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116761657delT								DPP10 (159721 upstream) : None (None downstream)																							atgagtaatcttttttttttc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119536262	119536263	+	IGR	INS	-	G	G	rs140140787	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119536262_119536263insG								INSIG2 (668666 upstream) : EN1 (63485 downstream)																							gacaggcacgtggggagaacac	0.000													0	6	---	---	---	---	
PROC	5624	broad.mit.edu	37	2	128186724	128186724	+	3'UTR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128186724delG	uc002tok.2	+	9					PROC_uc002tol.2_3'UTR|PROC_uc010yzi.1_3'UTR|PROC_uc010yzj.1_3'UTR|PROC_uc010yzk.1_3'UTR|PROC_uc002tom.2_3'UTR	NM_000312	NP_000303	P04070	PROC_HUMAN	protein C						blood coagulation|leukocyte migration|negative regulation of apoptosis|negative regulation of blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|Golgi lumen|plasma membrane	calcium ion binding|protein binding|serine-type endopeptidase activity				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	tctgtggggtgggGaggagca	0.060													4	2	---	---	---	---	
UGGT1	56886	broad.mit.edu	37	2	128945388	128945388	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128945388delT	uc002tps.2	+						UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1						'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						AATTGCTATGTTTTTTTTTTT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130124162	130124162	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130124162delT								None (None upstream) : LOC389033 (556273 downstream)																							ctgtaaaggattttttatttg	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133139703	133139704	+	IGR	INS	-	GA	GA			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133139703_133139704insGA								NCRNA00164 (124161 upstream) : GPR39 (34443 downstream)																							tattgcaataggagagagagat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134418527	134418527	+	IGR	DEL	A	-	-	rs112404079		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134418527delA								NCKAP5 (92496 upstream) : MGAT5 (593303 downstream)																							ACAGGCTTGCAAAAAAAAAAA	0.368													10	5	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	141986474	141986474	+	Intron	DEL	T	-	-	rs300387	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141986474delT	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTCAGTGGAATAAAAAAATCA	0.294										TSP Lung(27;0.18)			4	2	---	---	---	---	
GTDC1	79712	broad.mit.edu	37	2	145033545	145033546	+	Intron	DEL	AT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145033545_145033546delAT	uc002tvp.2	-						GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)		Tcacacacacatacacagacac	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	147277334	147277335	+	IGR	DEL	CA	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147277334_147277335delCA								None (None upstream) : PABPC1P2 (67290 downstream)																							CTCTCTCTCTcacacacacaca	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	152041059	152041059	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152041059delT								RND3 (696879 upstream) : RBM43 (63670 downstream)																							AACCCTTTCATTTTTACCTAA	0.353													4	2	---	---	---	---	
FMNL2	114793	broad.mit.edu	37	2	153437047	153437047	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153437047delT	uc002tye.2	+							NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3						GATTTTGAACTTTTTTTTTTG	0.338													4	2	---	---	---	---	
LRP2	4036	broad.mit.edu	37	2	170066497	170066497	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170066497delA	uc002ues.2	-							NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	tggatccactaaaacatcaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173399860	173399860	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173399860delT								ITGA6 (28679 upstream) : PDK1 (20241 downstream)																							acttaatctgttttttttttt	0.000													3	3	---	---	---	---	
HOXD8	3234	broad.mit.edu	37	2	176995902	176995903	+	Intron	INS	-	TA	TA	rs138795034	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176995902_176995903insTA	uc002uko.2	+						uc002ukl.1_5'Flank|uc002ukm.1_5'Flank|HOXD8_uc002ukn.2_Intron|HOXD8_uc002ukp.2_Intron	NM_019558	NP_062458	P13378	HXD8_HUMAN	homeobox D8						anterior/posterior axis specification, embryo	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		CCTGCACACCCTATATATATAT	0.401													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177445528	177445529	+	IGR	INS	-	AG	AG			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177445528_177445529insAG								MTX2 (242777 upstream) : MIR1246 (20179 downstream)																							CAACAATCTCCAGAGTTCACAA	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177630383	177630384	+	IGR	INS	-	TT	TT	rs141491059	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177630383_177630384insTT								MIR1246 (164603 upstream) : HNRNPA3 (447038 downstream)																							AGAAAATGTGATTTTTTTAGTG	0.431													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	183564297	183564297	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183564297delA								PDE1A (176790 upstream) : DNAJC10 (16702 downstream)																							ATACCTCTTCAAAAAAAATAG	0.279													4	3	---	---	---	---	
GULP1	51454	broad.mit.edu	37	2	189235595	189235596	+	Intron	DEL	TG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189235595_189235596delTG	uc010fru.2	+						GULP1_uc002uqc.3_Intron|GULP1_uc002uqd.2_Intron|GULP1_uc010zfw.1_Intron|GULP1_uc002uqe.2_Intron|GULP1_uc002uqf.2_Intron|GULP1_uc002uqg.2_Intron	NM_016315	NP_057399	Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing						apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			CATGTGTGTATGTGTGTGTGTG	0.351													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	199486080	199486080	+	IGR	DEL	C	-	-	rs66502856		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199486080delC								PLCL1 (471474 upstream) : SATB2 (648144 downstream)																							TACTTTTTTTCCTTACATTTC	0.313													4	3	---	---	---	---	
BMPR2	659	broad.mit.edu	37	2	203285199	203285199	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203285199delA	uc002uzf.3	+						BMPR2_uc010ftr.2_Intron|BMPR2_uc002uze.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II						anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9						TAACATTACTAAATATGCGTT	0.284													4	2	---	---	---	---	
ADAM23	8745	broad.mit.edu	37	2	207436214	207436214	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207436214delA	uc002vbq.2	+						ADAM23_uc010ziv.1_Intron	NM_003812	NP_003803	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23 preproprotein						cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		aacaaaaaggaaaaaaaaaat	0.154													11	5	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	214677590	214677590	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214677590delT	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		ATATGTTATCTTTTTTTTTTG	0.303													4	3	---	---	---	---	
ABCA12	26154	broad.mit.edu	37	2	215847360	215847360	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215847360delA	uc002vew.2	-						ABCA12_uc002vev.2_Intron|ABCA12_uc010zjn.1_Intron	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TAATACTCAGAAAAAAACACA	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217902376	217902376	+	IGR	DEL	T	-	-	rs34702643		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217902376delT								TNP1 (177594 upstream) : DIRC3 (246372 downstream)																							AACTGCAGTGTTTATGGAAAC	0.433													3	4	---	---	---	---	
RUFY4	285180	broad.mit.edu	37	2	218941968	218941969	+	Intron	INS	-	CT	CT	rs34926758		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218941968_218941969insCT	uc002vgw.2	+						RUFY4_uc002vgy.1_Intron|RUFY4_uc010fvl.1_Intron	NM_198483	NP_940885	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4								metal ion binding			pancreas(1)	1		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CTCCGTTTCTCCTGCTCAGTGT	0.460													3	3	---	---	---	---	
EPHA4	2043	broad.mit.edu	37	2	222313847	222313848	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222313847_222313848insA	uc002vmq.2	-						EPHA4_uc002vmr.2_Intron|EPHA4_uc010zlm.1_Intron|EPHA4_uc010zln.1_Intron	NM_004438	NP_004429	P54764	EPHA4_HUMAN	ephrin receptor EphA4 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(6)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	12		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		GGAAATGGCTGAAAAAAAACCA	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	233881721	233881721	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233881721delT								NGEF (3770 upstream) : NEU2 (15661 downstream)																							ATTATAAGACTTTTTTTTTAA	0.259													4	2	---	---	---	---	
HDAC4	9759	broad.mit.edu	37	2	240058006	240058006	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240058006delG	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron|HDAC4_uc010fyy.2_Intron|HDAC4_uc010znz.1_Intron|HDAC4_uc010fzb.1_Intron	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		ttctgtgcctggcttagttca	0.015													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41614831	41614831	+	Intron	DEL	T	-	-	rs11359795		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41614831delT	uc003ckv.3	-							NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCGTGAAAAATGACCAGCCTT	0.423													6	3	---	---	---	---	
ARHGEF3	50650	broad.mit.edu	37	3	57031758	57031758	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57031758delA	uc003dih.2	-							NM_001128615	NP_001122087	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		GACGAAGGGTAAATGATCCAA	0.488													4	2	---	---	---	---	
SLMAP	7871	broad.mit.edu	37	3	57899168	57899168	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57899168delT	uc003dje.1	+						SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_Intron|SLMAP_uc011bez.1_Intron|SLMAP_uc011bfa.1_Intron|SLMAP_uc003djh.2_Intron|SLMAP_uc003dji.1_Intron|SLMAP_uc011bfb.1_Intron|SLMAP_uc011bfc.1_Intron	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		ATACTTCAGCTTTTTTTTTTC	0.333													4	3	---	---	---	---	
ARHGAP31	57514	broad.mit.edu	37	3	119062897	119062898	+	Intron	INS	-	C	C	rs148466528	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119062897_119062898insC	uc003ecj.3	+							NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						CTGGCCGGGGGCGCAAAGAGTG	0.356													3	5	---	---	---	---	
PARP14	54625	broad.mit.edu	37	3	122431997	122431997	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122431997delT	uc003efq.3	+						PARP14_uc010hrk.2_Intron|PARP14_uc003efr.2_Intron|PARP14_uc003efs.1_Intron	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		atttgtcctgtttttagttgt	0.040													4	2	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124397368	124397369	+	Intron	INS	-	T	T	rs148867215	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124397368_124397369insT	uc003ehg.2	+						KALRN_uc003ehk.2_Intron	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						AAGTAAGTACCTTTTTTTTCTT	0.317													9	4	---	---	---	---	
SPSB4	92369	broad.mit.edu	37	3	140784152	140784152	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140784152delG	uc003ett.2	+						SPSB4_uc010hum.2_5'Flank	NM_080862	NP_543138	Q96A44	SPSB4_HUMAN	splA/ryanodine receptor domain and SOCS box						intracellular signal transduction	cytoplasm	protein binding				0						CCATGTCCCTGGTGACCCTGC	0.557													4	2	---	---	---	---	
PCOLCE2	26577	broad.mit.edu	37	3	142552606	142552606	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142552606delT	uc003evd.2	-							NM_013363	NP_037495	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2							extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3						ttttacccccttttttttcct	0.035													4	2	---	---	---	---	
MME	4311	broad.mit.edu	37	3	154889729	154889734	+	Intron	DEL	ATAAAT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154889729_154889734delATAAAT	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)	GCATTTGTAAATAAATTTGATTTGTC	0.218													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157487654	157487654	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157487654delA								C3orf55 (168635 upstream) : SHOX2 (326147 downstream)																							AGATCACTTCAAAAAAAAAAA	0.438													4	2	---	---	---	---	
IFT80	57560	broad.mit.edu	37	3	160075055	160075055	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160075055delT	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_Intron|IFT80_uc003fdd.1_Intron|IFT80_uc003fde.1_Intron	NM_020800	NP_065851	Q9P2H3	IFT80_HUMAN	WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			aactggctaatttttttttgt	0.065													4	2	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170174250	170174250	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170174250delT	uc011bpt.1	+							NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			aagtatttGAttttttttttt	0.005													6	3	---	---	---	---	
PLD1	5337	broad.mit.edu	37	3	171456094	171456094	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171456094delA	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	aaaacaagagaaaaaaaaaag	0.284													4	3	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173597429	173597429	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173597429delT	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			tttctgtgtgttttttttttt	0.000													4	2	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173688333	173688333	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173688333delA	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TGCTTACAATAAAAAAAAAAG	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	183278865	183278865	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183278865delG								KLHL6 (5366 upstream) : KLHL24 (74546 downstream)																							ACAATGACACGGGGTCTGCCT	0.483													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184241260	184241260	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184241260delA								CHRD (133641 upstream) : EPHB3 (38327 downstream)																							attattatccaaggagaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195427029	195427029	+	RNA	DEL	T	-	-	rs75389211		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195427029delT	uc011btd.1	+	1		c.208delT			uc003fux.1_RNA					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		gcaacaggaattttttcaggc	0.015													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	196405913	196405913	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196405913delA								LRRC33 (17041 upstream) : C3orf34 (27236 downstream)																							attctaaaacaaaaaaatttt	0.020													4	2	---	---	---	---	
DLG1	1739	broad.mit.edu	37	3	196786504	196786505	+	Intron	INS	-	CACTAGTCACTATTTACACTAGTCA	CACTAGTCACTATTTACACTAGTCA	rs147285389	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196786504_196786505insCACTAGTCACTATTTACACTAGTCA	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron	NM_001098424	NP_001091894	Q12959	DLG1_HUMAN	discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		acttcagtagccactagtcaca	0.208													5	3	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	67191	67191	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67191delA	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		cttaaagtttaaaaaaaaaGG	0.090													4	2	---	---	---	---	
ZNF876P	642280	broad.mit.edu	37	4	213376	213376	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:213376delT	uc010iba.2	+							NR_027481				Homo sapiens cDNA clone IMAGE:4828836.												0						ctcttttttcttttttttgag	0.154													4	2	---	---	---	---	
SH3TC1	54436	broad.mit.edu	37	4	8242814	8242814	+	3'UTR	DEL	T	-	-	rs67520179		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8242814delT	uc003gkv.3	+	18					SH3TC1_uc003gkw.3_3'UTR|SH3TC1_uc003gkx.3_RNA|SH3TC1_uc003gky.2_RNA	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1								binding			large_intestine(2)|pancreas(1)	3						ATGGGTTTTGTTTTTTTTTTG	0.552													4	2	---	---	---	---	
SLC2A9	56606	broad.mit.edu	37	4	9836923	9836924	+	Intron	DEL	AT	-	-	rs143827717		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9836923_9836924delAT	uc003gmc.2	-						SLC2A9_uc003gmd.2_Intron	NM_020041	NP_064425	Q9NRM0	GTR9_HUMAN	solute carrier family 2, member 9 protein						glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3						ccaaaCTCACATGTGGTCTCAG	0.287													2	4	---	---	---	---	
KLHL5	51088	broad.mit.edu	37	4	39105768	39105768	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39105768delG	uc003gts.2	+						KLHL5_uc003gtp.2_Intron|KLHL5_uc003gtq.2_Intron|KLHL5_uc003gtr.1_Intron|KLHL5_uc003gtt.2_Intron	NM_015990	NP_057074	Q96PQ7	KLHL5_HUMAN	kelch-like 5 isoform 1							cytoplasm|cytoskeleton	actin binding			ovary(1)	1						GAATGGTGGTGGGTACAGTAA	0.353													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54347688	54347688	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54347688delT	uc003haa.2	+						LNX1_uc003haf.3_Intron|LNX1_uc003hag.3_Intron|LNX1_uc003hah.3_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	TTCCTGCACCTTCTTCTCTCC	0.403			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54519798	54519798	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54519798delT	uc003haa.2	+						LNX1_uc003hah.3_5'Flank	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	CATGGCCTGATTGCCACTTTG	0.458			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54927909	54927909	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54927909delA	uc003haa.2	+						CHIC2_uc003haj.1_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	GAGCCATGTTAAAAAAAAAAG	0.363			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	55095489	55095490	+	5'UTR	DEL	AG	-	-	rs113739379		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55095489_55095490delAG	uc003han.3	+	1					PDGFRA_uc003haa.2_Intron|PDGFRA_uc003hal.2_5'UTR|PDGFRA_uc010igq.1_5'UTR|PDGFRA_uc003ham.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	GGAGAGAAACAGAGGAGGAGAC	0.450			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	72553754	72553754	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72553754delT								SLC4A4 (115951 upstream) : GC (53659 downstream)																							attccctatctttttttgccc	0.139													4	2	---	---	---	---	
NAAA	27163	broad.mit.edu	37	4	76839611	76839611	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76839611delA	uc003hjb.2	-						NAAA_uc003hja.2_Intron|NAAA_uc003hjc.3_Intron|NAAA_uc003hjd.3_Intron	NM_014435	NP_055250	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase isoform 1						lipid metabolic process	lysosome	hydrolase activity			skin(1)	1						ctggctcaagaaaaaaaaaaa	0.070													4	2	---	---	---	---	
ABCG2	9429	broad.mit.edu	37	4	89124361	89124362	+	Intron	INS	-	G	G			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89124361_89124362insG	uc003hrh.2	-									Q9UNQ0	ABCG2_HUMAN	RecName: Full=ATP-binding cassette sub-family G member 2; AltName: Full=Placenta-specific ATP-binding cassette transporter; AltName: Full=Breast cancer resistance protein; AltName: Full=Mitoxantrone resistance-associated protein; AltName: Full=CDw338; AltName: CD_antigen=CD338;						cellular iron ion homeostasis|urate metabolic process	integral to membrane|plasma membrane	ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030)	GAGAAGAGAGTGGGGGATGGAA	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	90237049	90237049	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90237049delA								GPRIN3 (7888 upstream) : SNCA (408202 downstream)																							TTCAGAGTTTAAAAACTAACA	0.269													4	2	---	---	---	---	
C4orf21	55345	broad.mit.edu	37	4	113527490	113527490	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113527490delA	uc003iau.2	-						C4orf21_uc003iaw.2_Intron	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like							integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		TTCTGATTCTAAATTTTTAAT	0.234													4	2	---	---	---	---	
KIAA1109	84162	broad.mit.edu	37	4	123170300	123170301	+	Intron	INS	-	TT	TT			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123170300_123170301insTT	uc003ieh.2	+						KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						AATTAATTGAATTTTTTTTTTA	0.218													4	2	---	---	---	---	
LRBA	987	broad.mit.edu	37	4	151226743	151226743	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151226743delG	uc010ipj.2	-						LRBA_uc010ipi.2_Intron|LRBA_uc003ils.3_Intron|LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron|LRBA_uc003ilr.3_Intron	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					attatgaatagggatgagtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	151996965	151996965	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151996965delT								LRBA (60086 upstream) : RPS3A (23789 downstream)																							GTGCTACAGAtttttttttta	0.159													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153849442	153849442	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153849442delA								ARFIP1 (16381 upstream) : FHDC1 (14693 downstream)																							TATGTCCCTCAAAAAAAAACT	0.458													2	4	---	---	---	---	
C4orf45	152940	broad.mit.edu	37	4	159938600	159938601	+	Intron	INS	-	T	T	rs113594311		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159938600_159938601insT	uc003iqf.1	-						C4orf45_uc010iqt.1_Intron	NM_152543	NP_689756	Q96LM5	CD045_HUMAN	hypothetical protein LOC152940												0						TCCTCCAACAAtttttttttta	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182124626	182124626	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182124626delT								None (None upstream) : MGC45800 (935533 downstream)																							gtttgttttgtttttttagtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190619582	190619584	+	IGR	DEL	ATA	-	-	rs147462794		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190619582_190619584delATA								None (None upstream) : FRG1 (242390 downstream)																							TACAACACACATAAGTACTTCCC	0.300													3	3	---	---	---	---	
TRIP13	9319	broad.mit.edu	37	5	913325	913325	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:913325delC	uc003jbr.2	+							NM_004237	NP_004228	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13						double-strand break repair|reciprocal meiotic recombination|synaptonemal complex assembly|transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			TGTTGGAGGTCCTCACGCACC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3883518	3883519	+	IGR	DEL	GT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3883518_3883519delGT								IRX1 (282002 upstream) : None (None downstream)																							gtgcacacgcgtgtgtacttgt	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36452431	36452432	+	IGR	INS	-	A	A	rs112644470		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36452431_36452432insA								RANBP3L (150420 upstream) : SLC1A3 (154025 downstream)																							AGACAGGAATGAAAAAAAAAAC	0.366													3	3	---	---	---	---	
LIFR	3977	broad.mit.edu	37	5	38542887	38542887	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38542887delC	uc010ive.1	-						LIFR_uc003jli.2_Intron	NM_001127671	NP_001121143	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor						positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)					ccttcccactccactcttcct	0.010			T	PLAG1	salivary adenoma								4	2	---	---	---	---	
DIMT1L	27292	broad.mit.edu	37	5	61689066	61689066	+	Intron	DEL	T	-	-	rs79936750		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61689066delT	uc003jta.2	-						DIMT1L_uc011cqq.1_Intron	NM_014473	NP_055288	Q9UNQ2	DIMT1_HUMAN	dimethyladenosine transferase							nucleolus	RNA binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			central_nervous_system(1)	1		Lung NSC(810;8.94e-06)|Prostate(74;0.0235)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.122)		AGCATGACaattttttttttt	0.100													4	2	---	---	---	---	
MAST4	375449	broad.mit.edu	37	5	66407366	66407366	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66407366delA	uc003jut.1	+						MAST4_uc003jus.2_Intron|MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron|MAST4_uc003juv.2_Intron|MAST4_uc003juw.2_Intron	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GGCTAAAAGGAAAAAAAAATC	0.418													5	3	---	---	---	---	
IQGAP2	10788	broad.mit.edu	37	5	75998629	75998632	+	Intron	DEL	CAGT	-	-	rs34100308		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75998629_75998632delCAGT	uc003kek.2	+						IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		CAAACCATAGCAGTCAGTTTCTCT	0.294													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	92159061	92159061	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92159061delG								None (None upstream) : FLJ42709 (586004 downstream)																							TTTCAACTCTGGGCCACCTTG	0.403													4	2	---	---	---	---	
SRP19	6728	broad.mit.edu	37	5	112198502	112198505	+	Intron	DEL	TTTG	-	-	rs145538201		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112198502_112198505delTTTG	uc003kqc.2	+						SRP19_uc003kqb.1_Intron|SRP19_uc011cvu.1_Intron|SRP19_uc011cvv.1_Intron	NM_003135	NP_003126	P09132	SRP19_HUMAN	signal recognition particle 19kDa						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)		TTAATGAGCCTTTGTTTGTAAAGG	0.387													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	118107298	118107299	+	IGR	INS	-	C	C	rs141530013	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118107298_118107299insC								None (None upstream) : DTWD2 (65272 downstream)																							aacagcatgtgcagggccctga	0.000													4	2	---	---	---	---	
FBN2	2201	broad.mit.edu	37	5	127693372	127693372	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127693372delT	uc003kuu.2	-						FBN2_uc003kuv.2_Intron	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor						bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ATAAATTGGATTTTTTTTTCC	0.383													4	3	---	---	---	---	
FSTL4	23105	broad.mit.edu	37	5	132778203	132778203	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132778203delA	uc003kyn.1	-							NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AAGGTTAAGGAAAAAAAAAAA	0.323													3	6	---	---	---	---	
PCDHGA2	56113	broad.mit.edu	37	5	140756840	140756840	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140756840delA	uc003ljk.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTAATGTGGGAAAAAAAATAA	0.249													2	5	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142229938	142229939	+	Intron	DEL	CT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142229938_142229939delCT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTACAGATGCTCTCTCTCTCT	0.332													6	3	---	---	---	---	
LARS	51520	broad.mit.edu	37	5	145540213	145540214	+	Intron	INS	-	ATTT	ATTT	rs140796536	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145540213_145540214insATTT	uc003lnx.1	-						LARS_uc011dbq.1_Intron|LARS_uc011dbr.1_Intron|LARS_uc011dbs.1_Intron	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	CAATTACTTTAATTTACTTAAA	0.208													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	145683027	145683027	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145683027delG								RBM27 (14245 upstream) : POU4F3 (35560 downstream)																							cttttggggtgggtactctta	0.144													4	2	---	---	---	---	
ABLIM3	22885	broad.mit.edu	37	5	148623931	148623931	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148623931delC	uc003lpy.2	+						ABLIM3_uc003lpz.1_Intron|ABLIM3_uc003lqa.1_Intron|ABLIM3_uc003lqb.2_Intron|ABLIM3_uc003lqc.1_Intron|ABLIM3_uc003lqd.1_Intron|ABLIM3_uc003lqf.2_Intron|ABLIM3_uc003lqe.1_Intron	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3						axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			ovary(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tttgctgactccctgtctagc	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157154456	157154456	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157154456delT								C5orf52 (47296 upstream) : THG1L (3867 downstream)																							tacccatcccttttttttttc	0.000													8	5	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167293741	167293741	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167293741delA	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		GTGCATTCAGAAAGATGTTAG	0.353													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168347814	168347814	+	Intron	DEL	T	-	-	rs112817808		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168347814delT	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)			TCTCTCCCTATTTTTTTTAAA	0.353													4	3	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169151755	169151756	+	Intron	INS	-	T	T	rs111517758		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169151755_169151756insT	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTTCTTTTGTCTTTTTTTTTTT	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171222772	171222772	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171222772delA								FGF18 (338610 upstream) : FBXW11 (65784 downstream)																							AGAGATCATTAAAAATGTTTA	0.413													4	2	---	---	---	---	
SH3PXD2B	285590	broad.mit.edu	37	5	171800822	171800823	+	Intron	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171800822_171800823insT	uc003mbr.2	-							NM_001017995	NP_001017995	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B						adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGTGCTCCCTGTACAGGAAAGA	0.342													163	126	---	---	---	---	
NEURL1B	54492	broad.mit.edu	37	5	172086808	172086808	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172086808delC	uc003mbt.2	+							NM_001142651	NP_001136123	A8MQ27	NEU1B_HUMAN	neuralized homolog 1B								ligase activity|zinc ion binding				0						attctcatctccaggcctttg	0.000													4	2	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	1769173	1769173	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1769173delT	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		TTTGAGTTCCTTTTAATATTC	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	4474441	4474441	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4474441delC								PECI (338610 upstream) : CDYL (231952 downstream)																							gttaagtgtgcctagactcct	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29775232	29775232	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29775232delA								HCG4 (14382 upstream) : HLA-G (19524 downstream)																							tttagaagttaaaaaacatta	0.005													4	2	---	---	---	---	
MAPK14	1432	broad.mit.edu	37	6	36017998	36018001	+	Intron	DEL	AGAC	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36017998_36018001delAGAC	uc003olp.2	+						MAPK14_uc011dth.1_Intron|MAPK14_uc003olo.2_Intron|MAPK14_uc003olq.2_Intron|MAPK14_uc003olr.2_Intron|MAPK14_uc011dti.1_Intron	NM_001315	NP_001306	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14 isoform 1						activation of MAPK activity|cellular component movement|cellular response to ionizing radiation|chemotaxis|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of muscle cell differentiation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|signal transduction in response to DNA damage|stress-activated MAPK cascade|stress-induced premature senescence|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase activity|MAP kinase kinase activity|protein binding			ovary(2)|stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	6						tacatcagagagacagacagacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	81387481	81387482	+	IGR	DEL	TC	-	-	rs6940662	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81387481_81387482delTC								BCKDHB (331494 upstream) : None (None downstream)																							gggttttttttctgtactgatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	81387482	81387482	+	IGR	DEL	C	-	-	rs6940662	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81387482delC								BCKDHB (331495 upstream) : None (None downstream)																							ggttttttttctgtactgatt	0.000													4	2	---	---	---	---	
PGM3	5238	broad.mit.edu	37	6	83896511	83896513	+	Intron	DEL	CTC	-	-	rs150128226		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83896511_83896513delCTC	uc003pjv.2	-						PGM3_uc003pjw.2_Intron|PGM3_uc011dyz.1_Intron	NM_015599	NP_056414	O95394	AGM1_HUMAN	phosphoglucomutase 3						dolichol-linked oligosaccharide biosynthetic process|embryo development ending in birth or egg hatching|glucose 1-phosphate metabolic process|hemopoiesis|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	magnesium ion binding|phosphoacetylglucosamine mutase activity|phosphoglucomutase activity				0		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		CAGCTATAATCTCCTATAGTACT	0.325													8	4	---	---	---	---	
FOXO3	2309	broad.mit.edu	37	6	108907701	108907701	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108907701delT	uc003psk.2	+						FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Intron	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A						antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		CTTGTGAATATTTTTTTGACG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	116915990	116915990	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116915990delA								RWDD1 (1558 upstream) : RSPH4A (21652 downstream)																							TGCCTCCAGTAAAAAATACAT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138029638	138029638	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138029638delT								OLIG3 (214107 upstream) : TNFAIP3 (158943 downstream)																							ACTTGACCCCTGCAGTTCCTT	0.378													4	2	---	---	---	---	
AIG1	51390	broad.mit.edu	37	6	143571095	143571095	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143571095delC	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron	NM_016108	NP_057192	Q9NVV5	AIG1_HUMAN	androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)		CTGGCTTTGACCAGGAAAGTG	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147287549	147287550	+	Intron	DEL	TC	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147287549_147287550delTC	uc003qlt.1	-						uc003qlu.1_Intron|uc003qlv.2_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																		tctctctctgtctctctctctc	0.000													4	2	---	---	---	---	
TIAM2	26230	broad.mit.edu	37	6	155520906	155520907	+	Intron	DEL	GA	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155520906_155520907delGA	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GTCAGGTCTTGACTGCGGTAGA	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156796813	156796813	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156796813delC								MIR1202 (528800 upstream) : ARID1B (302273 downstream)																							TAATGGAAGACCCAGAGCTCA	0.209													4	2	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	2094709	2094709	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2094709delG	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		CACAAAGGGCGGGGGCAGCAG	0.672													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6701827	6701827	+	5'Flank	DEL	T	-	-	rs2464878	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6701827delT	uc003sqr.1	+											Homo sapiens cDNA FLJ41306 fis, clone BRAMY2042549.																		agcagatttatttttttggct	0.025													4	2	---	---	---	---	
SOSTDC1	25928	broad.mit.edu	37	7	16519536	16519536	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16519536delA	uc003sth.2	-							NM_015464	NP_056279	Q6X4U4	SOSD1_HUMAN	sclerostin domain containing 1 precursor						Wnt receptor signaling pathway					ovary(2)|central_nervous_system(1)	3	Lung NSC(10;0.185)			UCEC - Uterine corpus endometrioid carcinoma (126;0.177)		TGTTCGATCTAAAAAAAAAGA	0.313													4	2	---	---	---	---	
CREB5	9586	broad.mit.edu	37	7	28849846	28849846	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28849846delA	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron|CREB5_uc003szs.2_Intron	NM_182898	NP_878901	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						TTATCAGCAGAAAAAAAAAAA	0.368													4	2	---	---	---	---	
CHN2	1124	broad.mit.edu	37	7	29452510	29452513	+	Intron	DEL	GGGT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29452510_29452513delGGGT	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2						GAATTTGTAGGGGTGGGTGGGTGG	0.441													4	2	---	---	---	---	
FKBP9	11328	broad.mit.edu	37	7	33020351	33020351	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33020351delT	uc003tdh.2	+						AVL9_uc011kai.1_Intron|FKBP9_uc011kak.1_Intron|FKBP9_uc011kal.1_Intron|FKBP9_uc011kam.1_Intron|FKBP9_uc003tdg.2_Intron	NM_007270	NP_009201	O95302	FKBP9_HUMAN	FK506 binding protein 9 precursor						protein folding	endoplasmic reticulum|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity			central_nervous_system(13)|ovary(1)	14			GBM - Glioblastoma multiforme(11;0.0156)			tctttctttctttttttttga	0.169													4	2	---	---	---	---	
INHBA	3624	broad.mit.edu	37	7	41740083	41740083	+	5'UTR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41740083delT	uc003thq.2	-	1					LOC285954_uc003tht.3_Intron|INHBA_uc003thr.2_5'UTR|LOC285954_uc003ths.2_Intron	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor						cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity			lung(5)|ovary(1)	6						ttttttggtgttttttttttc	0.338										TSP Lung(11;0.080)			7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	47736288	47736288	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47736288delC								C7orf65 (35042 upstream) : PKD1L1 (78002 downstream)																							tctttatcctcctccaggata	0.139													4	2	---	---	---	---	
C7orf72	100130988	broad.mit.edu	37	7	50144059	50144060	+	Intron	INS	-	TA	TA	rs146114368	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50144059_50144060insTA	uc011kcj.1	+							NM_001161834	NP_001155306			hypothetical protein LOC100130988											ovary(1)	1						tttcattgtattatatatatat	0.188													40	33	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53063304	53063304	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53063304delG								None (None upstream) : POM121L12 (40045 downstream)																							gcagaggcaaggaagtatgag	0.129													4	2	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	71176675	71176681	+	Intron	DEL	TCTTCTC	-	-	rs72492803		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71176675_71176681delTCTTCTC	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ctcctctctatcttctctcttctctct	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84561097	84561097	+	IGR	DEL	A	-	-	rs77016522		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84561097delA								SEMA3A (736880 upstream) : SEMA3D (63777 downstream)																							agtgaagaagaaaaaaaaaac	0.000													4	2	---	---	---	---	
DMTF1	9988	broad.mit.edu	37	7	86811354	86811354	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86811354delT	uc003uih.2	+						DMTF1_uc003uii.2_5'UTR|DMTF1_uc003uij.2_Intron|DMTF1_uc011khb.1_Intron|DMTF1_uc003uik.2_RNA|DMTF1_uc003uil.2_Intron|DMTF1_uc003uin.2_Intron	NM_001142327	NP_001135799	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1						cell cycle	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(14;0.0058)					TTGCTGCCTGTTTTTTTTTCA	0.418													5	3	---	---	---	---	
ADAM22	53616	broad.mit.edu	37	7	87577495	87577495	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87577495delA	uc003ujn.2	+						ADAM22_uc003uji.1_Intron|ADAM22_uc003ujj.1_Intron|ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			ATTTCCCCCCACTCTATTTCT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	100607644	100607644	+	Intron	DEL	T	-	-	rs5886153		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100607644delT	uc003uxk.1	+						uc003uxl.1_Intron|uc003uxm.1_Intron|uc003uxn.1_Intron|uc010lhn.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																		ACCTCTGCCCTCTTTCCCCCT	0.577													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101973498	101973498	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101973498delC								SH2B2 (11321 upstream) : SPDYE6 (12695 downstream)																							tcacttgcagccccctccctt	0.020													4	2	---	---	---	---	
COG5	10466	broad.mit.edu	37	7	106910150	106910150	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106910150delA	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						tatgtttatcaatgttttgtg	0.005													4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126890641	126890642	+	Intron	INS	-	A	A	rs148764921	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126890641_126890642insA	uc003vlt.2	-						GRM8_uc010lkz.1_Intron	NM_001127323	NP_001120795	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform b						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	AATTGCATTTTAAAAAACCTTG	0.366										HNSCC(24;0.065)			6	4	---	---	---	---	
METTL2B	55798	broad.mit.edu	37	7	128127855	128127858	+	Intron	DEL	CAAG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128127855_128127858delCAAG	uc003vnf.2	+						METTL2B_uc003vng.2_Intron|METTL2B_uc011kop.1_Intron	NM_018396	NP_060866	Q6P1Q9	MTL2B_HUMAN	methyltransferase like 2B								methyltransferase activity			skin(1)	1						GTGGTGCTATCAAGCAAGGCTTCA	0.422													10	7	---	---	---	---	
FLNC	2318	broad.mit.edu	37	7	128496167	128496167	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128496167delC	uc003vnz.3	+						FLNC_uc003voa.3_Intron	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a						cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12						CCCTGTTGGTCCACCTTCTCC	0.612													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149335719	149335719	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149335719delT								ZNF767 (13838 upstream) : KRBA1 (76383 downstream)																							ACACTGCCTCTTTGGGCCATG	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149856270	149856271	+	IGR	INS	-	A	A	rs142655888	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149856270_149856271insA								ATP6V0E2 (278484 upstream) : ACTR3C (88031 downstream)																							aacaaagctggaaaaaAATATC	0.248													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	2910305	2910307	+	Intron	DEL	TTC	-	-	rs71199530		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2910305_2910307delTTC	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ttttttttctttctttttttttt	0.089													4	2	---	---	---	---	
XPO7	23039	broad.mit.edu	37	8	21807226	21807229	+	Intron	DEL	TGTT	-	-	rs67297450		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21807226_21807229delTGTT	uc003xaa.3	+						XPO7_uc010lti.2_Intron|XPO7_uc010ltj.1_Intron	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b						mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		ATGGCCAGGCTGTttgttgttgtt	0.284													4	3	---	---	---	---	
LSM1	27257	broad.mit.edu	37	8	38021012	38021013	+	3'UTR	INS	-	A	A	rs34402880		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38021012_38021013insA	uc003xkw.2	-	4					LSM1_uc003xkx.2_RNA	NM_014462	NP_055277	O15116	LSM1_HUMAN	Lsm1 protein						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|mRNA processing|RNA splicing, via transesterification reactions	cytosol|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0	Colorectal(12;0.000442)					ATTTTGTTATTAAAAAAAAAAC	0.322													3	3	---	---	---	---	
ASPH	444	broad.mit.edu	37	8	62465283	62465284	+	Intron	DEL	AC	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62465283_62465284delAC	uc003xuj.2	-						ASPH_uc011leg.1_Intron	NM_004318	NP_004309	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	acacacacagacacacacacac	0.183													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62923620	62923620	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62923620delA								ASPH (296421 upstream) : NKAIN3 (237881 downstream)																							TGGCAGTGATAAAAAATAGAG	0.343													4	2	---	---	---	---	
CA13	377677	broad.mit.edu	37	8	86213930	86213930	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86213930delT	uc003ydf.1	+									Q8N1Q1	CAH13_HUMAN	Homo sapiens cDNA FLJ36434 fis, clone THYMU2012002.						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0						TTGTAAATACTTTTTTAATGT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	87247764	87247764	+	IGR	DEL	T	-	-	rs77698384		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87247764delT								SLC7A13 (5155 upstream) : WWP1 (107230 downstream)																							tttatttttatttttttttta	0.000													4	2	---	---	---	---	
RBM12B	389677	broad.mit.edu	37	8	94745438	94745438	+	3'UTR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745438delA	uc003yfz.2	-	3						NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TTTAAATTTGAAAAAAAAAAA	0.284													7	4	---	---	---	---	
INTS8	55656	broad.mit.edu	37	8	95866386	95866387	+	Intron	INS	-	TGAGCTGAAA	TGAGCTGAAA	rs143503531	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95866386_95866387insTGAGCTGAAA	uc003yhb.2	+						INTS8_uc003yha.1_Intron|INTS8_uc011lgq.1_Intron|INTS8_uc011lgr.1_Intron|INTS8_uc010mba.2_Intron	NM_017864	NP_060334	Q75QN2	INT8_HUMAN	integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)					ggaggttggagttgcatcattg	0.040													4	3	---	---	---	---	
PABPC1	26986	broad.mit.edu	37	8	101728028	101728028	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101728028delA	uc003yjs.1	-						PABPC1_uc011lhc.1_Intron|PABPC1_uc011lhd.1_Intron|PABPC1_uc003yjt.1_Intron|PABPC1_uc003yju.2_Intron	NM_002568	NP_002559	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1						mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CTACAATCACAAAAAAAAAAC	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	108699709	108699709	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108699709delA								ANGPT1 (189455 upstream) : RSPO2 (211836 downstream)																							AAACCCCTCCAAAAAAAAATA	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117532012	117532012	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117532012delC								TRPS1 (850784 upstream) : EIF3H (125044 downstream)																							TGCTTTTGTTCCCCATTGTGC	0.378													4	2	---	---	---	---	
TNFRSF11B	4982	broad.mit.edu	37	8	119936331	119936331	+	3'UTR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119936331delT	uc003yon.3	-	5						NM_002546	NP_002537	O00300	TR11B_HUMAN	osteoprotegerin precursor						apoptosis|skeletal system development		cytokine activity|receptor activity			central_nervous_system(2)	2	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			TGGAGTCTAGTTTTTTTTTTT	0.318													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136668643	136668644	+	IGR	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136668643_136668644insT								KHDRBS3 (8797 upstream) : None (None downstream)																							GGAGAACCTACTTTTTTAAAAA	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142675572	142675572	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142675572delA								FLJ43860 (158242 upstream) : MIR1302-7 (192031 downstream)																							cccggaggggaatgacctcgc	0.000													4	2	---	---	---	---	
GLIS3	169792	broad.mit.edu	37	9	4214244	4214245	+	Intron	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4214244_4214245insT	uc003zhx.1	-						GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron	NM_001042413	NP_001035878	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform a						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TCAAGTGCGCATTTTTGTGGAA	0.386													4	2	---	---	---	---	
PTPLAD2	401494	broad.mit.edu	37	9	21029024	21029025	+	Intron	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21029024_21029025insT	uc010miq.1	-						PTPLAD2_uc003zoj.1_Intron|PTPLAD2_uc010mir.1_Intron	NM_001010915	NP_001010915	Q5VWC8	HACD4_HUMAN	protein tyrosine phosphatase-like A domain						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	lyase activity			skin(1)	1				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)		TACAGAATGGAAAAGGAACAAT	0.406													3	3	---	---	---	---	
DDX58	23586	broad.mit.edu	37	9	32459124	32459125	+	Intron	INS	-	T	T	rs140196507	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32459124_32459125insT	uc003zra.2	-						DDX58_uc010mjj.2_Intron|DDX58_uc010mji.2_Intron	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide						detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		tgacctcgtgatcgcccacctt	0.025													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66464673	66464674	+	Intron	DEL	TG	-	-	rs113415960		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66464673_66464674delTG	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		GTCAAAACACTGTACTGATTCC	0.356													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66694812	66694813	+	Intron	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66694812_66694813insT	uc004aej.2	-											Homo sapiens cDNA clone IMAGE:4668947, partial cds.																		GTTCACAGGGAttttttttttc	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69056465	69056466	+	IGR	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69056465_69056466insT								MIR1299 (54144 upstream) : PGM5P2 (23779 downstream)																							taagacaaaaaaatcaccaaca	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69810304	69810304	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69810304delT								LOC100133920 (145355 upstream) : FOXD4L5 (365405 downstream)																							CTGCTTAACCTTTTTTGATTT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	76463006	76463006	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76463006delA								ANXA1 (677699 upstream) : RORB (649246 downstream)																							ACATTATTTTAAAAAAACTAG	0.308													4	2	---	---	---	---	
LOC100129066	100129066	broad.mit.edu	37	9	92295683	92295684	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92295683_92295684insA	uc004aqs.2	+							NR_024280				Homo sapiens cDNA FLJ42342 fis, clone UTERU2000794.												0						GAAAGTAAGCTAAAAAAAAAAA	0.460													5	4	---	---	---	---	
INVS	27130	broad.mit.edu	37	9	102921536	102921536	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102921536delT	uc004bap.1	+						INVS_uc010mta.1_Intron|INVS_uc011lve.1_Intron|INVS_uc004bao.1_Intron|INVS_uc004baq.1_Intron|INVS_uc004bar.1_Intron|INVS_uc010mtb.1_Intron	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a						negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|membrane|microtubule|nucleus|spindle	calmodulin binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.056)				caatgagaagttttagggaag	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107879378	107879378	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107879378delG								ABCA1 (188942 upstream) : SLC44A1 (127551 downstream)																							AGTTGGAGTTGGGGGACAGTG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111141174	111141174	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111141174delT								KLF4 (889127 upstream) : ACTL7B (475697 downstream)																							CCACTCAACCTCTCTCAGCCA	0.507													4	2	---	---	---	---	
SVEP1	79987	broad.mit.edu	37	9	113225006	113225007	+	Intron	DEL	AG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113225006_113225007delAG	uc010mtz.2	-						SVEP1_uc010mua.1_Intron	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						ACAGAGAGACAGAGAGAGAGAG	0.356													4	2	---	---	---	---	
HSDL2	84263	broad.mit.edu	37	9	115139630	115139630	+	5'Flank	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115139630delA	uc004bga.1	+						HSDL2_uc011lwv.1_5'Flank|HSDL2_uc004bgb.1_5'Flank|HSDL2_uc004bgc.1_5'Flank|HSDL2_uc011lww.1_5'Flank	NM_032303	NP_115679	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2							peroxisome	oxidoreductase activity|sterol binding				0						atcttatctcaaaaaaacaaa	0.164													4	2	---	---	---	---	
MAPKAP1	79109	broad.mit.edu	37	9	128350939	128350939	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128350939delA	uc004bpv.2	-						MAPKAP1_uc011lzt.1_Intron|MAPKAP1_uc010mwz.2_Intron|MAPKAP1_uc011lzu.1_Intron|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc010mxb.1_Intron|MAPKAP1_uc004bqa.2_Intron|MAPKAP1_uc010mxc.1_Intron	NM_001006617	NP_001006618	Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4						aacagttcccaaattattcta	0.010													4	2	---	---	---	---	
FAM73B	84895	broad.mit.edu	37	9	131823751	131823752	+	Intron	INS	-	GA	GA			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131823751_131823752insGA	uc004bxa.2	+						FAM73B_uc004bwy.2_Intron|FAM73B_uc004bwz.2_Intron|FAM73B_uc011mbn.1_Intron	NM_032809	NP_116198	Q7L4E1	FA73B_HUMAN	hypothetical protein LOC84895							integral to membrane				skin(1)	1						GGCTGCCTGAGGGCCGTGGTGA	0.579													4	2	---	---	---	---	
NCS1	23413	broad.mit.edu	37	9	132985664	132985664	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132985664delT	uc004bzi.2	+						NCS1_uc010myz.1_Intron	NM_014286	NP_055101	P62166	NCS1_HUMAN	frequenin homolog isoform 1						negative regulation of calcium ion transport via voltage-gated calcium channel activity|regulation of neuron projection development	cell junction|Golgi cisterna membrane|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|protein binding				0						gtccttagccttttttttttg	0.214													5	3	---	---	---	---	
EXOSC2	23404	broad.mit.edu	37	9	133573868	133573868	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133573868delG	uc004bzu.2	+						EXOSC2_uc011mbz.1_Intron|EXOSC2_uc011mca.1_Intron	NM_014285	NP_055100	Q13868	EXOS2_HUMAN	exosome component 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|positive regulation of cell growth|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|7S RNA binding|protein binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		TCCATGGGGTGGGATCCCAAC	0.468													4	2	---	---	---	---	
GTPBP4	23560	broad.mit.edu	37	10	1038982	1038983	+	Intron	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1038982_1038983insT	uc001ift.2	+						GTPBP4_uc010qac.1_Intron|GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		CTTTCCAAGGGTTTTTTTTTTC	0.470													4	2	---	---	---	---	
GTPBP4	23560	broad.mit.edu	37	10	1061485	1061486	+	Intron	INS	-	TCT	TCT	rs11250220	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1061485_1061486insTCT	uc001ift.2	+						GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		gggtcctgagcgctgagcctgg	0.000													4	2	---	---	---	---	
GTPBP4	23560	broad.mit.edu	37	10	1061486	1061487	+	Intron	INS	-	AGCA	AGCA	rs11250220	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1061486_1061487insAGCA	uc001ift.2	+						GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)		ggtcctgagcgctgagcctggg	0.000													4	2	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1326064	1326064	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1326064delA	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CAAAGCCCAGAAAGAATCTAA	0.438													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12850186	12850186	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12850186delC	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		ttcctccactcccacaaagct	0.095													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14073873	14073873	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14073873delT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						CTGACTTAGATTTTTTTTTTT	0.393													7	4	---	---	---	---	
ITGA8	8516	broad.mit.edu	37	10	15687599	15687599	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15687599delT	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6						TGCTGAGAACTTTTTTTCAAA	0.299													4	2	---	---	---	---	
FAM188A	80013	broad.mit.edu	37	10	15858580	15858580	+	Intron	DEL	A	-	-	rs72001657		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15858580delA	uc001iod.1	-						FAM188A_uc001ioe.1_Intron|FAM188A_uc001iof.1_Intron	NM_024948	NP_079224	Q9H8M7	F188A_HUMAN	chromosome 10 open reading frame 97						apoptosis	nucleus	calcium ion binding			ovary(1)	1						GTGATTTCTGAAAAAAATCAA	0.244													3	4	---	---	---	---	
PLXDC2	84898	broad.mit.edu	37	10	20517794	20517794	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20517794delA	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron|PLXDC2_uc009xkc.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						aagtcaagttaaaaaaaacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	22372988	22372988	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22372988delA								DNAJC1 (80338 upstream) : COMMD3 (232311 downstream)																							acactgcgataaagaaatacc	0.154													4	2	---	---	---	---	
SVIL	6840	broad.mit.edu	37	10	29760362	29760362	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29760362delG	uc001iut.1	-						LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|SVIL_uc010qdw.1_Intron|SVIL_uc001iuu.1_Intron	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2						cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)				GTGTTACTCAGGGAGGGTCTT	0.418													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	33782382	33782382	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33782382delA								NRP1 (158376 upstream) : PARD3 (617716 downstream)																							TTTCCTCCTTAAAAAAAAAAC	0.318													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42746830	42746833	+	IGR	DEL	AATT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42746830_42746833delAATT								None (None upstream) : LOC441666 (80482 downstream)																							ATCATGTGACAATTAATTTGATAA	0.284													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45157817	45157817	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45157817delC								CXCL12 (277275 upstream) : TMEM72 (248947 downstream)																							CTCTTTGGGACCCCCTGACCC	0.562													4	2	---	---	---	---	
GPRIN2	9721	broad.mit.edu	37	10	46997508	46997508	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46997508delT	uc001jec.2	+						GPRIN2_uc010qfq.1_5'Flank	NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth												0						TCTCTCACCCTCCGTGAGCTC	0.557													4	2	---	---	---	---	
ARHGAP22	58504	broad.mit.edu	37	10	49702213	49702214	+	Intron	DEL	TG	-	-	rs72286275		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49702213_49702214delTG	uc001jgt.2	-						ARHGAP22_uc001jgs.2_5'Flank|ARHGAP22_uc001jgu.2_Intron|ARHGAP22_uc010qgl.1_Intron|ARHGAP22_uc010qgm.1_Intron|ARHGAP22_uc001jgv.2_Intron	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 2						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1						acacatggtctgtgtcacagac	0.050													3	3	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	55585167	55585167	+	Intron	DEL	A	-	-	rs35654950		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55585167delA	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ATACATAGATAAAAATTCACT	0.244										HNSCC(58;0.16)			2	5	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73403316	73403317	+	Intron	INS	-	C	C	rs150881254	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73403316_73403317insC	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jry.2_5'Flank|CDH23_uc001jrz.2_5'Flank	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						AGGAGCCCTTGCCCCCCCCTCA	0.594													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80624117	80624119	+	IGR	DEL	CAT	-	-	rs72446586		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80624117_80624119delCAT								RPS24 (807547 upstream) : LOC283050 (78965 downstream)																							tcaCTGTCACCATCATCATCATT	0.251													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81784335	81784337	+	IGR	DEL	AAT	-	-	rs67544556		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81784335_81784337delAAT								MBL1P (73552 upstream) : LOC219347 (21654 downstream)																							TAAAGATAACAATCTTTGGAGAG	0.256													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85795431	85795432	+	IGR	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85795431_85795432insA								None (None upstream) : GHITM (103753 downstream)																							AGAAAAATTTCAAAAAAAAAGA	0.193													4	3	---	---	---	---	
OPN4	94233	broad.mit.edu	37	10	88423774	88423775	+	Intron	DEL	TG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88423774_88423775delTG	uc001kdq.2	+						LDB3_uc010qml.1_5'Flank|OPN4_uc001kdp.2_Intron|OPN4_uc010qmk.1_Intron|OPN4_uc009xsx.1_3'UTR	NM_033282	NP_150598	Q9UHM6	OPN4_HUMAN	opsin 4 isoform 1						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity			ovary(1)	1						GGTCTGCACATGTGTGTGTGTG	0.530													3	3	---	---	---	---	
FAM35A	54537	broad.mit.edu	37	10	88874594	88874594	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88874594delT	uc001kei.3	+							NM_019054	NP_061927	Q86V20	FA35A_HUMAN	hypothetical protein LOC54537											ovary(2)|skin(2)	4						ccaaaatatattttggagata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	94152943	94152944	+	IGR	INS	-	AC	AC	rs149222758	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94152943_94152944insAC								MARCH5 (39222 upstream) : IDE (60656 downstream)																							acacaacacatacacacacaca	0.020													4	2	---	---	---	---	
TMEM20	159371	broad.mit.edu	37	10	95661466	95661468	+	3'UTR	DEL	TTG	-	-	rs141308441		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95661466_95661468delTTG	uc001kjg.1	+	3					TMEM20_uc001kji.2_Intron|TMEM20_uc001kjf.1_3'UTR|TMEM20_uc001kjh.2_Intron|TMEM20_uc010qnw.1_3'UTR|TMEM20_uc001kjj.2_Intron	NM_001134658	NP_001128130	Q2M3R5	TMM20_HUMAN	transmembrane protein 20 isoform 1							integral to membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;3.46e-05)|Renal(717;0.018)|Ovarian(717;0.0228)|all_hematologic(284;0.189)		STAD - Stomach adenocarcinoma(243;0.00345)		TTGGTTTTTTTTGTTGTTGTTGT	0.296													4	3	---	---	---	---	
PDLIM1	9124	broad.mit.edu	37	10	97024889	97024889	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97024889delC	uc001kkh.2	-						PDLIM1_uc001kki.2_Intron|PDLIM1_uc009xuv.2_Intron|PDLIM1_uc001kkj.1_Intron	NM_020992	NP_066272	O00151	PDLI1_HUMAN	PDZ and LIM domain 1						response to oxidative stress	cytoplasm|cytoskeleton	zinc ion binding				0		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		ACAGCTGCCTCCAAAAGAGTT	0.353													4	2	---	---	---	---	
SMC3	9126	broad.mit.edu	37	10	112360493	112360493	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112360493delC	uc001kze.2	+							NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		ttctaagcctcagtttcttgt	0.080													10	6	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127685480	127685480	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127685480delT	uc001ljh.3	+						FANK1_uc009yan.2_Intron|FANK1_uc001lji.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)				TGGAATTCAATTTTTTTTTTT	0.318													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133265032	133265033	+	IGR	INS	-	T	T	rs146909232	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133265032_133265033insT								TCERG1L (155048 upstream) : PPP2R2D (482927 downstream)																							ccatttgtctgtttttttttac	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1359181	1359182	+	IGR	DEL	TC	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1359181_1359182delTC								TOLLIP (28342 upstream) : BRSK2 (51947 downstream)																							CTCCTCCTGGtctctctctgtc	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	9389563	9389563	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9389563delG								TMEM41B (53267 upstream) : IPO7 (16606 downstream)																							AGGAATGGGAGATGAGCCAAA	0.343													4	2	---	---	---	---	
NUCB2	4925	broad.mit.edu	37	11	17331796	17331796	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17331796delA	uc001mmw.2	+						NUCB2_uc001mms.1_Intron|NUCB2_uc001mmt.1_Intron|NUCB2_uc001mmv.1_Intron|NUCB2_uc009ygz.2_Intron	NM_005013	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2 precursor							cytosol|ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|plasma membrane	calcium ion binding|DNA binding				0						TTTTTTTTTTAAATCAACTTA	0.308													5	3	---	---	---	---	
TRAF6	7189	broad.mit.edu	37	11	36532147	36532149	+	5'Flank	DEL	AGG	-	-	rs3841219		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36532147_36532149delAGG	uc001mwr.1	-						TRAF6_uc001mws.1_5'Flank	NM_145803	NP_665802	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6						activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|ossification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell cytokine production|protein autoubiquitination|protein K63-linked ubiquitination|response to interleukin-1|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cell cortex|cytosol|endosome membrane|internal side of plasma membrane|nuclear membrane	histone deacetylase binding|mitogen-activated protein kinase kinase kinase binding|protein kinase B binding|protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)				CTCTCCAAGCAGGAGAAAACCCC	0.522											OREG0020894	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39976246	39976246	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39976246delA								None (None upstream) : LRRC4C (159507 downstream)																							AATAGCACCGAAAAAAAGCTA	0.284													4	2	---	---	---	---	
LOC440040	440040	broad.mit.edu	37	11	49644597	49644597	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49644597delT	uc010rhy.1	+						LOC440040_uc009ymb.2_Intron	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0						TTTTTtttccttttttttatt	0.129													4	2	---	---	---	---	
MACROD1	28992	broad.mit.edu	37	11	63920324	63920324	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63920324delG	uc001nyh.2	-							NM_014067	NP_054786	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1												0						TGCCCTCACTGTCACTGCATG	0.607											OREG0021046	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69643742	69643742	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69643742delC								FGF3 (9550 upstream) : ANO1 (280666 downstream)																							CTACCTGTCTCCAGGGTGCTG	0.597													4	2	---	---	---	---	
ANKRD42	338699	broad.mit.edu	37	11	82922676	82922676	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82922676delA	uc001ozz.1	+						ANKRD42_uc009yvi.1_Intron|ANKRD42_uc010rsv.1_Intron|ANKRD42_uc001paa.2_Intron|ANKRD42_uc001pab.1_Intron	NM_182603	NP_872409	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42											skin(1)	1						cactctctacaaaaaaaaaaa	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91738691	91738691	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91738691delT								None (None upstream) : FAT3 (346571 downstream)																							aaattgttccttttttttcct	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93741950	93741950	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93741950delA								C11orf90 (158282 upstream) : HEPHL1 (12428 downstream)																							ACCTTCAACCAACCAGTTCTA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	106167219	106167219	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106167219delA								AASDHPPT (197800 upstream) : GUCY1A2 (390691 downstream)																							aattataatgaaaaaaaaaag	0.000													4	2	---	---	---	---	
USP28	57646	broad.mit.edu	37	11	113733968	113733968	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113733968delA	uc001poh.2	-						USP28_uc010rwy.1_Intron|USP28_uc001poi.2_Intron|USP28_uc001poj.3_Intron|USP28_uc010rwz.1_Intron	NM_020886	NP_065937	Q96RU2	UBP28_HUMAN	ubiquitin specific protease 28						cell proliferation|DNA damage checkpoint|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|protein deubiquitination|response to ionizing radiation|ubiquitin-dependent protein catabolic process	nucleolus|nucleoplasm	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(2)|breast(2)|ovary(1)|large_intestine(1)|kidney(1)	7		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		ataagaaatcaaaaaggaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114912123	114912124	+	IGR	INS	-	A	A	rs140155280	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114912123_114912124insA								FAM55B (334471 upstream) : CADM1 (127829 downstream)																							aaacattgattaaaaaaaaGGA	0.183													4	2	---	---	---	---	
TMEM136	219902	broad.mit.edu	37	11	120199388	120199389	+	Intron	DEL	GT	-	-	rs36145001		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120199388_120199389delGT	uc001pxh.1	+						TMEM136_uc001pxg.2_Intron|TMEM136_uc010rzm.1_Intron|TMEM136_uc001pxj.2_Intron|TMEM136_uc009zas.1_Intron|TMEM136_uc001pxi.1_Intron	NM_174926	NP_777586	Q6ZRR5	TM136_HUMAN	transmembrane protein 136							integral to membrane				ovary(1)	1		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Hepatocellular(160;0.206)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.07e-06)		aacagtcatagtgtgtgtgtgt	0.045													4	3	---	---	---	---	
SORL1	6653	broad.mit.edu	37	11	121475640	121475640	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121475640delT	uc001pxx.2	+						SORL1_uc010rzp.1_Intron|SORL1_uc010rzq.1_Intron	NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		AAGATGTAACTTTTTTTtttt	0.169													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	123917180	123917181	+	IGR	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123917180_123917181insT								OR10G7 (7472 upstream) : VWA5A (68930 downstream)																							tgggagctaaattttttttttg	0.000													4	2	---	---	---	---	
PKNOX2	63876	broad.mit.edu	37	11	125283953	125283953	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125283953delG	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron|PKNOX2_uc001qbv.2_Intron	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		CCTCTCACCTGGGACCTCGGT	0.587													4	2	---	---	---	---	
ERC1	23085	broad.mit.edu	37	12	1421549	1421549	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1421549delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			AGTAAAGCAATTTTTTTTTTC	0.224													5	3	---	---	---	---	
KLRC2	3822	broad.mit.edu	37	12	10584769	10584770	+	Frame_Shift_Ins	INS	-	AA	AA			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10584769_10584770insAA	uc001qyk.2	-	5	526_527	c.519_520insTT	c.(517-522)ATTGGTfs	p.I173fs	KLRC3_uc001qyh.2_Intron|KLRC2_uc010she.1_Frame_Shift_Ins_p.I173fs	NM_002260	NP_002251	P26717	NKG2C_HUMAN	killer cell lectin-like receptor subfamily C,	173_174	Extracellular (Potential).|C-type lectin.				cellular defense response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0						CGAAACACACCAATCCATGAGG	0.287													136	163	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17591329	17591330	+	IGR	DEL	TT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17591329_17591330delTT								LMO3 (828571 upstream) : RERGL (642474 downstream)																							aaatgaatacttaagactgggt	0.010													4	2	---	---	---	---	
PTHLH	5744	broad.mit.edu	37	12	28119727	28119727	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28119727delA	uc001rik.2	-						PTHLH_uc001ril.2_Intron|PTHLH_uc001rim.2_Intron|PTHLH_uc001rin.2_Intron	NM_198966	NP_945317	P12272	PTHR_HUMAN	parathyroid hormone-like hormone isoform 1						activation of adenylate cyclase activity by G-protein signaling pathway|cAMP metabolic process|cell-cell signaling|epidermis development|female pregnancy|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|positive regulation of cAMP biosynthetic process|positive regulation of cell proliferation	cytoplasm|extracellular space|nucleus	hormone activity|peptide hormone receptor binding			breast(1)	1	Lung SC(9;0.184)					CTTCTCCTTTAAAAAAAAAAT	0.328													4	2	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31601796	31601796	+	Intron	DEL	C	-	-	rs67985192		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31601796delC	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						aacaaacaaaCAAAAACAAAT	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	32048833	32048833	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32048833delA								H3F3C (103658 upstream) : C12orf35 (63520 downstream)																							catgcaagacaaaaagcacac	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48428750	48428751	+	IGR	DEL	GT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48428750_48428751delGT								COL2A1 (30465 upstream) : SENP1 (8007 downstream)																							GCGTGGCTGCGTGTGTGTGTGC	0.550													4	2	---	---	---	---	
FMNL3	91010	broad.mit.edu	37	12	50092940	50092941	+	Intron	INS	-	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50092940_50092941insC	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron	NM_175736	NP_783863	Q8IVF7	FMNL3_HUMAN	formin-like 3 isoform 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4						GAGAAATGTTTCCCCAGAATGG	0.545													4	2	---	---	---	---	
FAM186A	121006	broad.mit.edu	37	12	50727335	50727335	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50727335delA	uc001rwl.2	-						FAM186A_uc010smt.1_Intron	NM_001145475	NP_001138947	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A												0						aaagcaaaacaaaaaaaaaGg	0.005													4	2	---	---	---	---	
KRT80	144501	broad.mit.edu	37	12	52574912	52574913	+	Intron	DEL	CT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52574912_52574913delCT	uc001rzx.2	-						KRT80_uc001rzw.2_Intron|KRT80_uc001rzy.2_Intron	NM_182507	NP_872313	Q6KB66	K2C80_HUMAN	keratin 80 isoform a							keratin filament	structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.108)		ATGACACATCCTCTCTCTCTCC	0.411													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	52706861	52706861	+	IGR	DEL	G	-	-	rs67759898		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52706861delG								KRT86 (3916 upstream) : KRT83 (1224 downstream)																							GAAGGCGAGAGGCTGATATGA	0.562													3	3	---	---	---	---	
KRT8	3856	broad.mit.edu	37	12	53294652	53294652	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53294652delT	uc001sbd.2	-						KRT8_uc009zmj.2_Intron|KRT8_uc009zmk.1_Intron|KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TCACCTCTGCTTCCTGCAACA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	74604797	74604797	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74604797delT	uc009zrx.1	-						uc001sxc.2_Intron					Homo sapiens cDNA clone IMAGE:3926153, partial cds.																		ATTTTGGGAATTTTTTTTTTG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	74669120	74669120	+	Intron	DEL	T	-	-	rs113849001		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74669120delT	uc009zrx.1	-						uc001sxc.2_Intron					Homo sapiens cDNA clone IMAGE:3926153, partial cds.																		TTTTTTGGGGTTTTTTTTTTT	0.303													4	4	---	---	---	---	
PLXNC1	10154	broad.mit.edu	37	12	94665604	94665604	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94665604delT	uc001tdc.2	+						PLXNC1_uc010sut.1_Intron|PLXNC1_uc009zsv.2_Intron	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						GTCAGTATTCTTTTTGGTTGG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106007541	106007541	+	IGR	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106007541delC								C12orf75 (242246 upstream) : NUAK1 (449584 downstream)																							atcccttctgccccagggccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108265382	108265382	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108265382delT								ASCL4 (94962 upstream) : WSCD2 (258129 downstream)																							GAATGATCTCTTTTTTTTTCT	0.184													4	2	---	---	---	---	
ATXN2	6311	broad.mit.edu	37	12	111951477	111951477	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111951477delA	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsm.1_Intron	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2						TTAAAAATAGAAAAAAAAAAA	0.199													7	4	---	---	---	---	
CIT	11113	broad.mit.edu	37	12	120141850	120141850	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120141850delT	uc001txi.1	-						CIT_uc001txh.1_Intron|CIT_uc001txj.1_Intron	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		GAGCCCCCCCTTTTTTTTTTC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	121521864	121521864	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121521864delG								OASL (45084 upstream) : P2RX7 (48814 downstream)																							acatgggcaaggggtttctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128638049	128638049	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128638049delG								None (None upstream) : TMEM132C (261242 downstream)																							TTAGGAGCCTGGGAAGATGGG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23017967	23017967	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23017967delT								FGF9 (739327 upstream) : SGCG (737093 downstream)																							tttttgtttatttttgtggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51903030	51903030	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51903030delT								FAM124A (47414 upstream) : SERPINE3 (12138 downstream)																							TAAGTCTTTATTTTTTCTTAT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	69560508	69560509	+	IGR	INS	-	ATA	ATA	rs138891114	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69560508_69560509insATA								None (None upstream) : KLHL1 (714217 downstream)																							TATGAGATGCTATAATGAGCTA	0.307													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	70127095	70127096	+	IGR	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70127095_70127096insA								None (None upstream) : KLHL1 (147630 downstream)																							ACCATatttacaaaaaaaaatc	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73723992	73723992	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73723992delT								KLF5 (72317 upstream) : KLF12 (536158 downstream)																							AGCCCCTGTGTTTTTTTCTGG	0.274													4	2	---	---	---	---	
RBM26	64062	broad.mit.edu	37	13	79954631	79954632	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79954631_79954632insA	uc001vkz.2	-						RBM26_uc001vky.2_Intron|RBM26_uc001vla.2_Intron|RBM26_uc001vlc.1_Intron	NM_022118	NP_071401	Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26						mRNA processing		nucleotide binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		GGAAAGTTTTTAAAAAAAAAAA	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	93720581	93720581	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93720581delA								GPC5 (201096 upstream) : GPC6 (158497 downstream)																							GCCACTCTATAAAAGAAGTAA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	48565936	48565937	+	IGR	DEL	CT	-	-	rs146169026		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48565936_48565937delCT								MDGA2 (421948 upstream) : None (None downstream)																							tttcagttcactgtgatagatc	0.000													2	4	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50122177	50122178	+	Intron	DEL	AC	-	-	rs139602604		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50122177_50122178delAC	uc010anj.1	-						POLE2_uc010ann.2_Intron|POLE2_uc001wwu.2_Intron|POLE2_uc001wwv.2_Intron|POLE2_uc010ano.2_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		ATGACTATAAacacacacacac	0.089													7	4	---	---	---	---	
GNG2	54331	broad.mit.edu	37	14	52321667	52321667	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52321667delC	uc001wzh.2	+									P59768	GBG2_HUMAN	Homo sapiens guanine nucleotide binding protein gamma 2 (GNG2) mRNA, complete cds.						cellular response to glucagon stimulus|energy reserve metabolic process|platelet activation|synaptic transmission	heterotrimeric G-protein complex	protein binding|signal transducer activity				0	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)	CCTCCTCCAGCCGCCTTCTTC	0.517													4	2	---	---	---	---	
C14orf101	54916	broad.mit.edu	37	14	57082524	57082524	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57082524delA	uc001xcm.2	+						C14orf101_uc001xcj.2_Intron|C14orf101_uc010aot.1_Intron|C14orf101_uc001xcl.1_Intron|C14orf101_uc001xcn.2_Intron|C14orf101_uc010trf.1_Intron|C14orf101_uc001xco.2_5'UTR	NM_017799	NP_060269	Q9NX78	CN101_HUMAN	hypothetical protein LOC54916							integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)		TTCCAACTTTAAAAGACAAAA	0.294													35	16	---	---	---	---	
TTC9	23508	broad.mit.edu	37	14	71133571	71133573	+	Intron	DEL	TGA	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71133571_71133573delTGA	uc001xmi.2	+							NM_015351	NP_056166	Q92623	TTC9A_HUMAN	tetratricopeptide repeat domain 9								binding				0				all cancers(60;0.00545)|BRCA - Breast invasive adenocarcinoma(234;0.00747)|OV - Ovarian serous cystadenocarcinoma(108;0.0538)		gCCatgatggtgatgatgatgat	0.049													4	2	---	---	---	---	
LIN52	91750	broad.mit.edu	37	14	74636142	74636142	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74636142delC	uc001xpp.2	+						LIN52_uc010asb.2_Intron	NM_001024674	NP_001019845	Q52LA3	LIN52_HUMAN	lin-52 homolog											breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00471)		AGCCTTATTTCCATGTTTTTT	0.403													4	2	---	---	---	---	
C14orf143	90141	broad.mit.edu	37	14	90301551	90301552	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90301551_90301552insA	uc001xxt.2	-						C14orf143_uc001xxs.2_Intron|uc001xxu.2_Intron	NM_145231	NP_660274	Q9BUY7	EFC11_HUMAN	hypothetical protein LOC90141								calcium ion binding				0		all_cancers(154;0.136)		Epithelial(152;0.194)		gagaacacagcaggatgcccgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98112942	98112942	+	Intron	DEL	T	-	-	rs143182166		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98112942delT	uc001yfv.1	-											human full-length cDNA clone CS0DI087YB20 of Placenta of Homo sapiens (human).																		TTTTTTGTAGTTTTTTTTTAA	0.299													4	2	---	---	---	---	
HSP90AA1	3320	broad.mit.edu	37	14	102548966	102548966	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102548966delT	uc001yku.3	-						HSP90AA1_uc001ykv.3_Intron	NM_005348	NP_005339	P07900	HS90A_HUMAN	heat shock 90kDa protein 1, alpha isoform 2						axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction	cytosol|melanosome|plasma membrane	ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding			ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1)	7					Rifabutin(DB00615)	ACATGCACAAttttttttttg	0.154													4	2	---	---	---	---	
PPP1R13B	23368	broad.mit.edu	37	14	104216536	104216537	+	Intron	INS	-	G	G	rs145564336	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104216536_104216537insG	uc001yof.1	-						PPP1R13B_uc001yog.1_Intron	NM_015316	NP_056131	Q96KQ4	ASPP1_HUMAN	apoptosis-stimulating protein of p53, 1						apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				TACAGGAGACTAGTGCGGTGTT	0.490													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22470594	22470595	+	IGR	INS	-	AA	AA	rs77118326		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22470594_22470595insAA								OR4N3P (56209 upstream) : MIR1268 (42634 downstream)																							tcaagttgctgaaaaaaaaagc	0.005													4	2	---	---	---	---	
GOLGA9P	283796	broad.mit.edu	37	15	23258265	23258268	+	Intron	DEL	TCTC	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23258265_23258268delTCTC	uc001yvh.1	+						uc001yvi.2_5'Flank	NR_024074				RecName: Full=Putative golgin subfamily A member 6-like protein 11;												0						TAATGATTGTTCTCTCTACCTCTC	0.603													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26577381	26577382	+	IGR	INS	-	T	T	rs141404412	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26577381_26577382insT								ATP10A (467064 upstream) : GABRB3 (211313 downstream)																							TAATGTAACTATTTTTTTTAAT	0.376													2	4	---	---	---	---	
SCG5	6447	broad.mit.edu	37	15	32945498	32945498	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32945498delT	uc001zha.2	+						SCG5_uc001zgz.2_Intron	NM_001144757	NP_001138229	P05408	7B2_HUMAN	secretogranin V isoform 1						intracellular protein transport|neuropeptide signaling pathway|peptide hormone processing|regulation of hormone secretion	extracellular region|stored secretory granule	enzyme inhibitor activity|GTP binding|unfolded protein binding				0		all_lung(180;7.32e-08)		all cancers(64;6.48e-17)|Epithelial(43;1.23e-11)|GBM - Glioblastoma multiforme(186;1.39e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0212)		TGTGACTATCTTAGAATGTCA	0.358													4	2	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33677493	33677493	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33677493delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTAATAGTACTTTTTTTTTCC	0.358													4	2	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	34046969	34046970	+	Intron	INS	-	G	G	rs138029527	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34046969_34046970insG	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ATTTTGTTTTTTCTGTTTACAG	0.272													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	41438795	41438795	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41438795delA								INO80 (30455 upstream) : EXD1 (36138 downstream)																							actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
MAPKBP1	23005	broad.mit.edu	37	15	42073937	42073937	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42073937delT	uc001zok.3	+						MAPKBP1_uc001zoj.3_Intron|MAPKBP1_uc010bcj.2_Intron|MAPKBP1_uc010bci.2_Intron|MAPKBP1_uc010udb.1_Intron|MAPKBP1_uc010bck.2_Intron	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein											central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		ATATGGCTGATTTTTTTTTTT	0.308													3	3	---	---	---	---	
CAPN3	825	broad.mit.edu	37	15	42696238	42696239	+	Intron	INS	-	AGAG	AGAG	rs139850425	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42696238_42696239insAGAG	uc001zpn.1	+						CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Intron|CAPN3_uc001zpp.1_Intron|CAPN3_uc001zpq.1_Intron|CAPN3_uc010bcv.1_5'Flank|CAPN3_uc001zpr.1_5'Flank|CAPN3_uc001zps.1_5'Flank|CAPN3_uc001zpt.1_5'Flank	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a						muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		TTTGAACAATCGGAGGGAACAA	0.495													2	6	---	---	---	---	
ANXA2	302	broad.mit.edu	37	15	60653462	60653463	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60653462_60653463insA	uc002agn.2	-						ANXA2_uc002agk.2_Intron|ANXA2_uc002agl.2_Intron|ANXA2_uc002agm.2_Intron|ANXA2_uc010uhd.1_Intron|ANXA2_uc010bgj.2_Intron	NM_001136015	NP_001129487	P07355	ANXA2_HUMAN	annexin A2 isoform 2						angiogenesis|positive regulation of vesicle fusion|skeletal system development	basement membrane|melanosome|midbody|soluble fraction	calcium ion binding|calcium-dependent phospholipid binding|cytoskeletal protein binding|phospholipase inhibitor activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Tenecteplase(DB00031)	CGAAATTCCTTAAAATCCAAGT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	64189349	64189350	+	IGR	DEL	CA	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64189349_64189350delCA								MIR422A (26131 upstream) : DAPK2 (9886 downstream)																							cactcagatgcacacacacaca	0.347											OREG0031369	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	5	3	---	---	---	---	
IGDCC3	9543	broad.mit.edu	37	15	65647666	65647666	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65647666delC	uc002aos.2	-							NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule											ovary(3)	3						AGACTCCCATCCCCCCCGCTC	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	67489422	67489423	+	IGR	INS	-	TCCTTC	TCCTTC	rs140896383	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67489422_67489423insTCCTTC								SMAD3 (1890 upstream) : AAGAB (3946 downstream)																							tcttaaaaccatcctctggcct	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79774645	79774645	+	IGR	DEL	T	-	-	rs67595543		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79774645delT								KIAA1024 (10003 upstream) : MTHFS (362675 downstream)																							cttcagcacattttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84099866	84099866	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84099866delT								BNC1 (146398 upstream) : SH3GL3 (16225 downstream)																							tagttatcactttttttttga	0.000													4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	86975303	86975303	+	Intron	DEL	T	-	-	rs10718551		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86975303delT	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						CAGGATCAGGTTTTTAACTCT	0.517													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8438639	8438639	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8438639delA								A2BP1 (675299 upstream) : TMEM114 (180864 downstream)																							ctggagatttaaaaaaaaaaa	0.000													6	4	---	---	---	---	
PMM2	5373	broad.mit.edu	37	16	8945617	8945618	+	Intron	DEL	AT	-	-	rs146051165		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8945617_8945618delAT	uc002czg.1	+									O15305	PMM2_HUMAN	full-length cDNA clone CS0DJ003YA02 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).						dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	cytosol	phosphomannomutase activity			ovary(1)	1						CAGCGACCCCATAGAGTGGCCC	0.480													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12473688	12473688	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12473688delG	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						CCCGGTGAGTGGGGCCTGCCC	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17670482	17670482	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17670482delT								XYLT1 (105744 upstream) : NOMO2 (840701 downstream)																							ATCCTTTTTATTTTTTTGATC	0.363													4	2	---	---	---	---	
ACSM3	6296	broad.mit.edu	37	16	20781853	20781853	+	Intron	DEL	A	-	-	rs67292475		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20781853delA	uc002dhr.2	+						ACSM3_uc002dhq.2_Intron|ACSM3_uc010vba.1_Intron	NM_005622	NP_005613	Q53FZ2	ACSM3_HUMAN	SA hypertension-associated homolog isoform 1						regulation of blood pressure	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			ovary(1)	1						AGGTTGACTTAAAAAAAAAAA	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21515163	21515164	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21515163_21515164insA	uc002diq.3	+						LOC100271836_uc002dja.2_Intron|LOC100271836_uc002djb.2_Intron					Homo sapiens cDNA FLJ59829 complete cds.																		CTTGTGCAATTAAAAATTGTTA	0.401													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	22353493	22353493	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22353493delA								POLR3E (8152 upstream) : CDR2 (3766 downstream)																							aaaccttaagaaaaaaaaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33536120	33536122	+	IGR	DEL	AAT	-	-	rs72535057		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33536120_33536122delAAT								SLC6A10P (639657 upstream) : MIR1826 (429386 downstream)																							CCATTAAAAAAATGCCCATTTCC	0.261													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46425523	46425523	+	IGR	DEL	A	-	-	rs71223647		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46425523delA								None (None upstream) : ANKRD26P1 (77726 downstream)																							tggaatcatcaaatggactcg	0.000													4	2	---	---	---	---	
NETO2	81831	broad.mit.edu	37	16	47166212	47166212	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47166212delA	uc002eer.1	-						NETO2_uc002ees.1_Intron	NM_018092	NP_060562	Q8NC67	NETO2_HUMAN	neuropilin- and tolloid-like protein 2							integral to membrane	receptor activity				0		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				AGTTTTGTTTAAAAAAAAAAA	0.303										HNSCC(25;0.065)			6	3	---	---	---	---	
NKD1	85407	broad.mit.edu	37	16	50648249	50648249	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50648249delT	uc002egg.1	+							NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1						Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		attctggagctaaaaccatgt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54258261	54258261	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54258261delG								FTO (109883 upstream) : IRX3 (58951 downstream)																							cactgatgatggggagaggaa	0.114													4	2	---	---	---	---	
SLC12A3	6559	broad.mit.edu	37	16	56921123	56921123	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56921123delT	uc010ccm.2	+						SLC12A3_uc002ekd.3_Intron|SLC12A3_uc010ccn.2_Intron	NM_001126108	NP_001119580	P55017	S12A3_HUMAN	solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	GAGCCCCAACttttttttttt	0.289													8	4	---	---	---	---	
CIAPIN1	57019	broad.mit.edu	37	16	57464912	57464912	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57464912delT	uc002ell.1	-						CIAPIN1_uc002elk.1_Intron|CIAPIN1_uc002elm.1_Intron|CIAPIN1_uc002eln.1_Intron|CIAPIN1_uc010cda.1_Intron|CIAPIN1_uc002elo.1_Intron	NM_020313	NP_064709	Q6FI81	CPIN1_HUMAN	cytokine induced apoptosis inhibitor 1						anti-apoptosis|apoptosis	cytoplasm|nucleolus					0						gcctggctaattttttttttt	0.085													11	5	---	---	---	---	
CCDC135	84229	broad.mit.edu	37	16	57748532	57748533	+	Intron	DEL	TC	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57748532_57748533delTC	uc002emi.2	+						CCDC135_uc002emj.2_Intron|CCDC135_uc002emk.2_Intron	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135							cytoplasm				central_nervous_system(1)	1						agagagaGAGTCTCTCTCTCTC	0.218													5	3	---	---	---	---	
PLA2G15	23659	broad.mit.edu	37	16	68283590	68283590	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68283590delT	uc002evr.2	+						PLA2G15_uc010vld.1_Intron|PLA2G15_uc010vle.1_Intron|PLA2G15_uc010vlf.1_Intron	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)						fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1						CTACACACAAttttttttttc	0.269													3	4	---	---	---	---	
SLC7A6	9057	broad.mit.edu	37	16	68324111	68324111	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68324111delT	uc002evt.1	+						SLC7A6_uc010cfb.1_Intron|SLC7A6_uc002evu.1_Intron|SLC7A6_uc002evv.1_Intron|SLC7A6_uc010cfc.1_Intron	NM_001076785	NP_001070253	Q92536	YLAT2_HUMAN	solute carrier family 7 (cationic amino acid						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity|antiporter activity			central_nervous_system(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.0948)		TTAAATTATGtttttttttct	0.204													10	5	---	---	---	---	
GLG1	2734	broad.mit.edu	37	16	74486706	74486706	+	3'UTR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74486706delT	uc002fcy.3	-	26					GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_3'UTR	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						tttaaaaaaattttttttttt	0.363													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	79031782	79031782	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79031782delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		ACAttctttctttttttttta	0.214													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	83081580	83081580	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83081580delA	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CAGACTCCtcaaaaaaacatt	0.060													4	2	---	---	---	---	
KIAA0182	23199	broad.mit.edu	37	16	85701506	85701507	+	Intron	INS	-	GTCCA	GTCCA	rs148610400	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85701506_85701507insGTCCA	uc002fix.2	+						KIAA0182_uc002fiw.2_Intron|KIAA0182_uc002fiy.2_Intron|KIAA0182_uc002fiz.2_Intron|KIAA0182_uc010cho.2_Intron	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1								protein binding			large_intestine(3)|ovary(1)|skin(1)	5						CAACAAAAATGGTCCACGTACC	0.436													6	3	---	---	---	---	
GINS2	51659	broad.mit.edu	37	16	85721333	85721343	+	Intron	DEL	AGCGCCTCCTG	-	-	rs77861532		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85721333_85721343delAGCGCCTCCTG	uc002fja.2	-						GINS2_uc002fjb.2_Intron	NM_016095	NP_057179	Q9Y248	PSF2_HUMAN	DNA replication complex GINS protein PSF2						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	nucleoplasm	protein binding				0						CTCAGAACAAAGCGCCTCCTGAGCGGCTCCG	0.550													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86139826	86139826	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86139826delT								IRF8 (183617 upstream) : LOC732275 (225630 downstream)																							tctatctccattgcctggcac	0.159													4	2	---	---	---	---	
ZCCHC14	23174	broad.mit.edu	37	16	87505641	87505641	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87505641delA	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		ACCCTCCACTAAAAAAAACAA	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21253429	21253430	+	IGR	DEL	AT	-	-	rs148176633		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21253429_21253430delAT								MAP2K3 (34880 upstream) : KCNJ12 (26269 downstream)																							acgcggacacatgtgcacacat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21347043	21347044	+	IGR	DEL	AG	-	-	rs111380221		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21347043_21347044delAG								KCNJ12 (23864 upstream) : C17orf51 (84528 downstream)																							aagcacaggcagagttaattta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21519738	21519739	+	IGR	INS	-	T	T	rs144084040	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21519738_21519739insT								C17orf51 (42007 upstream) : FAM27L (305631 downstream)																							tcttgttgccactgttccctag	0.124													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25279602	25279603	+	IGR	INS	-	A	A	rs141912767		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25279602_25279603insA								None (None upstream) : WSB1 (341503 downstream)																							gaggatgggagaaaaaggaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35010795	35010796	+	IGR	DEL	AT	-	-	rs150886537		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35010795_35010796delAT								MRM1 (45389 upstream) : LHX1 (283703 downstream)																							CGGCACACACATGTGACAAACG	0.510													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35436212	35436212	+	IGR	DEL	T	-	-	rs36087491		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35436212delT								AATF (22042 upstream) : ACACA (5716 downstream)																							tttgacagcatttttttttct	0.000													5	3	---	---	---	---	
DDX52	11056	broad.mit.edu	37	17	36003614	36003614	+	5'Flank	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36003614delT	uc002hoi.1	-						DDX52_uc002hoh.1_5'Flank|DDX52_uc002hoj.1_5'Flank	NM_007010	NP_008941	Q9Y2R4	DDX52_HUMAN	ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)				ATTAtttatcttttttttttt	0.244													4	2	---	---	---	---	
HNF1B	6928	broad.mit.edu	37	17	36059424	36059425	+	Intron	INS	-	G	G	rs151038441	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36059424_36059425insG	uc002hok.3	-						HNF1B_uc010wdi.1_Intron	NM_000458	NP_000449	P35680	HNF1B_HUMAN	hepatocyte nuclear factor 1-beta isoform 1						endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			GGGAGAGACCACCTGCTCTCAG	0.530									Hereditary_Prostate_Cancer				6	6	---	---	---	---	
THRA	7067	broad.mit.edu	37	17	38215941	38215941	+	5'Flank	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38215941delG	uc010cwp.1	+							NM_199334	NP_955366	P10827	THA_HUMAN	thyroid hormone receptor, alpha isoform 1						negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|negative regulation of transcription initiation, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter	cytosol|nucleoplasm	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|TBP-class protein binding|thyroid hormone binding|thyroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding				0	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Levothyroxine(DB00451)|Liothyronine(DB00279)	GGCTGGTAGAGGGGCCTATCT	0.502													4	2	---	---	---	---	
GRN	2896	broad.mit.edu	37	17	42421694	42421694	+	5'Flank	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42421694delA	uc002igp.1	+							NM_002087	NP_002078	P28799	GRN_HUMAN	granulin precursor						signal transduction	extracellular space	cytokine activity|growth factor activity			ovary(2)|central_nervous_system(2)|skin(1)	5		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CACCTTGAGGAAAGGGCTTTG	0.483													4	2	---	---	---	---	
LRRC37A	9884	broad.mit.edu	37	17	44383558	44383559	+	Intron	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44383558_44383559insT	uc002ikg.2	+						ARL17A_uc002iki.3_Intron|ARL17A_uc002ikh.3_Intron|ARL17B_uc002ikf.2_Intron	NM_014834	NP_055649	A6NMS7	L37A1_HUMAN	leucine rich repeat containing 37A precursor							integral to membrane					0		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		TTCTGAAATAATTTTTTTTTTC	0.337													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	52742538	52742538	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52742538delA								KIF2B (839965 upstream) : TOM1L1 (235514 downstream)																							AGATGTTGCCAAAAAAAAAGC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	52828430	52828430	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52828430delA								KIF2B (925857 upstream) : TOM1L1 (149622 downstream)																							agacaacaccaaaaaaaaatg	0.005													4	2	---	---	---	---	
AKAP1	8165	broad.mit.edu	37	17	55197932	55197932	+	3'UTR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55197932delA	uc002iux.2	+	11					AKAP1_uc010wnl.1_3'UTR|AKAP1_uc010dcm.2_3'UTR	NM_003488	NP_003479	Q92667	AKAP1_HUMAN	A-kinase anchor protein 1 precursor						blood coagulation	cytosol|integral to membrane|mitochondrial outer membrane	protein binding|RNA binding			ovary(1)	1	Breast(9;5.46e-08)					TCAGCTGTTTAAAAAAAAAAA	0.413													6	3	---	---	---	---	
USP32	84669	broad.mit.edu	37	17	58371745	58371746	+	Intron	DEL	GT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58371745_58371746delGT	uc002iyo.1	-						USP32_uc010wov.1_Intron	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			TCCTGCAGGAgtgtgtgtgtgt	0.317													4	2	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	63856840	63856840	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63856840delA	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			tatcttacacaatggacaaaa	0.000													4	2	---	---	---	---	
BPTF	2186	broad.mit.edu	37	17	65882603	65882603	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65882603delT	uc002jgf.2	+						BPTF_uc002jge.2_Intron|BPTF_uc010wqm.1_Intron	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTATTTTTCATTTTTTTTTTA	0.239													6	3	---	---	---	---	
FBF1	85302	broad.mit.edu	37	17	73918403	73918403	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73918403delA	uc002jqc.2	-						FBF1_uc002jqa.1_Intron|FBF1_uc010wsp.1_Intron|FBF1_uc002jqd.1_Intron|FBF1_uc002jqb.2_5'Flank|FBF1_uc010dgr.1_5'Flank	NM_001080542	NP_001074011	Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1												0						TAGACACTGGAGTCAAGTTCA	0.498													4	2	---	---	---	---	
LGALS3BP	3959	broad.mit.edu	37	17	76971358	76971358	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76971358delT	uc002jwh.2	-						LGALS3BP_uc002jwi.2_Intron|LGALS3BP_uc010dhr.2_Intron	NM_005567	NP_005558	Q08380	LG3BP_HUMAN	galectin 3 binding protein						cell adhesion|cellular defense response	extracellular space|membrane|proteinaceous extracellular matrix	protein binding|scavenger receptor activity			central_nervous_system(3)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			GGATTGTTTCTTTTTTTTCCA	0.393													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77282225	77282226	+	Intron	INS	-	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77282225_77282226insC	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			AATGTCCCTGGCCTGCCTCTCC	0.540													4	2	---	---	---	---	
RAB40B	10966	broad.mit.edu	37	17	80619212	80619212	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80619212delA	uc002kft.2	-						RAB40B_uc002kfs.2_Intron	NM_006822	NP_006813	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			central_nervous_system(1)	1	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			TGTAGGCTTTAAAAAACTTGT	0.388													4	2	---	---	---	---	
RAB40B	10966	broad.mit.edu	37	17	80629147	80629148	+	Intron	INS	-	CA	CA	rs150104931	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80629147_80629148insCA	uc002kft.2	-						RAB40B_uc002kfs.2_Intron	NM_006822	NP_006813	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			central_nervous_system(1)	1	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			ACACACACAGTCACACATCCTG	0.515													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	94412	94412	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:94412delT								None (None upstream) : USP14 (64071 downstream)																							CTAtcttttcttttttttttt	0.139													11	6	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4197786	4197787	+	Intron	INS	-	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4197786_4197787insC	uc010wyz.1	-						uc002kmm.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				gtcagctaaaaccccgtgaatg	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5789191	5789191	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5789191delG	uc002kmw.2	+											Homo sapiens chromosome 18 unknown mRNA sequence.																		tctctggaatgggggtattag	0.000													4	2	---	---	---	---	
CHST9	83539	broad.mit.edu	37	18	24718465	24718466	+	Intron	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24718465_24718466insT	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)					CTAAGCCTTCATTTTTTTTTTA	0.396													4	2	---	---	---	---	
KIAA1012	22878	broad.mit.edu	37	18	29493091	29493091	+	Intron	DEL	A	-	-	rs79506184		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29493091delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron|KIAA1012_uc002kxe.2_Intron	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN	hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0						actctgtctcaaaaaaaaaaa	0.144													10	5	---	---	---	---	
C18orf34	374864	broad.mit.edu	37	18	30802728	30802729	+	Intron	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30802728_30802729insT	uc002kxn.2	-						C18orf34_uc010dme.1_Intron|C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1											ovary(1)	1						cttcttcttcatttttttttGG	0.168													4	2	---	---	---	---	
ZNF397OS	100101467	broad.mit.edu	37	18	32860347	32860348	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32860347_32860348insA	uc002kym.2	-						ZNF397OS_uc010xce.1_Intron|ZNF397OS_uc002kyn.1_Intron	NM_001112734	NP_001106205	Q86W11	ZSC30_HUMAN	zinc finger protein 397 opposite strand						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						AACACTTACTGAAAAAAAAGAA	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	55500077	55500077	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55500077delT								ATP8B1 (101038 upstream) : NEDD4L (211542 downstream)																							TGTCAGCATCTTTTTGGTGCA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	61996764	61996764	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61996764delT	uc002ljx.2	+											Homo sapiens hypothetical protein LOC284294, mRNA (cDNA clone IMAGE:4823205).																		GAGGGCTGACTTTTTCTTGTT	0.453													4	2	---	---	---	---	
ZNF516	9658	broad.mit.edu	37	18	74150365	74150365	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74150365delT	uc010dqx.1	-						ZNF516_uc002lme.2_Intron	NM_014643	NP_055458	Q92618	ZN516_HUMAN	zinc finger protein 516						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		TTAGATGCCCTTTCACCCCTC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76206808	76206809	+	IGR	INS	-	CA	CA	rs144261977	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76206808_76206809insCA								None (None upstream) : SALL3 (533466 downstream)																							GGACAGTGATTCACACACACAC	0.381													6	4	---	---	---	---	
ATP8B3	148229	broad.mit.edu	37	19	1805076	1805076	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1805076delG	uc002ltw.2	-						ATP8B3_uc002ltv.2_Intron|ATP8B3_uc002ltx.2_Intron|ATP8B3_uc002lty.1_Intron|ATP8B3_uc002ltz.1_Intron	NM_138813	NP_620168	O60423	AT8B3_HUMAN	ATPase, class I, type 8B, member 3						ATP biosynthetic process		ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ctgagctcaagcgagcctccc	0.005													6	4	---	---	---	---	
ATP8B3	148229	broad.mit.edu	37	19	1805078	1805079	+	Intron	DEL	GA	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1805078_1805079delGA	uc002ltw.2	-						ATP8B3_uc002ltv.2_Intron|ATP8B3_uc002ltx.2_Intron|ATP8B3_uc002lty.1_Intron|ATP8B3_uc002ltz.1_Intron	NM_138813	NP_620168	O60423	AT8B3_HUMAN	ATPase, class I, type 8B, member 3						ATP biosynthetic process		ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gagctcaagcgagcctcccacc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	8412649	8412649	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8412649delA								KANK3 (4503 upstream) : ANGPTL4 (16362 downstream)																							caacaacaacaaaaaacccca	0.075													4	2	---	---	---	---	
MYO1F	4542	broad.mit.edu	37	19	8586699	8586699	+	Intron	DEL	T	-	-	rs35658338		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8586699delT	uc002mkg.2	-							NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF							unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3						tctttaaaagttttttttttg	0.000													4	2	---	---	---	---	
OLFM2	93145	broad.mit.edu	37	19	10046218	10046219	+	Intron	DEL	CA	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10046218_10046219delCA	uc002mmp.2	-							NM_058164	NP_477512	O95897	NOE2_HUMAN	olfactomedin 2 precursor							extracellular region				large_intestine(1)|skin(1)	2						ACAGCGCTTGCACACACACACA	0.520													4	2	---	---	---	---	
CYP4F2	8529	broad.mit.edu	37	19	16006678	16006681	+	Intron	DEL	TCTG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16006678_16006681delTCTG	uc002nbs.1	-						CYP4F2_uc010xot.1_Intron|CYP4F2_uc010xou.1_Intron	NM_001082	NP_001073	P78329	CP4F2_HUMAN	cytochrome P450, family 4, subfamily F,						leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2						catatattcatctgtctgtctgct	0.039													3	3	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17800569	17800571	+	5'Flank	DEL	TTT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17800569_17800571delTTT	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						cCAGTTGTAAttttttttttttt	0.015													4	2	---	---	---	---	
ANKRD27	84079	broad.mit.edu	37	19	33140329	33140330	+	Intron	INS	-	G	G	rs35138364		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33140329_33140330insG	uc002ntn.1	-						ANKRD27_uc002nto.1_Intron	NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)						early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)					CACACGGCAGAAACCCCATCAC	0.564													5	3	---	---	---	---	
ANKRD27	84079	broad.mit.edu	37	19	33140330	33140331	+	Intron	INS	-	G	G	rs3815699		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33140330_33140331insG	uc002ntn.1	-						ANKRD27_uc002nto.1_Intron	NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)						early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)					ACACGGCAGAAACCCCATCACG	0.559													5	3	---	---	---	---	
SPTBN4	57731	broad.mit.edu	37	19	41071881	41071883	+	Intron	DEL	ATG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41071881_41071883delATG	uc002ony.2	+						SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGAAGGAGGAATGGGAGTCAGAA	0.557													17	8	---	---	---	---	
CEACAM3	1084	broad.mit.edu	37	19	42310043	42310044	+	Intron	INS	-	TG	TG	rs12973252		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42310043_42310044insTG	uc002orn.1	+						CEACAM3_uc010eia.1_Intron|CEACAM3_uc002oro.1_Intron	NM_001815	NP_001806	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion							integral to membrane				skin(1)	1						CTTCCtgttgtttgttgttgtt	0.243													4	3	---	---	---	---	
CEACAM3	1084	broad.mit.edu	37	19	42310046	42310047	+	Intron	INS	-	T	T	rs76630039		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42310046_42310047insT	uc002orn.1	+						CEACAM3_uc010eia.1_Intron|CEACAM3_uc002oro.1_Intron	NM_001815	NP_001806	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion							integral to membrane				skin(1)	1						CCtgttgtttgttgttgttgtt	0.238													4	3	---	---	---	---	
MEGF8	1954	broad.mit.edu	37	19	42840629	42840629	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42840629delT	uc002otl.3	+						MEGF8_uc002otm.3_5'Flank	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8							integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)				ccttcatgtatttacttattc	0.318													4	2	---	---	---	---	
SAE1	10055	broad.mit.edu	37	19	47658718	47658718	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47658718delT	uc002pgc.2	+						SAE1_uc002pgd.2_Intron|SAE1_uc010ekx.2_Intron|SAE1_uc010ekw.2_Intron|SAE1_uc010xyk.1_Intron|SAE1_uc002pge.2_Intron	NM_016402	NP_057486	Q9UBE0	SAE1_HUMAN	SubName: Full=SUMO-1 activating enzyme subunit 1, isoform CRA_b; SubName: Full=cDNA, FLJ96708, Homo sapiens SUMO-1 activating enzyme subunit 1 (SAE1), mRNA;						protein sumoylation|protein ubiquitination	nucleus	ATP-dependent protein binding|enzyme activator activity|ligase activity|protein C-terminus binding|protein heterodimerization activity|ubiquitin activating enzyme activity			ovary(1)	1		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		TGTCCCAAACttttttttttg	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	47747784	47747785	+	IGR	DEL	AT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47747784_47747785delAT								BBC3 (11761 upstream) : CCDC9 (11946 downstream)																							TGGACTATACATATATATAttt	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	49831701	49831701	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49831701delG								SLC6A16 (3227 upstream) : CD37 (6727 downstream)																							gattttgggtggggacacagc	0.000													4	2	---	---	---	---	
TEAD2	8463	broad.mit.edu	37	19	49866193	49866193	+	5'Flank	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49866193delT	uc002pnj.2	-						TEAD2_uc002png.2_5'Flank|TEAD2_uc002pnh.2_5'Flank|TEAD2_uc002pni.2_5'Flank|TEAD2_uc010yao.1_5'Flank|TEAD2_uc010emw.2_5'Flank|DKKL1_uc002pnk.2_5'Flank	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		gttttttttgttttttttttt	0.318													4	2	---	---	---	---	
MYH14	79784	broad.mit.edu	37	19	50752588	50752590	+	Intron	DEL	CTT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50752588_50752590delCTT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		tctctgtccccttctctctctgg	0.010													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57519399	57519399	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57519399delA								MIMT1 (159477 upstream) : USP29 (112110 downstream)																							AAAGAAAAAGAAAATGGCTCC	0.239													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15443976	15443976	+	Intron	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15443976delG	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				agtaatgggtgggaagagcca	0.134													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	16029955	16029956	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16029955_16029956insA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron|MACROD2_uc002wpd.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TTTAAAAATCTAAAAAAAATAA	0.168													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17426005	17426007	+	Intron	DEL	CTT	-	-	rs149842495		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17426005_17426007delCTT	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TACATCCCAACTTCTTCTTAATC	0.438													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19187731	19187732	+	IGR	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19187731_19187732insT								C20orf79 (392698 upstream) : SLC24A3 (5558 downstream)																							AGTGTAGCTTCTTTTTTTTTCC	0.312													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19804033	19804033	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19804033delT								SLC24A3 (100493 upstream) : RIN2 (66177 downstream)																							CTCTGCCTGCTTTTTTTTTTT	0.388													7	8	---	---	---	---	
NINL	22981	broad.mit.edu	37	20	25485856	25485856	+	Intron	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25485856delC	uc002wux.1	-						NINL_uc010gdn.1_Intron|NINL_uc010gdo.1_Intron|NINL_uc010ztf.1_Intron	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like						G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						ttagcagacacagaaagacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29607943	29607944	+	IGR	INS	-	T	T	rs74659149		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29607943_29607944insT								None (None upstream) : FRG1B (3935 downstream)																							aaaggacatgattttgttattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36502854	36502861	+	IGR	DEL	TTAATGAA	-	-	rs111658391		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36502854_36502861delTTAATGAA								CTNNBL1 (2335 upstream) : VSTM2L (28638 downstream)																							GTTGTGTGGTTTAATGAATTCACAAAAA	0.361													4	2	---	---	---	---	
CHD6	84181	broad.mit.edu	37	20	40083599	40083599	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40083599delT	uc002xka.1	-						CHD6_uc002xkd.2_Intron	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				GAAGGGATCATTTTTTTTTGG	0.358													5	3	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51774760	51774761	+	Intron	DEL	GT	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51774760_51774761delGT	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			gaaggcaaaagtggaagaggcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52230503	52230503	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52230503delT								ZNF217 (19702 upstream) : SUMO1P1 (260539 downstream)																							AGCAATTAAATTTTTTTTCCT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54602273	54602273	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54602273delT								CBLN4 (22261 upstream) : MC3R (221515 downstream)																							tatttagtgctttttctctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56031577	56031578	+	IGR	INS	-	TTTTG	TTTTG	rs138213018	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56031577_56031578insTTTTG								RBM38 (47193 upstream) : CTCFL (32302 downstream)																							acttgactcctttttgttttgt	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59546614	59546614	+	IGR	DEL	G	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59546614delG								MIR646 (662989 upstream) : CDH4 (280945 downstream)																							gaacagaggagagaacagaaa	0.000													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60408924	60408925	+	Intron	INS	-	C	C			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60408924_60408925insC	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)			TAAAACCATTTCCCAAAGTGAA	0.371													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11059001	11059003	+	Intron	DEL	AAG	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11059001_11059003delAAG	uc002yit.1	-						BAGE_uc002yiw.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)		GTGAACACATAAGAAGTCAGAAG	0.384													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11061508	11061510	+	Intron	DEL	CAC	-	-	rs60979732		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11061508_11061510delCAC	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)		ATCTATAAAACACAACAGAATGA	0.236													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11066883	11066884	+	Intron	INS	-	AA	AA	rs147216020		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11066883_11066884insAA	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTAGAATCCATAATACTCTCAG	0.094													5	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11100123	11100123	+	5'Flank	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11100123delA	uc002yit.1	-						BAGE_uc002yix.2_5'Flank	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)		aggatagaggaaagaagaggg	0.000													4	2	---	---	---	---	
TMEM50B	757	broad.mit.edu	37	21	34839088	34839088	+	Intron	DEL	A	-	-	rs67303406		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34839088delA	uc002yrt.1	-						TMEM50B_uc002yrs.1_Intron|TMEM50B_uc010gmb.1_Intron	NM_006134	NP_006125	P56557	TM50B_HUMAN	transmembrane protein 50B							endoplasmic reticulum|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						AAATATGAGGaaaaaaaaaaa	0.040													8	5	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37649590	37649590	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37649590delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						AGGACTGCACttttttttttg	0.289													5	3	---	---	---	---	
KCNJ6	3763	broad.mit.edu	37	21	39290656	39290659	+	5'Flank	DEL	ATTT	-	-	rs143282848		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39290656_39290659delATTT	uc002ywo.2	-							NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	GAATTCATTCATTTATTCCGTAGA	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	42507064	42507065	+	IGR	INS	-	T	T			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42507064_42507065insT								DSCAM (288025 upstream) : C21orf130 (6362 downstream)																							TCCTCCTCTTCTTTTTTTTTTT	0.327													3	3	---	---	---	---	
KRTAP12-1	353332	broad.mit.edu	37	21	46101556	46101556	+	3'UTR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46101556delT	uc002zfv.2	-	1					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181686	NP_859014	P59990	KR121_HUMAN	keratin associated protein 12-1							keratin filament				skin(2)	2						GACCCCAGACTTCCCTGGGGG	0.463													4	2	---	---	---	---	
GGT3P	2679	broad.mit.edu	37	22	18792136	18792137	+	Intron	INS	-	A	A			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18792136_18792137insA	uc002zob.1	-											Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						TCTCCAGACTTAAAAAAAAAAC	0.307													4	2	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	28874066	28874066	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28874066delA	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						GATGTTTGCTAAGCTGTGTAA	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	38338873	38338873	+	IGR	DEL	G	-	-	rs149162968	by1000genomes	TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38338873delG								MICALL1 (848 upstream) : C22orf23 (660 downstream)																							GATTTGTCCTGGGGGGTTCTC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	42657562	42657562	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42657562delT								TCF20 (46117 upstream) : NFAM1 (118853 downstream)																							TCATTCTACATTTTTTTTTTT	0.343													4	2	---	---	---	---	
PNPLA5	150379	broad.mit.edu	37	22	44277690	44277691	+	Intron	INS	-	GT	GT			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44277690_44277691insGT	uc003beg.2	-						PNPLA5_uc011aqc.1_Intron|PNPLA5_uc003beh.2_Intron	NM_138814	NP_620169	Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5						lipid catabolic process		hydrolase activity				0		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				AGAAGGGCCAGCAGCGTTGGCC	0.639													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45015083	45015084	+	IGR	DEL	GT	-	-	rs36220219		TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45015083_45015084delGT								NCRNA00207 (46754 upstream) : PRR5 (49509 downstream)																							gtactgtggagtgtgtgtgtgt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	561899	561899	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:561899delT								PPP2R3B (214272 upstream) : SHOX (23180 downstream)																							CAATTGTGTGTGGGCATTTTC	0.483													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1370025	1370026	+	IGR	INS	-	TATC	TATC			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1370025_1370026insTATC								CRLF2 (38495 upstream) : CSF2RA (17667 downstream)																							atgataggtgatatctaggtag	0.069													5	6	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2282024	2282026	+	Intron	DEL	GGA	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2282024_2282026delGGA	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				TGGGTGGGATGGAGGAGATAAGG	0.542													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	100981930	100981930	+	IGR	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100981930delT								ARMCX2 (67067 upstream) : NXF5 (105155 downstream)																							tggttaattgttttttttttc	0.000													9	5	---	---	---	---	
IL1RAPL2	26280	broad.mit.edu	37	X	105010791	105010791	+	Intron	DEL	T	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105010791delT	uc004elz.1	+							NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2						central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3						TTATAAGCAGTTTTTTTTTTT	0.348													4	2	---	---	---	---	
RNF128	79589	broad.mit.edu	37	X	105970595	105970595	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105970595delC	uc004eml.2	+	1	702	c.452delC	c.(451-453)ACCfs	p.T151fs	RNF128_uc004emk.2_Intron	NM_194463	NP_919445	Q8TEB7	RN128_HUMAN	ring finger protein 128 isoform 1	151	PA.					endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding			ovary(1)|central_nervous_system(1)	2						TTCCCCGGGACCCGCAATGAG	0.577													13	13	---	---	---	---	
CLIC2	1193	broad.mit.edu	37	X	154508230	154508230	+	Intron	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154508230delA	uc004fnf.2	-							NM_001289	NP_001280	O15247	CLIC2_HUMAN	chloride intracellular channel 2						signal transduction	chloride channel complex|cytoplasm|nucleus	voltage-gated chloride channel activity			large_intestine(1)|ovary(1)|skin(1)	3	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ctcaaaaaagaaaaaaaaaga	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9936726	9936726	+	IGR	DEL	A	-	-			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9936726delA								TTTY22 (285872 upstream) : None (None downstream)																							AGTCATTATTAAAGCAAAGTG	0.299													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13430917	13430918	+	IGR	INS	-	AA	AA			TCGA-CJ-5672-01A-11D-1534-10	TCGA-CJ-5672-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13430917_13430918insAA								None (None upstream) : None (None downstream)																							TTTAAACTTGGAAAAAATTGAA	0.361													4	2	---	---	---	---	
