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
PLEKHG5	57449	broad.mit.edu	37	1	6527729	6527729	+	Intron	SNP	T	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6527729T>G	uc001ano.1	-						PLEKHG5_uc001ann.1_Intron|PLEKHG5_uc001anq.1_Intron|PLEKHG5_uc001anp.1_Intron|TNFRSF25_uc001ana.2_5'Flank|TNFRSF25_uc001anb.2_5'Flank|TNFRSF25_uc001anc.2_5'Flank|TNFRSF25_uc001and.2_5'Flank|TNFRSF25_uc009vlz.2_5'Flank|TNFRSF25_uc001ane.2_5'Flank|TNFRSF25_uc001anf.2_5'Flank|TNFRSF25_uc001ang.2_5'Flank|TNFRSF25_uc001anh.2_5'Flank|TNFRSF25_uc001ani.1_5'Flank|PLEKHG5_uc001anj.1_Intron|PLEKHG5_uc009vma.1_Intron|PLEKHG5_uc010nzr.1_Intron|PLEKHG5_uc001ank.1_Intron|PLEKHG5_uc009vmb.1_Intron|PLEKHG5_uc001anl.1_Intron|PLEKHG5_uc001anm.1_Intron|PLEKHG5_uc001anr.1_3'UTR	NM_001042663	NP_001036128	O94827	PKHG5_HUMAN	pleckstrin homology domain containing family G						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|perinuclear region of cytoplasm	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		TCAGGCCCCTTCACTGCTGCC	0.647													5	12	---	---	---	---	PASS
FBXO42	54455	broad.mit.edu	37	1	16577186	16577186	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16577186G>C	uc001ayg.2	-	10	2349	c.2133C>G	c.(2131-2133)TAC>TAG	p.Y711*	FBXO42_uc001aye.3_Nonsense_Mutation_p.Y429*|FBXO42_uc001ayf.2_Nonsense_Mutation_p.Y618*	NM_018994	NP_061867	Q6P3S6	FBX42_HUMAN	F-box protein 42	711										upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		CTCGTACAAAGTACAAGGCGT	0.403													39	136	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16973855	16973855	+	RNA	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16973855G>A	uc009vow.2	+	5		c.665G>A			CROCCL1_uc001azg.1_5'Flank|CROCCL1_uc001azi.1_5'Flank|MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_Intron|MST1P2_uc009vox.2_5'Flank|MST1P2_uc001azm.3_5'Flank					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						CCGGGCTAGGGAAGGTCCAGG	0.692													3	26	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34238249	34238249	+	Silent	SNP	G	A	A	rs142181378		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34238249G>A	uc001bxn.1	-	13	1676	c.1647C>T	c.(1645-1647)CCC>CCT	p.P549P	CSMD2_uc001bxm.1_Silent_p.P589P	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	549	Sushi 3.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCTCAAAGGCGGGCTGGCACT	0.577													27	59	---	---	---	---	PASS
PCSK9	255738	broad.mit.edu	37	1	55529175	55529175	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55529175G>A	uc001cyf.1	+	12	2288	c.1997G>A	c.(1996-1998)AGC>AAC	p.S666N	PCSK9_uc010oom.1_RNA	NM_174936	NP_777596	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	666					cellular response to insulin stimulus|cellular response to starvation|cholesterol homeostasis|cholesterol metabolic process|kidney development|liver development|low-density lipoprotein particle receptor catabolic process|lysosomal transport|negative regulation of catalytic activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor recycling|neuron differentiation|positive regulation of neuron apoptosis|positive regulation of receptor internalization|protein autoprocessing|regulation of receptor activity	extracellular space|late endosome|lysosome|perinuclear region of cytoplasm	apolipoprotein receptor binding|identical protein binding|low-density lipoprotein particle receptor binding|serine-type endopeptidase activity|very-low-density lipoprotein particle receptor binding			ovary(2)|central_nervous_system(1)|skin(1)	4						ACTACAGGCAGCACCAGCGAA	0.677													5	11	---	---	---	---	PASS
DEPDC1	55635	broad.mit.edu	37	1	68947267	68947267	+	Silent	SNP	A	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68947267A>C	uc001dem.3	-	9	1908	c.1791T>G	c.(1789-1791)GTT>GTG	p.V597V	DEPDC1_uc001dej.3_5'UTR|DEPDC1_uc001dek.3_RNA|DEPDC1_uc001del.3_Silent_p.V313V	NM_001114120	NP_001107592	Q5TB30	DEP1A_HUMAN	DEP domain containing 1 isoform a	597					intracellular signal transduction|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	GTPase activator activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		CATCGATGGCAACCCTCTCTA	0.398													10	227	---	---	---	---	PASS
SLC16A4	9122	broad.mit.edu	37	1	110921863	110921863	+	Silent	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110921863A>G	uc001dzo.1	-	6	824	c.642T>C	c.(640-642)AGT>AGC	p.S214S	SLC16A4_uc009wfs.1_Silent_p.S166S|SLC16A4_uc001dzp.1_Intron|SLC16A4_uc010ovy.1_Silent_p.S152S|SLC16A4_uc001dzq.1_Intron|SLC16A4_uc010ovz.1_Silent_p.S104S	NM_004696	NP_004687	O15374	MOT5_HUMAN	solute carrier family 16, member 4	214	Cytoplasmic (Potential).					integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	GTGCAGACAAACTGCTGCCTT	0.443													6	385	---	---	---	---	PASS
LOC388692	388692	broad.mit.edu	37	1	149282615	149282615	+	RNA	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149282615G>A	uc010pbf.1	+	1		c.3140G>A				NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0						CCACACACGGGCACTCAGTTC	0.612													5	73	---	---	---	---	PASS
FCGR1A	2209	broad.mit.edu	37	1	149763191	149763191	+	3'UTR	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149763191G>A	uc001esp.3	+	6					HIST2H2BF_uc010pbj.1_Intron|FCGR1A_uc009wlg.2_RNA	NM_000566	NP_000557	P12314	FCGR1_HUMAN	Fc fragment of IgG, high affinity Ia, receptor						interferon-gamma-mediated signaling pathway|phagocytosis, engulfment	integral to membrane|plasma membrane	IgG binding|receptor activity|receptor signaling protein activity			ovary(1)	1	Breast(34;0.0124)|all_hematologic(923;0.127)				Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Methyl aminolevulinate(DB00992)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Porfimer(DB00707)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTCATGGTATGTAACTCTTAA	0.438													4	36	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152188392	152188392	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152188392C>T	uc001ezt.1	-	3	5789	c.5713G>A	c.(5713-5715)GGA>AGA	p.G1905R		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	1905	21.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GATGACTGTCCTGACCTAGAG	0.552													56	745	---	---	---	---	PASS
CREB3L4	148327	broad.mit.edu	37	1	153946103	153946103	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153946103T>A	uc001fdn.3	+	9	1171	c.905T>A	c.(904-906)CTT>CAT	p.L302H	CREB3L4_uc010pef.1_Missense_Mutation_p.L155H|CREB3L4_uc001fdo.3_Missense_Mutation_p.L282H|CREB3L4_uc001fdm.1_Missense_Mutation_p.L302H|CREB3L4_uc001fdp.1_Missense_Mutation_p.L282H|CREB3L4_uc001fdr.2_Missense_Mutation_p.L302H|CREB3L4_uc001fdq.2_Missense_Mutation_p.L282H	NM_130898	NP_570968	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like	302	Helical; Signal-anchor for type II membrane protein; (Potential).				response to unfolded protein	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CAGATTCTTCTTTTTTCCCTG	0.552													46	46	---	---	---	---	PASS
SHE	126669	broad.mit.edu	37	1	154471630	154471630	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154471630C>T	uc001ffb.2	-	2	763	c.676G>A	c.(676-678)GAC>AAC	p.D226N	SHE_uc001ffc.2_RNA	NM_001010846	NP_001010846	Q5VZ18	SHE_HUMAN	Src homology 2 domain containing E	226										breast(3)|ovary(2)|central_nervous_system(1)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			ATGTAACCGTCGTTCTCTCCG	0.428													14	600	---	---	---	---	PASS
OLFML2B	25903	broad.mit.edu	37	1	161953786	161953786	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161953786C>G	uc001gbu.2	-	8	2356	c.1932G>C	c.(1930-1932)GAG>GAC	p.E644D	OLFML2B_uc001gbt.2_Missense_Mutation_p.E127D|OLFML2B_uc010pkq.1_Missense_Mutation_p.E645D	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor	644	Olfactomedin-like.									skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			GGACAATGACCTCCTGGCTGA	0.607													60	75	---	---	---	---	PASS
RGL1	23179	broad.mit.edu	37	1	183853914	183853914	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183853914G>T	uc001gqo.2	+	7	950	c.793G>T	c.(793-795)GAT>TAT	p.D265Y	RGL1_uc010pof.1_Missense_Mutation_p.D70Y|RGL1_uc001gqm.2_Missense_Mutation_p.D300Y|RGL1_uc010pog.1_Missense_Mutation_p.D263Y|RGL1_uc010poh.1_Missense_Mutation_p.D263Y|RGL1_uc010poi.1_Missense_Mutation_p.D265Y	NM_015149	NP_055964	Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation	265	Ras-GEF.				cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	protein binding|Ral guanyl-nucleotide exchange factor activity			breast(5)|ovary(4)|lung(2)	11						GTCTCGAAGGGATAAGAAGGA	0.473													6	303	---	---	---	---	PASS
NEK7	140609	broad.mit.edu	37	1	198266325	198266325	+	Silent	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198266325A>G	uc001gun.3	+	9	1080	c.753A>G	c.(751-753)GAA>GAG	p.E251E		NM_133494	NP_598001	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	251	Protein kinase.					cytoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|lung(1)|ovary(1)	4						AGAAGATAGAACAGTGTGACT	0.368													6	420	---	---	---	---	PASS
GPR37L1	9283	broad.mit.edu	37	1	202097558	202097558	+	Silent	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202097558C>T	uc001gxj.2	+	2	1383	c.1320C>T	c.(1318-1320)GGC>GGT	p.G440G		NM_004767	NP_004758	O60883	ETBR2_HUMAN	G-protein coupled receptor 37 like 1 precursor	440	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2						AGGAGTGCGGCGGGGCTTCGG	0.567													24	17	---	---	---	---	PASS
FLVCR1	28982	broad.mit.edu	37	1	213046072	213046072	+	Silent	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213046072A>G	uc001hjt.2	+	3	1134	c.936A>G	c.(934-936)CAA>CAG	p.Q312Q		NM_014053	NP_054772	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular	312					cell death|cellular iron ion homeostasis|heme export|transmembrane transport	integral to plasma membrane	heme transporter activity|protein binding|receptor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		CAGCTCTTCAAGACAGTCCCC	0.353													6	413	---	---	---	---	PASS
MARK1	4139	broad.mit.edu	37	1	220789331	220789331	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220789331T>A	uc001hmn.3	+	7	1143	c.546T>A	c.(544-546)GAT>GAA	p.D182E	MARK1_uc009xdw.2_Missense_Mutation_p.D182E|MARK1_uc010pun.1_Missense_Mutation_p.D182E|MARK1_uc001hmm.3_Missense_Mutation_p.D160E	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	182	Protein kinase.	Proton acceptor (By similarity).			intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)		TTCACCGTGATCTTAAGGTAA	0.194													27	526	---	---	---	---	PASS
OR2AK2	391191	broad.mit.edu	37	1	248129529	248129529	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248129529T>C	uc010pzd.1	+	1	896	c.896T>C	c.(895-897)CTA>CCA	p.L299P	OR2L13_uc001ids.2_Intron	NM_001004491	NP_001004491	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK,	299	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			GTCACACCTCTACTGAACCCA	0.463													25	411	---	---	---	---	PASS
WDR35	57539	broad.mit.edu	37	2	20138115	20138115	+	Silent	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20138115C>G	uc002rdi.2	-	19	2115	c.2007G>C	c.(2005-2007)CGG>CGC	p.R669R	WDR35_uc002rdj.2_Silent_p.R658R|WDR35_uc010ext.2_RNA|WDR35_uc002rdh.2_Silent_p.R234R|WDR35_uc002rdk.3_Silent_p.R234R	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1	669										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCGCAGAGACCGAATCTCAA	0.368													18	240	---	---	---	---	PASS
MSH2	4436	broad.mit.edu	37	2	47707977	47707977	+	Silent	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47707977A>G	uc002rvy.1	+	15	2669	c.2601A>G	c.(2599-2601)GAA>GAG	p.E867E	MSH2_uc010yoh.1_Silent_p.E801E|MSH2_uc002rvz.2_Silent_p.E867E|MSH2_uc010fbg.2_Silent_p.E677E	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2	867					B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(2)		large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATATCATGGAACCAGCAGCAA	0.373			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				6	284	---	---	---	---	PASS
UPP2	151531	broad.mit.edu	37	2	158958612	158958612	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158958612A>G	uc002tzp.2	+	1	231	c.37A>G	c.(37-39)AGA>GGA	p.R13G	UPP2_uc002tzo.2_Missense_Mutation_p.R70G	NM_173355	NP_775491	O95045	UPP2_HUMAN	uridine phosphorylase 2 isoform a	13					nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0						TAGGTCCATGAGATCTGACAG	0.338													7	430	---	---	---	---	PASS
SCN3A	6328	broad.mit.edu	37	2	165948825	165948825	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165948825G>C	uc002ucx.2	-	27	5238	c.4746C>G	c.(4744-4746)CAC>CAG	p.H1582Q	SCN3A_uc010zcy.1_Missense_Mutation_p.H65Q|SCN3A_uc002ucy.2_Missense_Mutation_p.H1533Q|SCN3A_uc002ucz.2_Missense_Mutation_p.H1533Q	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1582						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)	TGAAGTAGTAGTGTCTGAGGG	0.433													24	221	---	---	---	---	PASS
PPIG	9360	broad.mit.edu	37	2	170463623	170463623	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170463623G>A	uc002uez.2	+	6	474	c.254G>A	c.(253-255)CGA>CAA	p.R85Q	PPIG_uc010fpx.2_Intron|PPIG_uc010fpy.2_Missense_Mutation_p.R81Q|PPIG_uc002ufa.2_Missense_Mutation_p.R85Q|PPIG_uc002ufb.2_Missense_Mutation_p.R85Q|PPIG_uc002ufc.1_Missense_Mutation_p.R85Q|PPIG_uc002ufd.2_Missense_Mutation_p.R85Q	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	85	PPIase cyclophilin-type.				protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	GGAAATGGACGAGGAGGGGAA	0.269													5	638	---	---	---	---	PASS
RFTN2	130132	broad.mit.edu	37	2	198436607	198436607	+	3'UTR	SNP	A	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198436607A>T	uc002uuo.3	-	9						NM_144629	NP_653230	Q52LD8	RFTN2_HUMAN	raftlin family member 2							plasma membrane					0						CATAGATTAGAGGAAAGGCTG	0.229													3	18	---	---	---	---	PASS
ARL8B	55207	broad.mit.edu	37	3	5215726	5215726	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5215726G>C	uc003bqg.2	+	5	618	c.397G>C	c.(397-399)GAT>CAT	p.D133H	ARL8B_uc011asx.1_Missense_Mutation_p.D124H|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654	Q9NVJ2	ARL8B_HUMAN	ADP-ribosylation factor-like 10C	133	GTP.				cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)		AAACAAGAGAGATCTTCCTAA	0.313													93	311	---	---	---	---	PASS
MTMR14	64419	broad.mit.edu	37	3	9712761	9712761	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9712761T>C	uc003brz.2	+	6	708	c.584T>C	c.(583-585)GTC>GCC	p.V195A	MTMR14_uc003bsa.2_Missense_Mutation_p.V195A|MTMR14_uc003bsb.2_Missense_Mutation_p.V195A|MTMR14_uc011ath.1_RNA|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_RNA	NM_001077525	NP_001070993	Q8NCE2	MTMRE_HUMAN	jumpy isoform 2	195						perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)					TTTGATAAGGTCAGAGGCTAT	0.458													5	142	---	---	---	---	PASS
NKTR	4820	broad.mit.edu	37	3	42680080	42680080	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42680080G>T	uc003clo.2	+	13	3031	c.2884G>T	c.(2884-2886)GGG>TGG	p.G962W	NKTR_uc003clm.1_Missense_Mutation_p.G709W|NKTR_uc003clp.2_Missense_Mutation_p.G709W|NKTR_uc011azp.1_Intron|NKTR_uc003clq.1_Missense_Mutation_p.G852W|NKTR_uc003clr.1_Missense_Mutation_p.G709W|NKTR_uc003cls.2_Missense_Mutation_p.G662W	NM_005385	NP_005376	P30414	NKTR_HUMAN	natural killer-tumor recognition sequence	962					protein folding	membrane	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TGACTCTGAGGGGTCCTGTTC	0.423													40	87	---	---	---	---	PASS
CHMP2B	25978	broad.mit.edu	37	3	87295011	87295011	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87295011A>G	uc003dqp.3	+	3	534	c.274A>G	c.(274-276)ATG>GTG	p.M92V	CHMP2B_uc011bgn.1_Missense_Mutation_p.M51V	NM_014043	NP_054762	Q9UQN3	CHM2B_HUMAN	chromatin modifying protein 2B	92					cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane|mitochondrion|nucleus	protein domain specific binding			skin(2)|ovary(1)	3	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		AACAAAAGTGATGAATTCCCA	0.328													5	237	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108214631	108214631	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108214631C>T	uc003dxa.1	-	8	824	c.767G>A	c.(766-768)CGT>CAT	p.R256H		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	256	Myosin head-like.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						ACTTACAAAACGAGAGGAGTT	0.333													7	576	---	---	---	---	PASS
PARP9	83666	broad.mit.edu	37	3	122247559	122247559	+	Silent	SNP	G	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122247559G>C	uc010hri.2	-	11	2362	c.2217C>G	c.(2215-2217)ACC>ACG	p.T739T	PARP9_uc003eff.3_Silent_p.T704T|PARP9_uc011bjs.1_Silent_p.T704T|PARP9_uc003efg.2_Silent_p.T284T|PARP9_uc003efi.2_Silent_p.T704T|PARP9_uc003efh.2_Silent_p.T739T	NM_001146102	NP_001139574	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	739	PARP catalytic.				cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)|prostate(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0519)		TGAGGTTCTTGGTGAAGTATA	0.378													61	192	---	---	---	---	PASS
PLXNA1	5361	broad.mit.edu	37	3	126733641	126733641	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126733641C>A	uc003ejg.2	+	13	2779	c.2775C>A	c.(2773-2775)TAC>TAA	p.Y925*		NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	948	IPT/TIG 1.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)		CACCACACTACCGCGCCCTGT	0.647													3	6	---	---	---	---	PASS
NPHP3	27031	broad.mit.edu	37	3	132409424	132409424	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132409424T>G	uc003epe.1	-	19	2718	c.2641A>C	c.(2641-2643)AAG>CAG	p.K881Q	NPHP3_uc003epd.1_Missense_Mutation_p.K123Q	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3	881					maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						TCATGCAGCTTCTGTTTACTT	0.383													63	159	---	---	---	---	PASS
PIK3CB	5291	broad.mit.edu	37	3	138474707	138474707	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138474707T>C	uc011bmq.1	-	2	286	c.286A>G	c.(286-288)ACA>GCA	p.T96A		NM_006219	NP_006210	P42338	PK3CB_HUMAN	catalytic phosphatidylinositol 3-kinase beta	96	PI3K-ABD.				activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5						AGTCTTCGTGTTTCATCTTCA	0.393													6	264	---	---	---	---	PASS
PRR23A	729627	broad.mit.edu	37	3	138724479	138724479	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138724479G>A	uc011bms.1	-	1	632	c.632C>T	c.(631-633)TCT>TTT	p.S211F		NM_001134659	NP_001128131	A6NEV1	PR23A_HUMAN	proline rich 23A	211	Pro-rich.										0						GGGGCCTGGAGAGTGTCCCTC	0.647													5	64	---	---	---	---	PASS
RNF7	9616	broad.mit.edu	37	3	141462359	141462359	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141462359C>G	uc003eud.2	+	2	317	c.184C>G	c.(184-186)CTT>GTT	p.L62V	RNF7_uc003euc.2_Silent_p.V59V|RNF7_uc003eue.2_RNA	NM_014245	NP_055060	Q9UBF6	RBX2_HUMAN	ring finger protein 7 isoform 1	62	RING-type.				anti-apoptosis|induction of apoptosis by oxidative stress|protein neddylation|response to redox state	cytoplasm|nucleus	copper ion binding|NEDD8 ligase activity|protein binding|zinc ion binding				0						AGATGCCTGTCTTAGATGTCA	0.363													9	806	---	---	---	---	PASS
IFT80	57560	broad.mit.edu	37	3	160021725	160021725	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160021725T>A	uc011boy.1	-	11	1562	c.1129A>T	c.(1129-1131)AGT>TGT	p.S377C	IFT80_uc003fda.2_RNA|IFT80_uc003fdb.1_Missense_Mutation_p.S240C|IFT80_uc003fdd.1_Missense_Mutation_p.S60C|IFT80_uc003fde.1_Missense_Mutation_p.S240C	NM_020800	NP_065851	Q9P2H3	IFT80_HUMAN	WD repeat domain 56	377						cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGAATCAAACTAACAGTTCCT	0.289													5	362	---	---	---	---	PASS
VPS8	23355	broad.mit.edu	37	3	184616402	184616402	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184616402T>C	uc003fpb.1	+	23	2219	c.2048T>C	c.(2047-2049)GTC>GCC	p.V683A	VPS8_uc010hyd.1_Missense_Mutation_p.V593A|VPS8_uc010hye.1_Missense_Mutation_p.V112A	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	685							zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			ATGATCTATGTCTACAACAGA	0.338													7	466	---	---	---	---	PASS
TP63	8626	broad.mit.edu	37	3	189590948	189590948	+	Intron	SNP	T	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189590948T>A	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsa.2_3'UTR|TP63_uc003fsb.2_Intron|TP63_uc003fsc.2_Intron|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Intron	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		GCAACCTTTTTTACGTGTCTT	0.368									Hay-Wells_syndrome	HNSCC(45;0.13)			6	26	---	---	---	---	PASS
ZBTB49	166793	broad.mit.edu	37	4	4303969	4303969	+	Silent	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4303969C>T	uc003ghu.2	+	3	581	c.406C>T	c.(406-408)CTA>TTA	p.L136L	ZBTB49_uc003ghv.2_Intron|ZBTB49_uc010icy.2_RNA|ZBTB49_uc010icz.2_5'Flank	NM_145291	NP_660334	Q6ZSB9	ZBT49_HUMAN	zinc finger protein 509	136					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2						TACATTGTCTCTACAAAGCAC	0.438													21	93	---	---	---	---	PASS
SORCS2	57537	broad.mit.edu	37	4	7398084	7398084	+	Splice_Site	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7398084T>C	uc003gkb.3	+	2	548	c.548_splice	c.e2+2	p.R183_splice	SORCS2_uc011bwi.1_Splice_Site_p.R11_splice	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						TCTGTGGCGGTAAGTCAGCCC	0.532													5	186	---	---	---	---	PASS
TSPAN5	10098	broad.mit.edu	37	4	99397581	99397581	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99397581C>T	uc003hub.2	-	6	957	c.607G>A	c.(607-609)GAT>AAT	p.D203N	TSPAN5_uc011cdz.1_Missense_Mutation_p.D132N	NM_005723	NP_005714	P62079	TSN5_HUMAN	transmembrane 4 superfamily member 9	203	Extracellular (Potential).					integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)		TGCCTGGCATCATAGCCACAC	0.448													63	138	---	---	---	---	PASS
LEF1	51176	broad.mit.edu	37	4	109004590	109004590	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109004590T>G	uc003hyt.1	-	5	1215	c.560A>C	c.(559-561)CAT>CCT	p.H187P	LEF1_uc011cfj.1_Missense_Mutation_p.H72P|LEF1_uc011cfk.1_Missense_Mutation_p.H119P|LEF1_uc003hyu.1_Missense_Mutation_p.H187P|LEF1_uc003hyv.1_Missense_Mutation_p.H187P|LEF1_uc010imb.1_RNA	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	187	Pro-rich.				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		AGCTGGAGGATGTCTGGACAT	0.438													71	219	---	---	---	---	PASS
SC4MOL	6307	broad.mit.edu	37	4	166262973	166262973	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166262973C>A	uc003ire.2	+	6	887	c.757C>A	c.(757-759)CAC>AAC	p.H253N	SC4MOL_uc003irf.2_Missense_Mutation_p.H122N	NM_006745	NP_006736	Q15800	ERG25_HUMAN	sterol-C4-methyl oxidase-like isoform 1	253	Histidine box-3.				cholesterol biosynthetic process|fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	C-4 methylsterol oxidase activity|iron ion binding				0	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0875)	NADH(DB00157)	TCATGATTTCCACCACATGAA	0.358													5	320	---	---	---	---	PASS
MYO10	4651	broad.mit.edu	37	5	16674991	16674991	+	Silent	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16674991A>G	uc003jft.3	-	35	5403	c.4935T>C	c.(4933-4935)ATT>ATC	p.I1645I	MYO10_uc011cnb.1_Silent_p.I274I|MYO10_uc011cnc.1_Silent_p.I524I|MYO10_uc011cnd.1_Silent_p.I1002I|MYO10_uc011cne.1_Silent_p.I1002I|MYO10_uc010itx.2_Silent_p.I1267I	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	1645	MyTH4.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						GATACTTGAGAATCCCTCGAC	0.572													5	16	---	---	---	---	PASS
ADAMTS12	81792	broad.mit.edu	37	5	33881335	33881335	+	Silent	SNP	G	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33881335G>C	uc003jia.1	-	2	541	c.378C>G	c.(376-378)CTC>CTG	p.L126L	ADAMTS12_uc010iuq.1_Silent_p.L126L|ADAMTS12_uc003jib.1_Silent_p.L126L	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	126					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						TAACATGGGAGAGGTTCCCAT	0.502										HNSCC(64;0.19)			25	67	---	---	---	---	PASS
C5orf28	64417	broad.mit.edu	37	5	43446548	43446548	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43446548A>T	uc003jny.2	-	3	567	c.424T>A	c.(424-426)TGC>AGC	p.C142S	C5orf28_uc003jnv.3_Missense_Mutation_p.C142S|C5orf28_uc003jnx.2_Missense_Mutation_p.C142S	NM_022483	NP_071928	Q0VDI3	CE028_HUMAN	hypothetical protein LOC64417	142						integral to membrane					0	Lung NSC(6;2.07e-05)					GGAAGAAAGCACCATGAGTCT	0.438													33	134	---	---	---	---	PASS
ERBB2IP	55914	broad.mit.edu	37	5	65339009	65339009	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65339009A>G	uc003juk.1	+	16	1719	c.1411A>G	c.(1411-1413)AGG>GGG	p.R471G	ERBB2IP_uc003juh.1_Missense_Mutation_p.R471G|ERBB2IP_uc003jui.1_Missense_Mutation_p.R471G|ERBB2IP_uc003juj.1_Missense_Mutation_p.R471G|ERBB2IP_uc011cqx.1_Missense_Mutation_p.R471G|ERBB2IP_uc011cqy.1_Missense_Mutation_p.R471G|ERBB2IP_uc011cqz.1_Intron|ERBB2IP_uc010iwx.1_Missense_Mutation_p.R471G|ERBB2IP_uc003jul.1_Missense_Mutation_p.R471G	NM_018695	NP_061165	Q96RT1	LAP2_HUMAN	ERBB2 interacting protein isoform 2	471					basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		CAAAGATGAAAGGGAGGCACC	0.378													6	343	---	---	---	---	PASS
MAST4	375449	broad.mit.edu	37	5	66460450	66460450	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66460450G>A	uc003jut.1	+	28	4944	c.4876G>A	c.(4876-4878)GCC>ACC	p.A1626T	MAST4_uc003juw.2_Missense_Mutation_p.A1554T|MAST4_uc003jux.2_5'Flank	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	1818						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)		CGGACCTCAGGCCTCCAAGAC	0.602													20	62	---	---	---	---	PASS
PRRC1	133619	broad.mit.edu	37	5	126883627	126883627	+	Intron	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126883627T>C	uc003kuk.2	+						PRRC1_uc003kuj.3_Missense_Mutation_p.L381P	NM_130809	NP_570721	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1							Golgi apparatus					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		GGTTTTCTCCTTTGCTTTTTC	0.353													7	647	---	---	---	---	PASS
ADAMTS2	9509	broad.mit.edu	37	5	178548695	178548695	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178548695C>G	uc003mjw.2	-	21	3145	c.3145G>C	c.(3145-3147)GAC>CAC	p.D1049H		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1049					collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GAGTCGGGGTCCGGGCGGGAC	0.622													12	85	---	---	---	---	PASS
BAT2	7916	broad.mit.edu	37	6	31598498	31598498	+	Silent	SNP	C	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31598498C>A	uc003nvb.3	+	15	2634	c.2385C>A	c.(2383-2385)GTC>GTA	p.V795V	BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Silent_p.V795V	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	795	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0						TAGGAGATGTCTTCACCGCCA	0.592													16	40	---	---	---	---	PASS
MDGA1	266727	broad.mit.edu	37	6	37606075	37606075	+	Silent	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37606075C>T	uc003onu.1	-	16	3861	c.2682G>A	c.(2680-2682)GGG>GGA	p.G894G	MDGA1_uc003onv.1_Silent_p.G163G	NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing	894	MAM.				brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2						GGCCTCGAACCCCCTCAAAAA	0.567													37	65	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54806400	54806400	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54806400C>G	uc003pck.2	+	5	2747	c.2631C>G	c.(2629-2631)TTC>TTG	p.F877L		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	877										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					AAAGCAAGTTCTTGGAAAGGG	0.428													35	82	---	---	---	---	PASS
CDCA7L	55536	broad.mit.edu	37	7	21945218	21945218	+	Missense_Mutation	SNP	C	T	T	rs146158399		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21945218C>T	uc010kuk.2	-	7	1073	c.953G>A	c.(952-954)CGT>CAT	p.R318H	CDCA7L_uc003sve.3_Missense_Mutation_p.R284H|CDCA7L_uc010kul.2_Missense_Mutation_p.R272H|CDCA7L_uc003svf.3_Missense_Mutation_p.R317H	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1	318					positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0						AGAAGATATACGGTGACGTCG	0.383													4	156	---	---	---	---	PASS
KCTD7	154881	broad.mit.edu	37	7	66103318	66103318	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66103318C>G	uc003tve.2	+	3	555	c.393C>G	c.(391-393)TAC>TAG	p.Y131*	RABGEF1_uc003tvf.2_5'UTR|KCTD7_uc003tvd.3_Nonsense_Mutation_p.Y131*	NM_153033	NP_694578	Q96MP8	KCTD7_HUMAN	potassium channel tetramerisation domain	131	BTB.					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)	3						AGGCCCAGTACTATGCCATCG	0.572													30	64	---	---	---	---	PASS
MOSPD3	64598	broad.mit.edu	37	7	100211260	100211260	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100211260C>T	uc003uvq.2	+	4	644	c.442C>T	c.(442-444)CCA>TCA	p.P148S	MOSPD3_uc003uvr.2_Missense_Mutation_p.P148S|MOSPD3_uc003uvs.2_Missense_Mutation_p.P148S|MOSPD3_uc003uvt.2_Missense_Mutation_p.P138S	NM_001040097	NP_001035186	O75425	MSPD3_HUMAN	motile sperm domain containing 3 isoform a	148						integral to membrane	structural molecule activity			ovary(2)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					TCAGGGACAGCCAGATCCAGC	0.622													6	21	---	---	---	---	PASS
ATP6V0A4	50617	broad.mit.edu	37	7	138417832	138417832	+	Silent	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138417832G>A	uc003vuf.2	-	16	1936	c.1698C>T	c.(1696-1698)TTC>TTT	p.F566F	ATP6V0A4_uc003vug.2_Silent_p.F566F|ATP6V0A4_uc003vuh.2_Silent_p.F566F	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	566	Helical; (Potential).				cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1						GAGTTCTTCTGAAGTATCTGG	0.378													41	161	---	---	---	---	PASS
MTMR9	66036	broad.mit.edu	37	8	11152719	11152719	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11152719G>T	uc003wtm.2	+	2	597	c.199G>T	c.(199-201)GGT>TGT	p.G67C	MTMR9_uc010lrx.2_5'UTR|MTMR9_uc011kxa.1_5'UTR	NM_015458	NP_056273	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	67						cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		AGGATCACTGGGTACCATCAT	0.294													5	316	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	131916170	131916170	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131916170T>G	uc003ytd.3	-	7	2015	c.1759A>C	c.(1759-1761)ATT>CTT	p.I587L	ADCY8_uc010mds.2_Missense_Mutation_p.I587L	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	587	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			GGCTGCTTAATTAAGTAAGTT	0.488										HNSCC(32;0.087)			23	64	---	---	---	---	PASS
KCNQ3	3786	broad.mit.edu	37	8	133141908	133141908	+	Silent	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133141908C>T	uc003ytj.2	-	15	2445	c.2220G>A	c.(2218-2220)ACG>ACA	p.T740T	KCNQ3_uc010mdt.2_Silent_p.T728T	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein	740					axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)			TCTCCACATACGTTGTTGCTG	0.592													6	12	---	---	---	---	PASS
PLEC	5339	broad.mit.edu	37	8	144995868	144995868	+	Silent	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144995868A>G	uc003zaf.1	-	32	8702	c.8532T>C	c.(8530-8532)AAT>AAC	p.N2844N	PLEC_uc003zab.1_Silent_p.N2707N|PLEC_uc003zac.1_Silent_p.N2711N|PLEC_uc003zad.2_Silent_p.N2707N|PLEC_uc003zae.1_Silent_p.N2675N|PLEC_uc003zag.1_Silent_p.N2685N|PLEC_uc003zah.2_Silent_p.N2693N|PLEC_uc003zaj.2_Silent_p.N2734N	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	2844	Plectin 1.|Globular 2.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9						TCAGCTTCTCATTGGTGGCCT	0.672													3	7	---	---	---	---	PASS
KDM4C	23081	broad.mit.edu	37	9	6849563	6849563	+	Silent	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6849563A>G	uc003zkh.2	+	5	1072	c.492A>G	c.(490-492)GAA>GAG	p.E164E	KDM4C_uc010mhu.2_Silent_p.E186E|KDM4C_uc010mhw.2_Silent_p.E164E|KDM4C_uc011lmi.1_Silent_p.E164E|KDM4C_uc011lmj.1_RNA|KDM4C_uc003zkg.2_Silent_p.E164E|KDM4C_uc011lmk.1_5'UTR	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1	164	JmjC.				positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						TGGTTGAAGAAGAGTGTGGCA	0.423													6	383	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	66459820	66459820	+	5'Flank	SNP	G	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66459820G>C	uc010mng.1	-						uc004aeb.2_5'Flank|uc004aec.2_RNA					Homo sapiens cDNA, FLJ98602.																		tttgtccccagtgccttattt	0.000													3	10	---	---	---	---	PASS
SARDH	1757	broad.mit.edu	37	9	136577831	136577831	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136577831C>G	uc004cep.3	-	10	1372	c.1238G>C	c.(1237-1239)GGA>GCA	p.G413A	SARDH_uc004ceo.2_Missense_Mutation_p.G413A|SARDH_uc011mdn.1_Missense_Mutation_p.G413A|SARDH_uc011mdo.1_Missense_Mutation_p.G245A	NM_001134707	NP_001128179	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase precursor	413					glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CAGCATCATTCCTGGCAGGAA	0.627													5	27	---	---	---	---	PASS
NEBL	10529	broad.mit.edu	37	10	21124538	21124538	+	Silent	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21124538T>C	uc001iqi.2	-	14	1750	c.1353A>G	c.(1351-1353)AAA>AAG	p.K451K	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Intron|NEBL_uc001iql.1_RNA	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	451	Nebulin 12.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						ACTCCAGGTCTTTCTTGTATT	0.393													6	453	---	---	---	---	PASS
NDST2	8509	broad.mit.edu	37	10	75567375	75567375	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75567375G>A	uc001jvk.2	-	3	1576	c.772C>T	c.(772-774)CGT>TGT	p.R258C	NDST2_uc010qks.1_5'Flank|NDST2_uc010qkt.1_Missense_Mutation_p.R135C|NDST2_uc009xro.2_5'Flank|NDST2_uc010qku.1_Missense_Mutation_p.R135C	NM_003635	NP_003626	P52849	NDST2_HUMAN	heparan glucosaminyl	258	Lumenal (Potential).|Heparan sulfate N-deacetylase 2.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			ovary(1)	1	Prostate(51;0.0112)					CGGGCCCGACGAAGAACTGGT	0.562													12	45	---	---	---	---	PASS
RNLS	55328	broad.mit.edu	37	10	90122392	90122392	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90122392A>G	uc001kfe.2	-	5	752	c.617T>C	c.(616-618)ATT>ACT	p.I206T	RNLS_uc010qms.1_Missense_Mutation_p.I123T|RNLS_uc001kfd.2_Missense_Mutation_p.I206T|RNLS_uc009xtj.2_Missense_Mutation_p.I38T	NM_001031709	NP_001026879	Q5VYX0	RNLS_HUMAN	renalase isoform 1	206						extracellular region	oxidoreductase activity			ovary(1)	1						AGGGACATCAATCTTCGTACC	0.468													50	181	---	---	---	---	PASS
MRGPRX3	117195	broad.mit.edu	37	11	18158742	18158742	+	5'UTR	SNP	T	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18158742T>G	uc001mnu.2	+	3						NM_054031	NP_473372	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2						AGACTGGGGTTTCTGAGCATG	0.393													10	41	---	---	---	---	PASS
ABTB2	25841	broad.mit.edu	37	11	34175891	34175891	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34175891G>A	uc001mvl.1	-	16	2473	c.2243C>T	c.(2242-2244)GCC>GTC	p.A748V		NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing	748							DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CCTCTGCAGGGCATCCAGCTG	0.617													3	40	---	---	---	---	PASS
OR8J1	219477	broad.mit.edu	37	11	56128098	56128098	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56128098A>C	uc010rjh.1	+	1	376	c.376A>C	c.(376-378)ATT>CTT	p.I126L		NM_001005205	NP_001005205	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J,	126	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					CTATGTGGCTATTTGTAACCC	0.498													7	333	---	---	---	---	PASS
CARNS1	57571	broad.mit.edu	37	11	67191044	67191044	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67191044C>A	uc009yrp.2	+	9	1908	c.1456C>A	c.(1456-1458)CAG>AAG	p.Q486K	PPP1CA_uc001okx.1_5'Flank|CARNS1_uc001olc.3_Missense_Mutation_p.Q625K	NM_020811	NP_065862	A5YM72	CRNS1_HUMAN	ATP-grasp domain containing 1	486					carnosine biosynthetic process		ATP binding|carnosine synthase activity|metal ion binding				0						CCTGCTCTGCCAGGAGCTAGG	0.652													4	36	---	---	---	---	PASS
CCDC81	60494	broad.mit.edu	37	11	86097136	86097136	+	Silent	SNP	G	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86097136G>T	uc001pbx.1	+	2	551	c.123G>T	c.(121-123)CGG>CGT	p.R41R	CCDC81_uc001pbw.1_Silent_p.R41R	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	41										skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				TTGTGAGACGGCAGTTAACCC	0.299													57	162	---	---	---	---	PASS
CCDC81	60494	broad.mit.edu	37	11	86097137	86097137	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86097137C>T	uc001pbx.1	+	2	552	c.124C>T	c.(124-126)CAG>TAG	p.Q42*	CCDC81_uc001pbw.1_Nonsense_Mutation_p.Q42*	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	42										skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				TGTGAGACGGCAGTTAACCCT	0.303													55	161	---	---	---	---	PASS
KIAA1826	84437	broad.mit.edu	37	11	105880163	105880163	+	3'UTR	SNP	G	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105880163G>C	uc001piy.2	-	3					KIAA1826_uc001piz.2_3'UTR	NM_032424	NP_115800	Q8NCY6	K1826_HUMAN	hypothetical protein LOC84437							nucleus				breast(1)	1		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.56e-05)|Epithelial(105;0.00432)|all cancers(92;0.0309)		ACTGACATTAGACAAGAAACC	0.353													5	65	---	---	---	---	PASS
LST-3TM12	338821	broad.mit.edu	37	12	21168657	21168657	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21168657A>G	uc010sin.1	+	1	28	c.28A>G	c.(28-30)AGG>GGG	p.R10G	SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_001009562	NP_001009562	Q71QF0	Q71QF0_HUMAN	liver-specific organic anion transporter 3TM12	10						membrane	transporter activity				0						TCAAATAGAAAGGAGATTTGA	0.328													7	596	---	---	---	---	PASS
ABCC9	10060	broad.mit.edu	37	12	22063879	22063879	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22063879C>A	uc001rfi.1	-	7	1065	c.1045G>T	c.(1045-1047)GAA>TAA	p.E349*	ABCC9_uc001rfh.2_Nonsense_Mutation_p.E349*|ABCC9_uc001rfj.1_Nonsense_Mutation_p.E349*	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	349	Extracellular (Potential).|ABC transmembrane type-1 1.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TAAGCGTTTTCAAGAAATTCC	0.383													13	181	---	---	---	---	PASS
NR4A1	3164	broad.mit.edu	37	12	52452615	52452615	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52452615C>A	uc001rzs.2	+	8	1998	c.1684C>A	c.(1684-1686)CTG>ATG	p.L562M	NR4A1_uc010sno.1_Missense_Mutation_p.L575M|NR4A1_uc001rzt.2_Missense_Mutation_p.L562M|NR4A1_uc009zmc.2_3'UTR	NM_002135	NP_002126	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	562					nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ACTGCCCGAGCTGCGGACCCT	0.637													4	20	---	---	---	---	PASS
GALNT4	8693	broad.mit.edu	37	12	89917147	89917147	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89917147A>T	uc001tbd.2	-	1	1389	c.1180T>A	c.(1180-1182)TTC>ATC	p.F394I	POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc001tbc.2_Intron|POC1B_uc010sun.1_Intron|GALNT4_uc001tbe.2_Missense_Mutation_p.F391I|GALNT4_uc010suo.1_Missense_Mutation_p.F86I	NM_003774	NP_003765	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	394	Lumenal (Potential).				carbohydrate metabolic process	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0						CTATTGTAGAAGTGCTCTTTG	0.458													74	225	---	---	---	---	PASS
RAN	5901	broad.mit.edu	37	12	131357428	131357428	+	Silent	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131357428A>G	uc001uir.2	+	3	149	c.84A>G	c.(82-84)AAA>AAG	p.K28K	RAN_uc010tbk.1_5'UTR|RAN_uc010tbl.1_5'UTR|RAN_uc001uis.2_Silent_p.K48K	NM_006325	NP_006316	P62826	RAN_HUMAN	ras-related nuclear protein	28					androgen receptor signaling pathway|cell division|DNA metabolic process|mitosis|mitotic spindle organization|positive regulation of transcription, DNA-dependent|protein export from nucleus|RNA export from nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|melanosome|nuclear pore|nucleoplasm	androgen receptor binding|chromatin binding|GTP binding|GTPase activity|transcription coactivator activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		CCTTCGTGAAACGTCATTTGA	0.393													8	782	---	---	---	---	PASS
SKA3	221150	broad.mit.edu	37	13	21729086	21729086	+	3'UTR	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21729086G>A	uc001unt.2	-	9					SKA3_uc001unv.2_3'UTR|SKA3_uc001unu.2_3'UTR	NM_145061	NP_659498	Q8IX90	SKA3_HUMAN	SKA3						cell division|chromosome segregation|mitosis|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytoplasm|spindle microtubule	protein binding				0						TGAATGACTGGGCTACATGTC	0.323													37	140	---	---	---	---	PASS
KBTBD6	89890	broad.mit.edu	37	13	41706026	41706026	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41706026A>C	uc001uxu.1	-	1	911	c.622T>G	c.(622-624)TCA>GCA	p.S208A	KBTBD6_uc010ace.1_Intron|KBTBD6_uc010tfe.1_Missense_Mutation_p.S142A|uc001uxv.1_5'Flank	NM_152903	NP_690867	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain-containing 6	208							protein binding			ovary(1)|skin(1)	2		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		TCCCGAATTGAACCCATGTGG	0.562													11	45	---	---	---	---	PASS
C13orf1	57213	broad.mit.edu	37	13	50502122	50502122	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50502122A>G	uc001vdl.2	-	3	585	c.323T>C	c.(322-324)CTT>CCT	p.L108P	C13orf1_uc001vdm.2_Missense_Mutation_p.L69P|C13orf1_uc010tgm.1_Intron|C13orf1_uc010adj.2_Missense_Mutation_p.L108P	NM_020456	NP_065189	Q5W111	SPRY7_HUMAN	chromosome 13 open reading frame 1 isoform 1	108	B30.2/SPRY.										0		Lung NSC(96;7.5e-06)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Acute lymphoblastic leukemia(7;0.117)		GBM - Glioblastoma multiforme(99;1.72e-10)|COAD - Colon adenocarcinoma(199;0.208)		GTTGTGGTAAAGGGCTCCATC	0.468													7	484	---	---	---	---	PASS
DIS3	22894	broad.mit.edu	37	13	73336063	73336063	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73336063T>G	uc001vix.3	-	17	2714	c.2340A>C	c.(2338-2340)AGA>AGC	p.R780S	DIS3_uc001viy.3_Missense_Mutation_p.R750S|DIS3_uc001viz.2_RNA	NM_014953	NP_055768	Q9Y2L1	RRP44_HUMAN	DIS3 mitotic control isoform a	780					CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		AAAAATACCTTCTAATGGGTG	0.318										Multiple Myeloma(4;0.011)			44	125	---	---	---	---	PASS
SRP54	6729	broad.mit.edu	37	14	35487921	35487921	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35487921T>C	uc001wso.2	+	12	1348	c.997T>C	c.(997-999)TAT>CAT	p.Y333H	SRP54_uc010tpp.1_Missense_Mutation_p.Y284H|SRP54_uc010tpq.1_Missense_Mutation_p.Y269H	NM_003136	NP_003127	P61011	SRP54_HUMAN	signal recognition particle 54kDa isoform 1	333	M-domain.				GTP catabolic process|response to drug|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition|SRP-dependent cotranslational protein targeting to membrane, translocation	cytosol|nuclear speck|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|drug binding|endoplasmic reticulum signal peptide binding|GDP binding|GTP binding|nucleoside-triphosphatase activity|ribonucleoprotein binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)		GCGAGACATGTATGAGCAATT	0.289													6	615	---	---	---	---	PASS
RALGAPA1	253959	broad.mit.edu	37	14	36140632	36140632	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36140632A>G	uc001wti.2	-	25	4038	c.3647T>C	c.(3646-3648)GTA>GCA	p.V1216A	RALGAPA1_uc010amp.2_RNA|RALGAPA1_uc001wtj.2_Missense_Mutation_p.V1216A|RALGAPA1_uc010tpv.1_Missense_Mutation_p.V1229A|RALGAPA1_uc010tpw.1_Missense_Mutation_p.V1263A	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1	1216					activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						ACCAGCTGCTACAATAAAATC	0.358													4	134	---	---	---	---	PASS
GABRB3	2562	broad.mit.edu	37	15	26866641	26866641	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26866641T>C	uc001zaz.2	-	4	423	c.281A>G	c.(280-282)GAT>GGT	p.D94G	GABRB3_uc010uae.1_Missense_Mutation_p.D9G|GABRB3_uc001zba.2_Missense_Mutation_p.D94G|GABRB3_uc001zbb.2_Missense_Mutation_p.D150G|GABRB3_uc001zbc.2_RNA	NM_000814	NP_000805	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	94	Extracellular (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	GAGCCTTTTATCTCTCCAATA	0.433													5	186	---	---	---	---	PASS
TJP1	7082	broad.mit.edu	37	15	30064288	30064288	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30064288T>G	uc001zcr.2	-	4	766	c.291A>C	c.(289-291)AAA>AAC	p.K97N	TJP1_uc010azl.2_Missense_Mutation_p.K85N|TJP1_uc001zcq.2_Missense_Mutation_p.K101N|TJP1_uc001zcs.2_Missense_Mutation_p.K97N	NM_003257	NP_003248	Q07157	ZO1_HUMAN	tight junction protein 1 isoform a	97	PDZ 1.				cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TTTTCCCACTTTTCCTTAGTT	0.353													54	136	---	---	---	---	PASS
TMEM85	51234	broad.mit.edu	37	15	34520682	34520682	+	Silent	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34520682T>C	uc001zhq.2	+	4	479	c.408T>C	c.(406-408)TAT>TAC	p.Y136Y	TMEM85_uc001zhr.2_RNA|TMEM85_uc001zhs.2_Intron|TMEM85_uc010bat.2_Intron	NM_016454	NP_057538	Q5J8M3	TMM85_HUMAN	transmembrane protein 85	136	Helical; (Potential).				apoptosis	integral to membrane					0		all_lung(180;1.15e-06)		all cancers(64;1.03e-17)|GBM - Glioblastoma multiforme(113;3.33e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)|Lung(196;0.217)		GTTTGGTCTATCTCATTGGGA	0.448													6	444	---	---	---	---	PASS
IDH3A	3419	broad.mit.edu	37	15	78452354	78452354	+	Intron	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78452354A>G	uc002bdd.2	+						IDH3A_uc010umt.1_Intron|IDH3A_uc010umu.1_Intron|IDH3A_uc002bde.2_Intron|IDH3A_uc010umv.1_Intron|IDH3A_uc002bdf.2_Intron|IDH3A_uc002bdg.2_5'UTR	NM_005530	NP_005521	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha						carbohydrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NAD+) activity|magnesium ion binding|NAD binding				0					NADH(DB00157)	AAGTTGAAAAAGTTTGTTCAT	0.254													4	66	---	---	---	---	PASS
SRRM2	23524	broad.mit.edu	37	16	2809006	2809006	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2809006C>T	uc002crk.2	+	6	1163	c.614C>T	c.(613-615)CCT>CTT	p.P205L	SRRM2_uc002crj.1_Missense_Mutation_p.P109L|SRRM2_uc002crl.1_Missense_Mutation_p.P205L|SRRM2_uc010bsu.1_Missense_Mutation_p.P109L	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	205	Sufficient for RNA-binding.|Lys-rich.|Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						AGCAGCTCTCCTCGACGGGAG	0.473													82	261	---	---	---	---	PASS
SNX20	124460	broad.mit.edu	37	16	50701972	50701972	+	3'UTR	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50701972A>G	uc010vgp.1	-	4					SNX20_uc002egi.3_Intron|uc002egj.2_5'Flank	NM_153337	NP_699168	Q7Z614	SNX20_HUMAN	sorting nexin 20 isoform 2						cell communication|protein transport	endosome membrane|nucleus|plasma membrane	phosphatidylinositol binding|protein binding			ovary(1)	1						GAAAGCCAAGAGTGGGCAATC	0.582													14	44	---	---	---	---	PASS
CDH11	1009	broad.mit.edu	37	16	64981780	64981780	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64981780G>A	uc002eoi.2	-	13	2551	c.2117C>T	c.(2116-2118)CCT>CTT	p.P706L	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_3'UTR|CDH11_uc010vin.1_Missense_Mutation_p.P580L	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	706	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CCGGAGCCCAGGTCTAGGCAT	0.517			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			41	117	---	---	---	---	PASS
ZFHX3	463	broad.mit.edu	37	16	72993014	72993014	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72993014T>A	uc002fck.2	-	2	1704	c.1031A>T	c.(1030-1032)AAC>ATC	p.N344I	ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	344					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				AAAGTTTTTGTTTTTTGGTTC	0.428													31	125	---	---	---	---	PASS
GLG1	2734	broad.mit.edu	37	16	74497273	74497273	+	Silent	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74497273G>A	uc002fcy.3	-	20	2822	c.2772C>T	c.(2770-2772)CGC>CGT	p.R924R	GLG1_uc002fcx.2_Silent_p.R924R|GLG1_uc002fcw.3_Silent_p.R913R|GLG1_uc002fcz.3_Silent_p.R341R	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3	924	Cys-rich GLG1 14.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						GGGTGATCTGGCGCTTGGTTA	0.458													6	754	---	---	---	---	PASS
NT5M	56953	broad.mit.edu	37	17	17250185	17250185	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17250185T>C	uc002grf.2	+	5	796	c.611T>C	c.(610-612)CTG>CCG	p.L204P	NT5M_uc002gre.2_Missense_Mutation_p.C203R|NT5M_uc002grg.2_Missense_Mutation_p.L210P	NM_020201	NP_064586	Q9NPB1	NT5M_HUMAN	5',3'-nucleotidase, mitochondrial precursor	204					DNA replication|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	5'-nucleotidase activity|metal ion binding|nucleotide binding				0						CACCTGCAGCTGCAGCCCCCC	0.672													3	8	---	---	---	---	PASS
TLCD1	116238	broad.mit.edu	37	17	27052361	27052361	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27052361C>G	uc002hco.2	-	3	436	c.321G>C	c.(319-321)CAG>CAC	p.Q107H	TLCD1_uc010waw.1_Missense_Mutation_p.Q60H	NM_138463	NP_612472	Q96CP7	TLCD1_HUMAN	TLC domain containing 1 isoform 1	107	TLC.					integral to membrane					0	Lung NSC(42;0.00431)					AGGCTCGCGTCTGTCCGCTAG	0.517													7	21	---	---	---	---	PASS
STAT5A	6776	broad.mit.edu	37	17	40453310	40453310	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40453310A>G	uc002hzj.1	+	10	1649	c.1007A>G	c.(1006-1008)AAG>AGG	p.K336R	STAT5A_uc010cya.1_Missense_Mutation_p.K336R|STAT5A_uc010cyb.1_Missense_Mutation_p.K336R|STAT5A_uc010cyc.1_Missense_Mutation_p.K306R	NM_003152	NP_003143	P42229	STA5A_HUMAN	signal transducer and activator of transcription	336					2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)		ATCATTGAGAAGCAGCCTCCT	0.612													5	116	---	---	---	---	PASS
MPP3	4356	broad.mit.edu	37	17	41903162	41903162	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41903162C>G	uc002iei.3	-	9	737	c.571G>C	c.(571-573)GTC>CTC	p.V191L	MPP3_uc002ieh.2_Missense_Mutation_p.V216L|MPP3_uc002iej.2_RNA|MPP3_uc010czi.1_Missense_Mutation_p.V191L|MPP3_uc010wik.1_Missense_Mutation_p.V216L	NM_001932	NP_001923	Q13368	MPP3_HUMAN	palmitoylated membrane protein 3	191	PDZ.				signal transduction	cell surface|integral to plasma membrane	guanylate kinase activity			large_intestine(1)|skin(1)	2		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		TTGTGCAGGACTGCGATCCCG	0.597													6	86	---	---	---	---	PASS
NMT1	4836	broad.mit.edu	37	17	43173564	43173564	+	Silent	SNP	A	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43173564A>C	uc002ihz.2	+	5	525	c.507A>C	c.(505-507)CTA>CTC	p.L169L	NMT1_uc002iia.2_RNA	NM_021079	NP_066565	P30419	NMT1_HUMAN	N-myristoyltransferase 1	169					activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|N-terminal protein myristoylation|protein lipoylation	actin cytoskeleton|cell junction|cytosol	glycylpeptide N-tetradecanoyltransferase activity				0		Prostate(33;0.155)				CTTTACAGCTAAAAGAACTGT	0.433													101	294	---	---	---	---	PASS
ZNF652	22834	broad.mit.edu	37	17	47394380	47394380	+	Silent	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47394380T>C	uc002iov.3	-	2	1172	c.708A>G	c.(706-708)AAA>AAG	p.K236K	ZNF652_uc002iow.2_Silent_p.K236K|ZNF652_uc002iou.3_Intron	NM_001145365	NP_001138837	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	236					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			CACACTTAGCTTTCTGGACTG	0.512													6	384	---	---	---	---	PASS
BPTF	2186	broad.mit.edu	37	17	65962753	65962753	+	Silent	SNP	T	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65962753T>A	uc002jgf.2	+	26	8581	c.8520T>A	c.(8518-8520)GGT>GGA	p.G2840G	BPTF_uc002jge.2_Silent_p.G2823G|BPTF_uc002jgg.2_Silent_p.G555G|BPTF_uc002jgh.2_Silent_p.G357G	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2966	Bromo.				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)			ATTATTATGGTGTTATTAAGG	0.348													9	525	---	---	---	---	PASS
CABLES1	91768	broad.mit.edu	37	18	20814600	20814600	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20814600T>C	uc002kuc.2	+	5	1117	c.1117T>C	c.(1117-1119)TCA>CCA	p.S373P	C18orf45_uc010xaq.1_Intron|CABLES1_uc002kub.2_Intron|CABLES1_uc002kud.2_Missense_Mutation_p.S108P	NM_001100619	NP_001094089	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1 isoform 2	373	Interacts with CDK3 (By similarity).				blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AGGAAGACAATCAACTGGTGC	0.502													59	196	---	---	---	---	PASS
ZNF407	55628	broad.mit.edu	37	18	72346773	72346773	+	Silent	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72346773T>C	uc002llw.2	+	1	3855	c.3798T>C	c.(3796-3798)GTT>GTC	p.V1266V	ZNF407_uc010xfc.1_Silent_p.V1266V|ZNF407_uc010dqu.1_Silent_p.V1266V|ZNF407_uc002llu.2_Silent_p.V1265V	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	1266					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		CTGTGCTCGTTGTGACAAGAA	0.562													19	54	---	---	---	---	PASS
ZNF562	54811	broad.mit.edu	37	19	9763689	9763689	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9763689C>A	uc010xks.1	-	6	1380	c.1217G>T	c.(1216-1218)GGG>GTG	p.G406V	ZNF562_uc002mly.2_Missense_Mutation_p.G406V|ZNF562_uc002mlx.2_Missense_Mutation_p.G334V|ZNF562_uc010xkt.1_Missense_Mutation_p.G369V|ZNF562_uc010xku.1_Missense_Mutation_p.G337V|ZNF562_uc010xkv.1_Missense_Mutation_p.G405V|ZNF562_uc010xkw.1_Missense_Mutation_p.G290V	NM_001130032	NP_001123504	Q6V9R5	ZN562_HUMAN	zinc finger protein 562 isoform a	406	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GAAGGTCTTCCCACATTCAAC	0.388													5	202	---	---	---	---	PASS
COL5A3	50509	broad.mit.edu	37	19	10112488	10112488	+	Missense_Mutation	SNP	C	T	T	rs139370027	byFrequency	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10112488C>T	uc002mmq.1	-	7	1005	c.919G>A	c.(919-921)GTC>ATC	p.V307I		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	307	Nonhelical 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)			GTGGAGGTGACGACCAAAGGC	0.582											OREG0025228	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	200	---	---	---	---	PASS
ZNF763	284390	broad.mit.edu	37	19	12089265	12089265	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12089265G>A	uc002msw.2	+	4	681	c.526G>A	c.(526-528)GAA>AAA	p.E176K	ZNF763_uc010xmf.1_Missense_Mutation_p.E196K|ZNF763_uc002msv.2_Missense_Mutation_p.E179K|ZNF763_uc010xmg.1_Missense_Mutation_p.E54K	NM_001012753	NP_001012771	Q0D2J5	ZN763_HUMAN	zinc finger protein 763	176	C2H2-type 2; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1						TGCTTGTAAAGAATGTGGAAA	0.418													45	108	---	---	---	---	PASS
RNASEH2A	10535	broad.mit.edu	37	19	12917911	12917911	+	Intron	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12917911G>A	uc002mvg.1	+						RNASEH2A_uc002mvf.1_5'UTR	NM_006397	NP_006388	O75792	RNH2A_HUMAN	ribonuclease H2, large subunit						DNA replication|RNA catabolic process	nucleus|ribonuclease H2 complex	metal ion binding|ribonuclease H activity|RNA binding			breast(2)|central_nervous_system(1)	3						CGAGGTGTGCGTCTGGGGAAG	0.602													13	35	---	---	---	---	PASS
CC2D1A	54862	broad.mit.edu	37	19	14034594	14034594	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14034594G>A	uc002mxo.2	+	17	2209	c.1910G>A	c.(1909-1911)CGC>CAC	p.R637H	CC2D1A_uc002mxp.2_Missense_Mutation_p.R637H|CC2D1A_uc010dzh.2_Missense_Mutation_p.R206H|CC2D1A_uc002mxq.1_Missense_Mutation_p.R282H	NM_017721	NP_060191	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	637					positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			CCCACCGCCCGCTTTGAGCAA	0.627													8	38	---	---	---	---	PASS
LSM4	25804	broad.mit.edu	37	19	18418165	18418165	+	3'UTR	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18418165G>A	uc002niq.2	-	5						NM_012321	NP_036453	Q9Y4Z0	LSM4_HUMAN	U6 snRNA-associated Sm-like protein 4						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|mRNA processing|RNA splicing	cytosol|U6 snRNP	protein binding|RNA binding				0						ACACGAAGGGGGTTCCCCCTG	0.557													2	2	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40376809	40376809	+	Silent	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40376809C>T	uc002omp.3	-	24	11621	c.11613G>A	c.(11611-11613)GGG>GGA	p.G3871G		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	3871	VWFD 9.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGGACAGTGGCCCTGTGGGGC	0.597													9	46	---	---	---	---	PASS
LILRA6	79168	broad.mit.edu	37	19	54744735	54744735	+	Silent	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54744735G>A	uc002qeu.1	-	5	1051	c.927C>T	c.(925-927)CCC>CCT	p.P309P	LILRB3_uc002qeh.1_Intron|LILRB3_uc002qeg.1_Intron|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Silent_p.P309P|LILRB3_uc010erh.1_Intron|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Silent_p.P309P|LILRA6_uc002qem.1_RNA|LILRB3_uc002qen.1_RNA|LILRB3_uc002qeo.1_Silent_p.P309P|LILRB3_uc002qep.1_Intron|LILRB3_uc002qeq.1_Silent_p.P309P|LILRB3_uc002qer.1_RNA|LILRB3_uc002qes.1_Intron|LILRA6_uc010yep.1_Silent_p.P309P|LILRA6_uc010yeq.1_Silent_p.P309P|LILRA6_uc002qet.3_RNA|LILRA6_uc002qev.1_Silent_p.P170P	NM_024318	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor,	309	Extracellular (Potential).|Ig-like C2-type 1.					integral to membrane	receptor activity			skin(2)	2	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGGGGTCGCTGGGGGCCGACC	0.677													7	28	---	---	---	---	PASS
ZNF814	730051	broad.mit.edu	37	19	58386268	58386268	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58386268G>T	uc002qqo.2	-	3	762	c.490C>A	c.(490-492)CAT>AAT	p.H164N	ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.1_Intron	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	164					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						CCTGACACATGCAACTTACAC	0.507													74	225	---	---	---	---	PASS
ANGPT4	51378	broad.mit.edu	37	20	896633	896633	+	Silent	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:896633G>A	uc002wei.2	-	1	328	c.225C>T	c.(223-225)AAC>AAT	p.N75N	ANGPT4_uc010zpn.1_Silent_p.N69N	NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4 precursor	75					anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2						GGTGCAGTGGGTTGGCCAGTG	0.607													22	75	---	---	---	---	PASS
C20orf194	25943	broad.mit.edu	37	20	3278767	3278767	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3278767G>C	uc002wii.2	-	22	1889	c.1838C>G	c.(1837-1839)CCT>CGT	p.P613R	C20orf194_uc002wij.3_Missense_Mutation_p.P352R|C20orf194_uc002wik.2_Missense_Mutation_p.P287R	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943	613											0						TGGGAGGTGAGGAAGCAATGA	0.428													88	310	---	---	---	---	PASS
GGTLC1	92086	broad.mit.edu	37	20	23966339	23966339	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23966339G>A	uc002wts.2	-	5	629	c.496C>T	c.(496-498)CCC>TCC	p.P166S	GGTLC1_uc002wtu.2_Missense_Mutation_p.P166S	NM_178312	NP_842564	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	166							gamma-glutamyltransferase activity			ovary(1)	1						GTGACGTTGGGCAGAAGCTGG	0.617													19	73	---	---	---	---	PASS
NCOA5	57727	broad.mit.edu	37	20	44692013	44692013	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44692013G>A	uc002xrd.2	-	6	1664	c.1136C>T	c.(1135-1137)ACC>ATC	p.T379I	NCOA5_uc002xrc.2_Missense_Mutation_p.T267I|NCOA5_uc002xre.2_Missense_Mutation_p.T379I	NM_020967	NP_066018	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	379					regulation of transcription, DNA-dependent|transcription, DNA-dependent|translation	nucleus	aminoacyl-tRNA ligase activity|ATP binding			central_nervous_system(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)				CAGAGAGTCGGTGCTGCTCCT	0.572													11	35	---	---	---	---	PASS
ADAMTS5	11096	broad.mit.edu	37	21	28337626	28337626	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28337626G>A	uc002ymg.2	-	1	1814	c.1085C>T	c.(1084-1086)GCT>GTT	p.A362V		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	362	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						AAACAGGATAGCTGCATCGTA	0.552													18	59	---	---	---	---	PASS
KIAA1644	85352	broad.mit.edu	37	22	44645504	44645504	+	3'UTR	SNP	G	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44645504G>T	uc003bet.2	-	5						NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor							integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				GTTCTTCTCGGAGGCTGCACC	0.522													7	96	---	---	---	---	PASS
RAI2	10742	broad.mit.edu	37	X	17819773	17819773	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17819773C>T	uc004cyf.2	-	3	928	c.358G>A	c.(358-360)GTG>ATG	p.V120M	RAI2_uc004cyg.2_Missense_Mutation_p.V120M|RAI2_uc010nfa.2_Missense_Mutation_p.V120M|RAI2_uc004cyh.3_Missense_Mutation_p.V120M|RAI2_uc011miy.1_Missense_Mutation_p.V70M	NM_021785	NP_068557	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	120					embryo development					ovary(1)|breast(1)	2	Hepatocellular(33;0.183)					GGCAGTTGCACGGGGCCCTGG	0.617													13	13	---	---	---	---	PASS
ITIH5L	347365	broad.mit.edu	37	X	54785277	54785277	+	Silent	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54785277G>A	uc004dtj.2	-	8	1260	c.1230C>T	c.(1228-1230)ATC>ATT	p.I410I		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	inter-alpha (globulin) inhibitor H5-like	410	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|skin(2)|ovary(1)|breast(1)	6						CATTGGAGAGGATCACACTGG	0.627													14	17	---	---	---	---	PASS
SPANXN2	494119	broad.mit.edu	37	X	142803720	142803720	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142803720T>C	uc004fbz.2	-	1	797	c.43A>G	c.(43-45)AGC>GGC	p.S15G		NM_001009615	NP_001009615	Q5MJ10	SPXN2_HUMAN	SPANX-N2 protein	15										ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					TCACAGGGGCTCTTCCTCTTC	0.308													7	542	---	---	---	---	PASS
UBE2NL	389898	broad.mit.edu	37	X	142967736	142967736	+	3'UTR	SNP	A	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142967736A>T	uc004fca.2	+	1						NM_001012989	NP_001013007	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like								acid-amino acid ligase activity				0	Acute lymphoblastic leukemia(192;6.56e-05)					CTTGCATTTAATGGACATAGT	0.333													3	37	---	---	---	---	PASS
CSAG1	158511	broad.mit.edu	37	X	151909301	151909301	+	3'UTR	SNP	G	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151909301G>A	uc004fge.2	+	5					CSAG1_uc004fgf.2_3'UTR|CSAG1_uc004fgd.2_RNA	NM_153478	NP_705611	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1 precursor											ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					ATCAAAATGCGCCACAGCAGG	0.537													28	15	---	---	---	---	PASS
ESPNP	284729	broad.mit.edu	37	1	17022494	17022495	+	Intron	DEL	GT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17022494_17022495delGT	uc001azn.1	-							NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						GCTGCTGGGGGTGTGTGTGGAG	0.361													4	2	---	---	---	---	
NBPF3	84224	broad.mit.edu	37	1	21791623	21791624	+	Intron	INS	-	C	C	rs144217242	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21791623_21791624insC	uc001ber.2	+						NBPF3_uc001bes.2_Intron|NBPF3_uc009vqb.2_Intron|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3							cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ATTTCCTTTTTTCAGAaatgag	0.183													2	4	---	---	---	---	
RUNX3	864	broad.mit.edu	37	1	25266886	25266886	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25266886delC	uc009vrj.2	-						RUNX3_uc001bjr.2_Intron|RUNX3_uc009vrk.2_Intron|RUNX3_uc009vrl.1_Intron	NM_001031680	NP_001026850	Q13761	RUNX3_HUMAN	runt-related transcription factor 3 isoform 1						cell proliferation|induction of apoptosis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|protein phosphorylation|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		gctctgggttcccaccttgcc	0.114													4	2	---	---	---	---	
MTF1	4520	broad.mit.edu	37	1	38300439	38300440	+	Intron	DEL	AA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38300439_38300440delAA	uc001cce.1	-						MTF1_uc009vvj.1_Intron	NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				agtgtgagggaaaaaagagtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	46968844	46968844	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46968844delT								FAAH (89324 upstream) : DMBX1 (3824 downstream)																							gtccttgctgttacctctgcc	0.000													4	2	---	---	---	---	
CYP4B1	1580	broad.mit.edu	37	1	47280497	47280498	+	Intron	INS	-	AACT	AACT	rs3841797		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47280497_47280498insAACT	uc001cqm.3	+						CYP4B1_uc009vyl.1_Intron|CYP4B1_uc001cqn.3_Intron|CYP4B1_uc009vym.2_Intron|CYP4B1_uc010omk.1_Intron	NM_000779	NP_000770	P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)					ccagtgagcagaacagtcaggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55392961	55392964	+	IGR	DEL	ACAC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55392961_55392964delACAC								DHCR24 (40040 upstream) : TMEM61 (53501 downstream)																							ATacacacatacacacacacacac	0.363													4	2	---	---	---	---	
BSND	7809	broad.mit.edu	37	1	55466875	55466876	+	Intron	DEL	GT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55466875_55466876delGT	uc001cye.2	+							NM_057176	NP_476517	Q8WZ55	BSND_HUMAN	barttin							basolateral plasma membrane|cytoplasm|integral to plasma membrane|protein complex				ovary(1)|skin(1)	2						CAGTGGGATCgtgtgtgtgtgt	0.233													3	3	---	---	---	---	
FGGY	55277	broad.mit.edu	37	1	59812470	59812470	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59812470delT	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron	NM_018291	NP_060761	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)					tccaaaatcATTTTTTTTtaa	0.000													4	2	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64260932	64260932	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64260932delA	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						TTGCAAGGGGAAAAATTGGCT	0.443													4	2	---	---	---	---	
IL12RB2	3595	broad.mit.edu	37	1	67787765	67787766	+	Intron	DEL	TC	-	-	rs71945445		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67787765_67787766delTC	uc001ddu.2	+						IL12RB2_uc010oqi.1_Intron|IL12RB2_uc010oqj.1_Intron|IL12RB2_uc010oqk.1_Intron|IL12RB2_uc010oql.1_Intron|IL12RB2_uc010oqm.1_Intron|IL12RB2_uc010oqn.1_Intron	NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor						positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3						ATTTGGCAAGtctctctctctc	0.342													4	2	---	---	---	---	
ASB17	127247	broad.mit.edu	37	1	76390179	76390180	+	Intron	DEL	CT	-	-	rs143012860		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76390179_76390180delCT	uc001dhe.1	-						ASB17_uc001dhf.1_Intron	NM_080868	NP_543144	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box-containing 17						intracellular signal transduction					ovary(1)	1						TTTGTCATAACTCTGTCACTGG	0.218													4	2	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	81964482	81964482	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81964482delA	uc001dis.2	+									O95490	LPHN2_HUMAN	SubName: Full=cDNA FLJ41428 fis, clone BRHIP2005236, highly similar to Latrophilin-2;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		TTGGGGAAAGAAAAAAAAAAT	0.313													3	3	---	---	---	---	
DPYD	1806	broad.mit.edu	37	1	98060470	98060470	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98060470delT	uc001drv.2	-							NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	ATACCCGGCCTTTTTTTTTTT	0.323													17	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98573685	98573685	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98573685delT								MIR137 (61958 upstream) : SNX7 (553551 downstream)																							cagagaggcattaaggagaac	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102535254	102535255	+	IGR	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102535254_102535255insT								OLFM3 (72464 upstream) : COL11A1 (806769 downstream)																							GTCTTTCATTCTTTTTTTCCTT	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143420942	143420942	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143420942delA								None (None upstream) : LOC100286793 (226697 downstream)																							TGTTCACCTTAAAAAAAATTG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143537017	143537019	+	IGR	DEL	AAA	-	-	rs3059621		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143537017_143537019delAAA								None (None upstream) : LOC100286793 (110620 downstream)																							aaaacaaaacaaaacCCCAGATT	0.069													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144009132	144009132	+	Intron	DEL	G	-	-	rs11364742		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144009132delG	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		tttttaatctgtttttttcag	0.204													4	6	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144678541	144678541	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144678541delT	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						ttccagggtatttttttttta	0.000													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144945778	144945778	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144945778delT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_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)		ACCCAGCACATTTTCAAGGAC	0.318			T	PDGFRB	MPD								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148898509	148898510	+	Intron	DEL	TG	-	-	rs150514410	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148898509_148898510delTG	uc009wkv.1	+											Homo sapiens cDNA, FLJ17483.																		ttttaccccatgttttttttat	0.000													6	5	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154823232	154823232	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154823232delT	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron|KCNN3_uc009wox.1_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			ATCTTTAGCGTTTTGTATCAT	0.428													4	2	---	---	---	---	
ADAM15	8751	broad.mit.edu	37	1	155024606	155024606	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155024606delG	uc001fgr.1	+						uc001fgo.2_5'Flank|ADAM15_uc001fgq.1_5'UTR|ADAM15_uc009wpc.1_Intron|ADAM15_uc010pet.1_Intron|ADAM15_uc010peu.1_Intron|ADAM15_uc001fgt.1_Intron|ADAM15_uc010pev.1_Intron|ADAM15_uc001fgs.1_Intron|ADAM15_uc001fgu.1_Intron|ADAM15_uc001fgw.1_Intron|ADAM15_uc001fgv.1_Intron|ADAM15_uc001fgx.1_Intron|ADAM15_uc001fgz.1_Intron|ADAM15_uc001fgy.1_Intron|ADAM15_uc001fha.1_Intron	NM_207197	NP_997080	Q13444	ADA15_HUMAN	a disintegrin and metalloproteinase domain 15						angiogenesis|cell-matrix adhesion|collagen catabolic process|proteolysis	acrosomal vesicle|adherens junction|endomembrane system|flagellum|integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			central_nervous_system(3)|skin(2)|ovary(1)	6	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			ATTGTGTGTTGGGGGGGTGGG	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	164221478	164221478	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164221478delT								NUF2 (895925 upstream) : PBX1 (307324 downstream)																							tgccagggtatttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168559470	168559470	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168559470delA								XCL1 (8155 upstream) : DPT (105237 downstream)																							ATGTCCTTTTAAAAACATTTT	0.408													4	2	---	---	---	---	
PRRX1	5396	broad.mit.edu	37	1	170674259	170674260	+	Intron	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170674259_170674260insT	uc001ghf.2	+						PRRX1_uc001ghe.2_Intron	NM_022716	NP_073207	P54821	PRRX1_HUMAN	paired mesoderm homeobox 1 isoform pmx-1b							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GTACCCCATTCTTTTTTTTTGT	0.381													4	2	---	---	---	---	
FMO1	2326	broad.mit.edu	37	1	171218843	171218844	+	Intron	DEL	TG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171218843_171218844delTG	uc009wvz.2	+						FMO1_uc010pme.1_Intron|FMO1_uc001ghl.2_Intron	NM_002021	NP_002012	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1						NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum lumen|integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					tgtgtgtgtatgtgtgtgtgtg	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	175791319	175791319	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175791319delC								TNR (78567 upstream) : RFWD2 (122648 downstream)																							TTTGCCTTATCCCCCTGTATT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177781494	177781494	+	IGR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177781494delG								FAM5B (529937 upstream) : SEC16B (115995 downstream)																							GTATGTATCTGGGGCATCAGG	0.348													4	2	---	---	---	---	
RALGPS2	55103	broad.mit.edu	37	1	178752474	178752474	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178752474delA	uc001glz.2	+						RALGPS2_uc001gly.1_Intron|RALGPS2_uc010pnb.1_Intron	NM_152663	NP_689876	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0						aaatagaatgaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	181325143	181325143	+	IGR	DEL	T	-	-	rs34486250		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181325143delT								IER5 (265166 upstream) : CACNA1E (127573 downstream)																							TTTTTGCTCATTTTTTTTGGC	0.338													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	185565488	185565488	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185565488delA	uc001gro.2	-											Homo sapiens clone IMAGp998C217408Q2 mRNA sequence.																		tatgaggggtAAAAAATAAGA	0.199													4	2	---	---	---	---	
PPP1R12B	4660	broad.mit.edu	37	1	202318343	202318343	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202318343delG	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)			GCCACCCCATGGGGAGTATCA	0.547													4	2	---	---	---	---	
LGTN	1939	broad.mit.edu	37	1	206766820	206766823	+	Intron	DEL	GAGC	-	-	rs141098886		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206766820_206766823delGAGC	uc001heh.2	-						LGTN_uc009xbw.2_Intron	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin						intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			gagagagagagagcgcgagagaga	0.211													8	4	---	---	---	---	
CD55	1604	broad.mit.edu	37	1	207508098	207508099	+	Intron	INS	-	AA	AA	rs144436733	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207508098_207508099insAA	uc001hfq.3	+						CD55_uc001hfp.3_Intron|CD55_uc001hfr.3_Intron|CD55_uc010psf.1_Intron|CD55_uc009xcf.2_Intron|CD55_uc009xce.2_Intron|CD55_uc009xcg.2_Intron	NM_000574	NP_000565	P08174	DAF_HUMAN	decay accelerating factor for complement isoform						complement activation, classical pathway|elevation of cytosolic calcium ion concentration|innate immune response|respiratory burst	anchored to membrane|extracellular region|integral to plasma membrane|membrane raft|soluble fraction	receptor activity			ovary(1)	1					Chloramphenicol(DB00446)	caaaagagaacgagagagagag	0.000													2	4	---	---	---	---	
SPATA17	128153	broad.mit.edu	37	1	217992766	217992767	+	Intron	INS	-	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217992766_217992767insC	uc001hlh.1	+						SPATA17_uc001hli.2_Intron	NM_138796	NP_620151	Q96L03	SPT17_HUMAN	spermatogenesis associated 17							cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		catctttctctctctatctctc	0.149													4	2	---	---	---	---	
EPRS	2058	broad.mit.edu	37	1	220207221	220207222	+	Intron	INS	-	T	T	rs71871201		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220207221_220207222insT	uc001hly.1	-						EPRS_uc010puf.1_Intron|EPRS_uc001hlz.1_Intron|EPRS_uc009xdt.1_Intron	NM_004446	NP_004437	P07814	SYEP_HUMAN	glutamyl-prolyl tRNA synthetase						glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)	ATGCTTTCTGCTTTTTTTTTTT	0.322													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222010799	222010799	+	IGR	DEL	T	-	-	rs71678974		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222010799delT								DUSP10 (95338 upstream) : HHIPL2 (684803 downstream)																							AAACTATGCATTTTTTTTCAG	0.174													3	3	---	---	---	---	
NVL	4931	broad.mit.edu	37	1	224461408	224461408	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224461408delA	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_Intron	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)		GGAAAGGAATAAAATCCAGAG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	224743476	224743476	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224743476delT								WDR26 (121744 upstream) : CNIH3 (60703 downstream)																							gagctaatcctttttttttcc	0.020													4	2	---	---	---	---	
ZNF678	339500	broad.mit.edu	37	1	227822348	227822349	+	Intron	DEL	GA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227822348_227822349delGA	uc001hqw.1	+						ZNF678_uc009xet.1_Intron|ZNF678_uc009xeu.1_Intron	NM_178549	NP_848644	F5GXA7	F5GXA7_HUMAN	zinc finger protein 678						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			pancreas(1)	1		Prostate(94;0.0885)				acaaaatgaggagagagagaag	0.000													4	2	---	---	---	---	
KCNK1	3775	broad.mit.edu	37	1	233769112	233769112	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233769112delT	uc010pxo.1	+						KCNK1_uc001hvw.2_Intron|KCNK1_uc001hvx.2_Intron	NM_002245	NP_002236	O00180	KCNK1_HUMAN	potassium channel, subfamily K, member 1							voltage-gated potassium channel complex	inward rectifier potassium channel activity			central_nervous_system(1)	1		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine(DB00908)	TTCATGTAGGTTATCATGTTA	0.318													4	2	---	---	---	---	
EFCAB2	84288	broad.mit.edu	37	1	245180866	245180867	+	Intron	INS	-	A	A	rs138222140	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245180866_245180867insA	uc001ibd.2	+						EFCAB2_uc001ibc.2_Intron|EFCAB2_uc010pyo.1_Intron|EFCAB2_uc010pyp.1_Intron|EFCAB2_uc001ibe.2_Intron	NR_026586		Q5VUJ9	EFCB2_HUMAN	RecName: Full=EF-hand calcium-binding domain-containing protein 2;								calcium ion binding				0	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			TTCCAACCTATAATTGTAAACT	0.243													5	5	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245826190	245826190	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245826190delT	uc001ibf.1	+						KIF26B_uc001ibg.1_Intron|KIF26B_uc001ibh.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCCTTGCTTGTTTTTTTGTAC	0.428													4	2	---	---	---	---	
SMYD3	64754	broad.mit.edu	37	1	245954120	245954120	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245954120delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		CCAAGACTGGATGACTCTGTT	0.383													3	3	---	---	---	---	
TPO	7173	broad.mit.edu	37	2	1444153	1444154	+	Intron	INS	-	C	C	rs148134283	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1444153_1444154insC	uc002qww.2	+						TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Intron|TPO_uc002qwr.2_Intron|TPO_uc002qwx.2_Intron|TPO_uc010yio.1_Intron|TPO_uc010yip.1_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a						cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GGTTTCTAAGGCTTGTTTTTCC	0.351													3	3	---	---	---	---	
RNF144A	9781	broad.mit.edu	37	2	7180601	7180601	+	3'UTR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7180601delT	uc002qys.2	+	9					RNF144A_uc002qyt.2_3'UTR	NM_014746	NP_055561	P50876	R144A_HUMAN	ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		TATTGTTGCATTTCCTTGATA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	9893587	9893588	+	IGR	DEL	AC	-	-	rs140540598		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9893587_9893588delAC								YWHAQ (122481 upstream) : TAF1B (89983 downstream)																							GCAAGTGCAGacacacacacac	0.485													2	4	---	---	---	---	
PLB1	151056	broad.mit.edu	37	2	28719379	28719379	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28719379delT	uc002rmb.1	+						PLB1_uc010ezj.1_Intron	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)					tggaccttgatttttttcatc	0.219													4	2	---	---	---	---	
CDKL4	344387	broad.mit.edu	37	2	39440878	39440878	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39440878delA	uc002rrm.2	-						CDKL4_uc010fal.1_Intron	NM_001009565	NP_001009565	Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)				gtaaaggaataaaaaaaagaa	0.194													4	2	---	---	---	---	
SLC8A1	6546	broad.mit.edu	37	2	40645011	40645012	+	Intron	DEL	AC	-	-	rs111437189		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40645011_40645012delAC	uc002rrx.2	-						SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron|SLC8A1_uc002rsb.1_Intron	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TTGGATGGATacacacacacac	0.327													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53036696	53036696	+	IGR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53036696delG								None (None upstream) : ASB3 (860422 downstream)																							tggggattatggggacaattc	0.085													4	2	---	---	---	---	
TET3	200424	broad.mit.edu	37	2	74272683	74272683	+	5'Flank	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74272683delA	uc002skb.3	+						TET3_uc010fez.1_5'Flank	NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3								metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						GTGCTTGGGGAGAGGCCTGAA	0.498													4	2	---	---	---	---	
DCTN1	1639	broad.mit.edu	37	2	74595418	74595418	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74595418delA	uc002skx.2	-						DCTN1_uc002skv.2_Intron|DCTN1_uc002sku.2_Intron|DCTN1_uc002skw.1_Intron|DCTN1_uc010ffd.2_Intron|DCTN1_uc002sky.2_Intron	NM_004082	NP_004073	Q14203	DCTN1_HUMAN	dynactin 1 isoform 1						cell death|G2/M transition of mitotic cell cycle|mitosis|nervous system development	centrosome|cytosol|kinetochore|microtubule|spindle pole	motor activity|protein binding			ovary(3)|skin(2)	5						TTGCATGGGGAAAGGGTAGTG	0.423													4	2	---	---	---	---	
LRRTM4	80059	broad.mit.edu	37	2	77282308	77282310	+	Intron	DEL	CTG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77282308_77282310delCTG	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		ACAGCCTGCCCTGCTGCTTTCTC	0.507													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91769732	91769733	+	IGR	INS	-	AATC	AATC	rs113868867		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91769732_91769733insAATC								None (None upstream) : LOC654342 (35459 downstream)																							AGGCAGTGATGAATCAGACAGT	0.554													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91801453	91801454	+	IGR	INS	-	T	T	rs149695974		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91801453_91801454insT								None (None upstream) : LOC654342 (3738 downstream)																							tgatttcattcttttttaaggc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91802160	91802161	+	IGR	INS	-	G	G	rs140424741		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91802160_91802161insG								None (None upstream) : LOC654342 (3031 downstream)																							aggttTCtcttgcctttttaaa	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96614105	96614106	+	Intron	INS	-	G	G	rs139182099		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96614105_96614106insG	uc010yug.1	-											Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		ATTTGCAAAGTAAAAAAAAATT	0.267													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106880765	106880766	+	IGR	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106880765_106880766insA								UXS1 (69970 upstream) : PLGLA (122003 downstream)																							CAGTGGATTTGAAAAAAAAATG	0.450													4	2	---	---	---	---	
ACOXL	55289	broad.mit.edu	37	2	111720896	111720897	+	Intron	INS	-	A	A	rs150940046	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111720896_111720897insA	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0						AAGAACGAGGTAAAAAAAAAAT	0.351													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119391079	119391080	+	IGR	DEL	CT	-	-	rs113248956		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119391079_119391080delCT								INSIG2 (523483 upstream) : EN1 (208668 downstream)																							ctctctctcgctctctctctct	0.485													4	2	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121534033	121534033	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121534033delT	uc010yyu.1	+						GLI2_uc002tmp.1_Intron			P10070	GLI2_HUMAN	SubName: Full=cDNA FLJ60878, highly similar to Homo sapiens GLI-Kruppel family member GLI2, mRNA;						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				TAGATGCATATTTTTCTTCTG	0.562													4	2	---	---	---	---	
ARHGAP15	55843	broad.mit.edu	37	2	144102737	144102737	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144102737delA	uc002tvm.3	+						ARHGAP15_uc010zbl.1_Intron	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		ATTTCCTAGTAATGTGATTTA	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	144590068	144590068	+	IGR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144590068delG								ARHGAP15 (64148 upstream) : GTDC1 (113515 downstream)																							TGAAGGAGGAGGGAAGGTGGT	0.303													4	2	---	---	---	---	
GALNT13	114805	broad.mit.edu	37	2	155252845	155252845	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155252845delA	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_Intron|GALNT13_uc010fod.2_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						AACATTGAACAAAAAAAAAAT	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157943272	157943272	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157943272delT								GPD2 (473025 upstream) : GALNT5 (171068 downstream)																							GTATGGATACTTTTTTTTTTa	0.154													4	3	---	---	---	---	
TANC1	85461	broad.mit.edu	37	2	160032684	160032685	+	Intron	DEL	TG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160032684_160032685delTG	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc002uai.1_5'Flank	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3						CTTTTGGCTCTGTGCTCCAGTT	0.332													7	5	---	---	---	---	
BAZ2B	29994	broad.mit.edu	37	2	160540399	160540399	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160540399delT	uc002uau.1	-									Q9UIF8	BAZ2B_HUMAN	SubName: Full=Putative uncharacterized protein DKFZp686H10114;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						ctacaaagtcttttttgcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	184602126	184602126	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184602126delC								NUP35 (575719 upstream) : ZNF804A (860967 downstream)																							tcatcattttccaagtggtta	0.109													4	2	---	---	---	---	
DNAH7	56171	broad.mit.edu	37	2	196712335	196712335	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196712335delA	uc002utj.3	-							NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						ttggttatgtaaaaaacctgc	0.085													4	2	---	---	---	---	
CPO	130749	broad.mit.edu	37	2	207803981	207803981	+	5'Flank	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207803981delT	uc002vby.2	+							NM_173077	NP_775100	Q8IVL8	CBPO_HUMAN	carboxypeptidase O precursor						proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			large_intestine(1)|ovary(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		GCAGGAATGATTGCTCCTGAG	0.458													4	2	---	---	---	---	
VWC2L	402117	broad.mit.edu	37	2	215316879	215316880	+	Intron	DEL	TG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215316879_215316880delTG	uc002vet.2	+						VWC2L_uc010zjl.1_Intron	NM_001080500	NP_001073969	B2RUY7	VWC2L_HUMAN	von Willebrand factor C domain-containing							extracellular region					0						tttggctttttGTGTGTGTGTT	0.045													4	2	---	---	---	---	
CCDC108	255101	broad.mit.edu	37	2	219877735	219877735	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219877735delA	uc002vjl.1	-							NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1							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)		TTGCTAAAGGAAAAAAAAATC	0.264													4	2	---	---	---	---	
RAD18	56852	broad.mit.edu	37	3	8955647	8955648	+	Intron	INS	-	AGTCA	AGTCA	rs144181000	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8955647_8955648insAGTCA	uc003brd.2	-						RAD18_uc003bre.2_Intron	NM_020165	NP_064550	Q9NS91	RAD18_HUMAN	postreplication repair protein hRAD18p						DNA repair	nucleus|replication fork	damaged DNA binding|ligase activity|ubiquitin protein ligase binding|Y-form DNA binding|zinc ion binding			skin(3)|ovary(2)	5				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		ATAACCACAAGAGTCAAGTCAT	0.272								Rad6_pathway					3	7	---	---	---	---	
RBMS3	27303	broad.mit.edu	37	3	29895431	29895431	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29895431delC	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)				ATTCTGGTAGCCCCAGGTGCC	0.517													4	2	---	---	---	---	
SMARCC1	6599	broad.mit.edu	37	3	47768998	47768998	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47768998delA	uc003crq.2	-						SMARCC1_uc011bbd.1_Intron	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		actacatctcaaaaaaaaaat	0.055													4	2	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52584515	52584515	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52584515delA	uc003des.2	-	29	4831	c.4819delT	c.(4819-4821)TCAfs	p.S1607fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.S1500fs|PBRM1_uc003der.2_Frame_Shift_Del_p.S1520fs|PBRM1_uc003det.2_Frame_Shift_Del_p.S1515fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.S1570fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.S1552fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.S1527fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.S1500fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1607					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TAGGCCTCTGAGTGAAGAAGC	0.522			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								156	71	---	---	---	---	
ERC2	26059	broad.mit.edu	37	3	55744382	55744383	+	Intron	INS	-	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55744382_55744383insC	uc003dhr.1	-						ERC2_uc003dhq.1_Intron	NM_015576	NP_056391	O15083	ERC2_HUMAN	cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		GCGATAACTTACCCCCCCAAAG	0.411													4	2	---	---	---	---	
CNTN3	5067	broad.mit.edu	37	3	74418792	74418792	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74418792delA	uc003dpm.1	-							NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor						cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		AATGAACAAGAAAAAAAAAAA	0.274													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	77726235	77726235	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77726235delA								ROBO2 (29574 upstream) : ROBO1 (920153 downstream)																							TAGATGGGCTAAGTAAAGTAT	0.468													4	2	---	---	---	---	
EPHA6	285220	broad.mit.edu	37	3	97325217	97325217	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97325217delA	uc010how.1	+						EPHA6_uc011bgo.1_Intron|EPHA6_uc011bgp.1_Intron|EPHA6_uc003drs.3_Intron|EPHA6_uc003drr.3_Intron|EPHA6_uc003drt.2_Intron|EPHA6_uc010hox.1_Intron	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						TGAGCAAGAGAAAGCAAAGGC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	101635146	101635146	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101635146delA								NFKBIZ (55281 upstream) : LOC152225 (24557 downstream)																							tttctgctggaaaaatgacca	0.035													4	2	---	---	---	---	
ZPLD1	131368	broad.mit.edu	37	3	102057510	102057510	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102057510delG	uc003dvs.1	+							NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1							integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5						TTGTTTTGGTGGGATAGCTGT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103968625	103968625	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103968625delC								None (None upstream) : None (None downstream)																							ATTAGAGCTTCCATTTTTTGC	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	106099616	106099616	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106099616delA								CBLB (511350 upstream) : LOC100302640 (456044 downstream)																							agatttctgcaaaaaaatgtt	0.050													4	2	---	---	---	---	
GTPBP8	29083	broad.mit.edu	37	3	112712193	112712196	+	Intron	DEL	TCTT	-	-	rs140713370		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112712193_112712196delTCTT	uc003dzn.2	+						GTPBP8_uc011bhy.1_Intron|GTPBP8_uc003dzp.2_Intron|GTPBP8_uc003dzo.2_Intron	NM_014170	NP_054889	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 isoform 1						barrier septum formation		GTP binding				0						CTTCAGAAAGTCTTTCTTTATCCA	0.328													5	7	---	---	---	---	
SIDT1	54847	broad.mit.edu	37	3	113292362	113292362	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113292362delG	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5						agaaatccctgggggttaagt	0.000													4	2	---	---	---	---	
UROC1	131669	broad.mit.edu	37	3	126219214	126219214	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126219214delA	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)		gcaactccctaaacaagcatt	0.259													4	2	---	---	---	---	
TMEM108	66000	broad.mit.edu	37	3	133072834	133072834	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133072834delT	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epj.1_Intron|TMEM108_uc003epk.2_Intron	NM_023943	NP_076432	Q6UXF1	TM108_HUMAN	transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4						TTAAGCTTGCTTAGCAATAAG	0.473													4	2	---	---	---	---	
STAG1	10274	broad.mit.edu	37	3	136413643	136413643	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136413643delA	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.1_Intron|STAG1_uc003ere.2_Intron	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						GCCTAATAATAAAGGGAAAAG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	153077477	153077478	+	IGR	DEL	TT	-	-	rs67476107		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153077477_153077478delTT								RAP2B (191216 upstream) : C3orf79 (124806 downstream)																							AATTATGCCCTTTTGGTCTTCC	0.361													1	5	---	---	---	---	
PLCH1	23007	broad.mit.edu	37	3	155314368	155314368	+	Intron	DEL	A	-	-	rs62708860		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155314368delA	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TTACTAACAGAAAAAAAAAAA	0.328													4	2	---	---	---	---	
FXR1	8087	broad.mit.edu	37	3	180676028	180676028	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180676028delT	uc003fkq.2	+						FXR1_uc003fkp.2_Intron|FXR1_uc003fkr.2_Intron|FXR1_uc011bqj.1_Intron|FXR1_uc003fks.2_Intron|FXR1_uc011bqk.1_Intron|FXR1_uc011bql.1_Intron	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1						apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			CCAAAAGGAAttttttttttc	0.149													4	2	---	---	---	---	
MCF2L2	23101	broad.mit.edu	37	3	182912742	182912742	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182912742delT	uc003fli.1	-							NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			aatttttgtatttttttttgt	0.000													4	2	---	---	---	---	
TRA2B	6434	broad.mit.edu	37	3	185637503	185637503	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185637503delA	uc003fpv.2	-						TRA2B_uc003fpt.2_Intron|TRA2B_uc003fpu.2_Intron|TRA2B_uc010hym.2_Intron|TRA2B_uc003fpw.2_Intron	NM_004593	NP_004584	P62995	TRA2B_HUMAN	splicing factor, arginine/serine-rich 10						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)	2						AAATGCTCTTAAAAAAAAAAA	0.328													4	2	---	---	---	---	
DGKG	1608	broad.mit.edu	37	3	186038536	186038536	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186038536delA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TGAGAATGTTAAAAAAAAAAG	0.398													6	3	---	---	---	---	
PPP2R2C	5522	broad.mit.edu	37	4	6536185	6536186	+	Intron	DEL	AC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6536185_6536186delAC	uc011bwd.1	-						PPP2R2C_uc011bwe.1_Intron	NM_181876	NP_870991	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						acacacaccaacacacacaccc	0.000													4	2	---	---	---	---	
AFAP1	60312	broad.mit.edu	37	4	7811103	7811103	+	Intron	DEL	T	-	-	rs112743348		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7811103delT	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0						TAAAGGGAAATTTTTTTTTTT	0.323													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13659429	13659429	+	RNA	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13659429delA	uc003gna.1	+	2		c.232delA								Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																		AGATATTGGCAATTTGGAGCA	0.393													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	31247532	31247532	+	IGR	DEL	A	-	-	rs71651578		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31247532delA								PCDH7 (99111 upstream) : None (None downstream)																							tcaatgaaagaaaaaaaaaaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	33837498	33837499	+	IGR	INS	-	T	T	rs150313499		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33837498_33837499insT								None (None upstream) : None (None downstream)																							TGTTACTTGAGTAAACTTTGTG	0.371													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	35430437	35430437	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35430437delA								None (None upstream) : ARAP2 (519407 downstream)																							ATAATCAGGGAAAAAAATTGC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	39042203	39042203	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39042203delC								TMEM156 (8162 upstream) : KLHL5 (4456 downstream)																							ATTTATATCTCCCCTTGGGGA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49261388	49261391	+	IGR	DEL	CAAA	-	-	rs138722230		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49261388_49261391delCAAA								CWH43 (197295 upstream) : None (None downstream)																							gattttgtctcaaaaaaaaaaagt	0.000													4	2	---	---	---	---	
KIAA1211	57482	broad.mit.edu	37	4	57173954	57173955	+	Intron	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57173954_57173955insT	uc003hbk.2	+						KIAA1211_uc010iha.2_Intron|KIAA1211_uc011bzz.1_5'Flank|KIAA1211_uc003hbl.2_5'Flank|KIAA1211_uc003hbm.1_5'Flank	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482											ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)					CAGCAGGGGAATTAGAGGGAGG	0.550													16	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58463025	58463025	+	IGR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58463025delG								IGFBP7 (486486 upstream) : None (None downstream)																							acctgttatagggagacaaca	0.000													4	2	---	---	---	---	
EREG	2069	broad.mit.edu	37	4	75228180	75228181	+	5'Flank	INS	-	AG	AG	rs138703311		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75228180_75228181insAG	uc003hie.1	+						EREG_uc003hid.2_5'Flank	NM_001432	NP_001423	O14944	EREG_HUMAN	epiregulin preproprotein						angiogenesis|cell-cell signaling|cytokine-mediated signaling pathway|epidermal growth factor receptor signaling pathway|female meiosis|keratinocyte differentiation|keratinocyte proliferation|luteinizing hormone signaling pathway|mRNA transcription|negative regulation of epithelial cell proliferation|negative regulation of smooth muscle cell differentiation|negative regulation of transcription, DNA-dependent|oocyte maturation|organ morphogenesis|ovarian cumulus expansion|ovulation|positive regulation of cell division|positive regulation of cytokine production|positive regulation of DNA replication|positive regulation of epidermal growth factor receptor activity|positive regulation of fibroblast proliferation|positive regulation of innate immune response|positive regulation of interleukin-6 biosynthetic process|positive regulation of mitosis|positive regulation of phosphorylation|positive regulation of smooth muscle cell proliferation|primary follicle stage|wound healing	extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|growth factor activity			breast(1)|skin(1)	2			Lung(101;0.196)			TAAAAAAAAAAAAGAAGAAGAA	0.277													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82906092	82906093	+	IGR	INS	-	C	C	rs143454331	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82906092_82906093insC								RASGEF1B (513031 upstream) : HNRNPD (368374 downstream)																							GCCATCTGTCACCCCAACCCAC	0.381													4	3	---	---	---	---	
ARHGAP24	83478	broad.mit.edu	37	4	86682665	86682665	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86682665delA	uc003hpk.2	+						ARHGAP24_uc003hpj.2_Intron	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		AGAGAAGGGGAAAGATAAAAC	0.373													4	2	---	---	---	---	
ADH1C	126	broad.mit.edu	37	4	100269259	100269260	+	Intron	INS	-	TTTTA	TTTTA	rs141490417	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100269259_100269260insTTTTA	uc003huu.2	-							NM_000669	NP_000660	P00326	ADH1G_HUMAN	class I alcohol dehydrogenase, gamma subunit						ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Fomepizole(DB01213)|NADH(DB00157)	AGGttattcttttttattttat	0.129									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	103168354	103168356	+	IGR	DEL	AGG	-	-	rs35890378		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103168354_103168356delAGG								BANK1 (172387 upstream) : SLC39A8 (3842 downstream)																							TCATCAAAGAAGGAGAACTAAAA	0.365													3	4	---	---	---	---	
PAPSS1	9061	broad.mit.edu	37	4	108539105	108539105	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108539105delA	uc003hyk.2	-							NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		ACTTAAGGGGAAAAAAACAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111141678	111141679	+	IGR	INS	-	TCTTC	TCTTC	rs143293470	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111141678_111141679insTCTTC								ELOVL6 (21858 upstream) : ENPEP (255550 downstream)																							atttagttgcttcttctcttct	0.000													6	3	---	---	---	---	
CAMK2D	817	broad.mit.edu	37	4	114481388	114481388	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114481388delT	uc003ibi.2	-						CAMK2D_uc003ibj.2_Intron|CAMK2D_uc003ibk.2_Intron|CAMK2D_uc003ibo.3_Intron|CAMK2D_uc003ibm.2_Intron|CAMK2D_uc003ibn.2_Intron|CAMK2D_uc003ibl.2_Intron	NM_001221	NP_001212	Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|regulation of cell growth|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		TCTCACAGCATTTTTTTTTTT	0.368													5	3	---	---	---	---	
NDUFC1	4717	broad.mit.edu	37	4	140213481	140213481	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140213481delA	uc003ihs.2	-						NDUFC1_uc003iht.2_Intron	NM_002494	NP_002485	O43677	NDUC1_HUMAN	NADH dehydrogenase (ubiquinone) 1, subcomplex						mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0	all_hematologic(180;0.162)				NADH(DB00157)	AACAACAAACAAAAAAAACCC	0.234													4	2	---	---	---	---	
MAML3	55534	broad.mit.edu	37	4	140757157	140757157	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140757157delG	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187	Q96JK9	MAML3_HUMAN	mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)					CTGCACCACAGGGGGCCAATG	0.507													4	2	---	---	---	---	
DCHS2	54798	broad.mit.edu	37	4	155341343	155341343	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155341343delA	uc003inx.2	-							NM_001142552	NP_001136024	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 2						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AAGAAGTGAGAAAAAAAAGGa	0.244													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	164162272	164162272	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164162272delT								NAF1 (74199 upstream) : NPY1R (82845 downstream)																							ttttattttctttaccttgaa	0.000													4	2	---	---	---	---	
MFAP3L	9848	broad.mit.edu	37	4	170923315	170923316	+	Intron	INS	-	AGG	AGG	rs147177904	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170923315_170923316insAGG	uc003isp.3	-						MFAP3L_uc003isn.3_Intron	NM_021647	NP_067679	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like isoform							integral to membrane|plasma membrane				ovary(1)	1		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		CTTTTCCATCTAGTTCTTCTCA	0.460													3	3	---	---	---	---	
ENPP6	133121	broad.mit.edu	37	4	185092940	185092941	+	Intron	INS	-	T	T	rs34370676		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185092940_185092941insT	uc003iwc.2	-							NM_153343	NP_699174	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						lipid catabolic process	extracellular region|integral to membrane|plasma membrane				central_nervous_system(1)	1		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		AAACACATTGATTTTTTTTTTT	0.163													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190653162	190653162	+	IGR	DEL	T	-	-	rs111944048		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190653162delT								None (None upstream) : FRG1 (208812 downstream)																							ccctatcccattttcccaaac	0.144													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8123978	8123979	+	IGR	INS	-	A	A	rs116543905		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8123978_8123979insA								MTRR (222745 upstream) : SEMA5A (911159 downstream)																							CCATGAAAAGTAAAAAAAAAAA	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10532988	10532988	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10532988delC								ROPN1L (67851 upstream) : DAP (146355 downstream)																							gcaggggggtcctcatcctta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	10968463	10968463	+	IGR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10968463delG								DAP (207076 upstream) : CTNND2 (3489 downstream)																							CACTCAGCTAGGAGTGCATCT	0.388													4	2	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11723114	11723114	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11723114delA	uc003jfa.1	-						CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						TCCCAAACACAAAAAGCATAC	0.294													4	2	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33546481	33546481	+	Intron	DEL	A	-	-	rs74463306		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33546481delA	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						CTCACTATTTAAAAAAAAAAA	0.318										HNSCC(64;0.19)			4	2	---	---	---	---	
NIPBL	25836	broad.mit.edu	37	5	37003113	37003113	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37003113delT	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TTTTCCAGAGTTTTTTTTTTT	0.244													6	3	---	---	---	---	
ARL15	54622	broad.mit.edu	37	5	53425218	53425219	+	Intron	DEL	AG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53425218_53425219delAG	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)				agagcatattagaagtagtaaa	0.000													4	2	---	---	---	---	
FLJ37543	285668	broad.mit.edu	37	5	60980581	60980582	+	Intron	INS	-	A	A	rs142610409	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60980581_60980582insA	uc003jst.1	+						uc003jsu.1_Intron|uc010iwo.1_Intron|uc003jsv.2_Intron	NM_173667	NP_775938	Q2M2E5	CE064_HUMAN	hypothetical protein LOC285668 precursor							extracellular region					0		Lung NSC(810;0.000468)|Prostate(74;0.0283)|Breast(144;0.237)				cTAATCCAACTAGATGCCTCAT	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	65121023	65121023	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65121023delT								NLN (1636 upstream) : ERBB2IP (101361 downstream)																							AGGACTTAACTTTTTTTTTTT	0.269													4	2	---	---	---	---	
AP3B1	8546	broad.mit.edu	37	5	77465078	77465079	+	Intron	DEL	TG	-	-	rs57558684		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77465078_77465079delTG	uc003kfj.2	-							NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GCATGAATTATGTTTTTCACCT	0.322									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
MTX3	345778	broad.mit.edu	37	5	79279310	79279311	+	3'UTR	INS	-	TGA	TGA	rs3841613		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79279310_79279311insTGA	uc010jag.2	-	9					MTX3_uc010jah.2_3'UTR|MTX3_uc003kge.3_3'UTR	NM_001010891	NP_001010891	Q5HYI7	MTX3_HUMAN	metaxin 3						protein targeting to mitochondrion	mitochondrial outer membrane					0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		AGCATTCTCTTTGTTATTAAAA	0.366													4	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96706256	96706256	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96706256delT								RIOK2 (187251 upstream) : None (None downstream)																							TTTGTAGTTCTTTTTTTTTTT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	101151451	101151451	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101151451delA								ST8SIA4 (912464 upstream) : SLCO4C1 (418243 downstream)																							TGTCTACAAGAAAAAAAAATC	0.373													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	101986192	101986192	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101986192delA								SLCO6A1 (151472 upstream) : PAM (215335 downstream)																							GGATCATAACAAAAAAAATGC	0.368													4	2	---	---	---	---	
CAMK4	814	broad.mit.edu	37	5	110776441	110776442	+	Intron	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110776441_110776442insT	uc011cvj.1	+						CAMK4_uc003kpf.2_Intron|CAMK4_uc010jbv.2_Intron	NM_001744	NP_001735	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		tttcactgagatttttggcagc	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	113159403	113159404	+	IGR	INS	-	G	G			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113159403_113159404insG								YTHDC2 (228424 upstream) : KCNN2 (538612 downstream)																							ACCAAGTGGGAGGGGGGTGGGT	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	140400651	140400651	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140400651delT								PCDHA1 (8722 upstream) : PCDHB1 (30328 downstream)																							CTTCTTTCCCTCTTTGCTTGT	0.348													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142449674	142449674	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142449674delG	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)			AGGCAAATGTGGGGGGGTTCC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	143868057	143868058	+	IGR	DEL	GA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143868057_143868058delGA								KCTD16 (11113 upstream) : None (None downstream)																							GACATTGAAGGAGATATATTTT	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	149938545	149938545	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149938545delC								NDST1 (773 upstream) : SYNPO (42097 downstream)																							CAGGTAGGGGCCCAGGCCAGT	0.368													4	2	---	---	---	---	
RBM22	55696	broad.mit.edu	37	5	150079019	150079021	+	Intron	DEL	AAC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150079019_150079021delAAC	uc003lst.2	-							NM_018047	NP_060517	Q9NW64	RBM22_HUMAN	RNA binding motif protein 22						protein import into nucleus, translocation	catalytic step 2 spliceosome|cytoplasm	calcium-dependent protein binding|nucleotide binding|RNA binding|zinc ion binding				0		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AACATACTATAACAACATATTAT	0.271													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	152725619	152725619	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152725619delT								NMUR2 (940779 upstream) : GRIA1 (143556 downstream)																							AATCACTCCCTCCCCTGTTCT	0.393													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155277429	155277430	+	Intron	DEL	AG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155277429_155277430delAG	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			agacagagacagagagagagag	0.347													3	3	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155608698	155608698	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155608698delT	uc003lwa.1	+							NM_172244	NP_758447	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 2						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			atttttttccttttataagtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157914668	157914669	+	IGR	DEL	GA	-	-	rs113259224		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157914668_157914669delGA								CLINT1 (628500 upstream) : EBF1 (208255 downstream)																							TGCAGAAGAGGAGAGAGAAAAG	0.421													3	3	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168450611	168450611	+	Intron	DEL	T	-	-	rs72022961		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168450611delT	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|uc003mad.1_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)			CCCTCTGTTCTTTTTTTTTTC	0.483													4	2	---	---	---	---	
FAM196B	100131897	broad.mit.edu	37	5	169290953	169290953	+	3'UTR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169290953delA	uc003mag.2	-	4					DOCK2_uc003maf.2_Intron|DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron	NM_001129891	NP_001123363	A6NMK8	F196B_HUMAN	hypothetical protein LOC100131897												0						GAGGTGTTGGAAGGTGTAGTG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170931999	170932000	+	IGR	DEL	GA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170931999_170932000delGA								FGF18 (47837 upstream) : FBXW11 (356556 downstream)																							aggctcagaggagagagagagA	0.050													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2937190	2937190	+	IGR	DEL	T	-	-	rs60791183		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2937190delT								SERPINB9 (33645 upstream) : SERPINB6 (11204 downstream)																							agccgtggtatgtttgctgag	0.000													13	6	---	---	---	---	
SLC22A23	63027	broad.mit.edu	37	6	3442511	3442511	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3442511delG	uc003mvm.3	-						SLC22A23_uc003mvn.3_Intron|SLC22A23_uc003mvo.3_Intron|SLC22A23_uc003mvp.1_Intron|SLC22A23_uc010jnn.2_Intron|SLC22A23_uc010jno.2_Intron	NM_015482	NP_056297	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				atggggagctggggtttcatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3610487	3610487	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3610487delC								SLC22A23 (153694 upstream) : C6orf145 (112349 downstream)																							TTCTCCTCCTCCCATGGTGTT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23089071	23089071	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23089071delT								HDGFL1 (518322 upstream) : None (None downstream)																							CCCTTCAAACTTTTTTTTGTC	0.378													4	2	---	---	---	---	
MRPL2	51069	broad.mit.edu	37	6	43021911	43021911	+	3'UTR	DEL	A	-	-	rs79913628		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43021911delA	uc003ots.1	-	7					CUL7_uc011dvb.1_5'Flank|CUL7_uc003otq.2_5'Flank|CUL7_uc010jyh.2_5'Flank|KLC4_uc003otr.1_Intron	NM_015950	NP_057034	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2 precursor						translation	mitochondrion|ribosome	structural constituent of ribosome				0		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		CCTCCCCCGCAAAAAAAAAAC	0.328													4	3	---	---	---	---	
GPR116	221395	broad.mit.edu	37	6	46834437	46834437	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46834437delA	uc003oyo.3	-						GPR116_uc011dwj.1_Intron|GPR116_uc011dwk.1_Intron|GPR116_uc003oyp.3_Intron|GPR116_uc003oyq.3_Intron|GPR116_uc010jzi.1_Intron	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			TCTCCCAATTAAAAAAAAAGG	0.259													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57392834	57392836	+	Intron	DEL	AAC	-	-	rs33971467		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57392834_57392836delAAC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TTTGAACTTTAACAACAACTTGG	0.325													11	6	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57472011	57472011	+	Intron	DEL	A	-	-	rs67396455		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57472011delA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AGAAGATTGTATAAAGTTTTA	0.284													6	3	---	---	---	---	
CD109	135228	broad.mit.edu	37	6	74439837	74439837	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74439837delG	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4						GGAGAGCAGTGGGCTATGTGT	0.473													4	2	---	---	---	---	
BACH2	60468	broad.mit.edu	37	6	90955689	90955689	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90955689delT	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		CACAAAGGGGTGGAAAGGATG	0.522													4	2	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112435035	112435035	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112435035delA	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GCGGGCACTTAAAAGGGAAAG	0.388													4	2	---	---	---	---	
HEY2	23493	broad.mit.edu	37	6	126081127	126081127	+	3'UTR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126081127delT	uc003qad.2	+	5					HEY2_uc011ebr.1_3'UTR	NM_012259	NP_036391	Q9UBP5	HEY2_HUMAN	hairy/enhancer-of-split related with YRPW motif						negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription initiation from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|Notch signaling pathway|smooth muscle cell differentiation|transcription, DNA-dependent	transcriptional repressor complex	histone deacetylase binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		TTTCTCTCCCTTTTTTGTTTG	0.393													4	2	---	---	---	---	
AHI1	54806	broad.mit.edu	37	6	135750869	135750869	+	Intron	DEL	A	-	-	rs76145516		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135750869delA	uc003qgi.2	-						AHI1_uc003qgf.2_Intron|AHI1_uc003qgg.2_Intron|AHI1_uc003qgh.2_Intron|AHI1_uc003qgj.2_Intron|AHI1_uc003qgk.3_Intron|AHI1_uc003qgl.3_Intron	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a							adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		gaagcaacataaaaaaaaaaa	0.015													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	165603292	165603292	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165603292delT								None (None upstream) : C6orf118 (89863 downstream)																							gaattatctgtttttttcata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168381566	168381566	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168381566delA								HGC6.3 (3947 upstream) : KIF25 (18206 downstream)																							tgtccccaccaaaaccaccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25296572	25296572	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25296572delT								NPVF (28467 upstream) : MIR148A (692967 downstream)																							TTCTGGTTCCTTCCCTGCCAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30215302	30215303	+	IGR	INS	-	A	A	rs149488714	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30215302_30215303insA								C7orf41 (12921 upstream) : ZNRF2 (108620 downstream)																							CTGGCACCTATAAAAAACTCCT	0.426													2	6	---	---	---	---	
PDE1C	5137	broad.mit.edu	37	7	31815524	31815524	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31815524delT	uc003tcm.1	-						PDE1C_uc003tcn.1_Intron|PDE1C_uc003tco.1_Intron	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)			GAGCATCGCCTTTGCCTTTGT	0.438													4	2	---	---	---	---	
EEPD1	80820	broad.mit.edu	37	7	36312117	36312118	+	Intron	INS	-	G	G	rs56338724		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36312117_36312118insG	uc003tfa.2	+							NM_030636	NP_085139	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0						ttgttgttgttttttttttttt	0.391													4	3	---	---	---	---	
LOC285954	285954	broad.mit.edu	37	7	41797976	41797976	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41797976delT	uc003tht.3	+							NR_027118				Homo sapiens cDNA FLJ38947 fis, clone NT2NE2017792.												0						taaacactgattttttttttc	0.000													2	4	---	---	---	---	
PSPH	5723	broad.mit.edu	37	7	56108071	56108072	+	Intron	INS	-	ATTT	ATTT	rs141633297	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56108071_56108072insATTT	uc003trj.2	-						PSPH_uc003trh.2_Intron|PSPH_uc003tri.2_Intron	NM_004577	NP_004568	P78330	SERB_HUMAN	phosphoserine phosphatase						L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			AAACAttattcatttatttact	0.119													21	17	---	---	---	---	
RABGEF1	27342	broad.mit.edu	37	7	66098581	66098581	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66098581delT	uc003tvf.2	+						KCTD7_uc003tvd.3_Intron|KCTD7_uc003tve.2_Intron	NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1						endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1						AAGAGATCAATTTTTTTTTTT	0.333													8	5	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70193812	70193813	+	Intron	DEL	TG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70193812_70193813delTG	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CTTGTATTTTTGTGTGTGTGGC	0.436													4	2	---	---	---	---	
STAG3L2	442582	broad.mit.edu	37	7	74304097	74304097	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74304097delA	uc003ubj.3	-						PMS2L5_uc003ubl.2_5'Flank|PMS2L5_uc003ubk.2_5'Flank|PMS2L5_uc010lbw.2_5'Flank|PMS2L5_uc003ubm.3_5'Flank|STAG3L2_uc011kfj.1_5'Flank	NM_001025202	NP_001020373	P0CL84	ST3L2_HUMAN	STAG3-like							nucleus	binding				0						TTTTCCCTTTAAAAAAAAAAT	0.338													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81135815	81135815	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81135815delA								SEMA3C (584140 upstream) : HGF (195630 downstream)																							CTCTGACTTCAAAAAAATATC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	85267446	85267447	+	IGR	DEL	TG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85267446_85267447delTG								SEMA3D (451275 upstream) : None (None downstream)																							TGACTAGACTTGTAGATTTTGG	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	93924083	93924083	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93924083delA								BET1 (290393 upstream) : COL1A2 (99790 downstream)																							ACTCTGGGGCAATCAATCCTT	0.284													4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103368369	103368372	+	Intron	DEL	AATT	-	-	rs56185917		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103368369_103368372delAATT	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TTTATTACTGAATTATTTATTTTT	0.270													7	5	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135322457	135322457	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135322457delA	uc003vsw.2	+						NUP205_uc003vsx.2_Intron	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						TTATTGCTTTAAAAAAAAAGG	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150311028	150311029	+	IGR	INS	-	CTCTAT	CTCTAT	rs141505392	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150311028_150311029insCTCTAT								GIMAP4 (39988 upstream) : GIMAP6 (11437 downstream)																							tctctatttacctctatctcta	0.094													3	4	---	---	---	---	
LONRF1	91694	broad.mit.edu	37	8	12592554	12592554	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12592554delA	uc003wwd.1	-						LONRF1_uc011kxv.1_Intron|LONRF1_uc010lsp.1_Intron	NM_152271	NP_689484	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|zinc ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(644;0.236)		ACTTTTGTTTAAAAAAAAAAA	0.408													3	3	---	---	---	---	
MTUS1	57509	broad.mit.edu	37	8	17611025	17611026	+	Intron	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17611025_17611026insT	uc003wxv.2	-						MTUS1_uc010lsy.2_Intron|MTUS1_uc003wxw.2_Intron|MTUS1_uc010lsz.2_Intron	NM_001001924	NP_001001924	Q9ULD2	MTUS1_HUMAN	mitochondrial tumor suppressor 1 isoform 1							Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)		GAAATTGAGGATTTTTTTTTCC	0.297													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	24509736	24509736	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24509736delT								ADAM7 (125255 upstream) : NEFM (261538 downstream)																							ttttccttgCTTTTTTTTTCC	0.299													4	2	---	---	---	---	
RAB11FIP1	80223	broad.mit.edu	37	8	37731890	37731891	+	Intron	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37731890_37731891insA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_5'Flank|RAB11FIP1_uc003xko.1_5'Flank|RAB11FIP1_uc003xkp.1_Intron	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			AGGGACTGGTTAAAAAAATAAT	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43129890	43129892	+	IGR	DEL	TCC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43129890_43129892delTCC								HGSNAT (71921 upstream) : POTEA (17693 downstream)																							AGAGCCTGCAtcctcctcctcct	0.330													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54192175	54192175	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54192175delT								OPRK1 (27981 upstream) : ATP6V1H (435941 downstream)																							aacttaggcctttttctctag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55474197	55474198	+	IGR	INS	-	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55474197_55474198insC								SOX17 (100742 upstream) : RP1 (54429 downstream)																							AAAAGTGAGATGTGGCTTTTCA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	71788176	71788176	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71788176delA								XKR9 (140000 upstream) : EYA1 (321494 downstream)																							AATGTAGAGGAAAAAAAAACT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78420997	78420997	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78420997delT								PEX2 (508473 upstream) : None (None downstream)																							CAAAGCACAATTTTAGGAAAT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81121508	81121509	+	IGR	DEL	GT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81121508_81121509delGT								TPD52 (37672 upstream) : ZBTB10 (276345 downstream)																							AAGAAAgtgagtgtgtgtgtgt	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	81220216	81220216	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81220216delA								TPD52 (136380 upstream) : ZBTB10 (177638 downstream)																							GTTTGGGAAGAAAGGGAAAGC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	82420517	82420518	+	IGR	INS	-	TAT	TAT	rs140563751	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82420517_82420518insTAT								FABP4 (25044 upstream) : FABP12 (16765 downstream)																							tataagaactaaaggggaacta	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	82605745	82605750	+	IGR	DEL	TGTATA	-	-	rs71268017	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82605745_82605750delTGTATA								IMPA1 (7156 upstream) : SLC10A5 (143 downstream)																							tgtgtgtgtgtgtATATATATATATG	0.291													4	2	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	97995471	97995471	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97995471delT	uc003yhw.2	+							NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					ttcttctatctttttgaggta	0.055													4	2	---	---	---	---	
UBR5	51366	broad.mit.edu	37	8	103289611	103289611	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103289611delT	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			AGATAACTACttttttttttt	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103989101	103989101	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103989101delT								AZIN1 (112704 upstream) : ATP6V1C1 (44147 downstream)																							ATAAATCAGATTGAACCAAAT	0.348													4	2	---	---	---	---	
TAF2	6873	broad.mit.edu	37	8	120768595	120768595	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120768595delA	uc003you.2	-							NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2						G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GAGAGTAATTAAAAAAAAATT	0.323													4	2	---	---	---	---	
KIAA0196	9897	broad.mit.edu	37	8	126050797	126050797	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126050797delA	uc003yrt.2	-						KIAA0196_uc011lir.1_Intron|KIAA0196_uc003yru.1_Intron	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin						cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			ACTGAACGGCAAACCCCAGTG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126983824	126983824	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126983824delA								TRIB1 (533182 upstream) : FAM84B (580863 downstream)																							AGAAAGAATGAAAAAAGTAGG	0.358													4	2	---	---	---	---	
PTPRD	5789	broad.mit.edu	37	9	8482282	8482284	+	Intron	DEL	AAT	-	-	rs35364543		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8482282_8482284delAAT	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		AGCAGCTACCAATAATGTATGCT	0.369										TSP Lung(15;0.13)			3	4	---	---	---	---	
FREM1	158326	broad.mit.edu	37	9	14747999	14748000	+	Intron	DEL	AC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14747999_14748000delAC	uc003zlm.2	-						FREM1_uc010mic.2_Intron|FREM1_uc003zlk.2_Intron|FREM1_uc003zll.2_Intron	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor						cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)		AGGTCCAAGAACACACACACAC	0.262													4	2	---	---	---	---	
CDKN2A	1029	broad.mit.edu	37	9	21979295	21979295	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21979295delG	uc003zpl.2	-						MTAP_uc003zpi.1_Intron	NM_058195	NP_478102	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 4						cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(197)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GCAAGGAAGTGGGGACACTGC	0.453		17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26293838	26293838	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26293838delA								TUSC1 (614982 upstream) : C9orf82 (546846 downstream)																							AGCCCACTGGAGAACTGTTCT	0.458													4	2	---	---	---	---	
AQP3	360	broad.mit.edu	37	9	33443723	33443724	+	Intron	INS	-	TT	TT			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33443723_33443724insTT	uc003zsx.2	-						SUGT1P1_uc010mjq.1_Intron|AQP3_uc003zsv.1_Frame_Shift_Ins_p.*92fs|AQP3_uc003zsw.2_5'Flank|AQP3_uc010mju.2_Intron	NM_004925	NP_004916	Q92482	AQP3_HUMAN	aquaporin 3						excretion|odontogenesis|positive regulation of immune system process|regulation of keratinocyte differentiation|response to calcium ion|response to retinoic acid|response to vitamin D	basolateral plasma membrane|cell-cell junction|cytoplasm	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.0899)		AGTGGGAATGCTATTGAGGGCC	0.569													26	13	---	---	---	---	
KIAA1539	80256	broad.mit.edu	37	9	35108319	35108319	+	5'UTR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35108319delG	uc003zwl.2	-	3					KIAA1539_uc003zwm.2_5'UTR|KIAA1539_uc003zwn.2_5'UTR|KIAA1539_uc003zwo.2_5'UTR|KIAA1539_uc003zwp.1_5'UTR|KIAA1539_uc010mkk.1_RNA	NM_025182	NP_079458	Q7L5A3	K1539_HUMAN	hypothetical protein LOC80256							nucleus				ovary(2)	2	all_epithelial(49;0.217)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CCTTTATGCTGGGCCTGGGCT	0.622													4	2	---	---	---	---	
GLIPR2	152007	broad.mit.edu	37	9	36163196	36163198	+	3'UTR	DEL	ACC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36163196_36163198delACC	uc003zyz.2	+	5					GLIPR2_uc003zza.2_RNA|GLIPR2_uc003zyy.1_3'UTR	NM_022343	NP_071738	Q9H4G4	GAPR1_HUMAN	GLI pathogenesis-related 2							extracellular region|Golgi membrane				skin(3)|central_nervous_system(1)	4						AAGTACCACTACCACCACCACCT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67917596	67917598	+	IGR	DEL	GAG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67917596_67917598delGAG								FAM27B (123407 upstream) : None (None downstream)																							CATGGAAGATGAGGAGTCCGTTG	0.468													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68330988	68330988	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68330988delT								FAM27B (536799 upstream) : MIR1299 (671251 downstream)																							ttggaaggagttttttttttt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68416882	68416883	+	IGR	INS	-	T	T	rs149366845		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68416882_68416883insT								FAM27B (622693 upstream) : MIR1299 (585356 downstream)																							catcaaaaaaaaaTGTAATTTA	0.020													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68431239	68431242	+	IGR	DEL	GTAA	-	-	rs145348306		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68431239_68431242delGTAA								FAM27B (637050 upstream) : MIR1299 (570997 downstream)																							CAATCTTTGTGTAAGTATCTTTGT	0.309													4	2	---	---	---	---	
MAMDC2	256691	broad.mit.edu	37	9	72671057	72671057	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72671057delG	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						GCTTCAGTGAGGAGCTGACTC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	83059745	83059745	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83059745delA								TLE4 (718088 upstream) : None (None downstream)																							atgtttttataaggaagtttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92756869	92756869	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92756869delC								LOC100129066 (422195 upstream) : DIRAS2 (615245 downstream)																							TGCACCCTGACCACATACTGT	0.443													4	2	---	---	---	---	
PHF2	5253	broad.mit.edu	37	9	96377044	96377044	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96377044delA	uc004aub.2	+						PHF2_uc011lug.1_Intron	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2						liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		TTAGCCCAGCAAAAAAAAGtg	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110908295	110908296	+	IGR	DEL	AA	-	-	rs11303557		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110908295_110908296delAA								KLF4 (656248 upstream) : ACTL7B (708575 downstream)																							gaaattatttaaaaaaaaaata	0.000													4	2	---	---	---	---	
SNX30	401548	broad.mit.edu	37	9	115609727	115609727	+	Intron	DEL	T	-	-	rs34501288		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115609727delT	uc004bgj.3	+						SNX30_uc004bgi.3_Intron	NM_001012994	NP_001013012	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30						cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0						acaagcattcttttttttttt	0.000													3	3	---	---	---	---	
FKBP15	23307	broad.mit.edu	37	9	115934127	115934127	+	Intron	DEL	T	-	-	rs112903769		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115934127delT	uc004bgs.2	-						FKBP15_uc004bgr.2_Intron|FKBP15_uc011lxc.1_Intron|FKBP15_uc011lxd.1_Intron	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa						endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3						TTTCAAATTCTTtttttttat	0.164													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118504990	118504991	+	IGR	DEL	TG	-	-	rs35424421		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118504990_118504991delTG								DEC1 (340067 upstream) : C9orf27 (145555 downstream)																							CTAATGACTCTGTTTGTTTTCC	0.426													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118649450	118649451	+	IGR	INS	-	T	T	rs10817845	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118649450_118649451insT								DEC1 (484527 upstream) : C9orf27 (1095 downstream)																							ATGTTTGTCTCTTTTTTTTGTT	0.450													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	123136570	123136570	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123136570delC								MIR147 (129242 upstream) : CDK5RAP2 (14578 downstream)																							gtatcaccaaccccctctcct	0.000													4	2	---	---	---	---	
C9orf171	389799	broad.mit.edu	37	9	135426670	135426670	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135426670delT	uc004cbn.2	+						C9orf171_uc004cbo.2_Intron	NM_207417	NP_997300	Q6ZQR2	CI171_HUMAN	hypothetical protein LOC389799											ovary(4)|large_intestine(1)	5						CTGGGTGCCCttttttttttt	0.259													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	139021861	139021862	+	IGR	INS	-	TT	TT	rs142558414		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139021861_139021862insTT								C9orf69 (11130 upstream) : LHX3 (66236 downstream)																							TTCCCTTTTTATTTTTTttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3481173	3481173	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3481173delG	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																		atttgtccaaggatataagta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3507051	3507052	+	Intron	DEL	GT	-	-	rs10534965		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3507051_3507052delGT	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																		TATTTCACAGGTGTGTGTGTGT	0.322													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8355340	8355341	+	IGR	INS	-	CA	CA	rs141608948	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8355340_8355341insCA								GATA3 (238178 upstream) : None (None downstream)																							tcgtgcacatgcacacacacac	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8452011	8452011	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8452011delC								GATA3 (334849 upstream) : None (None downstream)																							gtagatgggtcccttgacctt	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10923713	10923713	+	IGR	DEL	T	-	-	rs66534117		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10923713delT								SFTA1P (86836 upstream) : LOC254312 (53191 downstream)																							CTAGAATCCCTTTTTTTCAGA	0.413													0	6	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11158646	11158646	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11158646delA	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						TTCAGTGAAGAAAGAGACCCT	0.413													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11227067	11227067	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11227067delT	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbk.1_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc009xiw.1_Intron|CELF2_uc010qbo.1_Intron|CELF2_uc010qbp.1_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						ttttttaatgtttttttctga	0.000													4	2	---	---	---	---	
MPP7	143098	broad.mit.edu	37	10	28438645	28438646	+	Intron	INS	-	T	T	rs72515870		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28438645_28438646insT	uc001iua.1	-						MPP7_uc009xkz.1_Intron|MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1						CTCTCTCTCCAGAGTTTAAAGC	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36483782	36483783	+	IGR	DEL	TG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36483782_36483783delTG								FZD8 (553420 upstream) : ANKRD30A (931002 downstream)																							ttcatgtctctgtgtgtgtgtg	0.153													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65527084	65527085	+	IGR	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65527084_65527085insA								REEP3 (145113 upstream) : None (None downstream)																							TGATTCAAGAGAAAAAAAAAAT	0.396													4	2	---	---	---	---	
KIAA1274	27143	broad.mit.edu	37	10	72243554	72243554	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72243554delC	uc001jrd.3	+							NM_014431	NP_055246	Q9ULE6	PALD_HUMAN	KIAA1274											ovary(2)|central_nervous_system(1)	3						AAGGAGTTAACCCCTTTCCTG	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82057636	82057637	+	IGR	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82057636_82057637insT								MAT1A (8202 upstream) : DYDC1 (38227 downstream)																							GCTATGTAttcttttttttttt	0.223													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85421685	85421685	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85421685delC								NRG3 (674750 upstream) : GHITM (477500 downstream)																							TTTTCCTTCTCCCACAATACG	0.458													4	2	---	---	---	---	
BMPR1A	657	broad.mit.edu	37	10	88614675	88614675	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88614675delT	uc001kdy.2	+							NM_004329	NP_004320	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA						BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	8						CATTAAGTTCTTTTTTTttct	0.224			Mis|N|F			gastrointestinal polyps			Hereditary_Mixed_Polyposis_syndrome_type_2|Juvenile_Polyposis				4	2	---	---	---	---	
AGAP11	119385	broad.mit.edu	37	10	88753100	88753100	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88753100delT	uc001kee.2	+						AGAP11_uc001kef.2_5'Flank	NM_133447	NP_597704	Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						ATGAGTTTACTTTTTTTTTTA	0.303													6	3	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100865260	100865260	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100865260delT	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		gttgtaagagttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102470920	102470921	+	IGR	DEL	CA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102470920_102470921delCA								HIF1AN (157240 upstream) : PAX2 (34547 downstream)																							CCTGTACACGCACACACACACA	0.530													4	3	---	---	---	---	
C10orf76	79591	broad.mit.edu	37	10	103753009	103753010	+	Intron	DEL	GA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103753009_103753010delGA	uc009xwy.1	-						C10orf76_uc009xwx.1_5'Flank	NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		gcctgggggggagagagagaga	0.094													3	3	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	106449421	106449421	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106449421delT	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		caacttgaccttttttttcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112986080	112986081	+	IGR	INS	-	G	G	rs142274567	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112986080_112986081insG								ADRA2A (145420 upstream) : GPAM (923541 downstream)																							CTTCTGATAGAGGGAATGCAAG	0.500													5	3	---	---	---	---	
CASC2	255082	broad.mit.edu	37	10	119887321	119887322	+	Intron	INS	-	CT	CT			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119887321_119887322insCT	uc001ldm.3	+						CASC2_uc009xzc.2_Intron	NR_026939				Homo sapiens mRNA for IGM1 protein.												0						tcacacctttgctctctcacac	0.000													4	2	---	---	---	---	
PRDX3	10935	broad.mit.edu	37	10	120933610	120933610	+	Intron	DEL	A	-	-	rs35217475		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120933610delA	uc001lec.2	-							NM_006793	NP_006784	P30048	PRDX3_HUMAN	peroxiredoxin 3 isoform a precursor						cell redox homeostasis|hydrogen peroxide catabolic process|mitochondrion organization|myeloid cell differentiation|negative regulation of kinase activity|positive regulation of cell proliferation|positive regulation of NF-kappaB transcription factor activity|regulation of mitochondrial membrane potential|response to lipopolysaccharide	early endosome|mitochondrion	alkyl hydroperoxide reductase activity|caspase inhibitor activity|peroxidase activity|peroxiredoxin activity|protein C-terminus binding|protein kinase binding				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0245)		atattttaagaaaaaaaaatt	0.124													4	2	---	---	---	---	
PPAPDC1A	196051	broad.mit.edu	37	10	122256401	122256402	+	Intron	DEL	GA	-	-	rs5788420		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122256401_122256402delGA	uc001lev.1	+						PPAPDC1A_uc010qtd.1_Intron|PPAPDC1A_uc009xzl.1_Intron|PPAPDC1A_uc001lew.1_Intron|PPAPDC1A_uc001lex.1_Intron	NM_001030059	NP_001025230	Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain						phospholipid dephosphorylation	integral to membrane	phosphatidate phosphatase activity			breast(1)	1		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)		aaggaatagggagagagagaga	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	129453291	129453291	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129453291delT								NPS (102356 upstream) : FOXI2 (82247 downstream)																							cctttccttctttttttTTGT	0.179													4	2	---	---	---	---	
PSMD13	5719	broad.mit.edu	37	11	244939	244939	+	Intron	DEL	T	-	-	rs71462075		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:244939delT	uc001lol.2	+						PSMD13_uc010qvr.1_Intron|PSMD13_uc001loo.2_Intron|PSMD13_uc001lon.2_Intron|PSMD13_uc001lom.2_Intron	NM_002817	NP_002808	Q9UNM6	PSD13_HUMAN	proteasome 26S non-ATPase subunit 13 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding			ovary(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		attgcaaaccttttttttttt	0.000													6	4	---	---	---	---	
BTBD10	84280	broad.mit.edu	37	11	13441864	13441865	+	Intron	INS	-	T	T	rs150881151	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13441864_13441865insT	uc001mkz.2	-						BTBD10_uc010rcl.1_Intron|BTBD10_uc001mla.2_Intron|BTBD10_uc009ygn.2_Intron|BTBD10_uc010rcm.1_Intron|BTBD10_uc010rcn.1_Intron|BTBD10_uc009ygo.2_Intron	NM_032320	NP_115696	Q9BSF8	BTBDA_HUMAN	K+ channel tetramerization protein							nucleus					0				Epithelial(150;0.0214)		AGTAAGAAGTATTTTTTTTTAA	0.297													4	2	---	---	---	---	
BTBD10	84280	broad.mit.edu	37	11	13441869	13441870	+	Intron	INS	-	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13441869_13441870insC	uc001mkz.2	-						BTBD10_uc010rcl.1_Intron|BTBD10_uc001mla.2_Intron|BTBD10_uc009ygn.2_Intron|BTBD10_uc010rcm.1_Intron|BTBD10_uc010rcn.1_Intron|BTBD10_uc009ygo.2_Intron	NM_032320	NP_115696	Q9BSF8	BTBDA_HUMAN	K+ channel tetramerization protein							nucleus					0				Epithelial(150;0.0214)		GAAGTATTTTTTTTTAATGATT	0.292													4	2	---	---	---	---	
NUCB2	4925	broad.mit.edu	37	11	17318991	17318991	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17318991delA	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						TTTTCTGGGGAAAAGGTAATA	0.428													4	2	---	---	---	---	
TPH1	7166	broad.mit.edu	37	11	18042322	18042322	+	3'UTR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18042322delA	uc001mnp.2	-	10					TPH1_uc009yhe.2_RNA	NM_004179	NP_004170	P17752	TPH1_HUMAN	tryptophan hydroxylase 1						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	AGCTGCTACCAAAAAAAAAAA	0.303													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	18995377	18995377	+	IGR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18995377delG								MRGPRX1 (38828 upstream) : MRGPRX2 (80628 downstream)																							GAGGGAAATAGGGCTAGTATA	0.388													4	2	---	---	---	---	
SYT7	9066	broad.mit.edu	37	11	61305230	61305231	+	Intron	INS	-	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61305230_61305231insC	uc001nrv.2	-						SYT7_uc009ynr.2_Intron	NM_004200	NP_004191	O43581	SYT7_HUMAN	synaptotagmin VII							cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|pancreas(1)	4						TTCCCTTACATCCCCCCCGCCC	0.609													3	3	---	---	---	---	
MARK2	2011	broad.mit.edu	37	11	63647302	63647302	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63647302delT	uc001nxw.2	+						MARK2_uc001nxx.2_Intron|MARK2_uc001nxy.2_Intron|MARK2_uc001nxv.3_Intron	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2						cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3						TGTCCCAGTATTTTTTTCTGA	0.483													4	2	---	---	---	---	
CTTN	2017	broad.mit.edu	37	11	70281360	70281360	+	3'UTR	DEL	T	-	-	rs71463677		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70281360delT	uc001opv.3	+	18					CTTN_uc001opu.2_Intron|CTTN_uc001opw.3_3'UTR|CTTN_uc010rqm.1_Intron|CTTN_uc001opx.2_3'UTR	NM_005231	NP_005222	Q14247	SRC8_HUMAN	cortactin isoform a							cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		Gttttttctgttttttttttt	0.423													4	2	---	---	---	---	
FAM168A	23201	broad.mit.edu	37	11	73242032	73242033	+	Intron	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73242032_73242033insA	uc001otz.1	-						FAM168A_uc001oty.1_Intron|FAM168A_uc009ytp.1_Intron	NM_015159	NP_055974	Q92567	F168A_HUMAN	hypothetical protein LOC23201												0						gttggctgttgaaaaaaacgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74193640	74193640	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74193640delT								KCNE3 (15040 upstream) : LIPT2 (9284 downstream)																							GTCTCATGACTTTTTTATGTG	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	77247443	77247443	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77247443delA								PAK1 (62335 upstream) : AQP11 (52993 downstream)																							gacactatccaaaaaaaaaaa	0.000													5	3	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	79105943	79105943	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79105943delG	uc001ozl.3	-							NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						tgcaagccaaggagcaccaag	0.000													4	2	---	---	---	---	
TRIM77	390231	broad.mit.edu	37	11	89449396	89449396	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89449396delA	uc010rtw.1	+							NM_001146162	NP_001139634			tripartite motif-containing 77												0						TTAAGTGATTAAAAAAAAACA	0.274													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	107764020	107764021	+	IGR	INS	-	AGG	AGG	rs151314691	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107764020_107764021insAGG								SLC35F2 (34106 upstream) : RAB39 (35256 downstream)																							AAAGATAAATCAGGAGTCAGTT	0.332													4	6	---	---	---	---	
ACAT1	38	broad.mit.edu	37	11	108011163	108011168	+	Intron	DEL	TTATTA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108011163_108011168delTTATTA	uc001pjy.2	+						ACAT1_uc001pjx.2_Intron	NM_000019	NP_000010	P24752	THIL_HUMAN	acetyl-Coenzyme A acetyltransferase 1 precursor						acetoacetic acid biosynthetic process|branched chain family amino acid catabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	acetyl-CoA C-acetyltransferase activity|metal ion binding			ovary(3)	3		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	TTTGAGAAATTTATTAGAACTTTTTC	0.345													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	108846021	108846021	+	IGR	DEL	G	-	-	rs66510844		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108846021delG								DDX10 (34375 upstream) : C11orf87 (446854 downstream)																							AATATTTGCAGGCACACACAA	0.433													3	5	---	---	---	---	
FAM55B	120406	broad.mit.edu	37	11	114576807	114576808	+	Intron	INS	-	TTTAT	TTTAT	rs146079363	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114576807_114576808insTTTAT	uc009yyy.2	+						uc009yyz.1_5'Flank	NM_182495	NP_872301	Q96DL1	FA55B_HUMAN	hypothetical protein LOC120406							integral to membrane				ovary(1)	1						CTTTTCTAATAtttattttatt	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	118198807	118198807	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118198807delA								CD3E (11918 upstream) : CD3D (10982 downstream)																							atgagtctttaaaaaggaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	119700611	119700611	+	IGR	DEL	T	-	-	rs68033250		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119700611delT								PVRL1 (101176 upstream) : TRIM29 (281384 downstream)																							GCCCATCTACTTACTGGGGGT	0.592													3	3	---	---	---	---	
LOC399959	399959	broad.mit.edu	37	11	121976619	121976619	+	Intron	DEL	T	-	-	rs34426575		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121976619delT	uc009zba.2	-							NR_024430				Homo sapiens cDNA FLJ34394 fis, clone HCHON2000676.												0						TGTTTGACACTTTTTTTTGCC	0.373													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124314905	124314905	+	IGR	DEL	G	-	-	rs58540351		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124314905delG								OR8B8 (3924 upstream) : OR8B12 (97715 downstream)																							CCTACTTCCTGTCCTACCACC	0.413													2	6	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132691599	132691599	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132691599delC	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		ACACTTTCTTCCATTTGCCTT	0.244													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133380799	133380800	+	Intron	DEL	CA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133380799_133380800delCA	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		cacacacacgcacacacacaca	0.000													4	2	---	---	---	---	
ADIPOR2	79602	broad.mit.edu	37	12	1863865	1863866	+	Intron	INS	-	TAC	TAC	rs10082811	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1863865_1863866insTAC	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827	Q86V24	ADR2_HUMAN	adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			attattattattactactacta	0.178													6	4	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6205273	6205274	+	Intron	INS	-	GATG	GATG	rs151040407	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6205273_6205274insGATG	uc001qnn.1	-						VWF_uc010set.1_Intron|VWF_uc001qno.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	atggatggatagatggatggat	0.302													3	3	---	---	---	---	
LOH12CR1	118426	broad.mit.edu	37	12	12510571	12510571	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12510571delA	uc001ral.2	+						LOH12CR1_uc009zhu.2_Intron|LOH12CR2_uc001rak.2_5'Flank	NM_058169	NP_477517	Q969J3	L12R1_HUMAN	LOH1CR12											ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)		TGCTAGTAGGAAAAAAAAAAA	0.572													4	2	---	---	---	---	
ABCC9	10060	broad.mit.edu	37	12	21971393	21971398	+	Intron	DEL	TATATC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21971393_21971398delTATATC	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TCTCACtatatatatctatatctata	0.184													4	2	---	---	---	---	
ABCC9	10060	broad.mit.edu	37	12	21998071	21998072	+	Intron	INS	-	T	T	rs144586124	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21998071_21998072insT	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TCAAGGCTTGCTTAAAAGCAGA	0.446													7	4	---	---	---	---	
FGFR1OP2	26127	broad.mit.edu	37	12	27093024	27093024	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27093024delA	uc001rhm.2	+						C12orf11_uc001rhk.3_5'Flank|C12orf11_uc010sjk.1_5'Flank|FGFR1OP2_uc001rhl.2_Intron|FGFR1OP2_uc001rhn.2_Intron	NM_015633	NP_056448	Q9NVK5	FGOP2_HUMAN	FGFR1 oncogene partner 2							cytoplasm					0	Colorectal(261;0.0847)					tatatttgagaaatggagcag	0.035													4	2	---	---	---	---	
C12orf35	55196	broad.mit.edu	37	12	32145162	32145162	+	Intron	DEL	A	-	-	rs141471703		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32145162delA	uc001rks.2	+						C12orf35_uc001rkt.2_Intron	NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196											ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			ACAATTCTATAAGTGAAGAGC	0.383													6	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38597541	38597542	+	IGR	INS	-	GAGGAGGAGTTTGAGGAGTATGCT	GAGGAGGAGTTTGAGGAGTATGCT	rs139354000	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38597541_38597542insGAGGAGGAGTTTGAGGAGTATGCT								None (None upstream) : ALG10B (113015 downstream)																							CCACAGCTGACGAGGAGGAGGT	0.490													8	4	---	---	---	---	
GXYLT1	283464	broad.mit.edu	37	12	42537805	42537806	+	Intron	DEL	CA	-	-	rs113168111		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42537805_42537806delCA	uc001rms.3	-						GXYLT1_uc001rmt.3_Intron	NM_173601	NP_775872	Q4G148	GXLT1_HUMAN	glycosyltransferase 8 domain containing 3						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0						catatacactcacacacacaca	0.322													4	2	---	---	---	---	
NELL2	4753	broad.mit.edu	37	12	45310371	45310371	+	5'Flank	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45310371delT	uc010sla.1	-							NM_001145110	NP_001138582	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform d						cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		CCATCACACCTTCCTTGCACT	0.353													4	2	---	---	---	---	
BIN2	51411	broad.mit.edu	37	12	51714920	51714923	+	Intron	DEL	GAGA	-	-	rs112711340		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51714920_51714923delGAGA	uc001ryg.2	-						BIN2_uc009zlz.2_Intron|BIN2_uc001ryh.2_Intron|BIN2_uc010sng.1_Intron	NM_016293	NP_057377	Q9UBW5	BIN2_HUMAN	bridging integrator 2							cytoplasm	protein binding			ovary(1)	1						CTCTGTTCCTGAGAGAGGATCAGC	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	53375258	53375259	+	IGR	INS	-	T	T	rs34697038		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53375258_53375259insT								KRT18 (28574 upstream) : EIF4B (24803 downstream)																							GTGTTTATGTCTTTTTTTTTTT	0.248											OREG0021854	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
USP15	9958	broad.mit.edu	37	12	62747918	62747919	+	Intron	DEL	GT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62747918_62747919delGT	uc001src.1	+						USP15_uc001srb.1_Intron	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15						protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		gtgtgtgtgcgtgtgtgtgtgt	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	67358135	67358136	+	IGR	DEL	TG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67358135_67358136delTG								GRIP1 (160241 upstream) : CAND1 (304925 downstream)																							tataaacacatgtgtgtgtata	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	67468805	67468806	+	IGR	INS	-	A	A	rs35836464		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67468805_67468806insA								GRIP1 (270911 upstream) : CAND1 (194255 downstream)																							acttaatccagaaaaAAAAAAA	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	79894646	79894646	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79894646delT								SYT1 (48859 upstream) : PAWR (91101 downstream)																							aggggatgcctttccatttgt	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80090568	80090569	+	IGR	INS	-	CT	CT			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80090568_80090569insCT								PAWR (5778 upstream) : PPP1R12A (76775 downstream)																							cccatccttcactctgtttcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80496628	80496628	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80496628delT								PPP1R12A (167393 upstream) : PTPRQ (341498 downstream)																							aaggctcttcttttttttctc	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97527989	97527990	+	IGR	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97527989_97527990insA								NEDD1 (180528 upstream) : RMST (330809 downstream)																							ctgctattatgaaaaaaaaatc	0.104													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99223412	99223412	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99223412delG	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc010svd.1_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc009ztq.2_Intron|ANKS1B_uc010sve.1_Intron|ANKS1B_uc001tgh.3_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc009ztp.2_Intron|ANKS1B_uc010svf.1_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CACCTATGTTGGGCACCTCTG	0.493													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99621390	99621390	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99621390delG	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		gcatctggccGGGATCTGCAA	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106321683	106321683	+	IGR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106321683delG								C12orf75 (556388 upstream) : NUAK1 (135442 downstream)																							aaaaacatatggatattagaa	0.000													4	2	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112655141	112655142	+	Intron	DEL	AC	-	-	rs4767497		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112655141_112655142delAC	uc009zwc.2	-						C12orf51_uc001ttr.1_Intron	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						acacacacatacacacacacac	0.084													4	3	---	---	---	---	
PLBD2	196463	broad.mit.edu	37	12	113801781	113801781	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113801781delT	uc001tve.2	+						PLBD2_uc001tvf.2_Intron	NM_173542	NP_775813	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2 isoform 1						lipid catabolic process	lysosomal lumen	hydrolase activity				0						ACTTCTCGACTTTTTTTTGAA	0.438													4	2	---	---	---	---	
MSI1	4440	broad.mit.edu	37	12	120809497	120809497	+	5'Flank	DEL	A	-	-	rs112962110		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120809497delA	uc001tye.1	-							NM_002442	NP_002433	O43347	MSI1H_HUMAN	musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATTTTGGATTAAAAAAAAAAA	0.398													3	4	---	---	---	---	
MLXIP	22877	broad.mit.edu	37	12	122615622	122615623	+	Intron	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122615622_122615623insT	uc001ubq.2	+						MLXIP_uc001ubr.2_Intron|MLXIP_uc001ubs.1_Intron|MLXIP_uc001ubt.2_5'Flank	NM_014938	NP_055753	Q9HAP2	MLXIP_HUMAN	MLX interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial outer membrane|nucleus	DNA binding			ovary(2)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		AAACTGAACTGTTTTTTGTAGT	0.475											OREG0022218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125210037	125210037	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125210037delC								NCOR2 (158027 upstream) : SCARB1 (52138 downstream)																							cgtcacctctccgGGGATTAC	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23424824	23424825	+	IGR	DEL	AT	-	-	rs75222506		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23424824_23424825delAT								None (None upstream) : SGCG (330235 downstream)																							TTTAAAAATCATATAAATTTGA	0.267													4	4	---	---	---	---	
POMP	51371	broad.mit.edu	37	13	29242952	29242952	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29242952delT	uc001usf.2	+							NM_015932	NP_057016	Q9Y244	POMP_HUMAN	proteasome maturation protein						proteasome assembly	cytosol|endoplasmic reticulum|membrane|microsome|nucleus|proteasome complex					0		Lung SC(185;0.0367)		all cancers(112;0.141)|OV - Ovarian serous cystadenocarcinoma(117;0.216)		TTTTTCTGGGTTTTTTTTTTA	0.075													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31652818	31652818	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31652818delT								C13orf26 (103667 upstream) : HSPH1 (57947 downstream)																							aaataacttcttagaagtaat	0.199													4	2	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	33716002	33716002	+	Intron	DEL	A	-	-	rs139780195		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33716002delA	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GATATTTTACATCTTTACGCA	0.323													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	47524304	47524304	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47524304delA								HTR2A (53254 upstream) : SUCLA2 (992488 downstream)																							CAACTCATACAAAAAAACATA	0.328													4	2	---	---	---	---	
DACH1	1602	broad.mit.edu	37	13	72136093	72136094	+	Intron	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72136093_72136094insA	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937	Q9UI36	DACH1_HUMAN	dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		TCCATGGAATTAAAAAAAAAAA	0.302													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75254153	75254154	+	IGR	DEL	AA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75254153_75254154delAA								KLF12 (545759 upstream) : LOC647288 (557736 downstream)																							GTGGGTTACTAACCCAGTCATC	0.366													4	2	---	---	---	---	
PCCA	5095	broad.mit.edu	37	13	100819019	100819019	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100819019delT	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron	NM_000282	NP_000273	P05165	PCCA_HUMAN	propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	tatgctttcatttttttttgg	0.000													4	2	---	---	---	---	
BIVM	54841	broad.mit.edu	37	13	103493397	103493397	+	3'UTR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103493397delA	uc001vps.2	+	11					BIVM_uc010agc.2_3'UTR|ERCC5_uc001vpu.1_Intron|BIVM_uc001vpv.2_3'UTR	NM_017693	NP_060163	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif							cytoplasm|nucleus					0	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTTCCTTTTTAAAAATCATAT	0.353													4	2	---	---	---	---	
COL4A2	1284	broad.mit.edu	37	13	111012316	111012316	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111012316delC	uc001vqx.2	+							NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein						angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			TTAGAAATTGCTGGTTGAAGA	0.373													4	2	---	---	---	---	
C13orf35	400165	broad.mit.edu	37	13	113320035	113320036	+	Intron	INS	-	AT	AT	rs142304361		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113320035_113320036insAT	uc001vsh.1	+							NM_207440	NP_997323	Q6ZP68	CM035_HUMAN	hypothetical protein LOC400165											ovary(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)		all cancers(43;0.201)			tgtgtgtgtccgtgtgtgtaag	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23581721	23581721	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23581721delT								C14orf119 (12057 upstream) : CEBPE (4794 downstream)																							ttagtatgtattttttgagta	0.040													4	2	---	---	---	---	
SEC23A	10484	broad.mit.edu	37	14	39514144	39514144	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39514144delA	uc001wup.1	-						SEC23A_uc010tqa.1_Intron|SEC23A_uc010tqb.1_Intron	NM_006364	NP_006355	Q15436	SC23A_HUMAN	SEC23-related protein A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		catctcCTTTAAAAAAAAAAA	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	48565936	48565937	+	IGR	DEL	CT	-	-	rs146169026		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48565936_48565937delCT								MDGA2 (421948 upstream) : None (None downstream)																							tttcagttcactgtgatagatc	0.000													3	7	---	---	---	---	
NAA30	122830	broad.mit.edu	37	14	57870585	57870586	+	Intron	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57870585_57870586insT	uc001xcx.3	+						NAA30_uc010trk.1_Intron|NAA30_uc010aow.2_Intron	NM_001011713	NP_001011713	Q147X3	NAA30_HUMAN	N-acetyltransferase 12							cytoplasm	peptide alpha-N-acetyltransferase activity			skin(1)	1						CATTTATGTACTTTTTTTCCTG	0.302													4	2	---	---	---	---	
HIF1A	3091	broad.mit.edu	37	14	62199095	62199096	+	Intron	DEL	TC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62199095_62199096delTC	uc001xfq.2	+						HIF1A_uc001xfr.2_Intron|HIF1A_uc001xfs.2_Intron	NM_001530	NP_001521	Q16665	HIF1A_HUMAN	hypoxia-inducible factor 1, alpha subunit						cellular response to hypoxia|collagen metabolic process|connective tissue replacement involved in inflammatory response wound healing|elastin metabolic process|epithelial to mesenchymal transition|oxygen homeostasis|positive regulation of chemokine production|positive regulation of epithelial cell migration|positive regulation of hormone biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|regulation of transforming growth factor-beta2 production	cytoplasm|nucleolus|transcription factor complex	histone acetyltransferase binding|Hsp90 protein binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			kidney(3)|lung(1)	4				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)		TTTATCAGTGTCTCCCTTTTTT	0.322													96	43	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	94268288	94268288	+	IGR	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94268288delG								PRIMA1 (13522 upstream) : C14orf86 (102788 downstream)																							CAAAGAGGCAGGGGGCTGAGG	0.532													4	2	---	---	---	---	
PPP2R5C	5527	broad.mit.edu	37	14	102356107	102356107	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102356107delT	uc001yko.2	+						PPP2R5C_uc010txr.1_Intron|PPP2R5C_uc001ykk.2_Intron|PPP2R5C_uc010txt.1_Intron|PPP2R5C_uc001ykn.2_Intron|PPP2R5C_uc001ykp.2_Intron|PPP2R5C_uc001ykq.2_Intron	NM_002719	NP_002710	Q13362	2A5G_HUMAN	gamma isoform of regulatory subunit B56, protein						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of cell proliferation|proteasomal ubiquitin-dependent protein catabolic process|signal transduction	chromosome, centromeric region|nucleus|protein phosphatase type 2A complex	protein binding|protein binding|protein phosphatase type 2A regulator activity|protein phosphatase type 2A regulator activity			ovary(1)|breast(1)	2						ACTTCTACCCTTTGCAGGAAC	0.373													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106771126	106771126	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106771126delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						TATCCATGGTAAAAAAAAGAA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20848462	20848462	+	IGR	DEL	T	-	-	rs56862210		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20848462delT								GOLGA8C (67436 upstream) : BCL8 (21594 downstream)																							CCCATACCCCTAAAACAAACT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21099695	21099696	+	IGR	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21099695_21099696insA								POTEB (27718 upstream) : NF1P1 (22325 downstream)																							AGAAAAAGTTGAAAAAAAAGTT	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21900029	21900029	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21900029delA								NF1P1 (765404 upstream) : LOC646214 (32485 downstream)																							TCTGAAGAATAAAAAAGTTTA	0.224													4	2	---	---	---	---	
FMN1	342184	broad.mit.edu	37	15	33258857	33258857	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33258857delG	uc001zhf.3	-							NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CATACCAGGAGTCAAAAGCAA	0.358													4	2	---	---	---	---	
TTBK2	146057	broad.mit.edu	37	15	43075081	43075081	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43075081delT	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		TCACTAGTGATTTTTTTTTTG	0.403													9	4	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	48054739	48054739	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48054739delA	uc010bek.2	+						SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvx.1_Intron|SEMA6D_uc001zvy.2_Intron|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AGGTGACCTCAAAAAAAAAAG	0.418													4	2	---	---	---	---	
ATP8B4	79895	broad.mit.edu	37	15	50188400	50188400	+	Intron	DEL	A	-	-	rs35582055		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50188400delA	uc001zxu.2	-						ATP8B4_uc010ber.2_Intron|ATP8B4_uc010ufd.1_Intron|ATP8B4_uc010ufe.1_Intron|ATP8B4_uc001zxv.1_3'UTR	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		AGAGATTAACAAAAAAAAGGC	0.373													4	2	---	---	---	---	
MYO1E	4643	broad.mit.edu	37	15	59653397	59653398	+	Intron	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59653397_59653398insA	uc002aga.2	-							NM_004998	NP_004989	Q12965	MYO1E_HUMAN	myosin IE						actin filament-based movement	myosin complex	actin binding|ATP binding|ATPase activity, coupled|calmodulin binding|microfilament motor activity			central_nervous_system(3)	3				all cancers(107;0.207)		cattcccagccaagccactagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	59692460	59692460	+	IGR	DEL	A	-	-	rs35538190		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59692460delA								MYO1E (27389 upstream) : FAM81A (37912 downstream)																							gaaagtcaggagtcagcccaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70575417	70575424	+	IGR	DEL	ATGGATGG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70575417_70575424delATGGATGG								TLE3 (185161 upstream) : UACA (371471 downstream)																							gaatgggtaaatggatggatggatggat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	86594017	86594017	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86594017delT								KLHL25 (255828 upstream) : AGBL1 (91225 downstream)																							ACACAGTTTCTTAGATGTCTC	0.398													4	2	---	---	---	---	
ZNF710	374655	broad.mit.edu	37	15	90593519	90593519	+	Intron	DEL	G	-	-	rs12909164	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90593519delG	uc002bov.1	+							NM_198526	NP_940928	Q8N1W2	ZN710_HUMAN	zinc finger protein 710						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			TGGAGGCCCAGGGAGGAGTCA	0.582													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	93973226	93973228	+	Intron	DEL	TTT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93973226_93973228delTTT	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																		tttctttttcttttttttttttt	0.094													5	4	---	---	---	---	
ABCA3	21	broad.mit.edu	37	16	2374321	2374321	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2374321delT	uc002cpy.1	-						ABCA3_uc010bsk.1_Intron|ABCA3_uc010bsl.1_Intron|ABCA3_uc002cpz.1_Intron	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3						response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)				AAGCAGTGCCTTTTACAGGTT	0.587													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6905035	6905035	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6905035delG	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		TTTCACTGTTGGGAGGTGGGT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17840375	17840375	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17840375delT								XYLT1 (275637 upstream) : NOMO2 (670808 downstream)																							atcgtccccattttacagatg	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	18297907	18297907	+	IGR	DEL	T	-	-	rs72410668		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18297907delT								XYLT1 (733169 upstream) : NOMO2 (213276 downstream)																							TCTGCCTCTctttctgcaccc	0.214													2	6	---	---	---	---	
CACNG3	10368	broad.mit.edu	37	16	24303321	24303322	+	Intron	DEL	GA	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24303321_24303322delGA	uc002dmf.2	+							NM_006539	NP_006530	O60359	CCG3_HUMAN	voltage-dependent calcium channel gamma-3						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)		AGCCAGTGGGGAGAGAGAGAGA	0.500													4	2	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	28007428	28007429	+	Intron	DEL	CT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28007428_28007429delCT	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						AAACAGCGCCCTCTCTCTCTCT	0.391													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32152597	32152597	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32152597delA								ZNF267 (223971 upstream) : HERC2P4 (10013 downstream)																							TAAGGCACATAATGAGCAATT	0.318													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33042961	33042961	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33042961delT								SLC6A10P (146498 upstream) : MIR1826 (922547 downstream)																							AATTTCTATGTTTTTACTGCA	0.428													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33520463	33520463	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33520463delT								SLC6A10P (624000 upstream) : MIR1826 (445045 downstream)																							gaatgtttgctgttggctttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33530991	33530993	+	IGR	DEL	CTT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33530991_33530993delCTT								SLC6A10P (634528 upstream) : MIR1826 (434515 downstream)																							GGTAATAACACTTATTTCTACTT	0.310													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33919411	33919411	+	IGR	DEL	T	-	-	rs74917177		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33919411delT								None (None upstream) : MIR1826 (46097 downstream)																							tctacaaaaatacattttcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46495392	46495393	+	IGR	INS	-	TC	TC	rs139938147	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46495392_46495393insTC								None (None upstream) : ANKRD26P1 (7856 downstream)																							ACCATCACGTTTTTTTTCTCCA	0.356													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	61446987	61446987	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61446987delA								None (None upstream) : CDH8 (240248 downstream)																							GACCCGGCCTAAACTAGAACA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	63438620	63438620	+	IGR	DEL	T	-	-	rs11075505		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63438620delT								None (None upstream) : None (None downstream)																							ATTTAGATTATTTTTACTTGT	0.199													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	63548911	63548911	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63548911delT								None (None upstream) : None (None downstream)																							gaattgtgcctttgccactgg	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73606175	73606175	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73606175delT								HTA (478505 upstream) : PSMD7 (724506 downstream)																							TTTGGGGCTGTTTTTTTAAGA	0.428													4	2	---	---	---	---	
PSMD7	5713	broad.mit.edu	37	16	74335977	74335985	+	Intron	DEL	ATTTTTGCT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74335977_74335985delATTTTTGCT	uc002fcq.2	+						PSMD7_uc010vmr.1_Intron	NM_002811	NP_002802	P51665	PSD7_HUMAN	proteasome 26S non-ATPase subunit 7						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0						GCATAAATGCATTTTTGCTGAATATTCTG	0.287													53	23	---	---	---	---	
CMIP	80790	broad.mit.edu	37	16	81544268	81544268	+	Intron	DEL	T	-	-	rs80104478		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81544268delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0						AAGACCAATGTTTTTTTTTCC	0.144													4	2	---	---	---	---	
OSGIN1	29948	broad.mit.edu	37	16	83991464	83991465	+	Intron	INS	-	TTTA	TTTA	rs138450613	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83991464_83991465insTTTA	uc002fha.2	+						OSGIN1_uc002fhb.2_Intron|OSGIN1_uc002fhc.2_Intron	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0						ggggtttattttttatttattt	0.262													4	2	---	---	---	---	
FANCA	2175	broad.mit.edu	37	16	89874487	89874488	+	Intron	INS	-	AAA	AAA	rs66895019		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89874487_89874488insAAA	uc002fou.1	-						FANCA_uc010vpn.1_Intron|FANCA_uc002fov.1_Intron|FANCA_uc002fow.1_Intron|FANCA_uc002fox.1_Intron|FANCA_uc010ciu.1_Intron|FANCA_uc002foy.2_Intron	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		agacaaaaagcaaacaaaaCCA	0.158			D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				9	5	---	---	---	---	
FANCA	2175	broad.mit.edu	37	16	89874491	89874492	+	Intron	INS	-	AA	AA	rs67590431		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89874491_89874492insAA	uc002fou.1	-						FANCA_uc010vpn.1_Intron|FANCA_uc002fov.1_Intron|FANCA_uc002fow.1_Intron|FANCA_uc002fox.1_Intron|FANCA_uc010ciu.1_Intron|FANCA_uc002foy.2_Intron	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		aaaaagcaaacaaaaCCAAAAC	0.158			D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				9	5	---	---	---	---	
FANCA	2175	broad.mit.edu	37	16	89874496	89874497	+	Intron	INS	-	AA	AA	rs62054217		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89874496_89874497insAA	uc002fou.1	-						FANCA_uc010vpn.1_Intron|FANCA_uc002fov.1_Intron|FANCA_uc002fow.1_Intron|FANCA_uc002fox.1_Intron|FANCA_uc010ciu.1_Intron|FANCA_uc002foy.2_Intron	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		gcaaacaaaaCCAAAACACCAT	0.158			D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				9	5	---	---	---	---	
TCF25	22980	broad.mit.edu	37	16	89949564	89949565	+	Intron	INS	-	A	A	rs142705330	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89949564_89949565insA	uc002fpb.2	+						TCF25_uc010vpp.1_Intron|TCF25_uc002fpc.2_5'Flank	NM_014972	NP_055787	Q9BQ70	TCF25_HUMAN	NULP1						heart development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		GAGCTGCTGACAAAGTCCCCCT	0.550													6	8	---	---	---	---	
RABEP1	9135	broad.mit.edu	37	17	5266498	5266498	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5266498delT	uc002gbm.3	+						RABEP1_uc010clc.1_Intron|RABEP1_uc010cld.1_Intron|RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron|NUP88_uc002gbn.2_Intron	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1						apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2						AGGACTCTGCTTttttttttt	0.199													8	4	---	---	---	---	
TNFRSF13B	23495	broad.mit.edu	37	17	16839798	16839799	+	Intron	DEL	AT	-	-	rs66615973		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16839798_16839799delAT	uc010vwt.1	-						uc002gqr.1_5'Flank			O14836	TR13B_HUMAN	Homo sapiens transmembrane activator and CAML interactor (TACI) mRNA, complete cds.						cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding|receptor activity			kidney(2)	2						acacacacacatatatatatat	0.045									IgA_Deficiency_Selective				4	2	---	---	---	---	
C17orf39	79018	broad.mit.edu	37	17	17946230	17946232	+	Intron	DEL	TTG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17946230_17946232delTTG	uc002gsg.1	+							NM_024052	NP_076957	Q8IVV7	CQ039_HUMAN	hypothetical protein LOC79018											skin(1)	1	all_neural(463;0.228)					tcttgtgtttTTGTTGTTGTTGT	0.217													4	2	---	---	---	---	
MYO15A	51168	broad.mit.edu	37	17	18044663	18044665	+	Intron	DEL	ATA	-	-	rs74811365		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18044663_18044665delATA	uc010vxh.1	+							NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV						sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)					tgtataacgtataatatgtctaa	0.000											OREG0024223	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	19390603	19390604	+	IGR	INS	-	G	G	rs140161340	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19390603_19390604insG								RNF112 (70016 upstream) : SLC47A1 (46563 downstream)																							tcttttccaaaggggatctgga	0.238													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21323652	21323653	+	IGR	DEL	AC	-	-	rs148026879		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21323652_21323653delAC								KCNJ12 (473 upstream) : C17orf51 (107919 downstream)																							GGGTGAGGGAACACACACGGCC	0.564													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21343818	21343819	+	IGR	INS	-	G	G	rs151017738	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21343818_21343819insG								KCNJ12 (20639 upstream) : C17orf51 (87753 downstream)																							TTGATCCTCACTGGTGTTCTTC	0.460													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29871395	29871396	+	IGR	INS	-	A	A	rs141600569	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29871395_29871396insA								RAB11FIP4 (6163 upstream) : MIR193A (15619 downstream)																							cttgcagctgcatccagctgag	0.000													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31478479	31478480	+	Intron	INS	-	TGC	TGC	rs140989188		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31478479_31478480insTGC	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	gaaagttctcttgtggtttcct	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	34295168	34295168	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34295168delT								LYZL6 (24497 upstream) : CCL16 (8368 downstream)																							tctttctttcttttttttttc	0.030													6	3	---	---	---	---	
KRT34	3885	broad.mit.edu	37	17	39537782	39537783	+	Intron	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39537782_39537783insA	uc002hwm.2	-							NM_021013	NP_066293	O76011	KRT34_HUMAN	keratin 34						epidermis development	intermediate filament	protein binding|structural molecule activity			central_nervous_system(1)	1		Breast(137;0.000496)				GAAACACTTCCAAAAAAAACCA	0.366													4	2	---	---	---	---	
CNTD1	124817	broad.mit.edu	37	17	40956027	40956027	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40956027delT	uc002ibm.3	+						CNTD1_uc010wha.1_Intron	NM_173478	NP_775749	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1											central_nervous_system(1)	1		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		cacttggctattttttttttt	0.000													4	3	---	---	---	---	
UBTF	7343	broad.mit.edu	37	17	42292477	42292477	+	Intron	DEL	A	-	-	rs5820526		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42292477delA	uc002igb.2	-						UBTF_uc002igc.2_Intron|UBTF_uc010czs.2_Intron|UBTF_uc002igd.2_Intron|UBTF_uc010czt.2_Intron|UBTF_uc002ige.2_Intron	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GTGTGCGTGGAGAAGTGCACT	0.338													1	5	---	---	---	---	
CDC27	996	broad.mit.edu	37	17	45258678	45258678	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45258678delA	uc002ild.3	-						CDC27_uc002ile.3_Intron|CDC27_uc002ilf.3_Intron|CDC27_uc010wkp.1_Intron|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						ACCCTGGGGGAAAAAAAAACC	0.184													4	2	---	---	---	---	
MYCBPAP	84073	broad.mit.edu	37	17	48604975	48604975	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48604975delT	uc010wmr.1	+						MYCBPAP_uc002iqz.2_Intron	NM_032133	NP_115509	Q8TBZ2	MYBPP_HUMAN	Myc-binding protein-associated protein						cell differentiation|multicellular organismal development|spermatogenesis|synaptic transmission	cytoplasm|membrane	protein binding			urinary_tract(2)|skin(2)|ovary(1)|pancreas(1)	6	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			ACACCTTATCTTTTTTTTCTT	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49440564	49440564	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49440564delC								UTP18 (65274 upstream) : CA10 (267111 downstream)																							TTCTCTTTTACCCCATCCAGT	0.333													4	2	---	---	---	---	
CACNG4	27092	broad.mit.edu	37	17	65022494	65022495	+	Intron	DEL	GT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65022494_65022495delGT	uc002jft.1	+							NM_014405	NP_055220	Q9UBN1	CCG4_HUMAN	voltage-dependent calcium channel gamma-4						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane	voltage-gated calcium channel activity			central_nervous_system(1)	1	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			gaggaatgtggtgtgtgtgtgt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	76486622	76486623	+	IGR	INS	-	GTCT	GTCT	rs148797625	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76486622_76486623insGTCT								DNAH17 (17766 upstream) : CYTH1 (183508 downstream)																							tttattcccaggtctctcaccc	0.050													9	5	---	---	---	---	
CYTH1	9267	broad.mit.edu	37	17	76723068	76723069	+	Intron	DEL	TC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76723068_76723069delTC	uc002jvw.2	-							NM_017456	NP_059430	Q15438	CYH1_HUMAN	cytohesin 1 isoform 2						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						TCTTTCCAGTTCTCTCTCTCAG	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77868141	77868142	+	IGR	INS	-	TCA	TCA	rs145841588	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77868141_77868142insTCA								CBX4 (54928 upstream) : TBC1D16 (45679 downstream)																							cattgttgttgtcatcatcatc	0.114													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78660783	78660787	+	Intron	DEL	TTCAG	-	-	rs66898204		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78660783_78660787delTTCAG	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						CTCTTGTTCTTTCAGTTCAGTAACC	0.444													3	5	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	7717421	7717421	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7717421delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				ccccatcccctttttgtctcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	8987700	8987700	+	IGR	DEL	T	-	-	rs57797558		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8987700delT								KIAA0802 (154925 upstream) : NDUFV2 (114975 downstream)																							TGCAGAGCTGTGTGCATTTAG	0.463													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35662275	35662276	+	IGR	INS	-	AGGTATAGAA	AGGTATAGAA	rs144591167	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35662275_35662276insAGGTATAGAA								CELF4 (516275 upstream) : None (None downstream)																							GAAAAGGAGTCAGACAAACTCT	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	40838738	40838738	+	IGR	DEL	T	-	-	rs34380360		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40838738delT								RIT2 (143081 upstream) : SYT4 (9121 downstream)																							TCTTATGttcttttttttttt	0.174													4	3	---	---	---	---	
ZBTB7C	201501	broad.mit.edu	37	18	45627431	45627459	+	Intron	DEL	CCTCCTTGCTCCCTGGGGAAGGAGCCAGC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45627431_45627459delCCTCCTTGCTCCCTGGGGAAGGAGCCAGC	uc010dnv.2	-						ZBTB7C_uc002ldb.2_Intron|ZBTB7C_uc010dnu.2_Intron|ZBTB7C_uc010dnw.2_Intron|ZBTB7C_uc010dnx.1_Intron|ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449	A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						CTCTCTGACTCCTCCTTGCTCCCTGGGGAAGGAGCCAGCCCACAGGCCC	0.598													4	2	---	---	---	---	
VPS4B	9525	broad.mit.edu	37	18	61077240	61077240	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61077240delT	uc002lix.2	-						VPS4B_uc010dpx.2_Intron|VPS4B_uc010dpy.2_Intron|VPS4B_uc010dpz.1_Intron	NM_004869	NP_004860	O75351	VPS4B_HUMAN	vacuolar protein sorting factor 4B						cell cycle|cell division|cellular membrane organization|endosome to lysosome transport via multivesicular body sorting pathway|intracellular cholesterol transport|protein transport|response to lipid	cytosol|early endosome|late endosome membrane|lysosome|nucleus|vacuolar membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding			ovary(1)	1						gtcagcaaacttttttttgta	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	72057058	72057059	+	IGR	INS	-	A	A			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72057058_72057059insA								CYB5A (97837 upstream) : FAM69C (45905 downstream)																							ttattattatttttttttGACT	0.178													2	5	---	---	---	---	
CALR	811	broad.mit.edu	37	19	13050676	13050676	+	Intron	DEL	T	-	-	rs111588637		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13050676delT	uc002mvu.2	+							NM_004343	NP_004334	P27797	CALR_HUMAN	calreticulin precursor						cell cycle arrest|cellular senescence|glucocorticoid receptor signaling pathway|negative regulation of neuron differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of steroid hormone receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|peptide antigen assembly with MHC class I protein complex|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of phagocytosis|post-translational protein modification|protein export from nucleus|protein maturation by protein folding|protein N-linked glycosylation via asparagine|protein stabilization|regulation of apoptosis|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|extracellular space|MHC class I peptide loading complex|nucleus|perinuclear region of cytoplasm|polysome|proteinaceous extracellular matrix	androgen receptor binding|calcium ion binding|chaperone binding|complement component C1q binding|DNA binding|integrin binding|mRNA binding|protein binding involved in protein folding|sugar binding|ubiquitin protein ligase binding|unfolded protein binding|zinc ion binding			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGAGCACTGATTTTTTTTTTT	0.393													10	5	---	---	---	---	
CACNA1A	773	broad.mit.edu	37	19	13404928	13404929	+	Intron	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13404928_13404929insT	uc010dze.2	-						CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc010xne.1_Intron	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	atTGGTCTTTCTTTTTTTTTTA	0.158													4	2	---	---	---	---	
PODNL1	79883	broad.mit.edu	37	19	14044375	14044376	+	Intron	INS	-	T	T			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14044375_14044376insT	uc002mxr.2	-						PODNL1_uc010xni.1_Intron|PODNL1_uc010xnj.1_Intron|PODNL1_uc002mxs.2_Intron	NM_024825	NP_079101	Q6PEZ8	PONL1_HUMAN	podocan-like 1 isoform 1							proteinaceous extracellular matrix				central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			TAAGCTGGAGATTTTGACTTGG	0.584													5	3	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17774099	17774100	+	Intron	INS	-	C	C			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17774099_17774100insC	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						CTCCAGGCTAACCCCCCCCACC	0.604													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20441860	20441860	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20441860delT								LOC284441 (71357 upstream) : ZNF826 (9218 downstream)																							ATTCATGttattttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29398195	29398195	+	IGR	DEL	T	-	-	rs72021843		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29398195delT								None (None upstream) : LOC148145 (57845 downstream)																							AGAGAATGTATTTTTTTTCCC	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	40155374	40155374	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40155374delA								LOC100129935 (22333 upstream) : LOC400696 (14640 downstream)																							actctgtctcaaaaaaaaagt	0.000													6	3	---	---	---	---	
GPR77	27202	broad.mit.edu	37	19	47840143	47840143	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47840143delC	uc010ela.1	+						GPR77_uc002pgk.1_5'Flank	NM_018485	NP_060955	Q9P296	C5ARL_HUMAN	G protein-coupled receptor 77						chemotaxis	integral to membrane|plasma membrane	C5a anaphylatoxin receptor activity			ovary(1)	1		all_cancers(25;1.72e-06)|all_lung(116;2.15e-05)|all_epithelial(76;3.44e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.0652)|Ovarian(192;0.086)		all cancers(93;0.000129)|OV - Ovarian serous cystadenocarcinoma(262;0.000415)|Epithelial(262;0.0109)|GBM - Glioblastoma multiforme(486;0.0138)		AATACACACACCAAGTGGCCT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54535708	54535709	+	IGR	DEL	TT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54535708_54535709delTT								CACNG6 (19790 upstream) : VSTM1 (8376 downstream)																							GAAAAATTGAtttttttttttt	0.129													4	2	---	---	---	---	
NLRP13	126204	broad.mit.edu	37	19	56443860	56443861	+	5'Flank	INS	-	TTTTTT	TTTTTT			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56443860_56443861insTTTTTT	uc010ygg.1	-							NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing								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)		TGTTAGTACACttttttgttgt	0.198													9	5	---	---	---	---	
NLRP5	126206	broad.mit.edu	37	19	56555375	56555376	+	Intron	INS	-	T	T	rs148712289	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56555375_56555376insT	uc002qmj.2	+						NLRP5_uc002qmi.2_Intron	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5							mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		gtctcgaagggtttttcccatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7149023	7149023	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7149023delA								BMP2 (388113 upstream) : HAO1 (714608 downstream)																							AAAAATCAAGAAAGGCACAAA	0.284													4	2	---	---	---	---	
ESF1	51575	broad.mit.edu	37	20	13759865	13759865	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13759865delA	uc002woj.2	-						ESF1_uc002wok.1_Intron	NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1						AACAAAAAACAAAAAAAAACC	0.289													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	21563037	21563037	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21563037delT								NKX2-2 (68373 upstream) : PAX1 (123260 downstream)																							taatgtcctcttcctcatgga	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26200814	26200814	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26200814delA								MIR663 (11900 upstream) : None (None downstream)																							CATACACAACAAAAAGACTGA	0.164													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29628987	29628988	+	Intron	INS	-	C	C	rs138771657		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29628987_29628988insC	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						tctctctctcttttttaacagc	0.119													2	5	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29645742	29645743	+	Intron	DEL	AG	-	-	rs148671604	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29645742_29645743delAG	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						gactggataaagaaaatgtggt	0.000													4	2	---	---	---	---	
BPIL1	80341	broad.mit.edu	37	20	31607733	31607733	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31607733delC	uc002wyj.2	+							NM_025227	NP_079503	Q8N4F0	BPIL1_HUMAN	bactericidal/permeability-increasing							extracellular region	lipid binding			skin(2)|large_intestine(1)|ovary(1)	4						ctaggactctcccaccctggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36737958	36737958	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36737958delA								RPRD1B (17194 upstream) : TGM2 (18908 downstream)																							GATGATGGGGAACAGTTTAAC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38258947	38258948	+	IGR	INS	-	ATGGA	ATGGA	rs140838940	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38258947_38258948insATGGA								LOC339568 (405556 upstream) : None (None downstream)																							TGAGAGAGTTGCTGGACTGGAC	0.455													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42101066	42101068	+	IGR	DEL	GAT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42101066_42101068delGAT								SFRS6 (8824 upstream) : L3MBTL (35282 downstream)																							gcattttacagatgatgaaacag	0.167													4	2	---	---	---	---	
SNX21	90203	broad.mit.edu	37	20	44463023	44463037	+	In_Frame_Del	DEL	GACGAGGACGACGAG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44463023_44463037delGACGAGGACGACGAG	uc002xpv.1	+	2	294_308	c.205_219delGACGAGGACGACGAG	c.(205-219)GACGAGGACGACGAGdel	p.DEDDE74del	SNX21_uc002xps.1_In_Frame_Del_p.DEDDE74del|SNX21_uc002xpt.1_In_Frame_Del_p.DEDDE74del|SNX21_uc002xpu.1_In_Frame_Del_p.DEDDE74del|SNX21_uc002xpw.1_5'UTR|SNX21_uc002xpx.2_In_Frame_Del_p.DEDDE65del|SNX21_uc010zxd.1_In_Frame_Del_p.DEDDE65del|SNX21_uc002xpy.1_5'Flank	NM_033421	NP_219489	Q969T3	SNX21_HUMAN	sorting nexin 21 isoform a	74_78					cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding			breast(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)				CGCcgaggacgacgaggacgacgaggacgaggacg	0.572													5	3	---	---	---	---	
PREX1	57580	broad.mit.edu	37	20	47384056	47384056	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47384056delA	uc002xtw.1	-							NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GTTTCCACCTAACTCAGAGAA	0.512													3	4	---	---	---	---	
ARFGEF2	10564	broad.mit.edu	37	20	47558017	47558018	+	Intron	INS	-	CC	CC			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47558017_47558018insCC	uc002xtx.3	+							NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine						exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TGTTGTATCTTTTCTTAACAGA	0.446													5	3	---	---	---	---	
B4GALT5	9334	broad.mit.edu	37	20	48311376	48311377	+	Intron	INS	-	AC	AC	rs141181010	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48311376_48311377insAC	uc002xuu.3	-							NM_004776	NP_004767	O43286	B4GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	galactosyltransferase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;2.51e-06)			gacagacagatacacacacaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53294071	53294072	+	IGR	INS	-	G	G	rs140274215	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53294071_53294072insG								DOK5 (26362 upstream) : None (None downstream)																							cctaggggagagggtggcagcc	0.074													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53624504	53624504	+	IGR	DEL	A	-	-	rs159113	by1000genomes	TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53624504delA								DOK5 (356795 upstream) : CBLN4 (947993 downstream)																							CGAATGCTGGAAAGTTCTATC	0.343													4	2	---	---	---	---	
PHACTR3	116154	broad.mit.edu	37	20	58328860	58328860	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58328860delC	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_Intron|PHACTR3_uc002yax.2_Intron	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			tactgtttgtccaaacaggac	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61649777	61649777	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61649777delC	uc002yec.1	+											Homo sapiens cDNA FLJ46471 fis, clone THYMU3023394.																		GGTGCGTGTGCCCTGGCCGTG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11180395	11180396	+	IGR	INS	-	AA	AA	rs11429487		TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11180395_11180396insAA								BAGE (81458 upstream) : None (None downstream)																							catttcactgcaaaaaaaatat	0.000													3	3	---	---	---	---	
RCAN1	1827	broad.mit.edu	37	21	35960615	35960615	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35960615delA	uc002yue.2	-						RCAN1_uc002yuc.2_Intron|RCAN1_uc002yud.2_Intron	NM_004414	NP_004405	P53805	RCAN1_HUMAN	calcipressin 1 isoform a						blood circulation|calcium-mediated signaling|central nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						actggtgagtaatagctgggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16346782	16346782	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16346782delT								POTEH (58845 upstream) : OR11H1 (102044 downstream)																							CTAGTTCTAGTTTGAGTTAAA	0.388													4	2	---	---	---	---	
HIRA	7290	broad.mit.edu	37	22	19409792	19409793	+	Intron	DEL	AC	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19409792_19409793delAC	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)					TATTACATAAACACACACACAC	0.104													4	2	---	---	---	---	
UFD1L	7353	broad.mit.edu	37	22	19449712	19449712	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19449712delG	uc002zpm.2	-						UFD1L_uc002zpo.2_Intron|UFD1L_uc011agy.1_Intron|UFD1L_uc002zpp.2_Intron	NM_005659	NP_005650	Q92890	UFD1_HUMAN	ubiquitin fusion degradation 1-like isoform A						skeletal system development|ubiquitin-dependent protein catabolic process	cytosol|nucleus	protein binding|ubiquitin-specific protease activity				0	Colorectal(54;0.0993)					ttgtcgagatggggttttgcc	0.000													4	2	---	---	---	---	
AIFM3	150209	broad.mit.edu	37	22	21329207	21329207	+	Intron	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21329207delC	uc002ztj.2	+						AIFM3_uc002ztk.2_Intron|AIFM3_uc002ztl.2_Intron|AIFM3_uc011ahx.1_Intron|AIFM3_uc002ztm.1_Intron	NM_144704	NP_653305	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor,						activation of caspase activity by cytochrome c|cell redox homeostasis|electron transport chain|induction of apoptosis|mitochondrial depolarization|transport	endoplasmic reticulum|mitochondrial inner membrane	2 iron, 2 sulfur cluster binding|caspase activator activity|flavin adenine dinucleotide binding|metal ion binding|oxidoreductase activity|protein binding			ovary(2)|lung(2)	4	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			CGGCTGCCCTCCCTGCTTATG	0.438													4	2	---	---	---	---	
KIAA1671	85379	broad.mit.edu	37	22	25476526	25476526	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25476526delT	uc003abn.2	+						KIAA1671_uc003abl.2_Intron	NM_001145206	NP_001138678	Q9BY89	K1671_HUMAN	hypothetical protein LOC85379											lung(1)	1						tttatttttatttttttagag	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35443816	35443816	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35443816delT								None (None upstream) : ISX (18313 downstream)																							tctataccccttacttgttTA	0.224													4	2	---	---	---	---	
EFCAB6	64800	broad.mit.edu	37	22	43925103	43925103	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43925103delT	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				CACCTTTGCCTCCCTGAGGGG	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	46639787	46639787	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46639787delT								PPARA (134 upstream) : C22orf40 (124 downstream)																							GCACAGTCCCTTTTGTGTCCT	0.522													4	2	---	---	---	---	
CERK	64781	broad.mit.edu	37	22	47087342	47087342	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47087342delA	uc003bia.2	-						CERK_uc010hae.2_Intron	NM_022766	NP_073603	Q8TCT0	CERK1_HUMAN	ceramide kinase						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TTGTGAAATTAAAAAAAAAAA	0.274													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	904199	904200	+	IGR	INS	-	GAGA	GAGA			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:904199_904200insGAGA								SHOX (284054 upstream) : CRLF2 (410687 downstream)																							ataaagagaaggagagataaag	0.213													4	2	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1536650	1536651	+	Intron	DEL	TG	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1536650_1536651delTG	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				cgcacagacatgctccatgtca	0.040													4	4	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1536653	1536668	+	Intron	DEL	TCCATGTCACAGGTAT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1536653_1536668delTCCATGTCACAGGTAT	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				acagacatgctccatgtcacaggtatgctccagggc	0.074													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	43267855	43267855	+	IGR	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43267855delA								PPP1R2P9 (630369 upstream) : MAOA (247554 downstream)																							GCTGGACTGTAAAAAAAAAAG	0.383													5	3	---	---	---	---	
FAAH2	158584	broad.mit.edu	37	X	57368049	57368049	+	Intron	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57368049delT	uc004dvc.2	+							NM_174912	NP_777572	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2							integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3						ataatagttgttttttttttt	0.005										HNSCC(52;0.14)			6	3	---	---	---	---	
TAF1	6872	broad.mit.edu	37	X	70597397	70597397	+	Intron	DEL	G	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70597397delG	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2						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)				CCCAGATGCTGCTGTTTTCCC	0.428													64	70	---	---	---	---	
TRPC5	7224	broad.mit.edu	37	X	111095468	111095468	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111095468delA	uc004epl.1	-						TRPC5_uc004epm.1_Intron	NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,						axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1						CTCTCAGTGCAAAAGCTTAAT	0.388													31	26	---	---	---	---	
ODZ1	10178	broad.mit.edu	37	X	123838709	123838709	+	Intron	DEL	A	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123838709delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						GGTTAGGAAGAAAAAAAAAAA	0.353													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9789276	9789279	+	IGR	DEL	GTGT	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9789276_9789279delGTGT								TTTY22 (138422 upstream) : None (None downstream)																							GGAAGACAACgtgtgtgtgtgtgt	0.250													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13710450	13710450	+	IGR	DEL	T	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13710450delT								None (None upstream) : None (None downstream)																							tggaatgtagtccaaaggaaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58879928	58879928	+	IGR	DEL	C	-	-			TCGA-CJ-5675-01A-11D-1534-10	TCGA-CJ-5675-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58879928delC								None (None upstream) : None (None downstream)																							ttattccattcgagaccgtag	0.035													7	7	---	---	---	---	
