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
WDR65	149465	broad.mit.edu	37	1	43647495	43647495	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43647495G>T	uc001cip.1	+	3	569	c.448G>T	c.(448-450)GAC>TAC	p.D150Y	EBNA1BP2_uc001cio.2_Intron|WDR65_uc010ojz.1_Missense_Mutation_p.D139Y|WDR65_uc001ciq.1_Missense_Mutation_p.D150Y	NM_152498	NP_689711	Q96MR6	WDR65_HUMAN	WD repeat domain 65	150										skin(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGTTAGAATCGACACTCAGAA	0.348													11	46	---	---	---	---	PASS
BCL9	607	broad.mit.edu	37	1	147091598	147091598	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147091598C>G	uc001epq.2	+	8	2377	c.1637C>G	c.(1636-1638)CCG>CGG	p.P546R	BCL9_uc010ozr.1_Missense_Mutation_p.P472R	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	546	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					TCTCTGCCCCCGAGGGGCATG	0.592			T	IGH@|IGL@	B-ALL								5	14	---	---	---	---	PASS
INSRR	3645	broad.mit.edu	37	1	156812296	156812296	+	Missense_Mutation	SNP	C	T	T	rs138327752	byFrequency	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156812296C>T	uc010pht.1	-	18	3385	c.3131G>A	c.(3130-3132)CGT>CAT	p.R1044H	NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor	1044	Cytoplasmic (Potential).|Protein kinase.				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1)	20	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACCCAGGAGACGCACCTGGGA	0.512													3	30	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158618345	158618345	+	Missense_Mutation	SNP	C	T	T	rs148714399	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158618345C>T	uc001fst.1	-	26	3867	c.3668G>A	c.(3667-3669)CGA>CAA	p.R1223Q		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1223	Spectrin 12.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					CTCATGCCGTCGCTGAAGAGC	0.507													26	96	---	---	---	---	PASS
C1orf125	126859	broad.mit.edu	37	1	179452354	179452354	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179452354C>A	uc001gmo.2	+	18	2216	c.2089C>A	c.(2089-2091)CAC>AAC	p.H697N	C1orf125_uc009wxg.2_RNA|C1orf125_uc010pnl.1_RNA|C1orf125_uc001gmp.2_Missense_Mutation_p.H697N	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1	697											0						ACTTCAGCACCACGTATGTAC	0.373													6	381	---	---	---	---	PASS
RGL1	23179	broad.mit.edu	37	1	183891372	183891372	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183891372A>G	uc001gqo.2	+	17	2178	c.2021A>G	c.(2020-2022)AAA>AGA	p.K674R	RGL1_uc001gqm.2_Missense_Mutation_p.K709R|RGL1_uc010pog.1_Missense_Mutation_p.K672R|RGL1_uc010poh.1_Missense_Mutation_p.K672R|RGL1_uc010poi.1_Missense_Mutation_p.K645R	NM_015149	NP_055964	Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation	674	Ras-associating.				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						AGCCAGGATAAAACCCCCGCT	0.522											OREG0014047	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	38	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	185953431	185953431	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185953431C>T	uc001grq.1	+	19	3150	c.2921C>T	c.(2920-2922)TCT>TTT	p.S974F	HMCN1_uc001grr.1_Missense_Mutation_p.S315F	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	974	Ig-like C2-type 6.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AAAACTACCTCTGTGGTTGTG	0.398													82	286	---	---	---	---	PASS
DISP1	84976	broad.mit.edu	37	1	223179160	223179160	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223179160G>T	uc001hnu.1	+	8	4568	c.4421G>T	c.(4420-4422)AGG>ATG	p.R1474M		NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A	1474					diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)		GCTGGTTGTAGGTCTTGCCCA	0.428													23	55	---	---	---	---	PASS
ASXL2	55252	broad.mit.edu	37	2	26022316	26022316	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26022316C>T	uc002rgs.2	-	4	562	c.341G>A	c.(340-342)AGC>AAC	p.S114N		NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2	114	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTGCTGCTGCTGTTCTCAGA	0.458													5	393	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89102230	89102230	+	Intron	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89102230G>T	uc010fhg.2	+						FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_Intron	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						ATAACATCAGGTAGCTGTGAG	0.318													5	138	---	---	---	---	PASS
REV1	51455	broad.mit.edu	37	2	100017691	100017691	+	3'UTR	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100017691T>C	uc002tad.2	-	23					REV1_uc002tac.2_3'UTR	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1						DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2						AGCATCAGGCTCTCTGGTAAT	0.343								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					5	144	---	---	---	---	PASS
SLC9A4	389015	broad.mit.edu	37	2	103120043	103120043	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103120043T>A	uc002tbz.3	+	3	1314	c.857T>A	c.(856-858)TTT>TAT	p.F286Y		NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN	solute carrier family 9 (sodium/hydrogen	286	Helical; Name=H/M6; (Potential).				regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity			skin(2)|central_nervous_system(1)	3						GTTTTTGGATTTATTTCTGCA	0.413													122	500	---	---	---	---	PASS
NCKAP5	344148	broad.mit.edu	37	2	133540313	133540313	+	Silent	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133540313G>A	uc002ttp.2	-	14	4445	c.4071C>T	c.(4069-4071)AGC>AGT	p.S1357S	NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	1357							protein binding				0						GACTGCTGAAGCTGCCTGAGC	0.617													7	20	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179406075	179406075	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179406075T>A	uc010zfg.1	-	299	90249	c.90025A>T	c.(90025-90027)ATT>TTT	p.I30009F	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.I23704F|TTN_uc010zfi.1_Missense_Mutation_p.I23637F|TTN_uc010zfj.1_Missense_Mutation_p.I23512F	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	30936							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTGCATTAATGGCTGTGACA	0.433													22	103	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179516238	179516238	+	Silent	SNP	A	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179516238A>T	uc010zfg.1	-	161	32411	c.32187T>A	c.(32185-32187)GTT>GTA	p.V10729V	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc010fre.1_Intron|TTN_uc002umw.1_RNA|TTN_uc002umx.1_5'UTR	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	11656							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTTTCAGGAACAACCTCCT	0.463													30	127	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179634573	179634573	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179634573G>A	uc010zfg.1	-	37	8959	c.8735C>T	c.(8734-8736)TCC>TTC	p.S2912F	TTN_uc010zfh.1_Missense_Mutation_p.S2866F|TTN_uc010zfi.1_Missense_Mutation_p.S2866F|TTN_uc010zfj.1_Missense_Mutation_p.S2866F|TTN_uc002unb.2_Missense_Mutation_p.S2912F	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2912							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCCACATGGAAGGGACATT	0.423													7	139	---	---	---	---	PASS
ICA1L	130026	broad.mit.edu	37	2	203693769	203693769	+	Intron	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203693769T>C	uc002uzh.1	-						ICA1L_uc002uzi.1_Intron|ICA1L_uc002uzj.2_5'UTR|ICA1L_uc002uzk.1_Intron	NM_138468	NP_612477	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like isoform 1												0						ATTAAACTTCTTTTAAAAATT	0.204													6	272	---	---	---	---	PASS
ZDBF2	57683	broad.mit.edu	37	2	207171231	207171231	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207171231A>G	uc002vbp.2	+	5	2229	c.1979A>G	c.(1978-1980)AAC>AGC	p.N660S		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	660	Potential.						nucleic acid binding|zinc ion binding			ovary(3)	3						ATGGATATGAACTGTGAATCC	0.443													5	140	---	---	---	---	PASS
BARD1	580	broad.mit.edu	37	2	215632207	215632207	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215632207C>T	uc002veu.2	-	6	1702	c.1567G>A	c.(1567-1569)GTT>ATT	p.V523I	BARD1_uc010zjm.1_Missense_Mutation_p.V379I	NM_000465	NP_000456	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	523	ANK 3.				cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ACTACTTACACAGCATTTCTG	0.383									Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				16	120	---	---	---	---	PASS
SETD5	55209	broad.mit.edu	37	3	9483878	9483878	+	Silent	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9483878T>C	uc003brt.2	+	10	1461	c.1026T>C	c.(1024-1026)ACT>ACC	p.T342T	SETD5_uc003brs.1_Silent_p.T323T|SETD5_uc003bru.2_Silent_p.T244T|SETD5_uc003brv.2_Silent_p.T231T|SETD5_uc010hck.2_5'UTR|SETD5_uc003brw.1_5'Flank|SETD5_uc003brx.2_5'Flank	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	342	SET.									ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		ATGCCCGTACTTTCGGTAATG	0.403													6	267	---	---	---	---	PASS
CNOT10	25904	broad.mit.edu	37	3	32746384	32746384	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32746384A>G	uc003cfc.1	+	3	454	c.199A>G	c.(199-201)ACA>GCA	p.T67A	CNOT10_uc011axi.1_Translation_Start_Site|CNOT10_uc003cfd.1_Missense_Mutation_p.T67A|CNOT10_uc003cfe.1_Missense_Mutation_p.T67A|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Missense_Mutation_p.T127A|CNOT10_uc010hfw.1_Translation_Start_Site	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10	67					nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2						AATTTTGAATACAGCAGTAGC	0.299													8	217	---	---	---	---	PASS
CXCR6	10663	broad.mit.edu	37	3	45988547	45988547	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45988547C>T	uc003cpc.1	+	2	655	c.574C>T	c.(574-576)CTT>TTT	p.L192F	FYCO1_uc003cpb.3_Intron|FYCO1_uc011bal.1_Intron|CXCR6_uc010hix.1_Missense_Mutation_p.L192F	NM_006564	NP_006555	O00574	CXCR6_HUMAN	G protein-coupled receptor TYMSTR	192	Helical; Name=5; (Potential).				viral genome replication	integral to plasma membrane	coreceptor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CACTGTGGTTCTTGCCACCCA	0.463													26	59	---	---	---	---	PASS
MORC1	27136	broad.mit.edu	37	3	108822744	108822744	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108822744C>T	uc003dxl.2	-	4	262	c.175G>A	c.(175-177)GGG>AGG	p.G59R	MORC1_uc011bhn.1_Missense_Mutation_p.G59R	NM_014429	NP_055244	Q86VD1	MORC1_HUMAN	MORC family CW-type zinc finger 1	59					cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8						ATGAATCCCCCCTGCAGTTTT	0.368													5	352	---	---	---	---	PASS
SLC15A2	6565	broad.mit.edu	37	3	121615297	121615297	+	Silent	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121615297G>T	uc003eep.2	+	2	303	c.150G>T	c.(148-150)GTG>GTT	p.V50V	SLC15A2_uc011bjn.1_Silent_p.V50V	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	50					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)	CCTTCATTGTGGTGAATGAAT	0.438													5	331	---	---	---	---	PASS
IL20RB	53833	broad.mit.edu	37	3	136710849	136710849	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136710849T>C	uc003eri.1	+	5	850	c.601T>C	c.(601-603)TAC>CAC	p.Y201H	IL20RB_uc003erj.1_Intron|IL20RB_uc010hud.1_Missense_Mutation_p.Y59H	NM_144717	NP_653318	Q6UXL0	I20RB_HUMAN	interleukin 20 receptor beta precursor	201	Extracellular (Potential).|Fibronectin type-III 2.					integral to membrane	receptor activity			ovary(1)	1						AGGGGCTGCATACTGTGTGAA	0.502													30	59	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505839	195505839	+	Silent	SNP	A	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505839A>T	uc011bto.1	-	3	12688	c.12228T>A	c.(12226-12228)GGT>GGA	p.G4076G	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATG	0.597													4	12	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506839	195506839	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506839G>T	uc011bto.1	-	3	11688	c.11228C>A	c.(11227-11229)ACC>AAC	p.T3743N	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	645					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGAGGGGTGGCGTGACC	0.592													3	6	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195515290	195515290	+	Missense_Mutation	SNP	C	G	G	rs78535324	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195515290C>G	uc011bto.1	-	2	3621	c.3161G>C	c.(3160-3162)AGC>ACC	p.S1054T	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1053					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGAGGGGTGCTGTCACCTGT	0.572													5	17	---	---	---	---	PASS
AFAP1	60312	broad.mit.edu	37	4	7783208	7783208	+	Intron	SNP	C	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7783208C>A	uc003gkg.1	-						AFAP1_uc011bwk.1_Silent_p.L559L	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0						TGTCAGCAGACAGCCTAGAGG	0.537													20	83	---	---	---	---	PASS
PCDH7	5099	broad.mit.edu	37	4	30724917	30724917	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30724917G>T	uc003gsk.1	+	1	2881	c.1873G>T	c.(1873-1875)GTG>TTG	p.V625L	PCDH7_uc011bxw.1_Missense_Mutation_p.V578L|PCDH7_uc011bxx.1_Missense_Mutation_p.V625L	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	625	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						CAGCACTACGGTGATTGTGCA	0.493													17	81	---	---	---	---	PASS
EPHA5	2044	broad.mit.edu	37	4	66197808	66197808	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66197808G>T	uc003hcy.2	-	17	3084	c.2891C>A	c.(2890-2892)TCT>TAT	p.S964Y	EPHA5_uc003hcx.2_Missense_Mutation_p.S896Y|EPHA5_uc003hcz.2_Missense_Mutation_p.S942Y|EPHA5_uc011cah.1_Missense_Mutation_p.S965Y|EPHA5_uc011cai.1_Missense_Mutation_p.S943Y|EPHA5_uc003hda.2_Missense_Mutation_p.S965Y	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	964	Cytoplasmic (Potential).				cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24						GTAGGCCCCAGATCCTAGTGG	0.358										TSP Lung(17;0.13)			25	155	---	---	---	---	PASS
TMPRSS11D	9407	broad.mit.edu	37	4	68725379	68725379	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68725379G>A	uc003hdq.2	-	2	91	c.26C>T	c.(25-27)TCG>TTG	p.S9L	LOC550112_uc003hdl.3_Intron|TMPRSS11D_uc011caj.1_Intron	NM_004262	NP_004253	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	9	Cytoplasmic (Potential).				proteolysis|respiratory gaseous exchange	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1						TCTTGAAGTCGAAGTTACACG	0.393													36	109	---	---	---	---	PASS
IGJ	3512	broad.mit.edu	37	4	71527881	71527881	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71527881C>T	uc003hfn.3	-	2	257	c.116G>A	c.(115-117)CGG>CAG	p.R39Q	IGJ_uc010ihz.2_Missense_Mutation_p.R55Q	NM_144646	NP_653247	P01591	IGJ_HUMAN	immunoglobulin J chain	39					immune response	extracellular region	antigen binding				0			Lung(101;0.235)			GGAAGTAATCCGGGCACACTT	0.368													4	162	---	---	---	---	PASS
RUFY3	22902	broad.mit.edu	37	4	71655357	71655357	+	Intron	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71655357A>G	uc003hfq.2	+						RUFY3_uc003hfp.3_3'UTR|RUFY3_uc011cax.1_Intron|RUFY3_uc003hfr.2_Intron|RUFY3_uc011cay.1_Intron	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)			GTCAGTGCTGAAGTGAAAAGA	0.348													5	153	---	---	---	---	PASS
DMP1	1758	broad.mit.edu	37	4	88583134	88583134	+	Silent	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88583134C>T	uc003hqv.2	+	6	308	c.204C>T	c.(202-204)GAC>GAT	p.D68D	DMP1_uc003hqw.2_Silent_p.D52D	NM_004407	NP_004398	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1 isoform 1	68					biomineral tissue development|ossification	cytoplasm|nucleus|proteinaceous extracellular matrix	calcium ion binding|integrin binding			pancreas(1)|skin(1)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		ACCCCAGTGACAGCACTCAGT	0.463													7	68	---	---	---	---	PASS
INTU	27152	broad.mit.edu	37	4	128632123	128632123	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128632123C>A	uc003ifk.1	+	14	2495	c.2425C>A	c.(2425-2427)CAA>AAA	p.Q809K	INTU_uc011cgq.1_RNA	NM_015693	NP_056508	Q9ULD6	PDZD6_HUMAN	PDZ domain containing 6	809										ovary(1)	1						AGAAACAGTGCAAGGAATCTT	0.378													44	206	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151817595	151817595	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151817595T>C	uc010ipj.2	-	16	2492	c.2018A>G	c.(2017-2019)AAG>AGG	p.K673R	LRBA_uc003ilu.3_Missense_Mutation_p.K673R|LRBA_uc010ipk.1_Silent_p.K565K	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	673						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TTCATCTTCCTTTACTCCAGA	0.264													8	573	---	---	---	---	PASS
CBR4	84869	broad.mit.edu	37	4	169923257	169923257	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169923257G>A	uc003iry.2	-	4	682	c.500C>T	c.(499-501)GCA>GTA	p.A167V	CBR4_uc011cjy.1_RNA|CBR4_uc003irz.1_Missense_Mutation_p.A167V	NM_032783	NP_116172	Q8N4T8	CBR4_HUMAN	carbonic reductase 4	167					fatty acid biosynthetic process|protein homotetramerization	mitochondrial matrix	NADPH binding|NADPH dehydrogenase (quinone) activity|protein binding|quinone binding				0		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)		TTTCTTTCTTGCTACCTCTTT	0.368													18	273	---	---	---	---	PASS
RAI14	26064	broad.mit.edu	37	5	34813718	34813718	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34813718A>G	uc003jir.2	+	11	1001	c.805A>G	c.(805-807)ACT>GCT	p.T269A	RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Missense_Mutation_p.T269A|RAI14_uc010ius.1_Missense_Mutation_p.T198A|RAI14_uc003jis.2_Missense_Mutation_p.T272A|RAI14_uc003jit.2_Missense_Mutation_p.T269A|RAI14_uc011cok.1_Missense_Mutation_p.T261A	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a	269						cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					AAGAAGTGGAACTCCAAAAAA	0.413													7	515	---	---	---	---	PASS
PTCD2	79810	broad.mit.edu	37	5	71627175	71627175	+	Silent	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71627175A>G	uc003kcb.2	+	4	451	c.441A>G	c.(439-441)GAA>GAG	p.E147E	PTCD2_uc011csf.1_5'UTR|PTCD2_uc003kcc.2_5'UTR|PTCD2_uc011csg.1_Intron|PTCD2_uc011csh.1_Intron|PTCD2_uc003kcd.2_RNA	NM_024754	NP_079030	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	147											0		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)		ATCTCGAGGAATCTGCAGTGG	0.403													8	733	---	---	---	---	PASS
NSA2	10412	broad.mit.edu	37	5	74072544	74072544	+	3'UTR	SNP	A	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74072544A>C	uc003kdk.1	+	6						NM_014886	NP_055701	O95478	NSA2_HUMAN	NSA2 ribosome biogenesis homolog						rRNA processing	nucleolus|ribonucleoprotein complex				ovary(1)	1						AATTGAAGAAACTGCCATTAC	0.323													10	42	---	---	---	---	PASS
ANKRD34B	340120	broad.mit.edu	37	5	79855596	79855596	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79855596G>T	uc010jam.2	-	4	593	c.243C>A	c.(241-243)GAC>GAA	p.D81E	ANKRD34B_uc003kgw.2_Missense_Mutation_p.D81E|ANKRD34B_uc010jan.2_Missense_Mutation_p.D81E	NM_001004441	NP_001004441	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	81						cytoplasm|nucleus				pancreas(1)	1		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		TCCCAGATTTGTCCTGTATGT	0.468													28	137	---	---	---	---	PASS
RASA1	5921	broad.mit.edu	37	5	86564707	86564707	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86564707G>A	uc003kiw.2	+	1	557	c.439G>A	c.(439-441)GGG>AGG	p.G147R	RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_5'Flank|RASA1_uc011ctv.1_5'Flank|RASA1_uc011ctw.1_5'Flank|RASA1_uc010jaw.2_5'Flank|RASA1_uc011ctu.1_Missense_Mutation_p.G147R	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	147					cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		GCCCCCTTTGGGGGCGGGCCT	0.622													7	39	---	---	---	---	PASS
KIF4B	285643	broad.mit.edu	37	5	154394373	154394373	+	Silent	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154394373C>T	uc010jih.1	+	1	1114	c.954C>T	c.(952-954)TCC>TCT	p.S318S		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	318	Kinesin-motor.				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTGCTGACTCCAATCTAGAGG	0.428													69	412	---	---	---	---	PASS
RNF144B	255488	broad.mit.edu	37	6	18457398	18457398	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18457398A>G	uc003ncs.2	+	5	648	c.344A>G	c.(343-345)GAC>GGC	p.D115G		NM_182757	NP_877434	Q7Z419	R144B_HUMAN	IBR domain containing 2	115	IBR-type.				apoptosis|positive regulation of anti-apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			GTTCATCTGGACCCCTACCGA	0.468													5	107	---	---	---	---	PASS
UBR2	23304	broad.mit.edu	37	6	42637945	42637945	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42637945T>A	uc011dur.1	+	35	3997	c.3997T>A	c.(3997-3999)TGG>AGG	p.W1333R	UBR2_uc011dus.1_Missense_Mutation_p.W978R|UBR2_uc003osh.2_RNA	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1333					cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			CATAATGTGTTGGGGTAGCTG	0.418													33	91	---	---	---	---	PASS
RNGTT	8732	broad.mit.edu	37	6	89322274	89322274	+	3'UTR	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89322274A>G	uc003pmr.2	-	16					RNGTT_uc003pms.2_3'UTR|RNGTT_uc011dzu.1_3'UTR	NM_003800	NP_003791	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		GAATGCATCAAGTATTTACAG	0.343													4	8	---	---	---	---	PASS
ASCC3	10973	broad.mit.edu	37	6	101110412	101110412	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101110412C>T	uc003pqk.2	-	15	2616	c.2287G>A	c.(2287-2289)GTA>ATA	p.V763I	ASCC3_uc011eai.1_Missense_Mutation_p.V665I	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	763	Helicase C-terminal 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GACCTTTGTACCTAGATACCA	0.323													49	209	---	---	---	---	PASS
HACE1	57531	broad.mit.edu	37	6	105233140	105233140	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105233140C>A	uc003pqu.1	-	12	1406	c.1129G>T	c.(1129-1131)GAA>TAA	p.E377*	HACE1_uc010kcy.1_5'UTR|HACE1_uc010kcz.1_Nonsense_Mutation_p.E377*|HACE1_uc010kcx.1_5'UTR|HACE1_uc003pqt.1_Nonsense_Mutation_p.E30*	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3	377					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		TTCATCAATTCTGTGGCTATT	0.363													48	133	---	---	---	---	PASS
ETV1	2115	broad.mit.edu	37	7	13975450	13975450	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13975450G>A	uc011jxq.1	-	8	1176	c.437C>T	c.(436-438)TCC>TTC	p.S146F	ETV1_uc011jxn.1_Missense_Mutation_p.S106F|ETV1_uc011jxo.1_Intron|ETV1_uc011jxp.1_Missense_Mutation_p.S88F|ETV1_uc003ssw.3_Missense_Mutation_p.S146F|ETV1_uc003ssx.2_RNA|ETV1_uc011jxr.1_Missense_Mutation_p.S128F|ETV1_uc011jxs.1_Missense_Mutation_p.S128F|ETV1_uc010ktv.2_Missense_Mutation_p.S15F	NM_004956	NP_004947	P50549	ETV1_HUMAN	ets variant gene 1 isoform a	146					transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		TMPRSS2/ETV1(24)|EWSR1/ETV1(7)	prostate(24)|soft_tissue(4)|bone(3)|lung(2)|central_nervous_system(1)|ovary(1)	35						ATGCAGTGGGGACACTGGCGT	0.562			T	EWSR1|TMPRSS2|SLC45A3|C15orf21|HNRNPA2B1. ACSL3	Ewing sarcoma|prostate								52	174	---	---	---	---	PASS
ABCB5	340273	broad.mit.edu	37	7	20762763	20762763	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20762763C>T	uc003suw.3	+	12	1757	c.1211C>T	c.(1210-1212)GCC>GTC	p.A404V	ABCB5_uc010kuh.2_Missense_Mutation_p.A849V|ABCB5_uc003sux.1_Missense_Mutation_p.A27V	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	404	Cytoplasmic (Potential).|ABC transmembrane type-1.				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6						CCAGTACTTGCCGTGACAGGA	0.383													5	326	---	---	---	---	PASS
AMPH	273	broad.mit.edu	37	7	38431539	38431539	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38431539G>A	uc003tgu.2	-	19	1757	c.1688C>T	c.(1687-1689)GCA>GTA	p.A563V	AMPH_uc003tgv.2_Missense_Mutation_p.A521V|AMPH_uc003tgt.2_Missense_Mutation_p.A448V|AMPH_uc003tgw.1_Missense_Mutation_p.A586V|AMPH_uc010kxl.1_RNA	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	563					endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						CTTGGGCTCTGCACCTATAGT	0.592													15	49	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48314043	48314043	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48314043G>A	uc003toq.2	+	17	4805	c.4780G>A	c.(4780-4782)GGC>AGC	p.G1594S	ABCA13_uc010kyr.2_Missense_Mutation_p.G1097S	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	1594					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						AAACAGTGTAGGCAATTCCAT	0.323													31	118	---	---	---	---	PASS
GTF2I	2969	broad.mit.edu	37	7	74167453	74167453	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74167453T>A	uc003uau.2	+	29	2955	c.2585T>A	c.(2584-2586)GTT>GAT	p.V862D	GTF2I_uc003uav.2_Missense_Mutation_p.V841D|GTF2I_uc003uaw.2_Missense_Mutation_p.V842D|GTF2I_uc003uay.2_Missense_Mutation_p.V840D|GTF2I_uc003uax.2_Missense_Mutation_p.V821D|GTF2I_uc003uba.2_Missense_Mutation_p.V53D	NM_032999	NP_127492	P78347	GTF2I_HUMAN	general transcription factor IIi isoform 1	862	GTF2I-like 6.				negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						CTCTCGAAAGTTGAAAAAGCT	0.294													24	191	---	---	---	---	PASS
PIK3CG	5294	broad.mit.edu	37	7	106509653	106509653	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106509653C>A	uc003vdv.3	+	2	1732	c.1647C>A	c.(1645-1647)AAC>AAA	p.N549K	PIK3CG_uc003vdu.2_Missense_Mutation_p.N549K|PIK3CG_uc003vdw.2_Missense_Mutation_p.N549K	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	549					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						AAATGCCCAACCAGCTTCGCA	0.532													20	63	---	---	---	---	PASS
ING3	54556	broad.mit.edu	37	7	120614705	120614705	+	Intron	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120614705T>C	uc003vjn.2	+						ING3_uc003vjo.2_Intron|ING3_uc003vjp.2_3'UTR|ING3_uc011kns.1_Intron	NM_019071	NP_061944	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3 isoform 1						histone H2A acetylation|histone H4 acetylation|positive regulation of apoptosis|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Piccolo NuA4 histone acetyltransferase complex	zinc ion binding			ovary(1)	1	all_neural(327;0.117)					GATTATTCAGTCTCCTGAGCA	0.289													7	397	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131982903	131982903	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131982903C>A	uc003vra.3	-	4	1679	c.1450G>T	c.(1450-1452)GAT>TAT	p.D484Y		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	484	Extracellular (Potential).|Sema.					integral to membrane|intracellular|plasma membrane				ovary(1)	1						AAGGCCATATCCCGGAGGACT	0.577													9	22	---	---	---	---	PASS
DOCK5	80005	broad.mit.edu	37	8	25191637	25191637	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25191637A>G	uc003xeg.2	+	21	2254	c.2117A>G	c.(2116-2118)GAC>GGC	p.D706G	DOCK5_uc010luf.1_RNA|DOCK5_uc003xeh.1_Missense_Mutation_p.D420G|DOCK5_uc003xei.2_Missense_Mutation_p.D276G|DOCK5_uc003xej.2_RNA	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	706						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CTGATAGGAGACATCAAGTTC	0.373													6	257	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61732614	61732614	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61732614A>T	uc003xue.2	+	9	3139	c.2662A>T	c.(2662-2664)ATG>TTG	p.M888L	CHD7_uc003xuf.2_Missense_Mutation_p.M1L	NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	888	Chromo 2.				central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TGACCGGATAATGGACTTTGC	0.388													107	492	---	---	---	---	PASS
NOV	4856	broad.mit.edu	37	8	120435157	120435157	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120435157T>A	uc003yoq.2	+	5	1080	c.859T>A	c.(859-861)TAC>AAC	p.Y287N		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	287	CTCK.				regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CCTGCACACCTACAAGCCCAG	0.512													6	23	---	---	---	---	PASS
TMEM71	137835	broad.mit.edu	37	8	133764200	133764200	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133764200C>T	uc003ytp.2	-	4	374	c.145G>A	c.(145-147)GGC>AGC	p.G49S	TMEM71_uc003ytn.2_Missense_Mutation_p.G49S|TMEM71_uc003yto.2_Missense_Mutation_p.G49S	NM_144649	NP_653250	Q6P5X7	TMM71_HUMAN	transmembrane protein 71 isoform 1	49						integral to membrane				ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TCTATGGAGCCGCATTCAAAA	0.458													24	132	---	---	---	---	PASS
ZFAT	57623	broad.mit.edu	37	8	135521987	135521987	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135521987G>A	uc003yup.2	-	15	3542	c.3367C>T	c.(3367-3369)CGA>TGA	p.R1123*	ZFAT_uc011ljj.1_Nonsense_Mutation_p.R242*|ZFAT_uc003yun.2_Nonsense_Mutation_p.R1111*|ZFAT_uc003yuo.2_Nonsense_Mutation_p.R1111*|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Nonsense_Mutation_p.R1111*|ZFAT_uc010mej.2_Nonsense_Mutation_p.R1061*	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	1123					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			GGGTCCAGTCGGTCGCCTTAA	0.597													3	30	---	---	---	---	PASS
C9orf144	389715	broad.mit.edu	37	9	34834304	34834304	+	Silent	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34834304C>T	uc003zvp.3	-	4	2090	c.1176G>A	c.(1174-1176)AGG>AGA	p.R392R		NR_024481				RecName: Full=Uncharacterized protein C9orf144A;												0						ACAAGTGTGGCCTGGGGATGG	0.587													14	51	---	---	---	---	PASS
SYK	6850	broad.mit.edu	37	9	93636536	93636536	+	Silent	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93636536G>A	uc004aqz.2	+	8	1171	c.966G>A	c.(964-966)CCG>CCA	p.P322P	SYK_uc004ara.2_Silent_p.P299P|SYK_uc004arb.2_Silent_p.P299P|SYK_uc004arc.2_Silent_p.P322P|SYK_uc011ltr.1_RNA|SYK_uc011lts.1_RNA|SYK_uc011ltt.1_RNA	NM_003177	NP_003168	P43405	KSYK_HUMAN	spleen tyrosine kinase isoform 1	322	Linker.				cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly	cytosol|T cell receptor complex	ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5						CATTCAATCCGTATGAGCCAG	0.468			T	ETV6|ITK	MDS|peripheral T-cell lymphoma								39	99	---	---	---	---	PASS
AKNA	80709	broad.mit.edu	37	9	117139678	117139678	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117139678C>T	uc004biq.3	-	2	544	c.409G>A	c.(409-411)GCT>ACT	p.A137T	AKNA_uc004bio.3_5'Flank|AKNA_uc004bip.3_Missense_Mutation_p.A56T|AKNA_uc004bir.3_Missense_Mutation_p.A137T|AKNA_uc004bis.3_Missense_Mutation_p.A137T|AKNA_uc010mve.2_Missense_Mutation_p.A18T|AKNA_uc004biu.1_Intron|AKNA_uc004biv.1_Missense_Mutation_p.A137T|AKNA_uc004biw.1_Missense_Mutation_p.A137T	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	137					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6						CTCTCTCCAGCCTCCTCAACC	0.617													3	5	---	---	---	---	PASS
ECHDC3	79746	broad.mit.edu	37	10	11797428	11797428	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11797428C>G	uc001ikw.3	+	4	632	c.412C>G	c.(412-414)CAC>GAC	p.H138D	ECHDC3_uc009xix.2_Missense_Mutation_p.H7D	NM_024693	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl Coenzyme A hydratase domain containing 3	138						mitochondrion	catalytic activity				0						CATCCGGAACCACCCCGTTCC	0.552													5	17	---	---	---	---	PASS
SFTPD	6441	broad.mit.edu	37	10	81702178	81702178	+	Silent	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81702178G>A	uc001kbh.2	-	4	442	c.399C>T	c.(397-399)GGC>GGT	p.G133G	MBL1P_uc001kbf.2_Intron	NM_003019	NP_003010	P35247	SFTPD_HUMAN	pulmonary surfactant-associated protein D	133	Collagen-like.				cell junction assembly|innate immune response|lung alveolus development|macrophage chemotaxis|negative regulation of interleukin-2 biosynthetic process|negative regulation of T cell proliferation|positive regulation of phagocytosis|reactive oxygen species metabolic process|receptor-mediated endocytosis|respiratory gaseous exchange|surfactant homeostasis	collagen|endocytic vesicle|extracellular space|lysosome	bacterial cell surface binding|protein binding|sugar binding			skin(1)	1	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			GGCCTGGCTTGCCCTGAGGTC	0.597													15	47	---	---	---	---	PASS
SORBS1	10580	broad.mit.edu	37	10	97074670	97074670	+	3'UTR	SNP	T	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97074670T>G	uc001kkp.2	-	31					SORBS1_uc001kkk.2_3'UTR|SORBS1_uc001kkl.2_3'UTR|SORBS1_uc001kkn.2_3'UTR|SORBS1_uc001kkm.2_3'UTR|SORBS1_uc001kko.2_3'UTR|SORBS1_uc001kkq.2_3'UTR|SORBS1_uc001kkr.2_3'UTR|SORBS1_uc001kks.2_3'UTR|SORBS1_uc001kkt.2_RNA|SORBS1_uc001kku.2_3'UTR|SORBS1_uc001kkv.2_3'UTR|SORBS1_uc001kkw.2_3'UTR|SORBS1_uc010qoe.1_3'UTR	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		CAGGCTTGGGTTTTAAACACA	0.388													7	27	---	---	---	---	PASS
EIF3A	8661	broad.mit.edu	37	10	120809340	120809340	+	Silent	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120809340T>C	uc001ldu.2	-	17	2777	c.2631A>G	c.(2629-2631)AGA>AGG	p.R877R	EIF3A_uc010qsu.1_Silent_p.R843R|EIF3A_uc009xzg.1_5'UTR	NM_003750	NP_003741	Q14152	EIF3A_HUMAN	eukaryotic translation initiation factor 3,	877					formation of translation initiation complex	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|structural molecule activity|translation initiation factor activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		TATCGCCAAGTCTTCTCTCTT	0.338													7	366	---	---	---	---	PASS
CPXM2	119587	broad.mit.edu	37	10	125526488	125526488	+	Splice_Site	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125526488C>T	uc001lhk.1	-	10	1804	c.1479_splice	c.e10+1	p.T493_splice	CPXM2_uc001lhj.2_Splice_Site	NM_198148	NP_937791	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2						cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TTTTGACTCACCGTGGCATTT	0.468													18	124	---	---	---	---	PASS
PTPN5	84867	broad.mit.edu	37	11	18750477	18750477	+	3'UTR	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18750477G>A	uc001mpd.2	-	15					IGSF22_uc009yht.2_5'Flank|IGSF22_uc001mpa.2_5'Flank|PTPN5_uc001mpb.2_3'UTR|PTPN5_uc001mpc.2_3'UTR|PTPN5_uc001mpe.2_3'UTR|PTPN5_uc010rdj.1_3'UTR|PTPN5_uc001mpf.2_3'UTR|PTPN5_uc010rdk.1_3'UTR	NM_006906	NP_008837	P54829	PTN5_HUMAN	protein-tyrosine-phosphatase non-receptor 5							integral to membrane	phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(2)	2						TAGGAGAAGCGCAGTCATTCT	0.632													10	83	---	---	---	---	PASS
ANO5	203859	broad.mit.edu	37	11	22281068	22281068	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22281068T>C	uc001mqi.2	+	15	1728	c.1411T>C	c.(1411-1413)TCT>CCT	p.S471P	ANO5_uc001mqj.2_Missense_Mutation_p.S470P	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	471	Helical; (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4						TTCCCAGATGTCTCTTGTCGT	0.373													7	391	---	---	---	---	PASS
PDHX	8050	broad.mit.edu	37	11	35016627	35016627	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35016627T>C	uc001mvt.2	+	11	1940	c.1414T>C	c.(1414-1416)TCA>CCA	p.S472P	PDHX_uc010rep.1_Missense_Mutation_p.S457P|PDHX_uc010req.1_Missense_Mutation_p.S245P	NM_003477	NP_003468	O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	472					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			AGTCACAATGTCAAGTGACAG	0.478													6	134	---	---	---	---	PASS
PRPF19	27339	broad.mit.edu	37	11	60671329	60671329	+	Silent	SNP	A	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60671329A>T	uc001nqf.2	-	2	231	c.24T>A	c.(22-24)TCT>TCA	p.S8S		NM_014502	NP_055317	Q9UMS4	PRP19_HUMAN	PRP19/PSO4 pre-mRNA processing factor 19	8	U-box.				DNA repair|protein polyubiquitination|spliceosome assembly	catalytic step 2 spliceosome|nuclear speck|spindle|ubiquitin ligase complex	DNA binding|identical protein binding|ubiquitin-ubiquitin ligase activity			ovary(1)	1						GCACTTCGTTAGAGACTGTAG	0.512													10	44	---	---	---	---	PASS
DDB1	1642	broad.mit.edu	37	11	61081631	61081631	+	Silent	SNP	T	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61081631T>A	uc001nrc.3	-	14	1867	c.1641A>T	c.(1639-1641)GGA>GGT	p.G547G	DDB1_uc010rle.1_Intron|DDB1_uc010rlf.1_Silent_p.G547G	NM_001923	NP_001914	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1	547	Interaction with CDT1.|Interaction with CUL4A.				cell cycle checkpoint|interspecies interaction between organisms|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytoplasm|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4						CATTGCTGTCTCCTAATGGGG	0.493								NER					18	67	---	---	---	---	PASS
DDB1	1642	broad.mit.edu	37	11	61081632	61081632	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61081632C>T	uc001nrc.3	-	14	1866	c.1640G>A	c.(1639-1641)GGA>GAA	p.G547E	DDB1_uc010rle.1_Intron|DDB1_uc010rlf.1_Missense_Mutation_p.G547E	NM_001923	NP_001914	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1	547	Interaction with CDT1.|Interaction with CUL4A.				cell cycle checkpoint|interspecies interaction between organisms|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytoplasm|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4						ATTGCTGTCTCCTAATGGGGT	0.493								NER					17	69	---	---	---	---	PASS
BIRC2	329	broad.mit.edu	37	11	102221673	102221673	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102221673A>G	uc001pgy.2	+	3	2393	c.994A>G	c.(994-996)AGG>GGG	p.R332G	BIRC2_uc010ruq.1_Missense_Mutation_p.R283G|BIRC2_uc010rur.1_Missense_Mutation_p.R332G	NM_001166	NP_001157	Q13490	BIRC2_HUMAN	baculoviral IAP repeat-containing protein 2	332	BIR 3.				cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	CD40 receptor complex|cytosol|internal side of plasma membrane	protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		GTGGTTTCCAAGGTAATTGTT	0.378													164	589	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8082245	8082245	+	Intron	SNP	T	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082245T>G	uc001qtr.2	-						SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		GTGAAATACTTTAAGACACGT	0.254													5	75	---	---	---	---	PASS
RAPGEF3	10411	broad.mit.edu	37	12	48137448	48137448	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48137448T>C	uc009zkp.2	-	17	2004	c.1564A>G	c.(1564-1566)ATC>GTC	p.I522V	RAPGEF3_uc001rpw.2_5'Flank|RAPGEF3_uc001rpx.2_5'UTR|RAPGEF3_uc010sln.1_Intron|RAPGEF3_uc001rpy.2_RNA|RAPGEF3_uc009zkq.2_Missense_Mutation_p.I522V|RAPGEF3_uc001rpz.3_Missense_Mutation_p.I564V	NM_001098532	NP_001092002	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform	522					regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity			lung(2)|skin(1)|pancreas(1)	4	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		GGCCGGCAGATGTCATAGGGG	0.612													7	18	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	102030997	102030997	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102030997C>T	uc001vox.1	-	4	488	c.299G>A	c.(298-300)AGT>AAT	p.S100N	NALCN_uc001voy.2_5'UTR|NALCN_uc001voz.2_Missense_Mutation_p.S100N|NALCN_uc001vpa.2_Missense_Mutation_p.S100N	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	100	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity	p.S100R(1)		ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CACATAGGAACTATCCCCCTA	0.299													10	547	---	---	---	---	PASS
FAM70B	348013	broad.mit.edu	37	13	114514719	114514719	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114514719G>A	uc001vuh.2	+	9	851	c.824G>A	c.(823-825)CGC>CAC	p.R275H		NM_182614	NP_872420	Q8WV15	FA70B_HUMAN	family with sequence similarity 70, member B	275	Pro-rich.					integral to membrane					0	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.123)|all_epithelial(44;0.133)	all cancers(43;0.181)			CCCTGCAGCCGCTTCCCAGTT	0.652													6	16	---	---	---	---	PASS
PCNX	22990	broad.mit.edu	37	14	71514655	71514655	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71514655A>C	uc001xmo.2	+	22	4738	c.4292A>C	c.(4291-4293)GAG>GCG	p.E1431A	PCNX_uc010are.1_Missense_Mutation_p.E1320A|PCNX_uc010arf.1_Missense_Mutation_p.E291A	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	1431						integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GCTTTTTCAGAGACCATGCTG	0.358													82	255	---	---	---	---	PASS
INO80	54617	broad.mit.edu	37	15	41348899	41348899	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41348899C>T	uc001zni.2	-	17	2204	c.1991G>A	c.(1990-1992)CGT>CAT	p.R664H	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	664	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.|Helicase ATP-binding.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						GATCTTCCAACGAACACTGTT	0.408													4	187	---	---	---	---	PASS
CYP19A1	1588	broad.mit.edu	37	15	51507945	51507945	+	Silent	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51507945T>C	uc001zyz.3	-	8	1064	c.813A>G	c.(811-813)AAA>AAG	p.K271K	CYP19A1_uc001zza.3_Silent_p.K271K|CYP19A1_uc001zzb.2_Silent_p.K271K|CYP19A1_uc001zzc.1_RNA	NM_031226	NP_112503	P11511	CP19A_HUMAN	cytochrome P450, family 19	271					estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)	ATTCTTCCAGTTTCTCTTCTG	0.373													8	643	---	---	---	---	PASS
ADAM10	102	broad.mit.edu	37	15	58925453	58925453	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58925453G>T	uc002afd.1	-	9	1562	c.1118C>A	c.(1117-1119)CCT>CAT	p.P373H	ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Missense_Mutation_p.P72H|ADAM10_uc002afe.1_Intron	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor	373	Peptidase M12B.|Extracellular (Potential).				cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)		GACTTTGGGAGGTACATGAGA	0.343													86	317	---	---	---	---	PASS
ACSBG1	23205	broad.mit.edu	37	15	78526760	78526760	+	Silent	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78526760G>A	uc002bdh.2	-	1	140	c.84C>T	c.(82-84)AGC>AGT	p.S28S	ACSBG1_uc010umw.1_Silent_p.S28S|ACSBG1_uc010umx.1_5'UTR|ACSBG1_uc010umy.1_5'UTR	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin	28					long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1						TGTCCTGCCGGCTCTCCTGTG	0.483													19	78	---	---	---	---	PASS
MYLK3	91807	broad.mit.edu	37	16	46741538	46741538	+	3'UTR	SNP	T	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46741538T>G	uc002eei.3	-	13					MYLK3_uc010vge.1_3'UTR	NM_182493	NP_872299	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3						cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis	cytosol	ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	7		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GCCAAATTATTTAAATGTTTG	0.393													37	108	---	---	---	---	PASS
CTNS	1497	broad.mit.edu	37	17	3563239	3563239	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3563239C>A	uc002fwb.2	+	11	1533	c.940C>A	c.(940-942)CTG>ATG	p.L314M	CTNS_uc002fwa.2_Missense_Mutation_p.L314M|CTNS_uc010ckj.2_Missense_Mutation_p.L314M|CTNS_uc010vrv.1_Missense_Mutation_p.L167M|CTNS_uc010vrw.1_Missense_Mutation_p.L206M	NM_004937	NP_004928	O60931	CTNS_HUMAN	cystinosin isoform 2	314	Helical; (Potential).|PQ-loop 2.				ATP metabolic process|brain development|cognition|glutathione metabolic process	integral to membrane|late endosome|lysosomal membrane	L-cystine transmembrane transporter activity				0				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	CTTCAGCCTCCTGCAGATGTT	0.632													4	22	---	---	---	---	PASS
CDC27	996	broad.mit.edu	37	17	45232075	45232075	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45232075A>T	uc002ild.3	-	8	1047	c.920T>A	c.(919-921)GTA>GAA	p.V307E	CDC27_uc002ile.3_Missense_Mutation_p.V307E|CDC27_uc002ilf.3_Missense_Mutation_p.V307E|CDC27_uc010wkp.1_Missense_Mutation_p.V246E|CDC27_uc010wkq.1_RNA	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	307					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						CACATCAATTACAGGAGGTGT	0.378													5	161	---	---	---	---	PASS
CA10	56934	broad.mit.edu	37	17	50149723	50149723	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50149723C>T	uc002itw.3	-	2	1078	c.92G>A	c.(91-93)GGC>GAC	p.G31D	CA10_uc002itv.3_Missense_Mutation_p.G37D|CA10_uc002itx.3_Missense_Mutation_p.G31D|CA10_uc002ity.3_Missense_Mutation_p.G31D|CA10_uc002itz.2_Missense_Mutation_p.G31D	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	31					brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			TGCCCACCAGCCTTCATGGAT	0.388													96	348	---	---	---	---	PASS
GREB1L	80000	broad.mit.edu	37	18	19076571	19076571	+	Silent	SNP	A	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19076571A>G	uc010xam.1	+	21	3574	c.3303A>G	c.(3301-3303)AGA>AGG	p.R1101R	GREB1L_uc010dlp.1_Silent_p.R992R|GREB1L_uc010xan.1_Silent_p.R517R|GREB1L_uc010dlr.1_Silent_p.R212R	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast	1101						integral to membrane					0						AGCAGGAGAGAGCTGCTGTCA	0.602													4	46	---	---	---	---	PASS
DSC1	1823	broad.mit.edu	37	18	28712549	28712549	+	Silent	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28712549T>C	uc002kwn.2	-	14	2482	c.2220A>G	c.(2218-2220)GGA>GGG	p.G740G	DSC1_uc002kwm.2_Silent_p.G740G	NM_024421	NP_077739	Q08554	DSC1_HUMAN	desmocollin 1 isoform Dsc1a preproprotein	740	Cytoplasmic (Potential).				homophilic cell adhesion	desmosome|gap junction|integral to membrane|membrane fraction	calcium ion binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CTTCTCCAGGTCCTTCAGTAT	0.343													8	663	---	---	---	---	PASS
ZNF24	7572	broad.mit.edu	37	18	32919802	32919802	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32919802T>A	uc002kyt.2	-	3	716	c.559A>T	c.(559-561)AGG>TGG	p.R187W	ZNF24_uc002kys.2_Missense_Mutation_p.R187W|ZNF24_uc002kyu.1_Missense_Mutation_p.R187W	NM_006965	NP_008896	P17028	ZNF24_HUMAN	zinc finger protein 24	187					myelination|negative regulation of transcription, DNA-dependent|viral reproduction	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						CCACAGTGCCTTAGGGAATGG	0.507													21	76	---	---	---	---	PASS
LOXHD1	125336	broad.mit.edu	37	18	44114312	44114312	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44114312G>T	uc010xcw.1	-	27	4198	c.4198C>A	c.(4198-4200)CTC>ATC	p.L1400I	LOXHD1_uc002lcg.1_Missense_Mutation_p.L1122I|LOXHD1_uc002lce.3_Missense_Mutation_p.L193I|LOXHD1_uc002lcf.3_Missense_Mutation_p.L289I|LOXHD1_uc010xcv.1_Missense_Mutation_p.L333I|LOXHD1_uc010xcx.1_RNA	NM_144612	NP_653213	Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1 isoform 1	1122	PLAT 8.				sensory perception of sound	stereocilium	protein binding				0						TTATCCGGGAGGAGCCTGCGG	0.498													35	107	---	---	---	---	PASS
SMAD7	4092	broad.mit.edu	37	18	46469033	46469033	+	Intron	SNP	A	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46469033A>T	uc002ldg.2	-						SMAD7_uc002ldf.2_Translation_Start_Site|SMAD7_uc010xde.1_Intron	NM_005904	NP_005895	O15105	SMAD7_HUMAN	SMAD family member 7						adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex	activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding				0	Colorectal(1;0.0518)					ACACATTCCAAAAGGCTGACT	0.448													10	34	---	---	---	---	PASS
C19orf34	255193	broad.mit.edu	37	19	1954075	1954075	+	5'UTR	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1954075G>A	uc002lum.2	-	2					CSNK1G2_uc002lul.3_Intron	NM_152771	NP_689984			chromosome 19 open reading frame 34												0		Ovarian(11;0.000137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGGTGGGCGGCTTCCCTCC	0.602													3	16	---	---	---	---	PASS
COL5A3	50509	broad.mit.edu	37	19	10116391	10116391	+	Splice_Site	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10116391C>T	uc002mmq.1	-	4	524	c.438_splice	c.e4-1	p.R146_splice		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein						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)			ACGGTGCCACCTGCAAGGGGA	0.632													6	17	---	---	---	---	PASS
C19orf62	29086	broad.mit.edu	37	19	17387524	17387524	+	Intron	SNP	T	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17387524T>G	uc002nfu.2	+						C19orf62_uc010xpl.1_3'UTR|C19orf62_uc002nfv.2_Intron|C19orf62_uc010ean.2_Intron|C19orf62_uc002nfw.2_Intron	NM_014173	NP_054892	Q9NWV8	BABA1_HUMAN	mediator of Rap80 interactions and targeting 40						chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|protein K63-linked deubiquitination|response to ionizing radiation	BRCA1-A complex|BRISC complex|cytoplasm	protein binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2						GAGGCTGGGGTGCCTAGAGGT	0.602													11	40	---	---	---	---	PASS
ZNF180	7733	broad.mit.edu	37	19	44982255	44982255	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44982255C>T	uc002ozf.3	-	5	725	c.443G>A	c.(442-444)TGG>TAG	p.W148*	ZNF180_uc002ozh.3_5'UTR|ZNF180_uc002ozi.3_Nonsense_Mutation_p.W121*|ZNF180_uc002ozg.3_Nonsense_Mutation_p.W147*|ZNF180_uc010ejm.2_Nonsense_Mutation_p.W123*	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	148					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)				TGAAGATAACCAAGGATCATC	0.388													5	345	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	19	53418479	53418479	+	IGR	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53418479G>A								ZNF320 (17533 upstream) : ZNF321 (11909 downstream)																							TAATTCTCCAGCATCACGTCT	0.488													6	176	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29623176	29623176	+	5'Flank	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29623176G>A	uc010ztl.1	+						FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						AGGAACCATAGCCATTGAAAT	0.363													7	319	---	---	---	---	PASS
C20orf114	92747	broad.mit.edu	37	20	31873889	31873889	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31873889C>A	uc002wyw.1	+	2	171	c.10C>A	c.(10-12)CCG>ACG	p.P4T	C20orf114_uc010gej.1_Missense_Mutation_p.P4T	NM_033197	NP_149974	Q8TDL5	LPLC1_HUMAN	LPLUNC1 protein precursor	4						extracellular space	lipid binding			central_nervous_system(2)|skin(2)	4						GATGGCCGGCCCGTGGACCTT	0.617													15	51	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40713330	40713330	+	Silent	SNP	G	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40713330G>T	uc002xkg.2	-	29	4312	c.4128C>A	c.(4126-4128)GTC>GTA	p.V1376V	PTPRT_uc010ggj.2_Silent_p.V1395V|PTPRT_uc010ggi.2_Silent_p.V579V	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1376	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				ACAGGCAGTGGACCACAGTAC	0.607													12	32	---	---	---	---	PASS
ERG	2078	broad.mit.edu	37	21	39870326	39870326	+	Intron	SNP	C	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39870326C>T	uc010gnw.2	-						ERG_uc002yxa.2_5'UTR|ERG_uc011aek.1_5'UTR|ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc011aem.1_5'UTR|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				GTTTATTGATCGTTAATAAAT	0.338													49	273	---	---	---	---	PASS
TRAPPC10	7109	broad.mit.edu	37	21	45513966	45513966	+	Missense_Mutation	SNP	T	C	C	rs142768361		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45513966T>C	uc002zea.2	+	20	3189	c.3020T>C	c.(3019-3021)GTG>GCG	p.V1007A	TRAPPC10_uc010gpo.2_Missense_Mutation_p.V718A|TRAPPC10_uc011afa.1_Missense_Mutation_p.V385A|TRAPPC10_uc011afb.1_Missense_Mutation_p.V112A	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1007					vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2						AAGCAGTCGGTGTTCTTCGTC	0.537													23	125	---	---	---	---	PASS
ACOT9	23597	broad.mit.edu	37	X	23754070	23754070	+	Silent	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23754070G>A	uc004dap.2	-	2	230	c.84C>T	c.(82-84)AAC>AAT	p.N28N	ACOT9_uc004dao.2_Silent_p.N28N|ACOT9_uc004daq.2_5'UTR|ACOT9_uc004dar.2_Intron|ACOT9_uc011mjt.1_RNA|ACOT9_uc004das.2_5'UTR|ACOT9_uc004dat.1_Silent_p.N28N	NM_001033583	NP_001028755	Q9Y305	ACOT9_HUMAN	acyl-Coenzyme A thioesterase 2, mitochondrial	28					acyl-CoA metabolic process	mitochondrion	acetyl-CoA hydrolase activity|carboxylesterase activity			ovary(2)|pancreas(1)	3						GTTTCTTGGGGTTCTGGGGTC	0.448													99	146	---	---	---	---	PASS
KLF8	11279	broad.mit.edu	37	X	56292017	56292017	+	Silent	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56292017T>C	uc004dur.2	+	3	1432	c.486T>C	c.(484-486)ACT>ACC	p.T162T	KLF8_uc010nkg.2_Silent_p.T157T|KLF8_uc011mop.1_Silent_p.T162T|KLF8_uc010nkh.2_RNA	NM_007250	NP_009181	O95600	KLF8_HUMAN	Kruppel-like factor 8 isoform 1	162					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						TCATTCACACTATCCCCTCAG	0.512													17	20	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3863	3863	+	RNA	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3863T>C	uc004cos.3	+	2		c.2156T>C			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		CATAATATGATTTATCTCCAC	0.493													38	166	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14146	14146	+	RNA	SNP	T	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14146T>C	uc004cox.3	+	1		c.1810T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TCCTAATCACATAACCTATTC	0.393													71	272	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15375	15375	+	Silent	SNP	G	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15375G>A	uc004coy.2	+	1	615	c.540G>A	c.(538-540)AGG>AGA	p.R180R	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		CAACCCCCTAGGAATCACCTC	0.453											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	53	190	---	---	---	---	PASS
CROCC	9696	broad.mit.edu	37	1	17081047	17081048	+	Intron	INS	-	T	T	rs148428698		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17081047_17081048insT	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TCCTCGTCTAATTTTTTTTACA	0.361													4	2	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17205782	17205783	+	Intron	INS	-	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17205782_17205783insG	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		ATATATAGGATGGGGGAAAGGG	0.421													4	2	---	---	---	---	
IFI6	2537	broad.mit.edu	37	1	27996406	27996406	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27996406delT	uc001boo.1	-						IFI6_uc001bon.1_Intron|IFI6_uc001bop.1_Intron	NM_002038	NP_002029	P09912	IFI6_HUMAN	interferon, alpha-inducible protein 6 isoform a						anti-apoptosis|negative regulation of caspase activity|negative regulation of mitochondrial depolarization|release of cytochrome c from mitochondria|type I interferon-mediated signaling pathway	integral to membrane|mitochondrion	protein binding			ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;7.75e-05)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		ATCAACTTAATTTTTTTTTCA	0.254													4	2	---	---	---	---	
ERI3	79033	broad.mit.edu	37	1	44692209	44692209	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44692209delG	uc001clt.2	-						ERI3_uc010okv.1_Intron|ERI3_uc009vxg.2_Intron|ERI3_uc010okw.1_Intron|ERI3_uc001clu.2_Intron	NM_024066	NP_076971	O43414	ERI3_HUMAN	prion protein interacting protein							intracellular	exonuclease activity|metal ion binding|nucleic acid binding			ovary(2)|large_intestine(1)	3						TTGATGATGTGGGGGAAGTGG	0.269													4	2	---	---	---	---	
USP24	23358	broad.mit.edu	37	1	55545500	55545501	+	Intron	DEL	TG	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55545500_55545501delTG	uc001cyg.3	-							NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13						GCAGAGTACTTGcacacacagt	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56424535	56424535	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56424535delT								USP24 (743773 upstream) : PPAP2B (535898 downstream)																							TGACTCCTCCTTTTTTTTTCT	0.398													5	4	---	---	---	---	
C8A	731	broad.mit.edu	37	1	57348896	57348897	+	Intron	INS	-	TG	TG	rs138394769	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57348896_57348897insTG	uc001cyo.2	+							NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)|skin(1)	3						TCATCTGCATCtgtgtgtgtgt	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78028489	78028495	+	IGR	DEL	ACTCCTA	-	-	rs142353910		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78028489_78028495delACTCCTA								AK5 (2837 upstream) : ZZZ3 (1696 downstream)																							GCACACCTCCACTCCTAACACCTAGTG	0.353													5	3	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	86004608	86004608	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86004608delG	uc001dlc.2	-							NM_001134445	NP_001127917	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	TTCTTTTTCTGGTCCCCCTAC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	103182807	103182807	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103182807delT								OLFM3 (720017 upstream) : COL11A1 (159217 downstream)																							GAGATGCTGCTTTTTTTTTCT	0.448													4	2	---	---	---	---	
LRIG2	9860	broad.mit.edu	37	1	113635612	113635612	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113635612delA	uc001edf.1	+						LRIG2_uc009wgn.1_Intron	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like							cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		actctgtttcaaaaaaaaaag	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116718428	116718429	+	IGR	DEL	TG	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116718428_116718429delTG								C1orf161 (40567 upstream) : ATP1A1 (196575 downstream)																							gaacttggcatgtgtgtgtgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142550380	142550380	+	IGR	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142550380delC								None (None upstream) : None (None downstream)																							CCTCATCTTTCCCCTTTTGAG	0.348													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142561248	142561249	+	IGR	INS	-	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142561248_142561249insG								None (None upstream) : None (None downstream)																							ccaagaaatatgggactatgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143261370	143261371	+	IGR	INS	-	A	A	rs145912009		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143261370_143261371insA								None (None upstream) : LOC100286793 (386268 downstream)																							aaggagaattcaaaaaaccact	0.134													7	4	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148012478	148012478	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148012478delA	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc001eqq.2_Intron|NBPF14_uc010pad.1_5'Flank|NBPF14_uc001eqs.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						GTGGATCCTTATCACCTTCAT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148864080	148864081	+	IGR	DEL	TT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148864080_148864081delTT								NBPF16 (105769 upstream) : LOC645166 (64205 downstream)																							caagggactcttttaatggcaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148905694	148905695	+	IGR	INS	-	C	C	rs112554833		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148905694_148905695insC								NBPF16 (147383 upstream) : LOC645166 (22591 downstream)																							gcatgatgcatctccagtgcga	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	154882238	154882238	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154882238delA								KCNN3 (39484 upstream) : PMVK (14971 downstream)																							accccctctcaaaaaaaaGTT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	184190330	184190330	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184190330delG								TSEN15 (146989 upstream) : C1orf21 (165820 downstream)																							CAGGCAAAAAGGGTTTTTTAA	0.318													4	2	---	---	---	---	
PIK3C2B	5287	broad.mit.edu	37	1	204426840	204426840	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204426840delC	uc001haw.2	-						PIK3C2B_uc010pqv.1_Intron|PIK3C2B_uc001hax.1_Intron|PIK3C2B_uc009xbd.1_Intron	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta						cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CCTGCTAGCACCCTGGGCCCC	0.562													12	10	---	---	---	---	
PLXNA2	5362	broad.mit.edu	37	1	208216813	208216813	+	Intron	DEL	A	-	-	rs79055601		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208216813delA	uc001hgz.2	-							NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TTCAACAAGGAAAAAAAAGTA	0.299													4	2	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	216737933	216737933	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216737933delT	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	GAATGTAGTCTTTTTTTTTCT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	225907795	225907795	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225907795delT	uc001hpe.1	+											Homo sapiens cDNA FLJ42062 fis, clone SYNOV2005673.																		ctccatttaattacccatcca	0.000													4	2	---	---	---	---	
LYST	1130	broad.mit.edu	37	1	235955623	235955623	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235955623delT	uc001hxj.2	-						LYST_uc009xgb.1_Intron|LYST_uc010pxs.1_Intron|LYST_uc001hxl.1_Intron	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GATTTCAttctttttttttta	0.149									Chediak-Higashi_syndrome				5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238692479	238692479	+	IGR	DEL	A	-	-	rs33931796		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238692479delA								LOC339535 (43162 upstream) : CHRM3 (857386 downstream)																							actgtgtctcaaaaaaaaaaa	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244024754	244024754	+	IGR	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244024754delC								AKT3 (18201 upstream) : ZNF238 (189807 downstream)																							ctgtctccatcccagagtctg	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18553923	18553923	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18553923delA								KCNS3 (439699 upstream) : NT5C1B (182068 downstream)																							caagggtgggaaaaaaaagcc	0.000													4	2	---	---	---	---	
SFRS7	6432	broad.mit.edu	37	2	38975943	38975943	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38975943delT	uc002rqz.2	-						SFRS7_uc002rra.2_Intron|SFRS7_uc010ynp.1_Intron|GEMIN6_uc002rrb.2_5'Flank	NM_001031684	NP_001026854	Q16629	SRSF7_HUMAN	splicing factor, arginine/serine-rich 7						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding				0		all_hematologic(82;0.248)				TTGTTGAGTATTTTTTTTTTT	0.264													13	7	---	---	---	---	
PLEK	5341	broad.mit.edu	37	2	68615866	68615867	+	Intron	INS	-	A	A	rs141488159	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68615866_68615867insA	uc002sen.3	+						PLEK_uc010fde.2_Intron	NM_002664	NP_002655	P08567	PLEK_HUMAN	pleckstrin						actin cytoskeleton reorganization|cortical actin cytoskeleton organization|hemopoietic progenitor cell differentiation|inhibition of phospholipase C activity involved in G-protein coupled receptor signaling pathway|integrin-mediated signaling pathway|negative regulation of calcium-mediated signaling|negative regulation of inositol phosphate biosynthetic process|phosphatidylinositol metabolic process|platelet aggregation|positive regulation of actin filament bundle assembly|positive regulation of actin filament depolymerization|positive regulation of inositol-polyphosphate 5-phosphatase activity|positive regulation of integrin activation|positive regulation of platelet activation|protein kinase C signaling cascade|protein secretion by platelet|regulation of cell diameter|ruffle organization|thrombin receptor signaling pathway|vesicle docking involved in exocytosis	cytosol|extracellular region|membrane fraction|ruffle membrane|soluble fraction	phosphatidylinositol-3,4-bisphosphate binding|protein homodimerization activity|protein kinase C binding			ovary(1)	1		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		AATATCATAGGAAAAAAAAAGG	0.361													4	2	---	---	---	---	
TIA1	7072	broad.mit.edu	37	2	70441778	70441779	+	Intron	INS	-	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70441778_70441779insC	uc002sgj.3	-						TIA1_uc002sgk.3_Intron|TIA1_uc002sgl.3_Intron	NM_022173	NP_071505	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding						apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0						aaaaaaaaaaaaaaaaaaaaaa	0.312													4	2	---	---	---	---	
TCF7L1	83439	broad.mit.edu	37	2	85529896	85529896	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85529896delT	uc002soy.2	+							NM_031283	NP_112573	Q9HCS4	TF7L1_HUMAN	HMG-box transcription factor TCF-3						chromatin organization|regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|breast(1)|central_nervous_system(1)	3						agccttgtcattttttttttc	0.000													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89430749	89430749	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89430749delT	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		AGTTCGCATCTTTTTTTTTTC	0.264													4	2	---	---	---	---	
ITPRIPL1	150771	broad.mit.edu	37	2	96990632	96990632	+	5'Flank	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96990632delA	uc002svx.2	+						ITPRIPL1_uc010yuk.1_5'Flank|ITPRIPL1_uc002svy.2_5'Flank|ITPRIPL1_uc010yul.1_5'Flank	NM_001008949	NP_001008949	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-triphosphate receptor interacting							integral to membrane				central_nervous_system(2)|ovary(1)	3						TTGATATGAGAAAGGGGTTGG	0.502													4	2	---	---	---	---	
IL1RL2	8808	broad.mit.edu	37	2	102833499	102833499	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102833499delT	uc002tbs.2	+						IL1RL2_uc002tbt.2_Intron	NM_003854	NP_003845	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2 precursor						cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2						ctgaatttgattttgaattta	0.000													4	2	---	---	---	---	
EDAR	10913	broad.mit.edu	37	2	109512530	109512531	+	3'UTR	DEL	CA	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109512530_109512531delCA	uc002teq.3	-	12					EDAR_uc010fjn.2_3'UTR|EDAR_uc010yws.1_3'UTR	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor						apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						GAAGGCCATTCACATGTAGTGC	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113714425	113714426	+	IGR	INS	-	GT	GT			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113714425_113714426insGT								IL1F7 (37969 upstream) : IL1F9 (21180 downstream)																							TGTTTTTGTAAGTGTGTGTGCT	0.287													4	2	---	---	---	---	
C2orf76	130355	broad.mit.edu	37	2	120075309	120075310	+	Intron	DEL	GT	-	-	rs140331434		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120075309_120075310delGT	uc002tls.2	-						C2orf76_uc010flf.1_Intron|C2orf76_uc010yyg.1_Intron|C2orf76_uc002tlt.2_Intron|C2orf76_uc002tlu.2_Intron	NM_001017927	NP_001017927	Q3KRA6	CB076_HUMAN	hypothetical protein LOC130355												0						ACACACAGCAGTGTGTGTGTCA	0.322													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129226559	129226559	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129226559delT								HS6ST1 (150388 upstream) : None (None downstream)																							CCCTGAGATGTTTTTTAGTTT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129509592	129509592	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129509592delT								HS6ST1 (433421 upstream) : None (None downstream)																							gagtaaacagtttttttttct	0.025													4	2	---	---	---	---	
POTEE	445582	broad.mit.edu	37	2	131995418	131995418	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131995418delT	uc002tsn.2	+						PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_Intron|POTEE_uc002tsl.2_Intron	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,								ATP binding				0						TGCTGATTCATTTTTGGTAGA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133021069	133021070	+	IGR	INS	-	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133021069_133021070insG								NCRNA00164 (5527 upstream) : GPR39 (153077 downstream)																							ATTGGATAATAGAAAAAAACAC	0.312													6	3	---	---	---	---	
MMADHC	27249	broad.mit.edu	37	2	150438467	150438468	+	Intron	INS	-	CTTTTT	CTTTTT	rs150736499	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150438467_150438468insCTTTTT	uc002txb.2	-						MMADHC_uc002txc.2_Intron|MMADHC_uc010fnu.2_Intron	NM_015702	NP_056517	Q9H3L0	MMAD_HUMAN	methylmalonic aciduria (cobalamin deficiency)							mitochondrion				central_nervous_system(1)|skin(1)	2						ACTCTTTTTTCAATACTGTAGC	0.327													8	4	---	---	---	---	
KCNH7	90134	broad.mit.edu	37	2	163291064	163291067	+	Intron	DEL	TTAA	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163291064_163291067delTTAA	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	CAAAGCTTTTTTAATTCCAAAGAA	0.338													4	2	---	---	---	---	
GRB14	2888	broad.mit.edu	37	2	165413059	165413059	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165413059delT	uc002ucl.2	-						GRB14_uc010zcv.1_Intron|GRB14_uc002ucm.2_Intron	NM_004490	NP_004481	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14						blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|upper_aerodigestive_tract(1)|lung(1)	7						caatcctacatttttttctgt	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168620838	168620840	+	IGR	DEL	GAC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168620838_168620840delGAC								XIRP2 (504579 upstream) : B3GALT1 (54342 downstream)																							TCAATTATGTGACATAGTCCACA	0.345													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	192696653	192696653	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192696653delT								OBFC2A (143406 upstream) : SDPR (2388 downstream)																							tctttttttcttttttttttt	0.373													4	2	---	---	---	---	
KLF7	8609	broad.mit.edu	37	2	207998878	207998879	+	Intron	INS	-	TT	TT	rs35538720		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207998878_207998879insTT	uc002vbz.1	-						KLF7_uc002vca.1_Intron|KLF7_uc010zix.1_5'Flank	NM_003709	NP_003700	O75840	KLF7_HUMAN	Kruppel-like factor 7 (ubiquitous)						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			central_nervous_system(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)		GGCTACTGGGAttttttttttt	0.441													5	4	---	---	---	---	
COPS7B	64708	broad.mit.edu	37	2	232653655	232653656	+	Intron	DEL	GC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232653655_232653656delGC	uc002vsg.1	+						COPS7B_uc010fxy.1_Intron|COPS7B_uc002vsh.1_Intron|COPS7B_uc002vsi.1_Intron|COPS7B_uc002vsj.1_5'Flank	NM_022730	NP_073567	Q9H9Q2	CSN7B_HUMAN	COP9 constitutive photomorphogenic homolog						cullin deneddylation	cytoplasm|signalosome				ovary(1)|liver(1)|skin(1)	3		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		TTAGATTgttgctaataataac	0.193													4	2	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2223013	2223013	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2223013delT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GATATGTGGGTAGTGAGAGGT	0.398													4	2	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10081677	10081677	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10081677delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc003buv.2_3'UTR	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GATTTGACTTAAAAAAAAAAG	0.239			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	82261161	82261161	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82261161delT	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																		tttagcctgcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	114998900	114998900	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114998900delA								ZBTB20 (132773 upstream) : GAP43 (343251 downstream)																							TGCTAAATTTAAAAAAAAAAA	0.363													5	3	---	---	---	---	
UMPS	7372	broad.mit.edu	37	3	124463850	124463851	+	3'UTR	INS	-	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124463850_124463851insT	uc003ehl.3	+	6					UMPS_uc003ehm.3_RNA|UMPS_uc011bka.1_3'UTR|UMPS_uc011bkb.1_3'UTR|UMPS_uc011bkc.1_3'UTR|UMPS_uc003ehn.3_3'UTR|UMPS_uc011bkd.1_3'UTR	NM_000373	NP_000364	P11172	UMPS_HUMAN	uridine monophosphate synthase						'de novo' pyrimidine base biosynthetic process|'de novo' UMP biosynthetic process|pyrimidine nucleoside biosynthetic process	cytosol|nucleus	orotate phosphoribosyltransferase activity|orotidine-5'-phosphate decarboxylase activity			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.146)		gtttgggctcattttttcccct	0.089													4	2	---	---	---	---	
ATR	545	broad.mit.edu	37	3	142222057	142222057	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142222057delA	uc003eux.3	-							NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						AAACTTGAGGAAAAAAAAATG	0.318								Other_conserved_DNA_damage_response_genes					12	6	---	---	---	---	
MED12L	116931	broad.mit.edu	37	3	150968807	150968808	+	Intron	DEL	TC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150968807_150968808delTC	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|P2RY14_uc003eys.1_Intron|P2RY14_uc003eyr.1_5'Flank	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGATGATGATTCTCTCTGTGGT	0.267													4	2	---	---	---	---	
WDR49	151790	broad.mit.edu	37	3	167218345	167218346	+	Intron	INS	-	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167218345_167218346insT	uc003fev.1	-						WDR49_uc003feu.1_Intron|WDR49_uc011bpd.1_Intron|WDR49_uc003few.1_Intron	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49											large_intestine(1)|ovary(1)|skin(1)	3						TTTTTCTGCTATTTTCCCTTGA	0.292													4	2	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173911316	173911317	+	Intron	DEL	CA	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173911316_173911317delCA	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TGTCAGAGGCCACACACACAAA	0.371													4	2	---	---	---	---	
MAN2B2	23324	broad.mit.edu	37	4	6618067	6618067	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6618067delG	uc003gjf.1	+						MAN2B2_uc003gje.1_Intron|MAN2B2_uc011bwf.1_Intron	NM_015274	NP_056089	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2						mannose metabolic process	extracellular region	alpha-mannosidase activity|carbohydrate binding|zinc ion binding			ovary(2)	2						GATCAGGGATGGGACAGGAGA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11009299	11009299	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11009299delA								CLNK (322913 upstream) : MIR572 (361152 downstream)																							CAGGAACTCCAAACCAAAGCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13969834	13969834	+	IGR	DEL	G	-	-	rs1373378	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13969834delG								BOD1L (340506 upstream) : None (None downstream)																							CATATCCCACGGGGGCAGGAT	0.502													4	2	---	---	---	---	
DHX15	1665	broad.mit.edu	37	4	24548569	24548570	+	Intron	INS	-	T	T	rs145430439	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24548569_24548570insT	uc003gqx.2	-							NM_001358	NP_001349	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 15						mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)				GACACAAACAGTAAGTTTAAAA	0.287													4	2	---	---	---	---	
OCIAD1	54940	broad.mit.edu	37	4	48863059	48863059	+	3'UTR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48863059delA	uc003gyo.2	+	9					OCIAD1_uc003gyr.2_3'UTR|OCIAD1_uc003gyp.2_3'UTR|OCIAD1_uc003gys.2_3'UTR|OCIAD1_uc003gyq.2_3'UTR|OCIAD1_uc010igk.2_3'UTR	NM_017830	NP_060300	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1 isoform 1							endosome	protein binding				0						GATAACTCTTAAAAAACCGTC	0.348													4	2	---	---	---	---	
SRP72	6731	broad.mit.edu	37	4	57340709	57340709	+	Intron	DEL	T	-	-	rs112716931		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57340709delT	uc003hbv.2	+						SRP72_uc010ihe.2_Intron|SRP72_uc003hbw.1_Intron	NM_006947	NP_008878	O76094	SRP72_HUMAN	signal recognition particle 72kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)					tttctctctcttttttttttt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	60512634	60512634	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60512634delG								None (None upstream) : None (None downstream)																							GATAAAAGGAGGGATGACAAA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63972061	63972062	+	IGR	DEL	TG	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63972061_63972062delTG								None (None upstream) : None (None downstream)																							accctctttctgtgtgtgtgtc	0.094													4	2	---	---	---	---	
UNC5C	8633	broad.mit.edu	37	4	96471235	96471235	+	5'Flank	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96471235delA	uc003htp.1	-						UNC5C_uc010ilc.1_5'Flank|UNC5C_uc003htq.2_5'Flank	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		ACTCTCTTAGAAAAAAAAAAT	0.398													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	100933276	100933276	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100933276delA								LOC256880 (59656 upstream) : DDIT4L (173753 downstream)																							tgtatcttttaaaaaaatttt	0.000													4	2	---	---	---	---	
NHEDC1	150159	broad.mit.edu	37	4	103826510	103826511	+	Intron	DEL	CA	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103826510_103826511delCA	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		cctgagtagccaggaCTGGTTA	0.119													13	6	---	---	---	---	
DKK2	27123	broad.mit.edu	37	4	108056344	108056344	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108056344delT	uc010ilw.1	-									Q9UBU2	DKK2_HUMAN	Homo sapiens dickkopf-2 mRNA, complete cds.						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		tgtgtcattatttttttcttt	0.154													4	2	---	---	---	---	
HADH	3033	broad.mit.edu	37	4	108954652	108954652	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108954652delA	uc003hyq.2	+						HADH_uc010ilx.2_Intron|HADH_uc010ily.2_Intron|HADH_uc003hyr.2_Intron	NM_005327	NP_005318	Q16836	HCDH_HUMAN	L-3-hydroxyacyl-Coenzyme A dehydrogenase						fatty acid beta-oxidation	mitochondrial matrix	3-hydroxyacyl-CoA dehydrogenase activity|NAD+ binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000168)	NADH(DB00157)	GACCTTGAAGAAAAAAAAACC	0.229													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	113719454	113719455	+	IGR	INS	-	T	T	rs139523845	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113719454_113719455insT								LARP7 (140713 upstream) : ANK2 (19784 downstream)																							TATGGAttttcttttttttttg	0.139													4	2	---	---	---	---	
KIAA1109	84162	broad.mit.edu	37	4	123175763	123175763	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123175763delT	uc003ieh.2	+						KIAA1109_uc003iel.1_5'Flank|KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						TCTGACAGGCTTTTTTTTTTC	0.269													4	2	---	---	---	---	
NAA15	80155	broad.mit.edu	37	4	140255648	140255648	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140255648delA	uc003ihu.1	+							NM_057175	NP_476516	Q9BXJ9	NAA15_HUMAN	NMDA receptor regulated 1						angiogenesis|cell differentiation|N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	protein binding			ovary(1)|skin(1)	2						AGGAAAAGAGAAATAATAGGA	0.259													2	4	---	---	---	---	
GYPE	2996	broad.mit.edu	37	4	144805149	144805149	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144805149delT	uc003ijj.2	-						GYPE_uc010ion.2_Intron|GYPE_uc003ijk.3_Intron	NM_198682	NP_941391	P15421	GLPE_HUMAN	glycophorin E precursor							integral to plasma membrane					0	all_hematologic(180;0.158)					TAGAGAGGTGTTTTCAGTCTA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	159391194	159391196	+	IGR	DEL	TTT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159391194_159391196delTTT								TMEM144 (214756 upstream) : RXFP1 (51851 downstream)																							AGAACAGATCTTTAGCTGCAGGT	0.414													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	159391198	159391200	+	IGR	DEL	GCT	-	-	rs115061202	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159391198_159391200delGCT								TMEM144 (214760 upstream) : RXFP1 (51847 downstream)																							CAGATCTTTAGCTGCAGGTGTGT	0.399													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	160436359	160436359	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160436359delG								RAPGEF2 (155060 upstream) : None (None downstream)																							AAAAACTTTTGGATGTTTAGG	0.313													4	2	---	---	---	---	
SH3RF1	57630	broad.mit.edu	37	4	170028875	170028875	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170028875delG	uc003isa.1	-							NM_020870	NP_065921	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1							Golgi apparatus|lamellipodium|perinuclear region of cytoplasm	ligase activity|zinc ion binding			breast(2)|lung(1)	3		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		CTATTCCACAGGCATGGACGT	0.398													3	3	---	---	---	---	
FAM92A3	403315	broad.mit.edu	37	4	183960484	183960484	+	RNA	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183960484delA	uc003ivi.3	+	1		c.1667delA				NR_003612				Homo sapiens family with sequence similarity 92, member A3, mRNA (cDNA clone IMAGE:4822144).												0						TTCAACATCCAAAAAAAAAAA	0.308													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	185220157	185220157	+	IGR	DEL	A	-	-	rs115404122	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185220157delA								ENPP6 (81043 upstream) : IRF2 (88721 downstream)																							ATAAATACATAAAAAAAAAGA	0.373													9	4	---	---	---	---	
SNX25	83891	broad.mit.edu	37	4	186231584	186231585	+	Intron	INS	-	CT	CT	rs148164296	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186231584_186231585insCT	uc003ixh.2	+						SNX25_uc010ish.2_Intron	NM_031953	NP_114159	Q9H3E2	SNX25_HUMAN	sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		ATTTGTCAGTGGTATATTTAGA	0.267													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189663798	189663799	+	IGR	DEL	AG	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189663798_189663799delAG								TRIML1 (595149 upstream) : None (None downstream)																							TATATATCTTAGTGAATGTGCT	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190559024	190559024	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190559024delA								None (None upstream) : FRG1 (302950 downstream)																							ACATGCTTATAAAACATGGAG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190619768	190619772	+	IGR	DEL	AAAAC	-	-	rs36202645		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190619768_190619772delAAAAC								None (None upstream) : FRG1 (242202 downstream)																							TGTTCTCTTTaaaacaaaacaaaac	0.293													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190635014	190635014	+	IGR	DEL	A	-	-	rs112391585		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190635014delA								None (None upstream) : FRG1 (226960 downstream)																							CAGTTTTAATAAAAGGGAGTA	0.318													18	11	---	---	---	---	
SLC12A7	10723	broad.mit.edu	37	5	1076520	1076530	+	Intron	DEL	CAGGTTCCAGC	-	-	rs111668454		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1076520_1076530delCAGGTTCCAGC	uc003jbu.2	-							NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride						potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CAGGCCCCCTCAGGTTCCAGCCATCCTGTGA	0.630													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6837071	6837072	+	IGR	DEL	GT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6837071_6837072delGT								PAPD7 (79910 upstream) : ADCY2 (559271 downstream)																							GAGGGGGTGAGTGTGTGTGTGG	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8138311	8138311	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8138311delG								MTRR (237078 upstream) : SEMA5A (896827 downstream)																							AAATGCAGCTGGCACTATTTC	0.378													4	2	---	---	---	---	
CARD6	84674	broad.mit.edu	37	5	40852067	40852067	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40852067delA	uc003jmg.2	+							NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6						apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5						catctctattaaaaaaaaaaa	0.000													4	4	---	---	---	---	
ITGA1	3672	broad.mit.edu	37	5	52140126	52140126	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52140126delC	uc003jou.2	+						ITGA1_uc003jov.2_Intron	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TCCAGTCATTCCCCAAATCCT	0.438													4	2	---	---	---	---	
DIMT1L	27292	broad.mit.edu	37	5	61689066	61689066	+	Intron	DEL	T	-	-	rs79936750		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61689066delT	uc003jta.2	-						DIMT1L_uc011cqq.1_Intron	NM_014473	NP_055288	Q9UNQ2	DIMT1_HUMAN	dimethyladenosine transferase							nucleolus	RNA binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			central_nervous_system(1)	1		Lung NSC(810;8.94e-06)|Prostate(74;0.0235)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.122)		AGCATGACaattttttttttt	0.100													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	66993937	66993937	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66993937delT								CD180 (501320 upstream) : PIK3R1 (517667 downstream)																							tatcccaatcttttgctccct	0.000													4	2	---	---	---	---	
ERAP1	51752	broad.mit.edu	37	5	96117713	96117713	+	Intron	DEL	T	-	-	rs142478570		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96117713delT	uc003kmm.2	-						ERAP1_uc003kml.2_Intron|ERAP1_uc010jbm.1_Intron|ERAP1_uc003kmn.2_Intron	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding						angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		TCAGTTACAAttttttttttt	0.189													4	2	---	---	---	---	
EFNA5	1946	broad.mit.edu	37	5	106915486	106915486	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106915486delC	uc003kol.2	-						EFNA5_uc010jbr.1_Intron	NM_001962	NP_001953	P52803	EFNA5_HUMAN	ephrin-A5 precursor						cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		CTTCAATATGCCCCACCTTGC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133856358	133856358	+	IGR	DEL	T	-	-	rs10712727		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133856358delT								CDKN2AIPNL (108769 upstream) : PHF15 (3708 downstream)																							ctttgaatgcttttttttttc	0.000													3	3	---	---	---	---	
LOC153328	153328	broad.mit.edu	37	5	135179469	135179470	+	Intron	DEL	GT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135179469_135179470delGT	uc003laz.1	+						LOC153328_uc003lba.2_Intron			Q6ZT89	S2548_HUMAN	RecName: Full=Putative mitochondrial carrier protein FLJ44862;						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			aagaaggccagtgtgtgtgtgg	0.005													4	2	---	---	---	---	
SH3RF2	153769	broad.mit.edu	37	5	145316543	145316544	+	Intron	DEL	AC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145316543_145316544delAC	uc003lnt.2	+						SH3RF2_uc011dbl.1_5'Flank	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2								ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTTTCAGAGTACACACACACAC	0.426													4	2	---	---	---	---	
STK32A	202374	broad.mit.edu	37	5	146753177	146753178	+	Intron	INS	-	T	T	rs56315827		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146753177_146753178insT	uc010jgn.1	+						STK32A_uc003lom.2_Intron|STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCTGCTGGGGTTTTTTTTAAG	0.297													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	147302992	147302992	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147302992delT								C5orf46 (16891 upstream) : SPINK5 (140543 downstream)																							CAAGAGAATATTTTTTTTTAC	0.433													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154671696	154671697	+	IGR	INS	-	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154671696_154671697insT								KIF4B (274011 upstream) : SGCD (463366 downstream)																							CCATCCTCCCCTTTCCTCTTAG	0.446													4	2	---	---	---	---	
EBF1	1879	broad.mit.edu	37	5	158487580	158487580	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158487580delT	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCTTTTATCCTTTTTTTTTCT	0.303			T	HMGA2	lipoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	160403199	160403199	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160403199delG								LOC285629 (37566 upstream) : GABRB2 (312237 downstream)																							TGTGTATTGAGGGGACCCAGG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162172956	162172956	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162172956delA								GABRG2 (590412 upstream) : CCNG1 (691621 downstream)																							atagaaatagaaaaaaaatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165186808	165186808	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165186808delA								None (None upstream) : None (None downstream)																							acagtgtcacaaaggaaaagg	0.000													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167380619	167380619	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167380619delC	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		GCTGCTCTATCCCCAGGCACA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170959832	170959832	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170959832delT								FGF18 (75670 upstream) : FBXW11 (328724 downstream)																							tctttctttcttttttttgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172760737	172760738	+	IGR	INS	-	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172760737_172760738insT								STC2 (4231 upstream) : LOC285593 (245908 downstream)																							ttttgaaggtgttttttttttt	0.079													3	3	---	---	---	---	
C5orf45	51149	broad.mit.edu	37	5	179287208	179287209	+	5'Flank	DEL	GT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179287208_179287209delGT	uc003mky.2	-						C5orf45_uc011dgt.1_5'Flank|C5orf45_uc011dgu.1_5'Flank|C5orf45_uc003mla.2_5'Flank|C5orf45_uc003mlc.2_5'Flank|C5orf45_uc003mlb.2_5'Flank|uc003mle.2_5'UTR			Q6NTE8	CE045_HUMAN	RecName: Full=UPF0544 protein C5orf45;												0						ATTTTCTGGCGTGTGTGTGTGT	0.366													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3755305	3755305	+	IGR	DEL	A	-	-	rs11344281		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3755305delA								C6orf145 (3059 upstream) : FAM50B (94327 downstream)																							TTTATCATTTAAAAAAAAATG	0.338													4	3	---	---	---	---	
BMP6	654	broad.mit.edu	37	6	7834547	7834559	+	Intron	DEL	ATCATCAGAGTGA	-	-	rs68098879		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7834547_7834559delATCATCAGAGTGA	uc003mxu.3	+							NM_001718	NP_001709	P22004	BMP6_HUMAN	bone morphogenetic protein 6 preproprotein						BMP signaling pathway|cartilage development|growth|immune response|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction	extracellular space	BMP receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity			large_intestine(2)|ovary(1)	3	Ovarian(93;0.0721)					CAAAATGTGTATCATCAGAGTGAATCATCAGAG	0.324													19	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	13861375	13861397	+	IGR	DEL	TTACAGGGGTTGTTGTTTTACTC	-	-	rs12524298	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13861375_13861397delTTACAGGGGTTGTTGTTTTACTC								CCDC90A (46586 upstream) : RNF182 (63806 downstream)																							gtttgttgttttacaggggttgttgttttactctataattaaa	0.000													6	4	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38809879	38809879	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38809879delT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						AGTAGCAAGATTTTTTTTCTT	0.328													6	3	---	---	---	---	
SUPT3H	8464	broad.mit.edu	37	6	45047230	45047230	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45047230delA	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron|SUPT3H_uc011dvw.1_Intron	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3						aaggaggaagaAAAAAAGGAA	0.020													4	2	---	---	---	---	
HCRTR2	3062	broad.mit.edu	37	6	55147362	55147362	+	3'UTR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55147362delT	uc003pcl.2	+	7					HCRTR2_uc010jzv.2_RNA	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2						feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|breast(1)	6	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			CTTGTGGATCTTTTTTTTTTT	0.254													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57380824	57380825	+	Intron	INS	-	TT	TT	rs145567229		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57380824_57380825insTT	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)		gtcagcaaggcttatattcctt	0.000													4	2	---	---	---	---	
IBTK	25998	broad.mit.edu	37	6	82891377	82891378	+	Intron	INS	-	TAAA	TAAA	rs147217758	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82891377_82891378insTAAA	uc003pjl.1	-						IBTK_uc011dyu.1_Intron|IBTK_uc011dyv.1_Intron|IBTK_uc011dyw.1_Intron|IBTK_uc010kbi.1_Intron	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase						negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		aatgtatactttaaatatacgc	0.079													7	7	---	---	---	---	
BACH2	60468	broad.mit.edu	37	6	90971387	90971388	+	Intron	INS	-	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90971387_90971388insT	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)		tctaaagcttctttttatttgc	0.000													4	2	---	---	---	---	
FABP7	2173	broad.mit.edu	37	6	123105087	123105088	+	3'UTR	INS	-	GAA	GAA			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123105087_123105088insGAA	uc003pzf.2	+	4					FABP7_uc003pze.1_3'UTR	NM_001446	NP_001437	O15540	FABP7_HUMAN	fatty acid binding protein 7, brain						negative regulation of cell proliferation	cytoplasm	lipid binding|transporter activity				0				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|gamma-Homolinolenic acid(DB00154)|Icosapent(DB00159)	ATTTTAATCTGAAAATTTATCA	0.302													30	14	---	---	---	---	
C6orf192	116843	broad.mit.edu	37	6	133117941	133117941	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133117941delT	uc003qdw.1	-						C6orf192_uc011eco.1_Intron	NM_052831	NP_439896	Q6NT16	CF192_HUMAN	hypothetical protein LOC116843						transmembrane transport	integral to membrane				ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;0.00303)|GBM - Glioblastoma multiforme(226;0.0265)		TTTGACTGGATTTTTTTTCCT	0.303													4	2	---	---	---	---	
EYA4	2070	broad.mit.edu	37	6	133712781	133712783	+	Intron	DEL	TCA	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133712781_133712783delTCA	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron	NM_004100	NP_004091	O95677	EYA4_HUMAN	eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		CCTCTCTTTTTCATTATCTCAGT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170479479	170479480	+	IGR	DEL	CA	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170479479_170479480delCA								C6orf208 (276510 upstream) : LOC154449 (83942 downstream)																							gtacacacagcacacacacacg	0.361													4	2	---	---	---	---	
SUN1	23353	broad.mit.edu	37	7	871897	871897	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:871897delT	uc011jvp.1	+						SUN1_uc010ksa.1_Intron|SUN1_uc003sje.1_Intron|SUN1_uc003sjf.2_Intron|SUN1_uc011jvq.1_Intron	NM_001130965	NP_001124437	O94901	SUN1_HUMAN	unc-84 homolog A isoform a						cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0						CACTTTAGGGTTCCCCTGGTC	0.438													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945634	945634	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945634delA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						aggagaaaggagaaaggagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2572678	2572678	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2572678delT								LFNG (3870 upstream) : C7orf27 (4833 downstream)																							TTTGCCTCGGTTTTTCCCCCT	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	3123824	3123824	+	IGR	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3123824delC								CARD11 (40245 upstream) : SDK1 (217256 downstream)																							ATCTCATGGACACAAAGAAGG	0.522													4	2	---	---	---	---	
SP4	6671	broad.mit.edu	37	7	21522098	21522098	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21522098delT	uc003sva.2	+						SP4_uc003svb.2_Intron	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5						TGTGTTTTAGTTTTTTTTTTT	0.274													4	2	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	37077911	37077911	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37077911delC	uc003tfk.1	-						ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						CTGAACTCAGCCCCACCTTCA	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57383584	57383585	+	IGR	DEL	TG	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57383584_57383585delTG								ZNF479 (176013 upstream) : ZNF716 (126298 downstream)																							tgtctatgtatgtgtgtgtgtg	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57929464	57929464	+	IGR	DEL	G	-	-	rs76511107		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57929464delG								ZNF716 (396199 upstream) : None (None downstream)																							AGGACCTTTCGAAATAAAATG	0.423													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61815104	61815107	+	IGR	DEL	ATCT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61815104_61815107delATCT								None (None upstream) : LOC643955 (936565 downstream)																							ATTTTGGATGatctatctattata	0.093													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67892164	67892164	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67892164delG								None (None upstream) : None (None downstream)																							CTGACATCCTGGGGAAAAGGC	0.483													4	2	---	---	---	---	
YWHAG	7532	broad.mit.edu	37	7	75990797	75990797	+	5'Flank	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75990797delT	uc011kgj.1	-							NM_012479	NP_036611	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan						G2/M transition of mitotic cell cycle|regulation of neuron differentiation|regulation of signal transduction|regulation of synaptic plasticity	cytosol	insulin-like growth factor receptor binding|protein kinase C binding|protein kinase C inhibitor activity			ovary(1)|lung(1)	2						tttctttttcttttttttttt	0.164													4	2	---	---	---	---	
CDHR3	222256	broad.mit.edu	37	7	105532568	105532568	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105532568delG	uc003vdk.2	+									Q6ZTQ4	CDHR3_HUMAN	RecName: Full=Cadherin-like protein 28; Flags: Precursor;						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1						gaggtcttttggcaccttgat	0.000													4	2	---	---	---	---	
NRCAM	4897	broad.mit.edu	37	7	108049909	108049909	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108049909delT	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5						ACATCTCCTGTTGACCTCTCT	0.507													4	2	---	---	---	---	
CTTNBP2	83992	broad.mit.edu	37	7	117385674	117385675	+	Intron	INS	-	ATAACAAAAG	ATAACAAAAG	rs149512543	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117385674_117385675insATAACAAAAG	uc003vjf.2	-							NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2											ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		ATTAATGATTAATAACAAAAAG	0.361													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121081490	121081490	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121081490delT								FAM3C (45068 upstream) : PTPRZ1 (431669 downstream)																							CAAGGGAACATTTTTTTTTAA	0.224													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132207104	132207105	+	Intron	INS	-	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132207104_132207105insA	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron|PLXNA4_uc003vrb.2_Intron	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						ATGACCACCCCAACCCAACCCA	0.450													4	3	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	133221546	133221547	+	Intron	DEL	CC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133221546_133221547delCC	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				ccctcctggtccaaggtgggta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136423922	136423922	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136423922delG								LUZP6 (761718 upstream) : CHRM2 (129477 downstream)																							AAGGAGGCAAGGAGGAGGGGC	0.443													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152104372	152104373	+	Intron	INS	-	A	A	rs11428134		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152104372_152104373insA	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		TAAGAAACATTAAAAAATAACG	0.327			N		medulloblastoma								5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157279059	157279060	+	IGR	DEL	GT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157279059_157279060delGT								DNAJB6 (68927 upstream) : PTPRN2 (52691 downstream)																							GTTTGGAGGGgtgtgtgtgtgt	0.421													4	2	---	---	---	---	
TUSC3	7991	broad.mit.edu	37	8	15520003	15520004	+	Intron	INS	-	TAAA	TAAA	rs151070528	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15520003_15520004insTAAA	uc003wwt.2	+						TUSC3_uc003wwr.2_Intron|TUSC3_uc003wws.2_Intron|TUSC3_uc003wwu.2_Intron|TUSC3_uc003wwv.2_Intron|TUSC3_uc003www.2_Intron|TUSC3_uc003wwx.2_Intron|TUSC3_uc003wwy.2_Intron	NM_006765	NP_006756	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3 isoform a						cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)		CTTTTCACTGCATGTACTGTCC	0.327													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49437662	49437662	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49437662delT								UBE2V2 (463210 upstream) : EFCAB1 (185689 downstream)																							TCAGGATTCATTTTTTTTTGT	0.463													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55246290	55246291	+	IGR	INS	-	TT	TT	rs138383653	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55246290_55246291insTT								MRPL15 (185216 upstream) : SOX17 (124204 downstream)																							AGGAAGACAGATGTTAACTTGA	0.450													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64637370	64637370	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64637370delA								YTHDF3 (512025 upstream) : MIR124-2 (654336 downstream)																							aaaaggatggaaagattaaaa	0.000													4	2	---	---	---	---	
CRISPLD1	83690	broad.mit.edu	37	8	75897990	75897990	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75897990delA	uc003yan.2	+							NM_031461	NP_113649	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain							extracellular region				ovary(1)|central_nervous_system(1)	2	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			CCTCTGGAAGAAAAAAAATGG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79401075	79401076	+	IGR	DEL	AC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79401075_79401076delAC								None (None upstream) : PKIA (27260 downstream)																							accacctctgACACACACACAC	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79742723	79742723	+	IGR	DEL	G	-	-	rs150774988		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79742723delG								IL7 (24965 upstream) : STMN2 (780657 downstream)																							tcaacaatatggtattatata	0.000													3	3	---	---	---	---	
POP1	10940	broad.mit.edu	37	8	99168152	99168152	+	Intron	DEL	T	-	-	rs9785153		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99168152delT	uc003yij.3	+						POP1_uc011lgv.1_Intron|POP1_uc003yik.2_Intron	NM_001145860	NP_001139332	Q99575	POP1_HUMAN	processing of precursor 1						tRNA 5'-leader removal|tRNA catabolic process	nucleolar ribonuclease P complex|ribonuclease MRP complex	identical protein binding|ribonuclease MRP activity|ribonuclease P activity			ovary(1)|breast(1)	2	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.145)			tgtgtgtgtgtgtgtgtgtgt	0.109													5	3	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99606124	99606125	+	Intron	INS	-	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99606124_99606125insA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		CCTACCCCCCCAAAAAAAAATT	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101922661	101922662	+	IGR	DEL	CT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101922661_101922662delCT								PABPC1 (188346 upstream) : YWHAZ (8142 downstream)																							CTCCACCTCCCTCTCTCACACA	0.510													4	2	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102915013	102915013	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102915013delG	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			TTGCTTACCTGGCCTCTGACC	0.498													4	2	---	---	---	---	
RRM2B	50484	broad.mit.edu	37	8	103250717	103250717	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103250717delG	uc003ykn.2	-						RRM2B_uc003yko.2_Intron|RRM2B_uc010mbv.1_Intron|RRM2B_uc010mbw.1_Intron|RRM2B_uc010mbx.1_Intron|RRM2B_uc010mby.1_Intron	NM_015713	NP_056528	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process|DNA repair|nucleobase, nucleoside and nucleotide interconversion	nucleoplasm	ribonucleoside-diphosphate reductase activity|transition metal ion binding			ovary(2)	2	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;0.000728)			CGGTTTCCCTGGCCAGGGCTC	0.592								Direct_reversal_of_damage|Modulation_of_nucleotide_pools					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	110165312	110165312	+	IGR	DEL	T	-	-	rs78167649		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110165312delT								TRHR (33502 upstream) : NUDCD1 (87837 downstream)																							ACTGAGGACATTTTTTTTTCC	0.458													4	2	---	---	---	---	
RAD21	5885	broad.mit.edu	37	8	117858606	117858607	+	3'UTR	INS	-	AT	AT	rs144946900	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117858606_117858607insAT	uc003yod.2	-	14						NM_006265	NP_006256	O60216	RAD21_HUMAN	RAD21 homolog						apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding			lung(1)|skin(1)	2	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					AAAGTTAAGACATTCTGATAAT	0.297													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	119994236	119994236	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119994236delT								TNFRSF11B (29853 upstream) : COLEC10 (85188 downstream)																							TCACCCCTACTTTTTTTTTTT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	121133834	121133835	+	IGR	INS	-	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121133834_121133835insG								DEPDC6 (70678 upstream) : COL14A1 (3517 downstream)																							TCAGCATGGATGGGGGATCATG	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139536118	139536119	+	IGR	INS	-	A	A	rs151304933	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139536118_139536119insA								FAM135B (27053 upstream) : COL22A1 (64360 downstream)																							AACAAGTACTGAAAAGCTCCAT	0.510													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	140756840	140756841	+	Intron	INS	-	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140756840_140756841insC	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						ACAGGCTCTTTCCCCCCATCAG	0.574													4	3	---	---	---	---	
C9orf25	203259	broad.mit.edu	37	9	34401971	34401972	+	Intron	DEL	TT	-	-	rs150073334		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34401971_34401972delTT	uc011lok.1	-						C9orf25_uc003zuj.2_Intron|C9orf25_uc003zuk.2_Intron|C9orf25_uc011lol.1_Intron|C9orf25_uc003zul.2_Intron	NM_147202	NP_671735	Q8IW50	CI025_HUMAN	hypothetical protein LOC203259												0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.0858)		CCTTCTCATCTTTTTTTTTTTT	0.272													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66478299	66478299	+	IGR	DEL	G	-	-	rs139319632		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66478299delG								FAM74A4 (983913 upstream) : LOC442421 (18171 downstream)																							ttaagttctagggtacatgtg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66479112	66479113	+	IGR	INS	-	T	T	rs71293617		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66479112_66479113insT								FAM74A4 (984726 upstream) : LOC442421 (17357 downstream)																							ttttgatggtgtttttttcttg	0.000													3	3	---	---	---	---	
NTRK2	4915	broad.mit.edu	37	9	87465125	87465125	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87465125delA	uc004aoa.1	+						NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron|NTRK2_uc011lsz.1_Intron|NTRK2_uc011lta.1_Intron|NTRK2_uc004aoc.2_Intron	NM_001018064	NP_001018074	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16						TCTGGTGGGGAAAAAAAAAAC	0.229										TSP Lung(25;0.17)			4	2	---	---	---	---	
ROR2	4920	broad.mit.edu	37	9	94488677	94488677	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94488677delA	uc004arj.1	-						ROR2_uc004ari.1_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						TAGTTTACAGAAAAAAAAAAT	0.219													4	3	---	---	---	---	
SPTLC1	10558	broad.mit.edu	37	9	94871578	94871578	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94871578delT	uc004arl.1	-						SPTLC1_uc011ltv.1_Intron|SPTLC1_uc004arm.1_Intron|SPTLC1_uc004arn.1_Intron	NM_006415	NP_006406	O15269	SPTC1_HUMAN	serine palmitoyltransferase subunit 1 isoform a							integral to membrane|SPOTS complex	protein binding|pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			ovary(1)|breast(1)	2					L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)	TCTTCGCCGGTTTTTTCTGGG	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101674948	101674948	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101674948delT								GALNT12 (62590 upstream) : COL15A1 (31190 downstream)																							gctcccttcctcaccctcaat	0.299													4	2	---	---	---	---	
PAPPA	5069	broad.mit.edu	37	9	119062157	119062157	+	Intron	DEL	T	-	-	rs34938235		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119062157delT	uc004bjn.2	+						PAPPA_uc011lxp.1_Intron|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9						attacctccattttttttttt	0.065													2	4	---	---	---	---	
FNBP1	23048	broad.mit.edu	37	9	132756905	132756905	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132756905delA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		TATCTTGTTGAAAAAAAAAAC	0.189			T	MLL	AML								8	4	---	---	---	---	
NUP214	8021	broad.mit.edu	37	9	134098560	134098560	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134098560delT	uc004cag.2	+						NUP214_uc004cah.2_Intron|NUP214_uc004cai.2_Intron|NUP214_uc010mzg.2_Intron|NUP214_uc011mcg.1_Intron	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa						carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		tttttttttcttttttttttt	0.149			T	DEK|SET|ABL1	AML|T-ALL								4	4	---	---	---	---	
NEBL	10529	broad.mit.edu	37	10	21330394	21330394	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21330394delA	uc001iqk.2	-							NM_213569	NP_998734	O76041	NEBL_HUMAN	nebulette non-muscle isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						GACAACATGGAAAAAAGCCGA	0.413													4	2	---	---	---	---	
ARHGAP21	57584	broad.mit.edu	37	10	25007072	25007072	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25007072delT	uc001isb.2	-						ARHGAP21_uc009xkl.1_Intron|ARHGAP21_uc001isc.1_Intron|ARHGAP21_uc001isd.1_Intron	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21						signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8						TCCACAAGACTTTGCATATGA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	29505653	29505653	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29505653delT								BAMBI (533785 upstream) : LYZL1 (72337 downstream)																							catgtatttcttttttttttc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30517883	30517883	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30517883delG								KIAA1462 (113463 upstream) : MTPAP (80848 downstream)																							AGGACTGAGTGCAGTGAGGGG	0.512													4	2	---	---	---	---	
FRMPD2	143162	broad.mit.edu	37	10	49415183	49415184	+	Intron	INS	-	T	T	rs60100811		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49415183_49415184insT	uc001jgi.2	-						FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3						tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		TAGAATTTTCCTTTTTTTTTTT	0.282													4	2	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51073759	51073759	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51073759delA	uc001jif.2	-						PARG_uc001jih.2_Intron|PARG_uc001jig.2_Intron|PARG_uc010qgv.1_Intron|PARG_uc009xoi.2_Intron|PARG_uc010qgw.1_Intron|PARG_uc009xoj.2_Intron|PARG_uc010qgx.1_Intron	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		ACTTTTTTTTAAAAAAAAAAG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63554797	63554798	+	IGR	DEL	CC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63554797_63554798delCC								C10orf107 (28708 upstream) : ARID5B (106645 downstream)																							AATGTCTCATCCCTCACCTTCT	0.460													4	2	---	---	---	---	
ADK	132	broad.mit.edu	37	10	76341407	76341407	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76341407delA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712	P55263	ADK_HUMAN	adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)	agtaataaagaaaaaaaactt	0.000													4	2	---	---	---	---	
LOC283050	283050	broad.mit.edu	37	10	80791186	80791187	+	Intron	INS	-	AG	AG	rs146998324	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80791186_80791187insAG	uc001jzz.2	-						LOC283050_uc001jzx.2_Intron|LOC283050_uc001jzy.2_Intron|LOC283050_uc001kab.1_Intron	NR_024431				Homo sapiens cDNA FLJ40604 fis, clone THYMU2011806.												0						CACACAAACTCAGAGAGAGAGA	0.262													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81081764	81081765	+	IGR	DEL	GT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81081764_81081765delGT								ZMIZ1 (5479 upstream) : PPIF (25455 downstream)																							agtacctttagtgaataaatca	0.193													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	83953240	83953240	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83953240delA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		actgttgtataaaaactgatt	0.000													4	2	---	---	---	---	
KIF20B	9585	broad.mit.edu	37	10	91532223	91532223	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91532223delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron|KIF20B_uc001kgt.1_Intron|KIF20B_uc009xtw.1_Intron	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						Ctttatttgctttttttttgc	0.139													4	2	---	---	---	---	
CPXM2	119587	broad.mit.edu	37	10	125510465	125510465	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125510465delA	uc001lhk.1	-						CPXM2_uc001lhj.2_Intron	NM_198148	NP_937791	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2						cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TCACATTATGAAAAGCAGGAG	0.483													4	2	---	---	---	---	
UROS	7390	broad.mit.edu	37	10	127486057	127486057	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127486057delA	uc001liw.3	-						UROS_uc001liv.3_Intron|UROS_uc010quh.1_Intron|UROS_uc001lix.3_Intron|UROS_uc001liy.3_Intron	NM_000375	NP_000366	P10746	HEM4_HUMAN	uroporphyrinogen III synthase						heme biosynthetic process|uroporphyrinogen III biosynthetic process	cytosol|mitochondrion	uroporphyrinogen-III synthase activity				0		all_lung(145;0.00756)|Lung NSC(174;0.0116)|Colorectal(57;0.0855)|all_neural(114;0.0937)|Breast(234;0.203)				ctggtactccaaaccactGAT	0.234													4	2	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16177494	16177494	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16177494delC	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						GTCTTTAAGACCAAAGTTCCA	0.353													4	2	---	---	---	---	
UEVLD	55293	broad.mit.edu	37	11	18588235	18588240	+	Intron	DEL	TTAGAG	-	-	rs66773714		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18588235_18588240delTTAGAG	uc001mot.2	-						UEVLD_uc001mou.2_Intron|UEVLD_uc010rde.1_Intron|UEVLD_uc010rdf.1_Intron|UEVLD_uc010rdg.1_Intron|UEVLD_uc001mov.2_Intron|UEVLD_uc010rdh.1_Intron	NM_001040697	NP_001035787	Q8IX04	UEVLD_HUMAN	ubiquitin-conjugating enzyme E2-like isoform a						cellular carbohydrate metabolic process|protein modification process|protein transport		binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor				0						ATACATTCTTTTAGAGTTAGTCAAAA	0.150													10	6	---	---	---	---	
ANO3	63982	broad.mit.edu	37	11	26584943	26584950	+	Intron	DEL	TGTGTGTG	-	-	rs61877025		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26584943_26584950delTGTGTGTG	uc001mqt.3	+						ANO3_uc010rdr.1_Intron|ANO3_uc010rds.1_Intron|ANO3_uc010rdt.1_Intron|MUC15_uc001mqw.2_Intron|MUC15_uc001mqx.2_Intron|MUC15_uc001mqy.2_Intron	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C							chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TTTCTCTCTCtgtgtgtgtgtgtgtgtg	0.226													9	4	---	---	---	---	
PAX6	5080	broad.mit.edu	37	11	31815988	31815988	+	Intron	DEL	A	-	-	rs35883677		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31815988delA	uc001mtd.3	-						PAX6_uc001mte.3_Intron|PAX6_uc001mtg.3_Intron|PAX6_uc001mtf.3_Intron|PAX6_uc001mth.3_Intron|PAX6_uc009yjr.2_Intron	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a						blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)					acacacacacacacacacaca	0.184									Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33806439	33806439	+	IGR	DEL	T	-	-	rs71741225		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33806439delT								FBXO3 (10368 upstream) : LMO2 (73686 downstream)																							TATCACTCAGTTTTTTTTTTT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	37819176	37819176	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37819176delT								None (None upstream) : None (None downstream)																							TAGGTTTTACTTTTTTAGCTT	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74765523	74765524	+	IGR	INS	-	A	A	rs142473609		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74765523_74765524insA								NEU3 (46782 upstream) : OR2AT4 (34273 downstream)																							ttcaagtagttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ARRB1	408	broad.mit.edu	37	11	75046001	75046001	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75046001delA	uc001owe.1	-						ARRB1_uc001owf.1_Intron	NM_004041	NP_004032	P49407	ARRB1_HUMAN	arrestin beta 1 isoform A						G-protein coupled receptor internalization|histone H4 acetylation|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of histone acetylation|positive regulation of Rho protein signal transduction|positive regulation of transcription from RNA polymerase II promoter|post-Golgi vesicle-mediated transport|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|signal transduction|stress fiber assembly|transcription from RNA polymerase II promoter	chromatin|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane fraction|nucleus|plasma membrane|pseudopodium|soluble fraction	angiotensin receptor binding|enzyme inhibitor activity|GTPase activator activity|insulin-like growth factor receptor binding|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding			breast(2)	2						TGTTTGTTTTAAAAAAAAAAG	0.239													4	2	---	---	---	---	
ACER3	55331	broad.mit.edu	37	11	76674522	76674524	+	Intron	DEL	ACA	-	-	rs138955533		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76674522_76674524delACA	uc009yum.1	+						ACER3_uc010rsg.1_Intron|ACER3_uc009yul.1_Intron|ACER3_uc001oxu.2_Intron|ACER3_uc009yun.1_Intron|ACER3_uc009yuo.1_Intron|ACER3_uc010rsh.1_Intron|ACER3_uc010rsi.1_Intron|ACER3_uc010rsj.1_Intron	NM_018367	NP_060837	Q9NUN7	ACER3_HUMAN	phytoceramidase, alkaline						ceramide metabolic process|phytosphingosine biosynthetic process|positive regulation of cell proliferation|sphingosine biosynthetic process	integral to endoplasmic reticulum membrane|integral to Golgi membrane	phytoceramidase activity				0						aacacattagacaacgagaCCAG	0.054													3	3	---	---	---	---	
INTS4	92105	broad.mit.edu	37	11	77689786	77689787	+	Intron	INS	-	A	A	rs148185606	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77689786_77689787insA	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron|INTS4_uc001oyv.1_RNA	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4						snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			aggaccaaatgaaaaactgaat	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81624692	81624692	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81624692delC	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																		AATTTGTAGTCCCAGGGGAAA	0.323													4	2	---	---	---	---	
EED	8726	broad.mit.edu	37	11	85975481	85975482	+	Intron	INS	-	TATT	TATT	rs138959322	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85975481_85975482insTATT	uc001pbp.2	+						EED_uc010rtm.1_Intron|EED_uc001pbq.2_Intron|EED_uc001pbr.2_Intron|EED_uc001pbs.2_Intron|EED_uc010rtn.1_Intron	NM_003797	NP_003788	O75530	EED_HUMAN	embryonic ectoderm development isoform a						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|identical protein binding			skin(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				AGTAAAGACtatatttatttat	0.312													9	5	---	---	---	---	
ME3	10873	broad.mit.edu	37	11	86168160	86168160	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86168160delC	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_Intron	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor						aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)	gcctacttgtcccattattcc	0.000													4	2	---	---	---	---	
MAML2	84441	broad.mit.edu	37	11	95921807	95921807	+	Intron	DEL	T	-	-	rs112854219		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95921807delT	uc001pfw.1	-							NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				AGGAAGTCAGTTTTTTTTTTT	0.353			T	MECT1|CRTC3	salivary gland mucoepidermoid								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	104980978	104980978	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104980978delT								CASP1 (8820 upstream) : CARD18 (27692 downstream)																							ACACAACCAATAAGAAAAAGA	0.388													4	2	---	---	---	---	
BTG4	54766	broad.mit.edu	37	11	111369752	111369752	+	Intron	DEL	A	-	-	rs117900703	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111369752delA	uc001plj.2	-						BTG4_uc001plk.2_Intron	NM_017589	NP_060059	Q9NY30	BTG4_HUMAN	B-cell translocation gene 4						cell cycle arrest|negative regulation of cell proliferation|neuron differentiation						0		all_cancers(61;3.78e-13)|all_epithelial(67;5.29e-08)|Melanoma(852;3.15e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0204)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.22e-06)|BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|all cancers(92;2.18e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0509)		TTTTCAAAGGAAAAAAAAAAG	0.303													4	2	---	---	---	---	
BCO2	83875	broad.mit.edu	37	11	112052730	112052730	+	Intron	DEL	A	-	-	rs35381587		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112052730delA	uc001pnf.2	+						BCO2_uc001pne.1_Intron|BCO2_uc001png.2_Intron|BCO2_uc001pnh.2_Intron|BCO2_uc010rwt.1_Intron|BCO2_uc009yyn.2_Intron|BCO2_uc001pni.2_Intron	NM_031938	NP_114144	Q9BYV7	BCDO2_HUMAN	beta-carotene dioxygenase 2 isoform a						carotene metabolic process|retinal metabolic process|retinoic acid metabolic process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						aatttacaagaaaaaaatcaa	0.035													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127481792	127481792	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127481792delT								KIRREL3 (608437 upstream) : ETS1 (846864 downstream)																							GAGGCACACATTCCAAAAAAG	0.443													4	2	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11311936	11311937	+	Intron	INS	-	A	A	rs143791285	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11311936_11311937insA	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						TTCAGCCAGGCAAAAAATAAGC	0.386										HNSCC(22;0.051)			5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16342393	16342396	+	IGR	DEL	ATTA	-	-	rs66881403		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16342393_16342396delATTA								DERA (152079 upstream) : MGST1 (157680 downstream)																							AAATTATTTTATTAATTCTAATGC	0.260													8	5	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	21242654	21242655	+	Intron	INS	-	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21242654_21242655insA	uc010sil.1	+						LST-3TM12_uc010sim.1_Intron|LST-3TM12_uc010sin.1_Intron			Q9NPD5	SO1B3_HUMAN	SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					GCTTTGCATTTAAATAAAAAAA	0.119													7	4	---	---	---	---	
ABCC9	10060	broad.mit.edu	37	12	22041045	22041056	+	Intron	DEL	GACAGAGGGGTT	-	-	rs145112683		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22041045_22041056delGACAGAGGGGTT	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)	aattgctgaggacagaggggtttccaggacat	0.175													4	4	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	24375315	24375315	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24375315delT	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						gaatgtggaatttttttttct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31285810	31285810	+	Intron	DEL	A	-	-	rs71232209		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31285810delA	uc010sjy.1	-											RecName: Full=Ovostatin homolog 1; Flags: Precursor;																		CACATGATGGAAAAAAAAATA	0.343													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31298717	31298719	+	Intron	DEL	TTA	-	-	rs72203534		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31298717_31298719delTTA	uc010sjy.1	-											RecName: Full=Ovostatin homolog 1; Flags: Precursor;																		TATTTTTTAtttattattattat	0.113													4	3	---	---	---	---	
AMN1	196394	broad.mit.edu	37	12	31825530	31825530	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31825530delA	uc001rkq.3	-						AMN1_uc001rko.3_Intron|AMN1_uc010skc.1_Intron|AMN1_uc001rkp.3_Intron|AMN1_uc009zjs.2_Intron	NM_001113402	NP_001106873	Q8IY45	AMN1_HUMAN	antagonist of mitotic exit network 1 homolog												0	all_cancers(9;7.41e-12)|all_epithelial(9;1.18e-11)|all_lung(12;1.14e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.162)		OV - Ovarian serous cystadenocarcinoma(6;0.0014)			TTACTTGTTTAAAAAAAAAAA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	82319500	82319500	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82319500delT								PPFIA2 (166391 upstream) : CCDC59 (426590 downstream)																							gggctcgttcttTTTTTTTTC	0.010													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	83754265	83754265	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83754265delA								TMTC2 (226202 upstream) : None (None downstream)																							TTAGTTTTACAAAATAATAGC	0.289													4	2	---	---	---	---	
LRRIQ1	84125	broad.mit.edu	37	12	85548077	85548078	+	Intron	INS	-	T	T	rs143527245	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85548077_85548078insT	uc001tac.2	+							NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)		ACTATTTTTACTTTTTCGGCTC	0.277													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89280241	89280242	+	IGR	DEL	TT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89280241_89280242delTT								KITLG (306003 upstream) : DUSP6 (461597 downstream)																							gctcaattcgtttaacttttga	0.000													4	2	---	---	---	---	
CDK17	5128	broad.mit.edu	37	12	96728173	96728173	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96728173delA	uc001tep.1	-						CDK17_uc009ztk.2_Intron|CDK17_uc010svb.1_Intron	NM_002595	NP_002586	Q00537	CDK17_HUMAN	PCTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity			ovary(3)|lung(2)|kidney(1)|central_nervous_system(1)	7						TTATAAGaataaaaaaaatta	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102716883	102716884	+	IGR	INS	-	CTTT	CTTT	rs147750681	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102716883_102716884insCTTT								PMCH (125269 upstream) : IGF1 (72761 downstream)																							GTTATTTCTTAATTTTATTTAG	0.277													5	5	---	---	---	---	
CHST11	50515	broad.mit.edu	37	12	105070120	105070120	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105070120delT	uc001tkx.1	+						CHST11_uc001tky.2_Intron	NM_018413	NP_060883	Q9NPF2	CHSTB_HUMAN	carbohydrate sulfotransferase 11						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0						attagatgccttctgaatttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119220622	119220622	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119220622delG								SUDS3 (364783 upstream) : SRRM4 (198774 downstream)																							GAGTGGCTCTGGGGCCACAGC	0.433													4	2	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	129088664	129088664	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129088664delC	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						agtcagggttccccagagaca	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130536422	130536423	+	IGR	DEL	CT	-	-	rs34369137		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130536422_130536423delCT								LOC100190940 (9535 upstream) : FZD10 (110609 downstream)																							tgactcgcgcctctctctctct	0.203													4	2	---	---	---	---	
STX2	2054	broad.mit.edu	37	12	131293365	131293366	+	Intron	INS	-	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131293365_131293366insT	uc001uio.2	-						STX2_uc001uip.2_Intron|STX2_uc010tbj.1_Intron	NM_194356	NP_919337	P32856	STX2_HUMAN	syntaxin 2 isoform 2						acrosome reaction|ectoderm development|intracellular protein transport|organ morphogenesis|signal transduction	basolateral plasma membrane|integral to membrane|microsome|soluble fraction	calcium-dependent protein binding|SNAP receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		ACTAAAGCTAATGAACAAGTGA	0.208													19	9	---	---	---	---	
PDS5B	23047	broad.mit.edu	37	13	33164039	33164040	+	Intron	INS	-	A	A	rs71715968		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33164039_33164040insA	uc010abf.2	+						PDS5B_uc001uun.2_Intron|PDS5B_uc001uuo.2_Intron|PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		CTAACCATTTCCCCCATTACTT	0.381													4	2	---	---	---	---	
KIAA0564	23078	broad.mit.edu	37	13	42524369	42524372	+	Intron	DEL	CAAA	-	-	rs34219937		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42524369_42524372delCAAA	uc001uyj.2	-						KIAA0564_uc001uyk.2_Intron	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		AATGTGTTAGCAAACAAACAAACA	0.294													5	6	---	---	---	---	
COG3	83548	broad.mit.edu	37	13	46108633	46108633	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46108633delT	uc001vak.2	+						COG3_uc010tfv.1_Intron|COG3_uc010aci.2_Intron	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3						ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		TCTAAACAACTTTTTTTTTTT	0.214													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	74111333	74111334	+	IGR	DEL	TT	-	-	rs77805451		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74111333_74111334delTT								KLF5 (459658 upstream) : KLF12 (148816 downstream)																							TCTCGGCTCCTTTTTTTTTATT	0.436													4	2	---	---	---	---	
SCEL	8796	broad.mit.edu	37	13	78133646	78133650	+	Intron	DEL	AACAC	-	-	rs35778654		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78133646_78133650delAACAC	uc001vki.2	+						SCEL_uc001vkj.2_Intron|SCEL_uc010thx.1_Intron	NM_144777	NP_659001	O95171	SCEL_HUMAN	sciellin isoform 1						embryo development|keratinocyte differentiation	cornified envelope|cytoplasm|membrane	protein binding|zinc ion binding			ovary(4)|breast(1)	5		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)		AGTCTGATAAaacacaacacaacac	0.268													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	86615448	86615448	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86615448delG								SLITRK6 (241965 upstream) : None (None downstream)																							CGAACCTTCTGGGTCCACTTA	0.418													4	2	---	---	---	---	
ABCC4	10257	broad.mit.edu	37	13	95898883	95898883	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95898883delG	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	ATCCTCTTTTGACCAGGAGTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	97700296	97700296	+	IGR	DEL	C	-	-	rs28484571	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97700296delC								OXGR1 (53692 upstream) : MBNL2 (174278 downstream)																							acaacaacaacaaaaaAACAG	0.055													4	3	---	---	---	---	
ERCC5	2073	broad.mit.edu	37	13	103508647	103508648	+	Intron	INS	-	TA	TA	rs148306316	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103508647_103508648insTA	uc001vpw.2	+						ERCC5_uc001vpu.1_Intron|ERCC5_uc010tjb.1_Intron|ERCC5_uc010tjc.1_Intron|ERCC5_uc010tjd.1_Intron	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein						negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					ctacacacgtgtatatatatat	0.223			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	103662016	103662017	+	IGR	INS	-	CA	CA			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103662016_103662017insCA								LOC121952 (113633 upstream) : SLC10A2 (34333 downstream)																							TGGCCTTAGATCACACACACAC	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105187881	105187881	+	IGR	DEL	A	-	-	rs11342588		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105187881delA								None (None upstream) : DAOA (930335 downstream)																							agctatggttaaaaaaaaaaa	0.055													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105793871	105793871	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105793871delA								None (None upstream) : DAOA (324345 downstream)																							ATCTCTTATTAAAAAAAAAAT	0.328													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	53421273	53421273	+	IGR	DEL	T	-	-	rs67301850		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53421273delT								FERMT2 (3458 upstream) : DDHD1 (82186 downstream)																							GAAACTGGGATTTTTTTTTTC	0.378													4	2	---	---	---	---	
TTC7B	145567	broad.mit.edu	37	14	91254507	91254508	+	Intron	INS	-	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91254507_91254508insA	uc001xyp.2	-							NM_001010854	NP_001010854	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)				gactctgactcaaaaaaaagag	0.030													4	2	---	---	---	---	
PPP4R4	57718	broad.mit.edu	37	14	94659496	94659496	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94659496delT	uc001ycs.1	+						PPP4R4_uc001ycr.2_Intron	NM_058237	NP_478144	Q6NUP7	PP4R4_HUMAN	HEAT-like repeat-containing protein isoform 1							cytoplasm|protein serine/threonine phosphatase complex	protein binding			skin(3)|upper_aerodigestive_tract(1)	4						GAGGACAAACTTTTTTTTTTA	0.338													2	4	---	---	---	---	
SETD3	84193	broad.mit.edu	37	14	99932331	99932331	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99932331delA	uc001ygc.2	-						SETD3_uc001ygd.2_Intron|SETD3_uc001ygf.2_Intron	NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a						peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|peptidyl-lysine trimethylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone methyltransferase activity (H3-K36 specific)|transcription coactivator activity				0		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)				CTCAAATGGGAAAAAAAAAAA	0.313													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20163116	20163116	+	IGR	DEL	T	-	-	rs76322638		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20163116delT								None (None upstream) : GOLGA6L6 (573978 downstream)																							gtcatgctgaTTTTTTTTTTA	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39712253	39712253	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39712253delG								C15orf54 (165205 upstream) : THBS1 (161027 downstream)																							GCTATTCACAGGAAATCATCA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	53740589	53740589	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53740589delG								ONECUT1 (658380 upstream) : WDR72 (65349 downstream)																							GGAGGCAACAGGGAAAGTACA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	65253297	65253297	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65253297delG								ANKDD1A (2258 upstream) : SPG21 (2067 downstream)																							AGGAGTGAGTGGGGGTGGAGG	0.348													4	2	---	---	---	---	
PML	5371	broad.mit.edu	37	15	74297800	74297801	+	Intron	INS	-	T	T	rs151124961	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74297800_74297801insT	uc002awv.2	+						PML_uc002awm.2_Intron|PML_uc002awl.2_Intron|PML_uc002awj.1_Intron|PML_uc002awk.2_Intron|PML_uc002awn.2_Intron|PML_uc002awo.2_Intron|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002aww.1_Intron	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1						cell cycle arrest|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|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5						TGTTGCTTTGCTTTTTTCCCCG	0.356			T	RARA|PAX5	APL|ALL								3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85070266	85070267	+	IGR	INS	-	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85070266_85070267insA								GOLGA6L5 (10188 upstream) : UBE2Q2P1 (160 downstream)																							CAGAATCTCACAAAAAAAAAAC	0.366													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88108439	88108439	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88108439delA								AGBL1 (536156 upstream) : NCRNA00052 (11721 downstream)																							atagatgagtaataccagctt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90825347	90825347	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90825347delT								TTLL13 (9904 upstream) : GABARAPL3 (64418 downstream)																							AAAGGTTTTGTTTTTTTTTTG	0.358													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	13472943	13472944	+	IGR	DEL	CT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13472943_13472944delCT								SHISA9 (138671 upstream) : ERCC4 (541070 downstream)																							CCTCTAGGGACTCAAGATACCT	0.495													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	19138224	19138224	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19138224delA								ITPRIPL2 (5276 upstream) : SYT17 (41414 downstream)																							catctcgaagaaaaaaaaaaG	0.164													4	2	---	---	---	---	
NSMCE1	197370	broad.mit.edu	37	16	27249866	27249867	+	Intron	INS	-	C	C	rs10578763		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27249866_27249867insC	uc002doi.1	-						NSMCE1_uc002doj.1_Intron	NM_145080	NP_659547	Q8WV22	NSE1_HUMAN	non-SMC element 1 homolog						DNA recombination|DNA repair|intracellular signal transduction	nucleus	zinc ion binding				0						CTTTTTTCTTTTTTTTTTTTTA	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32848034	32848034	+	IGR	DEL	A	-	-	rs75274373		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32848034delA								TP53TG3B (159156 upstream) : SLC6A10P (40763 downstream)																							tatttctttcattaaaaaatt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33052524	33052524	+	IGR	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33052524delC								SLC6A10P (156061 upstream) : MIR1826 (912984 downstream)																							aacctgtgtactacattacta	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33530995	33530995	+	IGR	DEL	T	-	-	rs78777890		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33530995delT								SLC6A10P (634532 upstream) : MIR1826 (434513 downstream)																							ATAACACTTATTTCTACTTGG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33967927	33967927	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33967927delG								MIR1826 (2335 upstream) : UBE2MP1 (435875 downstream)																							GTAAAGAATAGGATCTTCGTT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52068441	52068442	+	IGR	INS	-	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52068441_52068442insA								SALL1 (883258 upstream) : TOX3 (403476 downstream)																							CAGAAAGCAACAAAAATAGAAA	0.361													4	2	---	---	---	---	
CES1	1066	broad.mit.edu	37	16	55855521	55855521	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55855521delG	uc002eim.2	-						CES1_uc002eil.2_Intron|CES1_uc002ein.2_Intron	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor						response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	GGTTCTCAGTGAACCCTTAAG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	56878704	56878704	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56878704delT								NUP93 (28 upstream) : MIR138-2 (13726 downstream)																							ttttattttcttttttttttt	0.134													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58693291	58693291	+	IGR	DEL	G	-	-	rs56029647	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58693291delG								CNOT1 (29541 upstream) : SLC38A7 (7007 downstream)																							GTCATTTTttgttgttgttgt	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	70407635	70407635	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70407635delT								DDX19A (356 upstream) : ST3GAL2 (5703 downstream)																							acaatgaacattttttttttc	0.000													4	3	---	---	---	---	
MTSS1L	92154	broad.mit.edu	37	16	70708094	70708111	+	Intron	DEL	AGTCTCAACAGCTATAGT	-	-	rs67662127		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70708094_70708111delAGTCTCAACAGCTATAGT	uc002ezj.2	-							NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like						filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1						CCTTCAGGCCAGTCTCAACAGCTATAGTAGTCTCAACA	0.367													4	2	---	---	---	---	
GLG1	2734	broad.mit.edu	37	16	74538004	74538005	+	Intron	INS	-	A	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74538004_74538005insA	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						TGTAACCATGCAAAAAATGCAG	0.431													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	82688911	82688912	+	Intron	DEL	GT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82688911_82688912delGT	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		aaagggtaaagtgtgacgaagg	0.000													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	83068833	83068833	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83068833delG	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TGGGCCAGCTGCTAGAGAAGA	0.483													4	2	---	---	---	---	
DOC2B	8447	broad.mit.edu	37	17	9669	9670	+	Intron	DEL	CA	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9669_9670delCA	uc010vpx.1	-							NM_003585	NP_003576	Q14184	DOC2B_HUMAN	double C2-like domains, beta						calcium ion-dependent exocytosis of neurotransmitter|positive regulation of calcium ion-dependent exocytosis|positive regulation of insulin secretion|positive regulation of vesicle fusion|protein localization	plasma membrane|synaptic vesicle	calcium-dependent phospholipid binding|transporter activity				0						cacacacgagcacacacacaca	0.144													6	3	---	---	---	---	
RTN4RL1	146760	broad.mit.edu	37	17	1884727	1884727	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1884727delT	uc002ftp.2	-							NM_178568	NP_848663	Q86UN2	R4RL1_HUMAN	reticulon 4 receptor-like 1 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0						CATCTTGGTATTTTTTTCTTT	0.328													4	2	---	---	---	---	
SGSM2	9905	broad.mit.edu	37	17	2251991	2251992	+	Intron	DEL	AC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2251991_2251992delAC	uc002fun.3	+						SGSM2_uc002fum.3_Intron|SGSM2_uc010vqw.1_Intron	NM_001098509	NP_001091979	O43147	SGSM2_HUMAN	RUN and TBC1 domain containing 1 isoform 2							intracellular	Rab GTPase activator activity				0				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		AATGCAGGCAACACACACAGCA	0.238													4	2	---	---	---	---	
EPN2	22905	broad.mit.edu	37	17	19236950	19236951	+	Intron	INS	-	G	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19236950_19236951insG	uc002gvd.3	+						EPN2_uc002gve.3_Intron|EPN2_uc002gvf.3_Intron|EPN2_uc010vyo.1_Intron|EPN2_uc010vyp.1_Intron|EPN2_uc010vyq.1_Intron|EPN2_uc002gvh.1_Intron|EPN2_uc002gvj.3_Intron	NM_014964	NP_055779	O95208	EPN2_HUMAN	epsin 2 isoform b						endocytosis		lipid binding			skin(1)	1	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					AGCTGATGGCTGGTGAAGGTGT	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21553561	21553561	+	IGR	DEL	T	-	-	rs113696343		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21553561delT								C17orf51 (75830 upstream) : FAM27L (271809 downstream)																							atgctgaggatgatgatgatg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21553563	21553564	+	IGR	DEL	AT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21553563_21553564delAT								C17orf51 (75832 upstream) : FAM27L (271806 downstream)																							gctgaggatgatgatgatgatg	0.000													5	3	---	---	---	---	
DHRS13	147015	broad.mit.edu	37	17	27229263	27229264	+	Intron	DEL	TC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27229263_27229264delTC	uc002hde.3	-						DHRS13_uc002hdd.3_Intron|DHRS13_uc010wba.1_Intron	NM_144683	NP_653284	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13							extracellular region	binding|oxidoreductase activity				0	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)			taaatctttttctcagtttttc	0.000													4	2	---	---	---	---	
SSH2	85464	broad.mit.edu	37	17	28229551	28229551	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28229551delA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						TGTTGCCCTTAAAAAAAAAAA	0.289													3	3	---	---	---	---	
SLFN14	342618	broad.mit.edu	37	17	33878295	33878296	+	Intron	DEL	TG	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33878295_33878296delTG	uc010ctu.1	-							NM_001129820	NP_001123292	P0C7P3	SLN14_HUMAN	schlafen family member 14								ATP binding			central_nervous_system(1)	1						AATATATTTTTGTGTGTGTGTG	0.193													4	2	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35632656	35632657	+	Intron	DEL	GG	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35632656_35632657delGG	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron|ACACA_uc002hnq.2_Intron	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CTGTGTACCTGGAACTAAATTT	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36609489	36609489	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36609489delG								SOCS7 (53472 upstream) : ARHGAP23 (4155 downstream)																							CTGTGTGTGTGGGGGGGATAG	0.542													4	2	---	---	---	---	
KRT28	162605	broad.mit.edu	37	17	38949668	38949668	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38949668delT	uc002hvh.1	-							NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D							cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)				TTCCATTTGATTTTTTTTTTT	0.284													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39215669	39215669	+	3'UTR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39215669delT	uc002hvx.2	-	1						NM_033184	NP_149440			keratin associated protein 2-4																		TATTTACTCGTTTTTTTTTTC	0.368													5	3	---	---	---	---	
EFTUD2	9343	broad.mit.edu	37	17	42966300	42966301	+	Intron	INS	-	ATAA	ATAA	rs149690543	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42966300_42966301insATAA	uc002ihn.2	-						EFTUD2_uc010wje.1_Intron|EFTUD2_uc010wjf.1_Intron	NM_004247	NP_004238	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain							Cajal body|catalytic step 2 spliceosome|cytoplasm|nuclear speck	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(33;0.109)				tctgagtcgtcataaagttatt	0.000													0	6	---	---	---	---	
PPP1R9B	84687	broad.mit.edu	37	17	48220617	48220617	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48220617delA	uc002iqh.3	-							NM_032595	NP_115984	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B						cell cycle arrest|cell differentiation|cell migration|filopodium assembly|negative regulation of cell growth|nervous system development|regulation of cell growth by extracellular stimulus|regulation of cell proliferation|regulation of exit from mitosis|RNA splicing	adherens junction|cytoskeleton|dendritic spine|filopodium|lamellipodium|nucleoplasm|protein phosphatase type 1 complex|ruffle membrane|synapse	actin binding|protein phosphatase 1 binding|protein phosphatase inhibitor activity				0						atGTCCAGCGAAAAAAAAGCT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48864887	48864887	+	IGR	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48864887delC								C17orf73 (19969 upstream) : WFIKKN2 (47124 downstream)																							ACTCTCTCCACCAGCCACCAT	0.333													4	2	---	---	---	---	
SPAG9	9043	broad.mit.edu	37	17	49134090	49134090	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49134090delT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron	NM_001130528	NP_001124000	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			CCCTAAACAGTTTTTTTTTTA	0.313													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	50630598	50630598	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50630598delG								CA10 (393221 upstream) : None (None downstream)																							ATACCTATCAGGGTTACCCAA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	61673450	61673450	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61673450delT								DCAF7 (1811 upstream) : TACO1 (4793 downstream)																							GAGAATTTAAttttttttttt	0.239													4	3	---	---	---	---	
ARSG	22901	broad.mit.edu	37	17	66269127	66269127	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66269127delT	uc002jhc.2	+						SLC16A6_uc002jgz.1_Intron|SLC16A6_uc002jha.1_Intron	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAAATATAACTTTTTTTTTTT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22636977	22636977	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22636977delG								HRH4 (577057 upstream) : ZNF521 (4911 downstream)																							GAAGTTAAATGGAGAAGCATT	0.453													4	2	---	---	---	---	
MRO	83876	broad.mit.edu	37	18	48349617	48349619	+	Intron	DEL	TCC	-	-	rs111680842		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48349617_48349619delTCC	uc002lex.3	-						MRO_uc010dpc.2_Intron	NM_031939	NP_114145	Q9BYG7	MSTRO_HUMAN	maestro isoform a							nucleolus	binding				0		Colorectal(6;0.0596)		Colorectal(21;0.082)		cacatttgcttcctcccacttct	0.246													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	52784335	52784335	+	Intron	DEL	A	-	-	rs61431480		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52784335delA	uc002lfu.1	-											Homo sapiens cDNA FLJ36621 fis, clone TRACH2016651.																		GAATTCAAAGAGAGAAGGAAA	0.428													3	3	---	---	---	---	
PDE4A	5141	broad.mit.edu	37	19	10572804	10572804	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10572804delT	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.2_Intron|PDE4A_uc002mom.2_Intron|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_Intron	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1						signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)	TCCttctttctttttttttgt	0.274													5	3	---	---	---	---	
CCDC151	115948	broad.mit.edu	37	19	11541264	11541264	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11541264delT	uc002mrs.2	-						CCDC151_uc002mrr.2_Intron|CCDC151_uc010dxz.2_Intron	NM_145045	NP_659482	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151											ovary(1)	1						ggcTGTGATGTTTTTTTTTTT	0.199													4	2	---	---	---	---	
ELAVL3	1995	broad.mit.edu	37	19	11565285	11565286	+	3'UTR	DEL	TC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11565285_11565286delTC	uc002mry.1	-	7					ELAVL3_uc002mrx.1_3'UTR	NM_001420	NP_001411	Q14576	ELAV3_HUMAN	ELAV-like protein 3 isoform 1						cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3						tctctctctttctctctctctc	0.574													4	2	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17777717	17777717	+	Intron	DEL	G	-	-	rs9797868		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17777717delG	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						gagagagagagagaaagacag	0.184													4	3	---	---	---	---	
FCHO1	23149	broad.mit.edu	37	19	17866830	17866830	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17866830delC	uc010ebb.2	+						FCHO1_uc002nhg.3_Intron|FCHO1_uc002nhh.2_Intron|FCHO1_uc010xpw.1_Intron	NM_001161358	NP_001154830	O14526	FCHO1_HUMAN	FCH domain only 1 isoform b											breast(1)	1						CAGGGGAGGGCCCAGGAGTCA	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29981239	29981239	+	Intron	DEL	C	-	-	rs67887172		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29981239delC	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		GAGTCCCTCACCCATTCCAAG	0.368													5	3	---	---	---	---	
ZNF461	92283	broad.mit.edu	37	19	37157556	37157557	+	Intron	INS	-	C	C	rs145412420	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37157556_37157557insC	uc002oem.2	-						ZNF461_uc002oen.2_Intron|ZNF461_uc010xtj.1_Intron	NM_153257	NP_694989	Q8TAF7	ZN461_HUMAN	gonadotropin inducible transcription repressor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CTATAGACATTCCCTTCCGCGG	0.525													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42094317	42094317	+	IGR	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42094317delC								CEACAM21 (1121 upstream) : CEACAM4 (31027 downstream)																							GACCCTGGATCCCACCTGCAC	0.323													4	2	---	---	---	---	
LYPD5	284348	broad.mit.edu	37	19	44300532	44300550	+	3'UTR	DEL	ATGAAAGTGTCCTGCACTC	-	-	rs573865	byFrequency	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44300532_44300550delATGAAAGTGTCCTGCACTC	uc002oxm.3	-	5					LYPD5_uc002oxn.3_3'UTR	NM_001031749	NP_001026919	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5 isoform A							anchored to membrane|plasma membrane					0		Prostate(69;0.0352)				TCATGCAGTTATGAAAGTGTCCTGCACTCATGAAAGTGT	0.201													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	3755708	3755710	+	IGR	DEL	AGG	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3755708_3755710delAGG								C20orf27 (7256 upstream) : SPEF1 (2442 downstream)																							gtctactacaAGGAGGAaaaagc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6497055	6497055	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6497055delT								FERMT1 (392864 upstream) : BMP2 (251690 downstream)																							gaattctagcttcaattctac	0.010													4	2	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9360474	9360475	+	Intron	DEL	TC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9360474_9360475delTC	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						AAAAATGTATTCTCTCTCTCTC	0.406													3	3	---	---	---	---	
BANF2	140836	broad.mit.edu	37	20	17674540	17674540	+	Intron	DEL	C	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17674540delC	uc010zrs.1	+							NM_001159495	NP_001152967	Q9H503	BAFL_HUMAN	barrier to autointegration factor 2 isoform 2							cytoplasm|nucleus	DNA binding			skin(1)	1						CATCTTCACACCACGGTGGCT	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19731126	19731126	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19731126delA								SLC24A3 (27586 upstream) : RIN2 (139084 downstream)																							tctccaaaagaaaaaaaaaaT	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19751263	19751264	+	IGR	INS	-	C	C	rs141836367	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19751263_19751264insC								SLC24A3 (47723 upstream) : RIN2 (118946 downstream)																							TCATGGCTCTGCCCCCAGCCTC	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26202318	26202318	+	IGR	DEL	T	-	-	rs77929867		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26202318delT								MIR663 (13404 upstream) : None (None downstream)																							aattacagaatctttatatct	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29431750	29431750	+	IGR	DEL	G	-	-	rs112192023		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29431750delG								None (None upstream) : FRG1B (180129 downstream)																							gtgtagatgtgtttttctctt	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29448101	29448101	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29448101delA								None (None upstream) : FRG1B (163778 downstream)																							TAGAAACAGCAAAAATGAAGA	0.274													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29638538	29638538	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29638538delT	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						AGAGCAAGAATTTTTAAAGAA	0.378													6	6	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29650349	29650349	+	Intron	DEL	C	-	-	rs138887197		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29650349delC	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						atagggtattctttctctgct	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	32538815	32538815	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32538815delT								CHMP4B (96646 upstream) : RALY (42917 downstream)																							agatgtgaaattccatccctt	0.000													4	2	---	---	---	---	
RBM39	9584	broad.mit.edu	37	20	34312260	34312260	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34312260delA	uc002xeb.2	-						RBM39_uc002xdz.2_Intron|RBM39_uc002xea.2_Intron|RBM39_uc010gfn.2_Intron|RBM39_uc010zvm.1_Intron|RBM39_uc002xeg.2_Intron|RBM39_uc002xec.2_Intron|RBM39_uc002xed.2_Intron|RBM39_uc002xee.2_Intron|RBM39_uc002xef.2_Intron|RBM39_uc010zvn.1_Intron	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					aaaacaaaacaaaaaaaaGGC	0.154													6	3	---	---	---	---	
RPN2	6185	broad.mit.edu	37	20	35865362	35865362	+	Intron	DEL	A	-	-	rs11477462		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35865362delA	uc002xgp.2	+						RPN2_uc002xgq.2_Intron	NM_002951	NP_002942	P04844	RPN2_HUMAN	ribophorin II isoform 1 precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|nucleus|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				GAAAATTATTAGCTTTATGAA	0.373													4	5	---	---	---	---	
TFAP2C	7022	broad.mit.edu	37	20	55208253	55208253	+	Intron	DEL	T	-	-	rs72357061		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55208253delT	uc002xya.2	+						TFAP2C_uc010zzi.1_Intron	NM_003222	NP_003213	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma						cell-cell signaling|male gonad development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Colorectal(105;0.229)			actcttattattttttttttt	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57955059	57955059	+	IGR	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57955059delG								EDN3 (54013 upstream) : PHACTR3 (197505 downstream)																							ACTGCATTGTGGGGAGAACCC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9417527	9417527	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9417527delT								None (None upstream) : None (None downstream)																							tggtttataatttttaatggt	0.164													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9577625	9577627	+	IGR	DEL	AAT	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9577625_9577627delAAT								None (None upstream) : None (None downstream)																							attctaagacaataagtttatgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9854127	9854128	+	IGR	INS	-	C	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9854127_9854128insC								None (None upstream) : None (None downstream)																							ttcaacctcctcacactgaatt	0.025													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9865569	9865570	+	IGR	INS	-	A	A	rs77497487	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9865569_9865570insA								None (None upstream) : None (None downstream)																							CTGCTGAGTTTAAATCTTCCTT	0.490													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11076406	11076407	+	Intron	DEL	TT	-	-	rs142727884		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11076406_11076407delTT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		taatttactattttttttttct	0.000													3	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11078640	11078642	+	Intron	DEL	CTC	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11078640_11078642delCTC	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		atggaaactactcctggtgaaaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11155113	11155113	+	IGR	DEL	A	-	-	rs149249762		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11155113delA								BAGE (56176 upstream) : None (None downstream)																							TGTAGATCTGAAAAAAAATGA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14367575	14367575	+	IGR	DEL	C	-	-	rs140643406		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14367575delC								None (None upstream) : C21orf99 (42912 downstream)																							atttctttttccacaataggc	0.000													5	3	---	---	---	---	
JAM2	58494	broad.mit.edu	37	21	27011450	27011450	+	5'Flank	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27011450delT	uc002ylp.1	+						JAM2_uc011ace.1_5'Flank|JAM2_uc002ylq.1_5'Flank|JAM2_uc011acf.1_5'Flank|JAM2_uc010glh.1_5'Flank|JAM2_uc002ylr.1_5'Flank|JAM2_uc010gli.1_5'Flank	NM_021219	NP_067042	P57087	JAM2_HUMAN	junctional adhesion molecule 2 precursor						blood coagulation|cell-cell adhesion|leukocyte migration	integral to plasma membrane|tight junction					0						TCTTGATTGCTTTTTTTTTTC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29367920	29367920	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29367920delT								NCRNA00113 (244368 upstream) : C21orf94 (17762 downstream)																							AACAAGATACTTTTTTTTAAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	31511840	31511840	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31511840delT								GRIK1 (199558 upstream) : CLDN17 (26423 downstream)																							gatatcttacttttttttttc	0.000													4	2	---	---	---	---	
HUNK	30811	broad.mit.edu	37	21	33362735	33362735	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33362735delT	uc002yph.2	+							NM_014586	NP_055401	P57058	HUNK_HUMAN	hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2						gacctcattcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	38647796	38647796	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38647796delA								DSCR3 (7963 upstream) : DYRK1A (92063 downstream)																							AGCATATATCAAAAAAAAGGA	0.234													4	2	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45376563	45376563	+	Intron	DEL	G	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45376563delG	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron|AGPAT3_uc002zdx.2_Intron|AGPAT3_uc002zdy.2_5'Flank	NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		tgggtgctgtggggttgcagg	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20114718	20114718	+	IGR	DEL	T	-	-	rs143470990		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20114718delT								RANBP1 (14 upstream) : ZDHHC8 (4647 downstream)																							ATTCAGGTTGTTTTTTTTTTT	0.313													11	10	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22939997	22939997	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22939997delT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0						gataaacaggtggccaacaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23327026	23327026	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23327026delA								LOC96610 (61944 upstream) : RTDR1 (74568 downstream)																							GGGATGGGTGAAAAGGAACCA	0.328													4	2	---	---	---	---	
CHEK2	11200	broad.mit.edu	37	22	29107647	29107647	+	Intron	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29107647delA	uc003adu.1	-						CHEK2_uc003ads.1_Intron|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Intron|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_Intron|CHEK2_uc010gvk.1_Intron|CHEK2_uc003adt.1_Intron|CHEK2_uc003adv.1_Intron|CHEK2_uc003adw.1_Intron|CHEK2_uc003adx.1_Intron|CHEK2_uc003ady.1_Intron|CHEK2_uc003adz.1_Intron	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a						cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20						TTGGAAGAAGAAAAAAAAAAA	0.184			F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				8	4	---	---	---	---	
BPIL2	254240	broad.mit.edu	37	22	32853547	32853558	+	5'Flank	DEL	TCCATCCATCCA	-	-	rs71320927	by1000genomes	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32853547_32853558delTCCATCCATCCA	uc003amn.2	-						BPIL2_uc010gwo.2_5'Flank|BPIL2_uc011amb.1_Intron|BPIL2_uc003amo.3_Intron	NM_174932	NP_777592	Q8NFQ6	BPIL2_HUMAN	bactericidal/permeability-increasing							extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)|skin(1)	2						catccatccgtccatccatccatccatccatc	0.057											OREG0003513	type=REGULATORY REGION|Gene=BPIL2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41063321	41063321	+	IGR	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41063321delT								MKL1 (30631 upstream) : MCHR1 (11861 downstream)																							GTGGGGCTGattttccatttg	0.144													4	2	---	---	---	---	
PHF21B	112885	broad.mit.edu	37	22	45299033	45299033	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45299033delT	uc003bfn.2	-						PHF21B_uc003bfm.2_Intron|PHF21B_uc011aqk.1_Intron|PHF21B_uc011aql.1_Intron|PHF21B_uc011aqm.1_Intron	NM_138415	NP_612424	Q96EK2	PF21B_HUMAN	PHD finger protein 21B isoform 1								zinc ion binding			ovary(2)|skin(1)	3		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		AAGCACTCCCTCCTCCAGCAC	0.498													4	2	---	---	---	---	
ARSD	414	broad.mit.edu	37	X	2827819	2827819	+	Intron	DEL	A	-	-	rs72256276		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2827819delA	uc004cqy.2	-						ARSD_uc004cqz.1_Intron	NM_001669	NP_001660	P51689	ARSD_HUMAN	arylsulfatase D isoform a precursor							lysosome	arylsulfatase activity|metal ion binding				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)				aaaaaCAATTAAAAAAAATCA	0.289													4	2	---	---	---	---	
SMS	6611	broad.mit.edu	37	X	21997306	21997307	+	Intron	INS	-	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21997306_21997307insT	uc004dag.2	+						SMS_uc010nfs.2_Intron|SMS_uc010nft.2_Intron	NM_004595	NP_004586	P52788	SPSY_HUMAN	spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)	AAAATTAATtcttttttttttt	0.158													5	5	---	---	---	---	
USP9X	8239	broad.mit.edu	37	X	41046084	41046084	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41046084delT	uc004dfb.2	+						USP9X_uc004dfc.2_Intron	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform						BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						GATGGGGTGAttttttttttt	0.124													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	140757920	140757920	+	IGR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140757920delA								SPANXC (85060 upstream) : SPANXE (27649 downstream)																							CCAAAAAATGAAAAAAAAAAT	0.299													5	3	---	---	---	---	
SLC10A3	8273	broad.mit.edu	37	X	153715751	153715751	+	3'UTR	DEL	A	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153715751delA	uc004flq.2	-	3					UBL4A_uc004flo.2_5'Flank|SLC10A3_uc004flr.2_3'UTR|SLC10A3_uc004flp.2_3'UTR	NM_001142392	NP_001135864	P09131	P3_HUMAN	solute carrier family 10, member 3 isoform 1						organic anion transport	integral to membrane	bile acid:sodium symporter activity			ovary(1)|skin(1)	2	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AAAAATCAGTAAAAAAAATAA	0.458													4	3	---	---	---	---	
CLIC2	1193	broad.mit.edu	37	X	154521949	154521949	+	Intron	DEL	T	-	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154521949delT	uc004fnf.2	-						CLIC2_uc010nvj.1_Intron	NM_001289	NP_001280	O15247	CLIC2_HUMAN	chloride intracellular channel 2						signal transduction	chloride channel complex|cytoplasm|nucleus	voltage-gated chloride channel activity			large_intestine(1)|ovary(1)|skin(1)	3	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					tagtcccagctactcgggagg	0.000													5	3	---	---	---	---	
CLIC2	1193	broad.mit.edu	37	X	154521951	154521952	+	Intron	INS	-	T	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154521951_154521952insT	uc004fnf.2	-						CLIC2_uc010nvj.1_Intron	NM_001289	NP_001280	O15247	CLIC2_HUMAN	chloride intracellular channel 2						signal transduction	chloride channel complex|cytoplasm|nucleus	voltage-gated chloride channel activity			large_intestine(1)|ovary(1)|skin(1)	3	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					gtcccagctactcgggaggctg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59019925	59019925	+	IGR	DEL	A	-	-	rs55674607		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59019925delA								None (None upstream) : None (None downstream)																							GGGCATTGCTAGGCAACCGCT	0.428													4	2	---	---	---	---	
