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
UBE2J2	118424	broad.mit.edu	37	1	1198752	1198752	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1198752C>T	uc001adn.2	-	3	456	c.146G>A	c.(145-147)CGA>CAA	p.R49Q	UBE2J2_uc001adm.2_Missense_Mutation_p.R14Q|UBE2J2_uc001ado.2_Missense_Mutation_p.R65Q|UBE2J2_uc001adp.2_Missense_Mutation_p.R49Q|UBE2J2_uc001adq.2_5'UTR|UBE2J2_uc001adr.2_5'UTR|UBE2J2_uc001ads.2_5'UTR|LOC100128842_uc010nyh.1_5'Flank	NM_194458	NP_919440	Q8N2K1	UB2J2_HUMAN	ubiquitin conjugating enzyme E2, J2 isoform 3	49	Cytoplasmic (Potential).				response to unfolded protein	endoplasmic reticulum membrane|integral to membrane	ATP binding|ubiquitin-protein ligase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.66e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.53e-21)|Colorectal(212;0.00019)|COAD - Colon adenocarcinoma(227;0.000215)|Kidney(185;0.00255)|BRCA - Breast invasive adenocarcinoma(365;0.00266)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0371)|Lung(427;0.205)		CTCTGGGCCTCGGACGACATA	0.448													19	218	---	---	---	---	PASS
UBE4B	10277	broad.mit.edu	37	1	10221342	10221342	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10221342C>T	uc001aqs.3	+	23	3909	c.3196C>T	c.(3196-3198)CGG>TGG	p.R1066W	UBE4B_uc001aqr.3_Missense_Mutation_p.R937W|UBE4B_uc010oai.1_RNA|UBE4B_uc010oaj.1_Missense_Mutation_p.R521W	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	1066					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CCAGTTGCCCCGGGTGAGGAC	0.542													9	86	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17084468	17084468	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17084468C>T	uc010ock.1	-	12	1630	c.1630G>A	c.(1630-1632)GGC>AGC	p.G544S	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_Missense_Mutation_p.G144S	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						AGCTGGGAGCCTGAGGGCCCA	0.612													3	37	---	---	---	---	PASS
PADI6	353238	broad.mit.edu	37	1	17720899	17720899	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17720899G>A	uc001bak.1	+	12	1286	c.1286G>A	c.(1285-1287)GGG>GAG	p.G429E		NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6	421					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	AAGGTCCAAGGGAAAGAGTAC	0.547													4	19	---	---	---	---	PASS
RHD	6007	broad.mit.edu	37	1	25633330	25633330	+	Intron	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25633330T>C	uc001bjz.2	+						RHD_uc010oep.1_3'UTR|RHD_uc001bkc.2_Intron|RHD_uc009vrm.2_Intron|RHD_uc001bka.2_Intron|RHD_uc001bkb.2_Intron|RHD_uc009vrn.2_Intron|RHD_uc009vro.2_Intron|RHD_uc009vrp.2_Intron|uc001bkd.1_5'Flank	NM_016124	NP_057208	Q02161	RHD_HUMAN	Rh blood group D antigen isoform 1							integral to plasma membrane				breast(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGGTGCTCAGTAGGCTTCGGT	0.522													8	12	---	---	---	---	PASS
AHDC1	27245	broad.mit.edu	37	1	27874531	27874531	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27874531C>T	uc009vsy.2	-	6	5065	c.4096G>A	c.(4096-4098)GAC>AAC	p.D1366N	AHDC1_uc009vsz.1_Missense_Mutation_p.D1366N	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1366							DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CTGGGCGAGTCGCAGTGGAAG	0.632													4	11	---	---	---	---	PASS
ZSCAN20	7579	broad.mit.edu	37	1	33960693	33960693	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33960693A>G	uc001bxj.3	+	8	2916	c.2749A>G	c.(2749-2751)ACC>GCC	p.T917A	ZSCAN20_uc009vui.2_Missense_Mutation_p.T916A	NM_145238	NP_660281	P17040	ZSC20_HUMAN	zinc finger protein 31	917	C2H2-type 6.				viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TAAGAGCTCCACCCTGGCCAA	0.512													6	57	---	---	---	---	PASS
C1orf94	84970	broad.mit.edu	37	1	34684328	34684328	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34684328A>G	uc001bxs.3	+	7	1592	c.1193A>G	c.(1192-1194)TAT>TGT	p.Y398C	C1orf94_uc001bxt.2_Missense_Mutation_p.Y588C	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b	398							protein binding				0		Myeloproliferative disorder(586;0.0393)				CACAGCCCCTATTTTTCTTCC	0.493													54	184	---	---	---	---	PASS
ZMYM1	79830	broad.mit.edu	37	1	35578915	35578915	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35578915T>A	uc001bym.2	+	11	1632	c.1484T>A	c.(1483-1485)TTT>TAT	p.F495Y	ZMYM1_uc001byn.2_Missense_Mutation_p.F495Y|ZMYM1_uc010ohu.1_Missense_Mutation_p.F476Y|ZMYM1_uc001byo.2_Missense_Mutation_p.F135Y|ZMYM1_uc009vut.2_Missense_Mutation_p.F420Y	NM_024772	NP_079048	Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM domain containing 1	495	TTF-type.					nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AGAGAGTCATTTGCAACCCAC	0.353													16	44	---	---	---	---	PASS
CSF3R	1441	broad.mit.edu	37	1	36939104	36939104	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36939104C>G	uc001caw.1	-	6	783	c.605G>C	c.(604-606)TGG>TCG	p.W202S	CSF3R_uc009vvc.1_5'Flank|CSF3R_uc001cau.1_5'Flank|CSF3R_uc001cav.1_Missense_Mutation_p.W202S|CSF3R_uc001cax.1_Missense_Mutation_p.W202S|CSF3R_uc001cay.1_Missense_Mutation_p.W202S	NM_000760	NP_000751	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor isoform a	202	Fibronectin type-III 1.|Extracellular (Potential).				cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity			central_nervous_system(2)|ovary(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	TGCCTGCACCCAGATGCCCAT	0.602													10	39	---	---	---	---	PASS
GJA9	81025	broad.mit.edu	37	1	39340771	39340771	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39340771A>C	uc001cct.1	-	2	1281	c.1000T>G	c.(1000-1002)TCC>GCC	p.S334A	RRAGC_uc001ccr.2_5'Flank|MYCBP_uc001ccs.2_5'Flank	NM_030772	NP_110399	P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	334	Cytoplasmic (Potential).				cell communication	connexon complex|integral to membrane					0	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			CTAAGTGTGGAAATCTCATTA	0.318													60	204	---	---	---	---	PASS
ZNF684	127396	broad.mit.edu	37	1	41012841	41012841	+	Silent	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41012841T>C	uc001cft.1	+	5	1097	c.846T>C	c.(844-846)TAT>TAC	p.Y282Y		NM_152373	NP_689586	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	282	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			CCTTCAGGTATAGTTCATCCC	0.383													19	71	---	---	---	---	PASS
YIPF1	54432	broad.mit.edu	37	1	54344347	54344347	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54344347A>G	uc001cvu.2	-	5	581	c.244T>C	c.(244-246)TAC>CAC	p.Y82H	YIPF1_uc001cvv.2_RNA|YIPF1_uc001cvw.2_RNA|YIPF1_uc001cvx.2_RNA|YIPF1_uc001cvy.2_RNA	NM_018982	NP_061855	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	82	Cytoplasmic (Potential).					integral to membrane|transport vesicle				large_intestine(1)|ovary(1)	2						AATGTTTGGTAGTATTCAAAT	0.363													5	306	---	---	---	---	PASS
DOCK7	85440	broad.mit.edu	37	1	62979390	62979390	+	Silent	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62979390A>G	uc001daq.2	-	32	4150	c.4116T>C	c.(4114-4116)TAT>TAC	p.Y1372Y	DOCK7_uc001dan.2_Silent_p.Y1233Y|DOCK7_uc001dao.2_Silent_p.Y1233Y|DOCK7_uc001dap.2_Silent_p.Y1341Y|DOCK7_uc001dam.2_Silent_p.Y552Y|DOCK7_uc010oov.1_Silent_p.Y111Y	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1372					activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						CACTTACTTTATACTCAAAGC	0.363													19	203	---	---	---	---	PASS
BRDT	676	broad.mit.edu	37	1	92470095	92470095	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92470095T>C	uc001dok.3	+	17	2862	c.2513T>C	c.(2512-2514)GTA>GCA	p.V838A	BRDT_uc001dol.3_Missense_Mutation_p.V838A|BRDT_uc010osz.1_Missense_Mutation_p.V842A|BRDT_uc009wdf.2_Missense_Mutation_p.V765A|BRDT_uc010ota.1_Missense_Mutation_p.V792A|BRDT_uc010otb.1_Missense_Mutation_p.V792A|BRDT_uc001dom.3_Missense_Mutation_p.V838A	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein	838					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		GAAAAGGAAGTAAAAGCTCGG	0.378													4	139	---	---	---	---	PASS
BCAS2	10286	broad.mit.edu	37	1	115113351	115113351	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115113351T>C	uc001efa.2	-	5	493	c.440A>G	c.(439-441)GAA>GGA	p.E147G	DENND2C_uc001eez.2_RNA	NM_005872	NP_005863	O75934	SPF27_HUMAN	breast carcinoma amplified sequence 2	147	Potential.				mRNA processing|RNA splicing, via transesterification reactions	nucleolus|spliceosomal complex	protein binding			large_intestine(1)	1	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTGTGCGTGTTCAATCATATG	0.284													5	181	---	---	---	---	PASS
SEC22B	9554	broad.mit.edu	37	1	145109641	145109641	+	Silent	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145109641G>A	uc001eml.1	+	5	443	c.303G>A	c.(301-303)AAG>AAA	p.K101K	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron	NM_004892	NP_004883	O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B	101	Longin.|Cytoplasmic (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|melanosome	protein binding				0						AGCATGGAAAGAAGGTGCCCA	0.438													48	729	---	---	---	---	PASS
ATP8B2	57198	broad.mit.edu	37	1	154307015	154307015	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154307015C>T	uc001fey.1	+	10	1031	c.842C>T	c.(841-843)ACA>ATA	p.T281I	ATP8B2_uc001few.2_Missense_Mutation_p.T262I|ATP8B2_uc001fex.2_Missense_Mutation_p.T295I	NM_001005855	NP_001005855	P98198	AT8B2_HUMAN	ATPase, class I, type 8B, member 2 isoform b	281	Cytoplasmic (Potential).				ATP biosynthetic process	plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(1)|skin(1)	2	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AGCGGCAGAACAAAGTTCAAA	0.542													10	116	---	---	---	---	PASS
INSRR	3645	broad.mit.edu	37	1	156814334	156814334	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156814334T>C	uc010pht.1	-	14	2911	c.2657A>G	c.(2656-2658)TAC>TGC	p.Y886C	NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor	886	Fibronectin type-III 3.|Extracellular (Potential).				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)					CCTGGCAGAGTAGTTTCCAGG	0.572													7	15	---	---	---	---	PASS
C1orf129	80133	broad.mit.edu	37	1	170985418	170985418	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170985418A>C	uc010plz.1	+	17	2003	c.1849A>C	c.(1849-1851)AAA>CAA	p.K617Q		NM_001163629	NP_001157101	Q5TGP6	CA129_HUMAN	hypothetical protein LOC80133 isoform 1	Error:Variant_position_missing_in_Q5TGP6_after_alignment							binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CGAACTGGACAAAGTGACCTA	0.413													67	217	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	185964002	185964002	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185964002A>T	uc001grq.1	+	24	3790	c.3561A>T	c.(3559-3561)AGA>AGT	p.R1187S		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	1187	Ig-like C2-type 9.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						TTGGTCAAAGAGTGGATATTC	0.418													6	259	---	---	---	---	PASS
PGBD5	79605	broad.mit.edu	37	1	230461073	230461073	+	Silent	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230461073G>A	uc010pwb.1	-	6	1155	c.1155C>T	c.(1153-1155)TAC>TAT	p.Y385Y	PGBD5_uc001htv.2_Silent_p.Y484Y	NM_024554	NP_078830	Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	385						integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		ATTTGTCATCGTATCTGCAGA	0.527													9	90	---	---	---	---	PASS
CHML	1122	broad.mit.edu	37	1	241798468	241798468	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241798468T>C	uc001hzd.2	-	1	765	c.601A>G	c.(601-603)AGC>GGC	p.S201G	OPN3_uc001hza.2_Intron|OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_001821	NP_001812	P26374	RAE2_HUMAN	choroideremia-like Rab escort protein 2	201					intracellular protein transport|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(4)|skin(2)	6	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			GTAGATTTGCTTTCATCTTTA	0.343													7	476	---	---	---	---	PASS
ZNF124	7678	broad.mit.edu	37	1	247320117	247320117	+	Silent	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247320117T>C	uc001ick.2	-	4	946	c.807A>G	c.(805-807)AAA>AAG	p.K269K	ZNF124_uc001ici.2_Intron|ZNF124_uc001icj.1_Silent_p.K207K	NM_003431	NP_003422	Q15973	ZN124_HUMAN	zinc finger protein 124	269	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			ATCTGAAGGCTTTCCCACATT	0.433													5	161	---	---	---	---	PASS
SNTG2	54221	broad.mit.edu	37	2	1094047	1094047	+	Silent	SNP	T	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1094047T>G	uc002qwq.2	+	4	404	c.276T>G	c.(274-276)TCT>TCG	p.S92S	SNTG2_uc002qwp.2_RNA|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	92	PDZ.				central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		AGGGAGGTTCTGAGCACAACG	0.393													52	180	---	---	---	---	PASS
VSNL1	7447	broad.mit.edu	37	2	17773470	17773470	+	Silent	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17773470A>G	uc002rcm.2	+	2	513	c.129A>G	c.(127-129)CTA>CTG	p.L43L		NM_003385	NP_003376	P62760	VISL1_HUMAN	visinin-like 1	43	EF-hand 1.						calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GTGGGAGGCTAAATCTCGAGG	0.428													54	132	---	---	---	---	PASS
C2orf44	80304	broad.mit.edu	37	2	24261142	24261142	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24261142A>T	uc002rep.2	-	2	1354	c.1223T>A	c.(1222-1224)CTC>CAC	p.L408H	C2orf44_uc010eya.2_Missense_Mutation_p.L408H	NM_025203	NP_079479	Q9H6R7	CB044_HUMAN	hypothetical protein LOC80304 isoform 1	408							protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTATCAGTGAGTTTTTGTTT	0.343													18	230	---	---	---	---	PASS
PRKCE	5581	broad.mit.edu	37	2	46313413	46313413	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46313413C>T	uc002rut.2	+	11	1701	c.1504C>T	c.(1504-1506)CGA>TGA	p.R502*		NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon	502	Protein kinase.				activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			TCAGCGCTCCCGAAAATTCGA	0.493													4	147	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89104384	89104384	+	RNA	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89104384G>A	uc010fhg.2	+	15		c.1417G>A			FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_RNA	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						ATCCTGCAGCGTTCAAGTTTG	0.289													4	187	---	---	---	---	PASS
CLASP1	23332	broad.mit.edu	37	2	122161972	122161972	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122161972C>A	uc002tnc.2	-	26	3098	c.2708G>T	c.(2707-2709)CGG>CTG	p.R903L	CLASP1_uc010yyv.1_5'UTR|CLASP1_uc002tmz.2_5'UTR|CLASP1_uc002tna.2_5'UTR|CLASP1_uc010yyw.1_RNA|CLASP1_uc002tnb.2_RNA|CLASP1_uc010yyx.1_RNA|CLASP1_uc010yyy.1_RNA|CLASP1_uc010yyz.1_Missense_Mutation_p.R883L|CLASP1_uc010yza.1_Missense_Mutation_p.R875L|CLASP1_uc010yzb.1_RNA|CLASP1_uc010yzc.1_RNA|CLASP1_uc002tng.1_Missense_Mutation_p.R874L	NM_015282	NP_056097	Q7Z460	CLAP1_HUMAN	CLIP-associating protein 1 isoform 1	903					axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)					AGCAAACATCCGAGTGAAGAT	0.368													6	250	---	---	---	---	PASS
GCA	25801	broad.mit.edu	37	2	163216776	163216776	+	3'UTR	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163216776A>G	uc002ucg.2	+	8					GCA_uc010zcu.1_3'UTR	NM_012198	NP_036330	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein						cellular membrane fusion	cytoplasm|plasma membrane	calcium ion binding|protein homodimerization activity				0						TTAAACCTGAAGAGACACTGT	0.303													6	201	---	---	---	---	PASS
ABI2	10152	broad.mit.edu	37	2	204267389	204267389	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204267389C>A	uc002vaa.2	+	9	1359	c.1124C>A	c.(1123-1125)CCT>CAT	p.P375H	ABI2_uc002uzz.2_Missense_Mutation_p.P308H|ABI2_uc010zih.1_Missense_Mutation_p.P23H|ABI2_uc010zii.1_Missense_Mutation_p.P369H|ABI2_uc010zij.1_Missense_Mutation_p.P252H|ABI2_uc002vab.2_Missense_Mutation_p.P263H|ABI2_uc010zik.1_Missense_Mutation_p.P100H|ABI2_uc010zil.1_Missense_Mutation_p.P210H|ABI2_uc010zim.1_Missense_Mutation_p.P161H|ABI2_uc002vac.2_Missense_Mutation_p.P161H|ABI2_uc010zin.1_Missense_Mutation_p.P23H	NM_005759	NP_005750	Q9NYB9	ABI2_HUMAN	abl interactor 2	375	Pro-rich.				actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0						AGACGCCCTCCTTCCATTACT	0.438													89	243	---	---	---	---	PASS
GLB1L	79411	broad.mit.edu	37	2	220104166	220104166	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220104166A>G	uc002vkm.2	-	10	1149	c.910T>C	c.(910-912)TTC>CTC	p.F304L	GLB1L_uc002vkk.2_Missense_Mutation_p.F61L|GLB1L_uc010zkx.1_Missense_Mutation_p.F214L|GLB1L_uc002vkn.2_Missense_Mutation_p.F304L	NM_024506	NP_078782	Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like precursor	304					carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds				0		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)		Epithelial(149;1.3e-11)|all cancers(144;2.07e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTCCATGGAACATGTACCTG	0.483													5	174	---	---	---	---	PASS
VPRBP	9730	broad.mit.edu	37	3	51505015	51505015	+	Silent	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51505015A>G	uc003dbe.1	-	4	285	c.117T>C	c.(115-117)TCT>TCC	p.S39S	VPRBP_uc003dbg.1_Silent_p.S39S	NM_014703	NP_055518	Q9Y4B6	VPRBP_HUMAN	HIV-1 Vpr binding protein	39					interspecies interaction between organisms	cytoplasm|nucleus	protein binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CAATCAATTGAGACATCCTAG	0.403													5	202	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52643561	52643561	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52643561G>A	uc003des.2	-	16	2347	c.2335C>T	c.(2335-2337)CAA>TAA	p.Q779*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.Q779*|PBRM1_uc003der.2_Nonsense_Mutation_p.Q747*|PBRM1_uc003det.2_Nonsense_Mutation_p.Q794*|PBRM1_uc003deu.2_Nonsense_Mutation_p.Q794*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.Q779*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.Q779*|PBRM1_uc003dey.2_Nonsense_Mutation_p.Q779*|PBRM1_uc003dez.1_Nonsense_Mutation_p.Q779*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.Q692*|PBRM1_uc003dfa.1_Nonsense_Mutation_p.Q125*|PBRM1_uc003dfc.2_Nonsense_Mutation_p.Q146*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	779					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding	p.Q779*(3)		kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ATAAGCTCTTGAATCAGCAAA	0.448			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								31	52	---	---	---	---	PASS
MAGI1	9223	broad.mit.edu	37	3	65428524	65428524	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65428524T>C	uc003dmn.2	-	8	1605	c.1079A>G	c.(1078-1080)GAA>GGA	p.E360G	MAGI1_uc003dmm.2_Missense_Mutation_p.E360G|MAGI1_uc003dmo.2_Missense_Mutation_p.E360G|MAGI1_uc003dmp.2_Missense_Mutation_p.E360G|MAGI1_uc010hny.2_Missense_Mutation_p.E245G	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	360	WW 2.				cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		AGCAGGCAGTTCTGAAAAATA	0.383													5	144	---	---	---	---	PASS
CASR	846	broad.mit.edu	37	3	122003164	122003164	+	Missense_Mutation	SNP	T	A	A	rs104893701		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122003164T>A	uc003eev.3	+	7	2735	c.2363T>A	c.(2362-2364)TTC>TAC	p.F788Y	CASR_uc003eew.3_Missense_Mutation_p.F798Y	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	788	Helical; Name=5; (Potential).		F -> C (in FIH; leftward shift in the concentration-response curve for the mutant receptor; cells cotransfected with both the wild-type and the mutant receptor show an EC(50) similar to the mutant; a gain-of-function mutation rendering the receptor more sensitive than normal to activation).|F -> L (in FIH; induces a significant shift to the left relative to the wild- type protein in the MAPK response to increasing extracellular calcium concentrations).		anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	GCCATCTGCTTCTTCTTTGCC	0.547													6	16	---	---	---	---	PASS
PARP14	54625	broad.mit.edu	37	3	122418640	122418640	+	Silent	SNP	A	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122418640A>T	uc003efq.3	+	6	1298	c.1239A>T	c.(1237-1239)ATA>ATT	p.I413I	PARP14_uc010hrk.2_RNA|PARP14_uc003efr.2_Silent_p.I130I|PARP14_uc003efs.1_Silent_p.I130I	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	413					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		GGGACACCATAAAAAATGATG	0.398													36	140	---	---	---	---	PASS
SLC33A1	9197	broad.mit.edu	37	3	155571204	155571204	+	Missense_Mutation	SNP	T	A	A	rs148999356		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155571204T>A	uc003fan.3	-	1	964	c.583A>T	c.(583-585)ATT>TTT	p.I195F	SLC33A1_uc003fao.1_Missense_Mutation_p.I195F	NM_004733	NP_004724	O00400	ACATN_HUMAN	acetyl-coenzyme A transporter	195	Helical; (Potential).				cell death|transmembrane transport	endoplasmic reticulum membrane|Golgi membrane|integral to plasma membrane|membrane fraction	acetyl-CoA transporter activity			ovary(2)|large_intestine(1)|pancreas(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TCGACGGCAATGTCCTGAGTG	0.498													11	57	---	---	---	---	PASS
LAMP3	27074	broad.mit.edu	37	3	182871951	182871951	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182871951T>C	uc003flh.3	-	2	502	c.278A>G	c.(277-279)AAC>AGC	p.N93S		NM_014398	NP_055213	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	93	Lumenal (Potential).|Thr-rich.				cell proliferation	integral to membrane|lysosomal membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			GGTTGCAGTGTTTTTTGTAGT	0.488													131	525	---	---	---	---	PASS
BCL6	604	broad.mit.edu	37	3	187446247	187446247	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187446247G>A	uc003frp.3	-	6	1898	c.1441C>T	c.(1441-1443)CAG>TAG	p.Q481*	BCL6_uc011bsf.1_Nonsense_Mutation_p.Q481*|BCL6_uc010hza.2_Nonsense_Mutation_p.Q379*|BCL6_uc003frq.1_Nonsense_Mutation_p.Q481*	NM_001130845	NP_001124317	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1	481					negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		TGTGGGGACTGAGAGCCGCAG	0.612			T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								5	35	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511283	195511283	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511283C>T	uc011bto.1	-	2	7628	c.7168G>A	c.(7168-7170)GCT>ACT	p.A2390T	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)		GCTGAGGAAGCGTCGGTGACA	0.592													4	47	---	---	---	---	PASS
C3orf34	84984	broad.mit.edu	37	3	196434643	196434643	+	Nonsense_Mutation	SNP	C	A	A	rs139813132	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196434643C>A	uc011btw.1	-	3	665	c.283G>T	c.(283-285)GAA>TAA	p.E95*		NM_032898	NP_116287	Q96LK0	CEP19_HUMAN	hypothetical protein LOC84984	91						centriole|spindle pole					0	all_cancers(143;1.48e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;1.08e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00301)		TGAATTTGTTCCATTGTTTCT	0.428													108	445	---	---	---	---	PASS
CPLX1	10815	broad.mit.edu	37	4	780370	780370	+	Silent	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:780370C>T	uc003gbi.2	-	4	515	c.324G>A	c.(322-324)GAG>GAA	p.E108E	CPLX1_uc003gbj.2_Silent_p.E87E	NM_006651	NP_006642	O14810	CPLX1_HUMAN	complexin 1	108					glutamate secretion	cytosol					0				Colorectal(103;0.187)		CCTCCTCCACCTCGTCCCCGC	0.701													3	12	---	---	---	---	PASS
ACOX3	8310	broad.mit.edu	37	4	8416589	8416589	+	Missense_Mutation	SNP	T	C	C	rs114127771	byFrequency	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8416589T>C	uc010idk.2	-	4	590	c.445A>G	c.(445-447)AGG>GGG	p.R149G	ACOX3_uc003glc.3_Missense_Mutation_p.R149G|ACOX3_uc003gld.3_Missense_Mutation_p.R149G|ACOX3_uc003gle.1_Missense_Mutation_p.R54G	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a	149					bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1						ACCTCCATCCTGAAGATCTTT	0.413													6	228	---	---	---	---	PASS
CLRN2	645104	broad.mit.edu	37	4	17516859	17516859	+	5'UTR	SNP	G	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17516859G>C	uc003gpg.1	+	1						NM_001079827	NP_001073296	A0PK11	CLRN2_HUMAN	clarin 2							integral to membrane					0						CTGCTGCTCGGAGACCTTGGG	0.522													20	89	---	---	---	---	PASS
PI4K2B	55300	broad.mit.edu	37	4	25256736	25256736	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25256736T>C	uc003grk.2	+	3	606	c.473T>C	c.(472-474)CTC>CCC	p.L158P	PI4K2B_uc011bxs.1_Missense_Mutation_p.L62P	NM_018323	NP_060793	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	158	PI3K/PI4K.					cytoplasm|membrane	1-phosphatidylinositol 4-kinase activity|ATP binding			ovary(2)|skin(2)	4		Breast(46;0.173)				TATGGTCAACTCAATCCAAAA	0.393													5	85	---	---	---	---	PASS
PTPN13	5783	broad.mit.edu	37	4	87672210	87672210	+	Silent	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87672210T>C	uc003hpz.2	+	19	3579	c.3099T>C	c.(3097-3099)AGT>AGC	p.S1033S	PTPN13_uc003hpy.2_Silent_p.S1033S|PTPN13_uc003hqa.2_Silent_p.S1033S|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1033						cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TAAATAGAAGTCCTGAAAGGA	0.388													6	370	---	---	---	---	PASS
PDE5A	8654	broad.mit.edu	37	4	120442144	120442144	+	Silent	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120442144A>G	uc003idh.2	-	13	2006	c.1851T>C	c.(1849-1851)CAT>CAC	p.H617H	uc003ide.3_Intron|PDE5A_uc003idf.2_Silent_p.H575H|PDE5A_uc003idg.2_Silent_p.H565H|uc003idi.3_Intron	NM_001083	NP_001074	O76074	PDE5A_HUMAN	phosphodiesterase 5A isoform 1	617	Catalytic (By similarity).	Divalent metal cation 1.			platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)	TATTAAAGGCATGTCTCCAAT	0.338													22	80	---	---	---	---	PASS
HSPA4L	22824	broad.mit.edu	37	4	128751820	128751820	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128751820A>G	uc003ifm.2	+	18	2447	c.2194A>G	c.(2194-2196)ACT>GCT	p.T732A	HSPA4L_uc011cgr.1_Missense_Mutation_p.T699A	NM_014278	NP_055093	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	732					protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						TCTGGATCCTACTGAAATGGA	0.338													4	182	---	---	---	---	PASS
ZNF330	27309	broad.mit.edu	37	4	142151366	142151366	+	Silent	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142151366A>G	uc003iiq.3	+	7	685	c.465A>G	c.(463-465)GAA>GAG	p.E155E	ZNF330_uc011chl.1_Silent_p.E95E	NM_014487	NP_055302	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	155						chromosome, centromeric region|midbody|nucleolus	protein binding|zinc ion binding				0	all_hematologic(180;0.162)					TTCTCTGTGAAGATGATCAAT	0.294													6	415	---	---	---	---	PASS
FBXW7	55294	broad.mit.edu	37	4	153273982	153273982	+	Intron	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153273982C>A	uc003ims.2	-						FBXW7_uc011cii.1_Intron|FBXW7_uc003imt.2_Intron|FBXW7_uc003imq.2_5'UTR|FBXW7_uc003imr.2_Intron	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform						interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				CTTGACTGAACAGATTCCTCC	0.453			Mis|N|D|F		colorectal|endometrial|T-ALL								6	33	---	---	---	---	PASS
ACCN5	51802	broad.mit.edu	37	4	156757933	156757933	+	Missense_Mutation	SNP	T	G	G	rs142739848		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156757933T>G	uc003ipe.1	-	8	1190	c.1143A>C	c.(1141-1143)GAA>GAC	p.E381D		NM_017419	NP_059115	Q9NY37	ACCN5_HUMAN	amiloride-sensitive cation channel 5,	381	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)		TGGCCGGGTATTCTATTTCTT	0.373													47	174	---	---	---	---	PASS
DCTD	1635	broad.mit.edu	37	4	183812459	183812459	+	3'UTR	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183812459G>A	uc003ivf.2	-	6					DCTD_uc003ivg.2_3'UTR|DCTD_uc010irw.2_3'UTR|DCTD_uc003ivh.2_3'UTR	NM_001921	NP_001912	P32321	DCTD_HUMAN	dCMP deaminase isoform b						nucleotide biosynthetic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide metabolic process	cytosol	dCMP deaminase activity|zinc ion binding				0		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)		ATACTGGCTAGTAAGAAGTTA	0.368													6	96	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14364016	14364016	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14364016T>G	uc003jff.2	+	14	2573	c.2567T>G	c.(2566-2568)GTC>GGC	p.V856G	TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_Missense_Mutation_p.V807G|TRIO_uc003jfh.1_Missense_Mutation_p.V505G	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	856					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					CTGCAGTATGTCAATGAGGTC	0.498													8	117	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14497119	14497119	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14497119C>A	uc003jff.2	+	50	8018	c.8012C>A	c.(8011-8013)TCT>TAT	p.S2671Y	TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2671					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					AACAAGGTATCTGTGAAGGTG	0.493													40	136	---	---	---	---	PASS
RANBP3L	202151	broad.mit.edu	37	5	36255599	36255599	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36255599C>A	uc003jkh.2	-	11	1490	c.997G>T	c.(997-999)GAC>TAC	p.D333Y	RANBP3L_uc011cow.1_Missense_Mutation_p.D358Y	NM_145000	NP_659437	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like isoform 2	333	RanBD1.				intracellular transport					ovary(1)	1	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			GTTCCACAGTCAGTGCTTGCT	0.373													12	138	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41045851	41045851	+	Silent	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41045851C>T	uc003jmj.3	-	18	2323	c.1833G>A	c.(1831-1833)GAG>GAA	p.E611E	HEATR7B2_uc003jmi.3_Silent_p.E166E	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	611	HEAT 7.						binding			ovary(6)|central_nervous_system(2)	8						AACCAACCTTCTCAGTGGAGT	0.294													34	117	---	---	---	---	PASS
CDC25C	995	broad.mit.edu	37	5	137621505	137621505	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137621505C>A	uc003lcp.1	-	14	1569	c.1298G>T	c.(1297-1299)TGC>TTC	p.C433F	CDC25C_uc003lcq.1_Missense_Mutation_p.C360F|CDC25C_uc003lcr.1_Missense_Mutation_p.C433F|CDC25C_uc011cyp.1_Missense_Mutation_p.C450F|CDC25C_uc003lcs.1_Missense_Mutation_p.C511F	NM_001790	NP_001781	P30307	MPIP3_HUMAN	cell division cycle 25C isoform a	433					cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm	protein tyrosine phosphatase activity|WW domain binding			lung(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			ATGCATAGGGCAGTAGCTCTG	0.512													11	117	---	---	---	---	PASS
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139876554	139876554	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139876554G>T	uc003lfs.1	+	15	2819	c.2695G>T	c.(2695-2697)GTT>TTT	p.V899F	ANKHD1_uc003lfq.1_Missense_Mutation_p.V918F|ANKHD1_uc003lfr.2_Missense_Mutation_p.V899F|ANKHD1_uc003lft.1_Intron|ANKHD1_uc003lfu.1_Missense_Mutation_p.V379F|ANKHD1_uc003lfv.1_Intron	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	899						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTACCTCAGGTTGACACAAT	0.448													51	79	---	---	---	---	PASS
ZMAT2	153527	broad.mit.edu	37	5	140085370	140085370	+	3'UTR	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140085370C>A	uc003lgy.1	+	6						NM_144723	NP_653324	Q96NC0	ZMAT2_HUMAN	zinc finger, matrin type 2							nucleus	DNA binding|zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGACTTTGGCCTATGCTGGAC	0.488													44	346	---	---	---	---	PASS
FCHSD1	89848	broad.mit.edu	37	5	141021013	141021013	+	3'UTR	SNP	A	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141021013A>C	uc003llk.2	-	20					FCHSD1_uc010jgg.2_3'UTR|FCHSD1_uc003llj.2_RNA	NM_033449	NP_258260	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1										FCHSD1/BRAF(2)	skin(2)|ovary(1)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGTCTGACAGCTTGAAGAT	0.582													8	41	---	---	---	---	PASS
PPARGC1B	133522	broad.mit.edu	37	5	149225491	149225491	+	Intron	SNP	A	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149225491A>C	uc003lrc.2	+						PPARGC1B_uc003lrb.1_Missense_Mutation_p.K995N|PPARGC1B_uc003lrd.2_Intron|PPARGC1B_uc003lrf.2_Intron|PPARGC1B_uc003lre.1_Missense_Mutation_p.K974N	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor						estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			AGCCCCTGAAACCCAGCCACA	0.567													4	6	---	---	---	---	PASS
HLA-DQB2	3120	broad.mit.edu	37	6	32725567	32725567	+	Intron	SNP	C	T	T	rs77504727		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32725567C>T	uc003oby.3	-						HLA-DQB2_uc003obz.2_Missense_Mutation_p.R247H	NR_003937		Q5SR06	Q5SR06_HUMAN	SubName: Full=Major histocompatibility complex, class II, DQ beta 2; SubName: Full=Putative uncharacterized protein ENSP00000372579;						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	integral to membrane|MHC class II protein complex					0						ACCCCTGTGACGGATGATAAG	0.552													8	34	---	---	---	---	PASS
CRISP1	167	broad.mit.edu	37	6	49819726	49819726	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49819726G>T	uc003ozw.2	-	3	262	c.183C>A	c.(181-183)AAC>AAA	p.N61K	CRISP1_uc003ozx.2_Missense_Mutation_p.N61K	NM_001131	NP_001122	P54107	CRIS1_HUMAN	acidic epididymal glycoprotein-like 1 isoform 1	61					fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)					TCTTCAGCATGTTGCTGGCTG	0.378													41	182	---	---	---	---	PASS
EEF1A1	1915	broad.mit.edu	37	6	74227570	74227570	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74227570A>T	uc003phi.2	-	7	1389	c.1352T>A	c.(1351-1353)GTC>GAC	p.V451D	EEF1A1_uc003phd.2_Missense_Mutation_p.V176D|EEF1A1_uc003phe.2_Missense_Mutation_p.V441D|EEF1A1_uc003phf.2_Missense_Mutation_p.V444D|EEF1A1_uc003phg.2_3'UTR|EEF1A1_uc003phh.2_Missense_Mutation_p.V297D|EEF1A1_uc003phj.2_Missense_Mutation_p.V451D|EEF1A1_uc003phk.2_Missense_Mutation_p.V451D|EEF1A1_uc003phl.2_Silent_p.G95G|EEF1A1_uc003phm.1_RNA	NM_001402	NP_001393	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha	451						cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0						AGACTTGGTGACCTTGCCAGC	0.473											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	15	34	---	---	---	---	PASS
SENP6	26054	broad.mit.edu	37	6	76331327	76331327	+	Silent	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76331327A>G	uc003pid.3	+	2	751	c.132A>G	c.(130-132)GGA>GGG	p.G44G	SENP6_uc003pie.3_Silent_p.G44G|SENP6_uc003pic.2_Silent_p.G44G	NM_015571	NP_056386	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6 isoform 1	44					proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)				AAAGTGAAGGAGATACAGATA	0.289													7	556	---	---	---	---	PASS
ORC3L	23595	broad.mit.edu	37	6	88367719	88367719	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88367719C>A	uc003pmh.2	+	16	1718	c.1674C>A	c.(1672-1674)TTC>TTA	p.F558L	ORC3L_uc011dzn.1_RNA|ORC3L_uc003pmg.2_Missense_Mutation_p.F559L|ORC3L_uc003pmi.2_Missense_Mutation_p.F521L|ORC3L_uc011dzo.1_Missense_Mutation_p.F415L|ORC3L_uc011dzp.1_Missense_Mutation_p.F415L	NM_012381	NP_036513	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3 isoform 2	558					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)		TTGTGAACTTCATTGACTGTC	0.333													16	163	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117674152	117674152	+	Splice_Site	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117674152C>A	uc003pxp.1	-	26	4520	c.4321_splice	c.e26+1	p.D1441_splice	ROS1_uc011ebi.1_Splice_Site|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		GACTTTATTACCTGGAAAAGG	0.443			T	GOPC|ROS1	glioblastoma|NSCLC								55	166	---	---	---	---	PASS
ECT2L	345930	broad.mit.edu	37	6	139206666	139206666	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139206666C>A	uc003qif.1	+	15	2155	c.2052C>A	c.(2050-2052)TTC>TTA	p.F684L	ECT2L_uc011edq.1_Intron	NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	epithelial cell transforming sequence 2	684	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0						TACCAGCATTCCGAACTTTCC	0.453													60	149	---	---	---	---	PASS
RAET1E	135250	broad.mit.edu	37	6	150210680	150210680	+	Silent	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150210680G>A	uc003qnl.1	-	3	486	c.426C>T	c.(424-426)ACC>ACT	p.T142T	uc003qni.1_Intron|RAET1E_uc003qnj.2_Silent_p.T142T|RAET1E_uc003qnk.1_Silent_p.T106T|RAET1E_uc010kih.1_RNA	NM_139165	NP_631904	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E precursor	142	Extracellular (Potential).|MHC class I alpha-2 like.			AT -> TI (in Ref. 7; AAL76417).	antigen processing and presentation|immune response|regulation of immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		TCTCTCCATTGGTGGCGAACT	0.473													33	117	---	---	---	---	PASS
HECW1	23072	broad.mit.edu	37	7	43548639	43548639	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43548639G>T	uc003tid.1	+	24	4543	c.3938G>T	c.(3937-3939)GGA>GTA	p.G1313V	HECW1_uc011kbi.1_Missense_Mutation_p.G1279V|uc003tig.1_RNA	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	1313	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						CCTTACTATGGACTCTTTGAG	0.488													56	186	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48353926	48353926	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48353926C>A	uc003toq.2	+	26	9804	c.9779C>A	c.(9778-9780)TCT>TAT	p.S3260Y	ABCA13_uc010kys.1_Missense_Mutation_p.S334Y|ABCA13_uc003tos.1_Missense_Mutation_p.S86Y	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3260					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						CTTAGCGATTCTAATATGTTT	0.363													92	219	---	---	---	---	PASS
CDC14C	168448	broad.mit.edu	37	7	48965645	48965645	+	3'UTR	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48965645A>G	uc010kyv.1	+	1						NR_003595				SubName: Full=Putative uncharacterized protein MGC26484;												0						AGCCATCAGGACCCCCTGACA	0.418													4	66	---	---	---	---	PASS
VSTM2A	222008	broad.mit.edu	37	7	54610387	54610387	+	5'UTR	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54610387G>T	uc010kzf.2	+	1					VSTM2A_uc010kze.2_5'UTR|VSTM2A_uc003tqc.3_5'UTR	NM_182546	NP_872352	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2							extracellular region					0			STAD - Stomach adenocarcinoma(5;0.0525)			CTTTTCGGCTGTTGGCTACAC	0.502													28	329	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82545945	82545945	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82545945T>G	uc003uhx.2	-	7	11646	c.11357A>C	c.(11356-11358)GAG>GCG	p.E3786A	PCLO_uc003uhv.2_Missense_Mutation_p.E3786A|PCLO_uc010lec.2_Missense_Mutation_p.E751A	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3717					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TTCATCAAGCTCTGCTTGTTT	0.433													29	257	---	---	---	---	PASS
ABCB4	5244	broad.mit.edu	37	7	87069080	87069080	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87069080C>T	uc003uiv.1	-	14	1710	c.1634G>A	c.(1633-1635)CGT>CAT	p.R545H	ABCB4_uc003uiw.1_Missense_Mutation_p.R545H|ABCB4_uc003uix.1_Missense_Mutation_p.R545H	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	545	ABC transporter 1.|Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					AACCAGGGCACGTGCAATGGC	0.542													8	109	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88965798	88965798	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88965798C>T	uc011khi.1	+	4	4040	c.3502C>T	c.(3502-3504)CAT>TAT	p.H1168Y		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1168						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AGCCCAGCAGCATATGCAGAA	0.453										HNSCC(36;0.09)			13	58	---	---	---	---	PASS
DNAJC2	27000	broad.mit.edu	37	7	102956305	102956305	+	Silent	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102956305T>C	uc003vbo.2	-	15	1793	c.1542A>G	c.(1540-1542)AAA>AAG	p.K514K	PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_Silent_p.K139K|DNAJC2_uc010lix.2_Silent_p.K461K|DNAJC2_uc003vbp.2_Silent_p.K139K	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	514					'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1						TTATGTCATCTTTTTGATGAG	0.294													8	540	---	---	---	---	PASS
ATXN7L1	222255	broad.mit.edu	37	7	105254953	105254953	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105254953C>T	uc003vde.2	-	10	1855	c.1828G>A	c.(1828-1830)GTC>ATC	p.V610I	ATXN7L1_uc003vdf.2_Missense_Mutation_p.V486I|ATXN7L1_uc003vdg.3_Missense_Mutation_p.V270I|ATXN7L1_uc003vdh.3_Missense_Mutation_p.V394I	NM_020725	NP_065776	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1 isoform 1	610	Ser-rich.										0						GAAGGGATGACGGCTGGTATC	0.552													8	329	---	---	---	---	PASS
CLEC2L	154790	broad.mit.edu	37	7	139221070	139221070	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139221070A>C	uc010lnd.2	+	2	241	c.241A>C	c.(241-243)ATC>CTC	p.I81L		NM_001080511	NP_001073980	P0C7M8	CLC2L_HUMAN	C-type lectin domain family 2, member L	81	Helical; (Potential).					integral to membrane	sugar binding				0	Melanoma(164;0.233)					TCTGTTCGCCATCTTGGTGGT	0.522													75	182	---	---	---	---	PASS
MKRN1	23608	broad.mit.edu	37	7	140155662	140155662	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140155662A>G	uc003vvt.2	-	6	1250	c.1025T>C	c.(1024-1026)ATT>ACT	p.I342T	MKRN1_uc003vvs.2_Missense_Mutation_p.I278T|MKRN1_uc011krd.1_Missense_Mutation_p.I76T	NM_013446	NP_038474	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1 isoform 1	342							ligase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.00956)					CTCACTTGGAATGACAAAGTT	0.473													13	168	---	---	---	---	PASS
CUL1	8454	broad.mit.edu	37	7	148495072	148495072	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148495072A>G	uc010lpg.2	+	19	2517	c.1991A>G	c.(1990-1992)AAG>AGG	p.K664R	CUL1_uc003wey.2_Missense_Mutation_p.K664R|CUL1_uc003wez.2_Missense_Mutation_p.K554R|CUL1_uc003wfa.2_Missense_Mutation_p.K325R	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	664					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			GTGGAATTGAAGCCAGATACC	0.373													6	190	---	---	---	---	PASS
INSIG1	3638	broad.mit.edu	37	7	155095544	155095544	+	Intron	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155095544T>C	uc003wly.2	+						INSIG1_uc011kvu.1_Missense_Mutation_p.F120L|INSIG1_uc003wlz.2_Intron	NM_005542	NP_005533	O15503	INSI1_HUMAN	insulin induced gene 1 isoform 1						cell proliferation|ER-nuclear sterol response pathway	endoplasmic reticulum membrane|integral to membrane	protein binding				0	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCTGATACCCTTCTGTGAGGA	0.403													8	454	---	---	---	---	PASS
DLC1	10395	broad.mit.edu	37	8	13356561	13356561	+	Silent	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13356561T>C	uc003wwm.2	-	2	1464	c.1020A>G	c.(1018-1020)AGA>AGG	p.R340R	DLC1_uc003wwn.2_Silent_p.R340R|DLC1_uc011kxy.1_Silent_p.R340R	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	340					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7						GTCTTACCTTTCTCTTACGAA	0.388													5	248	---	---	---	---	PASS
SGCZ	137868	broad.mit.edu	37	8	13947906	13947906	+	3'UTR	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13947906G>A	uc003wwq.2	-	8					SGCZ_uc010lss.2_3'UTR	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		TGAAGCAGACGGACAGGAACA	0.512													5	53	---	---	---	---	PASS
TRAM1	23471	broad.mit.edu	37	8	71508498	71508498	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71508498G>A	uc003xyo.1	-	5	655	c.485C>T	c.(484-486)ACA>ATA	p.T162I	TRAM1_uc011lfc.1_Missense_Mutation_p.T131I	NM_014294	NP_055109	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	162	Helical; (Potential).|TLC.				cotranslational protein targeting to membrane|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	protein binding|receptor activity			ovary(1)	1			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)			AATGACTTACGTCATCAGGTT	0.363													51	154	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	133911118	133911118	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133911118C>A	uc003ytw.2	+	14	3334	c.3293C>A	c.(3292-3294)CCA>CAA	p.P1098Q	TG_uc010mdw.2_5'UTR	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	1098	Thyroglobulin type-1 9.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CAAGAAAACCCATCTCCAAAA	0.532													12	38	---	---	---	---	PASS
KIAA1432	57589	broad.mit.edu	37	9	5763718	5763718	+	Silent	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5763718C>T	uc003zji.2	+	18	2547	c.2454C>T	c.(2452-2454)TTC>TTT	p.F818F	KIAA1432_uc003zjh.2_Silent_p.F818F|KIAA1432_uc003zjl.3_Silent_p.F781F|KIAA1432_uc003zjj.1_Silent_p.F360F	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a	897						integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		TCCCCCTCTTCCTGCAGACAG	0.498													36	94	---	---	---	---	PASS
ADAMTSL1	92949	broad.mit.edu	37	9	18684860	18684860	+	Intron	SNP	T	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18684860T>G	uc003zne.3	+						ADAMTSL1_uc003znc.3_3'UTR	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)		GAAAGCAGTGTCTCACTGGTT	0.378													24	78	---	---	---	---	PASS
PLIN2	123	broad.mit.edu	37	9	19116527	19116527	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19116527G>C	uc003zno.2	-	8	1212	c.1033C>G	c.(1033-1035)CAC>GAC	p.H345D	PLIN2_uc011lna.1_Missense_Mutation_p.H317D	NM_001122	NP_001113	Q99541	PLIN2_HUMAN	adipose differentiation-related protein	345					cellular lipid metabolic process	endoplasmic reticulum|extracellular region|lipid particle				ovary(2)	2						ACCCCCATGTGCTTGGCTTGA	0.547													6	92	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68414462	68414462	+	RNA	SNP	A	G	G	rs149255248		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68414462A>G	uc004aex.2	+	1		c.1017A>G								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		ctcattgaccactctgaaaat	0.000													3	11	---	---	---	---	PASS
GOLM1	51280	broad.mit.edu	37	9	88648293	88648293	+	Silent	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88648293G>A	uc004aol.2	-	9	1231	c.1033C>T	c.(1033-1035)CTG>TTG	p.L345L	GOLM1_uc004aom.2_Silent_p.L345L	NM_016548	NP_057632	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	345	Lumenal (Potential).					Golgi apparatus|integral to plasma membrane					0						TCTCCTCTCAGTTTCTGCTGG	0.428													127	403	---	---	---	---	PASS
GPSM1	26086	broad.mit.edu	37	9	139228923	139228923	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139228923G>C	uc004chd.2	+	2	308	c.88G>C	c.(88-90)GAG>CAG	p.E30Q	GPSM1_uc004chc.2_Missense_Mutation_p.E30Q	NM_001145638	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1 (AGS3-like, C.	30	TPR 1.|Mediates association with membranes (By similarity).				cell differentiation|nervous system development|signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|plasma membrane	binding|GTPase activator activity				0		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GTCCTGCCTAGAGCTGGCGCT	0.657													5	6	---	---	---	---	PASS
PTCHD3	374308	broad.mit.edu	37	10	27702296	27702296	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27702296A>G	uc001itu.2	-	1	1002	c.884T>C	c.(883-885)CTC>CCC	p.L295P		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	295					spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4						GGTCAGGTAGAGGGGATGCCT	0.612													3	19	---	---	---	---	PASS
ZDHHC6	64429	broad.mit.edu	37	10	114201991	114201991	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114201991A>G	uc001kzv.2	-	4	902	c.478T>C	c.(478-480)TTC>CTC	p.F160L	ZDHHC6_uc001kzw.2_Missense_Mutation_p.F156L|ZDHHC6_uc009xya.1_Missense_Mutation_p.F160L	NM_022494	NP_071939	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	160	Helical; (Potential).					integral to membrane	acyltransferase activity|zinc ion binding				0		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)		ACAAAAATGAAAGCAGCATGG	0.373													48	173	---	---	---	---	PASS
LOC494141	494141	broad.mit.edu	37	11	18231485	18231485	+	RNA	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18231485G>A	uc009yhh.2	+	2		c.509G>A			LOC494141_uc001mnx.3_RNA|LOC494141_uc009yhi.1_RNA	NR_026541				Homo sapiens cDNA FLJ29025 fis, clone PRS03236.												0						CTTGTATCGGGGAATCTTTCC	0.458													6	62	---	---	---	---	PASS
BTBD18	643376	broad.mit.edu	37	11	57512173	57512173	+	Silent	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57512173C>T	uc009ymm.2	-	2	1758	c.1572G>A	c.(1570-1572)ACG>ACA	p.T524T	CTNND1_uc001nlf.1_Intron|BTBD18_uc010rjy.1_Silent_p.T524T	NM_001145101	NP_001138573	B2RXH4	BTBDI_HUMAN	BTB (POZ) domain containing 18	524											0						GGTAGGTAGGCGTTCTGCAGC	0.537													4	122	---	---	---	---	PASS
MIR192	406967	broad.mit.edu	37	11	64658636	64658636	+	RNA	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64658636A>G	hsa-mir-192|MI0000234	-			c.83A>G			uc009ypx.2_Intron|uc010rnr.1_RNA																	0						CATACCTGTGACCTATGGAAT	0.622													3	10	---	---	---	---	PASS
C11orf82	220042	broad.mit.edu	37	11	82639936	82639936	+	Silent	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82639936T>C	uc001ozt.2	+	4	475	c.231T>C	c.(229-231)AGT>AGC	p.S77S	C11orf82_uc010rsr.1_5'UTR|C11orf82_uc010rss.1_Intron|C11orf82_uc009yvd.2_Silent_p.S77S	NM_145018	NP_659455	Q8IXT1	NOXIN_HUMAN	nitric oxide-inducible gene protein	77					apoptosis|cell cycle arrest	cytoplasm|nucleus				ovary(2)	2						TATTTGGAAGTTGCTTAGATA	0.348													6	460	---	---	---	---	PASS
CCDC90B	60492	broad.mit.edu	37	11	82972989	82972989	+	Silent	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82972989C>T	uc001pae.2	-	9	1091	c.729G>A	c.(727-729)CTG>CTA	p.L243L	CCDC90B_uc001pac.2_Silent_p.L142L|CCDC90B_uc001pad.2_Silent_p.L142L|CCDC90B_uc001paf.2_Silent_p.L234L	NM_021825	NP_068597	Q9GZT6	CC90B_HUMAN	coiled-coil domain containing 90B precursor	243	Helical; (Potential).					integral to membrane|mitochondrion|mitochondrion					0		Acute lymphoblastic leukemia(157;0.103)				ATGCTATTGCCAGGCAAGTAA	0.368													16	215	---	---	---	---	PASS
SLC6A12	6539	broad.mit.edu	37	12	300301	300301	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:300301C>T	uc001qhz.2	-	17	2321	c.1778G>A	c.(1777-1779)GGC>GAC	p.G593D	SLC6A12_uc001qhx.2_Missense_Mutation_p.G250D|SLC6A12_uc001qhy.2_Missense_Mutation_p.G149D|SLC6A12_uc001qia.2_Missense_Mutation_p.G593D|SLC6A12_uc001qib.2_Missense_Mutation_p.G593D|SLC6A12_uc009zdh.1_Missense_Mutation_p.G593D	NM_003044	NP_003035	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter	593	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			AAAGTTCCGGCCAGCACTGCC	0.612													21	56	---	---	---	---	PASS
SLC6A13	6540	broad.mit.edu	37	12	336752	336752	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:336752T>C	uc001qic.1	-	8	967	c.914A>G	c.(913-915)AAG>AGG	p.K305R	SLC6A13_uc009zdj.1_Missense_Mutation_p.K305R|SLC6A13_uc010sdl.1_Missense_Mutation_p.K213R|SLC6A13_uc010sdm.1_Missense_Mutation_p.K186R	NM_016615	NP_057699	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter	305					neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GTTGTGGTACTTGTTGTAGCT	0.567													11	27	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13906469	13906469	+	Silent	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13906469C>A	uc001rbt.2	-	3	971	c.792G>T	c.(790-792)GGG>GGT	p.G264G		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	264	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TGTCTGTATCCCCTGCCACCA	0.542													34	81	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13906470	13906470	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13906470C>T	uc001rbt.2	-	3	970	c.791G>A	c.(790-792)GGG>GAG	p.G264E		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	264	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	GTCTGTATCCCCTGCCACCAG	0.537													34	82	---	---	---	---	PASS
C12orf70	341346	broad.mit.edu	37	12	27628533	27628533	+	Silent	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27628533C>T	uc010sjq.1	+	5	557	c.381C>T	c.(379-381)TTC>TTT	p.F127F		NM_001145010	NP_001138482	A6NFE2	CL070_HUMAN	hypothetical protein LOC341346	127						integral to membrane					0						AGGGCATGTTCCTCAAGCTAA	0.378													33	113	---	---	---	---	PASS
KRT6A	3853	broad.mit.edu	37	12	52884675	52884675	+	Silent	SNP	G	A	A	rs398542		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52884675G>A	uc001sam.2	-	4	1088	c.879C>T	c.(877-879)GAC>GAT	p.D293D		NM_005554	NP_005545	P02538	K2C6A_HUMAN	keratin 6A	293	Coil 1B.|Rod.				cell differentiation|ectoderm development|positive regulation of cell proliferation	keratin filament	protein binding|structural constituent of cytoskeleton			ovary(4)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.189)		AGTTGATCTCGTCTGTGAGAG	0.498													4	302	---	---	---	---	PASS
RAB3IP	117177	broad.mit.edu	37	12	70209176	70209176	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70209176A>G	uc001svp.2	+	11	1828	c.1381A>G	c.(1381-1383)AGA>GGA	p.R461G	RAB3IP_uc001svm.2_Missense_Mutation_p.R445G|RAB3IP_uc001svn.2_3'UTR|RAB3IP_uc001svo.2_RNA|RAB3IP_uc001svq.2_3'UTR|RAB3IP_uc001svr.2_RNA|RAB3IP_uc001svs.2_RNA|RAB3IP_uc001svt.2_Missense_Mutation_p.R239G	NM_175623	NP_783322	Q96QF0	RAB3I_HUMAN	RAB3A interacting protein isoform alpha 2	461					cilium assembly|Golgi to plasma membrane transport|protein localization to organelle|protein transport	actin cortical patch|centrosome|cytosol|lamellipodium|microtubule basal body|nucleus	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Esophageal squamous(21;0.187)		Lung(24;0.000381)|OV - Ovarian serous cystadenocarcinoma(12;0.00168)|STAD - Stomach adenocarcinoma(21;0.00694)			TATGCAGTTGAGAAAAGAGAT	0.373													7	714	---	---	---	---	PASS
EEA1	8411	broad.mit.edu	37	12	93195423	93195423	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93195423G>T	uc001tck.2	-	20	2990	c.2725C>A	c.(2725-2727)CTT>ATT	p.L909I		NM_003566	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1, 162kD	909	Potential.				early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3						TGTTCCTTAAGTGTGTTTTCC	0.259													46	562	---	---	---	---	PASS
UBC	7316	broad.mit.edu	37	12	125397153	125397153	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125397153T>C	uc001ugs.3	-	2	1613	c.1165A>G	c.(1165-1167)ACT>GCT	p.T389A	UBC_uc001ugr.2_Intron|UBC_uc001ugu.1_Intron|UBC_uc001ugt.2_Intron|UBC_uc001ugv.2_Intron	NM_021009	NP_066289	P0CG48	UBC_HUMAN	ubiquitin C	389	Ubiquitin-like 6.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		GTCTTACCAGTCAGGGTCTTC	0.532													54	229	---	---	---	---	PASS
UGGT2	55757	broad.mit.edu	37	13	96515926	96515926	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96515926C>T	uc001vmt.2	-	31	3771	c.3601G>A	c.(3601-3603)GAT>AAT	p.D1201N		NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2	1201					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3						TCATCTTCATCGGTAAGGATA	0.313													6	746	---	---	---	---	PASS
COL4A1	1282	broad.mit.edu	37	13	110833684	110833684	+	Silent	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110833684C>T	uc001vqw.3	-	29	2270	c.2148G>A	c.(2146-2148)CCG>CCA	p.P716P	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	716	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CATTAAATCCCGGGCGACCTG	0.502													3	32	---	---	---	---	PASS
PSMB5	5693	broad.mit.edu	37	14	23504076	23504076	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23504076G>T	uc001wii.2	-	1	279	c.15C>A	c.(13-15)AGC>AGA	p.S5R	PSMB5_uc001wij.2_Missense_Mutation_p.S5R|PSMB5_uc010tni.1_Intron	NM_002797	NP_002788	P28074	PSB5_HUMAN	proteasome beta 5 subunit isoform 1	5				LASV -> IRGR (in Ref. 7; BAA06097).|LAS -> HEG (in Ref. 5; BC004146).	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus	protein binding|threonine-type endopeptidase activity			ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)	TCTCCAACACGCTGGCAAGCG	0.572													8	15	---	---	---	---	PASS
LGMN	5641	broad.mit.edu	37	14	93185156	93185156	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93185156G>T	uc001yav.2	-	4	498	c.172C>A	c.(172-174)CGC>AGC	p.R58S	LGMN_uc001yat.2_Missense_Mutation_p.R58S|LGMN_uc001yau.2_Missense_Mutation_p.R58S|LGMN_uc001yaw.2_Missense_Mutation_p.R58S|LGMN_uc010aul.2_5'UTR|LGMN_uc001yax.2_Missense_Mutation_p.R58S|LGMN_uc001yay.2_Missense_Mutation_p.R58S	NM_001008530	NP_001008530	Q99538	LGMN_HUMAN	legumain preproprotein	58					hormone biosynthetic process|negative regulation of neuron apoptosis|vitamin D metabolic process	lysosome	cysteine-type endopeptidase activity|protein serine/threonine kinase activity			skin(1)	1		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		ATCCCATTGCGGTGAATGATC	0.478													4	270	---	---	---	---	PASS
JAG2	3714	broad.mit.edu	37	14	105624079	105624079	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105624079C>A	uc001yqg.2	-	3	843	c.439G>T	c.(439-441)GAG>TAG	p.E147*	JAG2_uc001yqh.2_Nonsense_Mutation_p.E147*	NM_002226	NP_002217	Q9Y219	JAG2_HUMAN	jagged 2 isoform a precursor	147	Extracellular (Potential).				auditory receptor cell fate commitment|cell communication|cell cycle|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation|spermatogenesis|thymic T cell selection	integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding			lung(3)|breast(2)	5		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		TCCCAGGCCTCCACGATGAGG	0.657													5	8	---	---	---	---	PASS
SPRED1	161742	broad.mit.edu	37	15	38643718	38643718	+	Silent	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38643718C>T	uc001zka.3	+	7	1523	c.1188C>T	c.(1186-1188)AGC>AGT	p.S396S		NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain	396	SPR.				inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		GTGACACTAGCGACGACAAGT	0.458									Legius_syndrome				4	216	---	---	---	---	PASS
RCN2	5955	broad.mit.edu	37	15	77236100	77236100	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77236100T>C	uc002bcd.2	+	4	670	c.449T>C	c.(448-450)CTT>CCT	p.L150P	RCN2_uc002bce.2_Missense_Mutation_p.L222P|RCN2_uc010bks.2_Missense_Mutation_p.L103P	NM_002902	NP_002893	Q14257	RCN2_HUMAN	reticulocalbin 2 precursor	150	EF-hand 3.					endoplasmic reticulum lumen	calcium ion binding				0						TTTTCAAAGCTTCACTTAAAG	0.274													6	343	---	---	---	---	PASS
AKAP13	11214	broad.mit.edu	37	15	86123604	86123604	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86123604A>G	uc002blv.1	+	7	2475	c.2305A>G	c.(2305-2307)ATG>GTG	p.M769V	AKAP13_uc002blt.1_Missense_Mutation_p.M769V|AKAP13_uc002blu.1_Missense_Mutation_p.M769V|AKAP13_uc010bne.1_5'Flank	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	769					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						TGTCCCTAAAATGGAGAAAGA	0.433													40	75	---	---	---	---	PASS
TTLL13	440307	broad.mit.edu	37	15	90796515	90796515	+	Silent	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90796515G>A	uc002bpd.1	+	4	621	c.333G>A	c.(331-333)GAG>GAA	p.E111E	TTLL13_uc002bpe.1_RNA	NM_001029964	NP_001025135	A6NNM8	TTL13_HUMAN	tubulin tyrosine ligase-like family, member 13	111	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity				0	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			GCCTGAAGGAGGTGGGGGAGG	0.562													5	76	---	---	---	---	PASS
ARRDC4	91947	broad.mit.edu	37	15	98509153	98509153	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98509153T>G	uc010bom.2	+	3	562	c.403T>G	c.(403-405)TAT>GAT	p.Y135D	ARRDC4_uc002bui.3_Missense_Mutation_p.Y48D	NM_183376	NP_899232	Q8NCT1	ARRD4_HUMAN	arrestin domain containing 4	135					signal transduction						0	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)			TACTGGGAAATATGGAAGCAT	0.418													33	416	---	---	---	---	PASS
ZC3H7A	29066	broad.mit.edu	37	16	11845212	11845212	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11845212G>C	uc002dbk.2	-	22	3075	c.2877C>G	c.(2875-2877)GAC>GAG	p.D959E	ZC3H7A_uc002dbh.2_Missense_Mutation_p.D99E|ZC3H7A_uc002dbi.2_Missense_Mutation_p.D147E|ZC3H7A_uc002dbj.2_RNA|ZC3H7A_uc002dbl.2_Missense_Mutation_p.D959E	NM_014153	NP_054872	Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	959						nucleus	nucleic acid binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						ATTTTCCAAAGTCATTATCAT	0.333													125	325	---	---	---	---	PASS
RSL1D1	26156	broad.mit.edu	37	16	11935566	11935566	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11935566T>G	uc002dbp.1	-	7	914	c.841A>C	c.(841-843)AAT>CAT	p.N281H	RSL1D1_uc010buv.1_Missense_Mutation_p.N280H|RSL1D1_uc010uyw.1_Missense_Mutation_p.N61H|RSL1D1_uc010buw.2_RNA	NM_015659	NP_056474	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	281	Potential.				regulation of protein localization|translation	large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0						TTCTTCTTATTAAGCAAAGAT	0.383													35	277	---	---	---	---	PASS
LOC440354	440354	broad.mit.edu	37	16	29538827	29538827	+	Intron	SNP	A	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29538827A>T	uc002dsp.3	-						uc002dtf.2_Intron|LOC440354_uc002dth.2_RNA					Homo sapiens IMAA mRNA for hLAT1-3TM, complete cds.												0						aagcaaaattaaaaaaaAAAA	0.124													3	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													5	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268081	70268081	+	RNA	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268081G>A	uc010cfp.1	-	3		c.334C>T								Homo sapiens cDNA, FLJ98908.																		TCTTACTGTTGGCTAAAAGGC	0.373													4	24	---	---	---	---	PASS
ZC3H18	124245	broad.mit.edu	37	16	88690383	88690383	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88690383C>T	uc002fky.2	+	11	2011	c.1811C>T	c.(1810-1812)TCG>TTG	p.S604L	ZC3H18_uc010voz.1_Missense_Mutation_p.S628L|ZC3H18_uc010chw.2_RNA	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	604	Ser-rich.					nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		TCCTTCTCTTCGTCCCCGTCC	0.652													8	59	---	---	---	---	PASS
FANCA	2175	broad.mit.edu	37	16	89836339	89836339	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89836339C>T	uc002fou.1	-	26	2452	c.2410G>A	c.(2410-2412)GGT>AGT	p.G804S	FANCA_uc010vpn.1_Missense_Mutation_p.G804S	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform	804					DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GCAGGAGGACCCACATCCACC	0.637			D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				3	16	---	---	---	---	PASS
MYH13	8735	broad.mit.edu	37	17	10261145	10261145	+	Splice_Site	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10261145C>T	uc002gmk.1	-	8	736	c.646_splice	c.e8-1	p.G216_splice		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle						muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						CTAGGGTTCCCTAATAATAAA	0.453													45	103	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	21731002	21731002	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21731002G>A	uc002gyy.3	+	2	429	c.304G>A	c.(304-306)GTG>ATG	p.V102M						SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																		CATCGAAAATGTGAAGGCCAA	0.552													14	57	---	---	---	---	PASS
HEXIM1	10614	broad.mit.edu	37	17	43226612	43226612	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43226612A>C	uc002iig.2	+	1	1929	c.55A>C	c.(55-57)ACA>CCA	p.T19P		NM_006460	NP_006451	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	19					negative regulation of cyclin-dependent protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	cyclin-dependent protein kinase inhibitor activity|protein binding|snRNA binding			ovary(1)	1						TAGCAACTGTACAGGTGCTGC	0.552											OREG0024474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	17	---	---	---	---	PASS
ACSF2	80221	broad.mit.edu	37	17	48551987	48551987	+	3'UTR	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48551987T>C	uc002iqu.2	+	16					ACSF2_uc010wml.1_3'UTR|ACSF2_uc010wmm.1_3'UTR|ACSF2_uc010wmn.1_3'UTR|ACSF2_uc010wmo.1_3'UTR|ACSF2_uc010dbt.1_3'UTR	NM_025149	NP_079425	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			tttatgcacctagatgtcccc	0.343													16	44	---	---	---	---	PASS
DSEL	92126	broad.mit.edu	37	18	65181609	65181609	+	Silent	SNP	A	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65181609A>T	uc002lke.1	-	2	1491	c.267T>A	c.(265-267)TCT>TCA	p.S89S		NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	79						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	6		Esophageal squamous(42;0.129)				GGCTTGCACGAGACTTTTGTC	0.408													38	98	---	---	---	---	PASS
TUBB4	10382	broad.mit.edu	37	19	6496076	6496076	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6496076G>T	uc002mfg.1	-	4	541	c.434C>A	c.(433-435)TCC>TAC	p.S145Y	TUBB4_uc002mff.1_Missense_Mutation_p.S73Y	NM_006087	NP_006078	P04350	TBB4_HUMAN	tubulin, beta 4	145	GTP (Potential).				'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(2)	2		Hepatocellular(1079;0.00213)|Renal(1328;0.0183)		Lung(535;3.23e-05)|STAD - Stomach adenocarcinoma(1328;8.24e-05)|GBM - Glioblastoma multiforme(1328;0.00839)|READ - Rectum adenocarcinoma(264;0.155)		GCCCATTCCGGACCCCGTGCC	0.637													9	22	---	---	---	---	PASS
ZNF833	401898	broad.mit.edu	37	19	11793448	11793448	+	5'UTR	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11793448G>A	uc010dyg.2	+	2					ZNF833_uc002msl.3_RNA	NM_001013691	NP_001013713			zinc finger protein 833												0						TCTCTACAGAGATGTGATGTG	0.463													4	87	---	---	---	---	PASS
UNC13A	23025	broad.mit.edu	37	19	17743642	17743642	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17743642T>C	uc002nhd.2	-	28	3641	c.3641A>G	c.(3640-3642)GAG>GGG	p.E1214G		NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A	1126	MHD1.				exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						CGTCACATACTCATTGTAGAG	0.557													5	68	---	---	---	---	PASS
ZNF708	7562	broad.mit.edu	37	19	21477264	21477264	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21477264G>T	uc002npq.1	-	4	702	c.504C>A	c.(502-504)TTC>TTA	p.F168L	ZNF708_uc002npr.1_Missense_Mutation_p.F104L|ZNF708_uc010ecs.1_Missense_Mutation_p.F104L	NM_021269	NP_067092	P17019	ZN708_HUMAN	zinc finger protein 708	168	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(4)|skin(2)	6						CTTTACATTTGAAAGGATTTT	0.328													6	234	---	---	---	---	PASS
ZNF570	148268	broad.mit.edu	37	19	37975663	37975663	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37975663A>G	uc002ogk.1	+	5	1668	c.1139A>G	c.(1138-1140)CAT>CGT	p.H380R	ZNF570_uc010efl.1_Missense_Mutation_p.H436R|ZNF570_uc010xtr.1_Missense_Mutation_p.H177R	NM_144694	NP_653295	Q96NI8	ZN570_HUMAN	zinc finger protein 570	380	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CAGAGAATACATACTGGAGAG	0.423													18	57	---	---	---	---	PASS
PSG11	5680	broad.mit.edu	37	19	43519423	43519423	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43519423T>C	uc002ovm.1	-	4	916	c.809A>G	c.(808-810)CAG>CGG	p.Q270R	PSG11_uc002ouw.2_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG11_uc002ovn.1_Missense_Mutation_p.Q276R|PSG11_uc002ovo.1_Missense_Mutation_p.Q148R|PSG11_uc002ovp.1_Missense_Mutation_p.Q148R	NM_002785	NP_002776	Q9UQ72	PSG11_HUMAN	pregnancy specific beta-1-glycoprotein 11	270	Ig-like C2-type 2.				female pregnancy	extracellular region					0		Prostate(69;0.00682)				CCAAGAATACTGTGCTGGTGG	0.458													52	213	---	---	---	---	PASS
ZFP112	7771	broad.mit.edu	37	19	44833539	44833539	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44833539A>T	uc010ejj.2	-	5	902	c.789T>A	c.(787-789)TAT>TAA	p.Y263*	ZFP112_uc002ozc.3_Nonsense_Mutation_p.Y257*|ZFP112_uc010xwy.1_Nonsense_Mutation_p.Y280*|ZFP112_uc010xwz.1_Nonsense_Mutation_p.Y262*	NM_001083335	NP_001076804	Q9UJU3	ZF112_HUMAN	zinc finger protein 228 isoform 1	263	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)	5						AGGCTTTTCTATACCCAGTAC	0.433													42	97	---	---	---	---	PASS
NAPSA	9476	broad.mit.edu	37	19	50868922	50868922	+	5'UTR	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50868922T>C	uc002prx.2	-	1					NR1H2_uc002prv.3_Intron	NM_004851	NP_004842	O96009	NAPSA_HUMAN	napsin A preproprotein						proteolysis	extracellular region	aspartic-type endopeptidase activity				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)		GGGGCCTCATTTTCTTTCCCC	0.458													3	19	---	---	---	---	PASS
ZNF671	79891	broad.mit.edu	37	19	58232944	58232944	+	Silent	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58232944G>A	uc002qpz.3	-	4	609	c.510C>T	c.(508-510)GGC>GGT	p.G170G	ZNF776_uc002qpx.2_Intron|ZNF671_uc010eug.2_Silent_p.G93G|ZNF671_uc010yhf.1_Silent_p.G72G	NM_024833	NP_079109	Q8TAW3	ZN671_HUMAN	zinc finger protein 671	170					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TCAATATTGGGCCACATATGT	0.473													4	174	---	---	---	---	PASS
PRNT	149830	broad.mit.edu	37	20	4721284	4721284	+	RNA	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4721284C>A	uc002wlb.2	-	1		c.31G>T			PRNT_uc010zqp.1_RNA|PRNT_uc010zqq.1_RNA	NR_024268				Homo sapiens mRNA for putative M8 protein, isoform 2.												0						CTGCAGCTGGCACCCAATCTT	0.413											OREG0025751	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	149	---	---	---	---	PASS
PCNA	5111	broad.mit.edu	37	20	5099285	5099285	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5099285C>T	uc002wlp.2	-	3	561	c.358G>A	c.(358-360)GAT>AAT	p.D120N	PCNA_uc002wlq.2_Missense_Mutation_p.D120N|PCNA_uc010zqs.1_3'UTR	NM_182649	NP_872590	P12004	PCNA_HUMAN	proliferating cell nuclear antigen	120					cell proliferation|DNA strand elongation involved in DNA replication|mismatch repair|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|positive regulation of deoxyribonuclease activity|regulation of DNA replication|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair|translesion synthesis	cytoplasm|DNA replication factor C complex|microtubule cytoskeleton|nuclear replication fork|nucleoplasm|PCNA complex|PCNA-p21 complex	dinucleotide insertion or deletion binding|DNA polymerase processivity factor activity|MutLalpha complex binding|purine-specific mismatch base pair DNA N-glycosylase activity			lung(1)	1						ACATCTAAATCCATCAACTTC	0.358								DNA_polymerases_(catalytic_subunits)					81	260	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11026722	11026722	+	Splice_Site	SNP	C	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11026722C>A	uc002yit.1	-	8	1713	c.1505_splice	c.e8+1		TPTE_uc002yis.1_Splice_Site	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)		GCAAGCCTCACCCCAGGCAAT	0.438													14	28	---	---	---	---	PASS
MICAL3	57553	broad.mit.edu	37	22	18382309	18382309	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18382309C>T	uc002zng.3	-	7	1206	c.853G>A	c.(853-855)GAC>AAC	p.D285N	MICAL3_uc011agl.1_Missense_Mutation_p.D285N|MICAL3_uc002znh.2_Missense_Mutation_p.D285N|MICAL3_uc002znj.1_5'UTR|MICAL3_uc002znk.1_Missense_Mutation_p.D285N|MICAL3_uc002znl.1_Intron|MICAL3_uc010grf.2_Missense_Mutation_p.D285N|MICAL3_uc011agm.1_Missense_Mutation_p.D285N	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin	285						cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)		TTCTCCAAGTCAATACCTGGG	0.453													89	271	---	---	---	---	PASS
SLC5A4	6527	broad.mit.edu	37	22	32614520	32614520	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32614520A>G	uc003ami.2	-	15	1963	c.1961T>C	c.(1960-1962)ATT>ACT	p.I654T		NM_014227	NP_055042	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (low affinity glucose	654	Helical; (Potential).				carbohydrate transport|sodium ion transport	integral to membrane	symporter activity				0						GTAGCCGTGAATAAAGACCAC	0.403													5	92	---	---	---	---	PASS
C22orf23	84645	broad.mit.edu	37	22	38347530	38347530	+	Splice_Site	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38347530C>T	uc003auj.1	-	3	195	c.104_splice	c.e3-1	p.V35_splice	C22orf23_uc003auk.1_Splice_Site_p.V35_splice|POLR2F_uc010gxi.2_5'Flank|POLR2F_uc003aul.2_5'Flank|POLR2F_uc003aum.2_5'Flank	NM_032561	NP_115950	Q9BZE7	EVG1_HUMAN	hypothetical protein LOC84645												0	Melanoma(58;0.045)					TTCATCATCACTGCACGACAA	0.378													4	157	---	---	---	---	PASS
GPR64	10149	broad.mit.edu	37	X	19026097	19026097	+	Splice_Site	SNP	C	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19026097C>T	uc004cyx.2	-	19	1730	c.1566_splice	c.e19+1	p.Q522_splice	GPR64_uc004cyy.2_Splice_Site_p.Q519_splice|GPR64_uc004cyz.2_Splice_Site_p.Q508_splice|GPR64_uc004czb.2_Splice_Site_p.Q522_splice|GPR64_uc004czc.2_Splice_Site_p.Q506_splice|GPR64_uc004czd.2_Splice_Site_p.Q498_splice|GPR64_uc004cze.2_Splice_Site_p.Q492_splice|GPR64_uc004czf.2_Splice_Site_p.Q484_splice|GPR64_uc004cza.2_Splice_Site_p.Q500_splice|GPR64_uc004cyw.2_Splice_Site_p.Q506_splice|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)					AGCAGTTTTACCTGAAACAAA	0.408													41	53	---	---	---	---	PASS
USP9X	8239	broad.mit.edu	37	X	41084019	41084019	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41084019T>C	uc004dfb.2	+	40	7409	c.6776T>C	c.(6775-6777)TTT>TCT	p.F2259S	USP9X_uc004dfc.2_Missense_Mutation_p.F2259S	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	2259					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						CCCAATCCTTTTGGTGATCCT	0.328													5	210	---	---	---	---	PASS
COX7B	1349	broad.mit.edu	37	X	77160816	77160816	+	3'UTR	SNP	A	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77160816A>G	uc004ecu.1	+	3						NM_001866	NP_001857	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb precursor						respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0						TTGATGCCAAATTAAAGCACT	0.343													5	87	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2145	2145	+	5'Flank	SNP	G	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2145G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		AAACCTTGTAGAGAGAGTAAA	0.383													57	92	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	11830309	11830309	+	5'Flank	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11830309delA	uc001asz.2	+											RecName: Full=Uncharacterized protein C1orf167;																		GACCAGAAAGAAAAAAAAAAA	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20746982	20746982	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20746982delA	uc001bdf.1	-											Homo sapiens cDNA clone IMAGE:5269505.																		ggattctcataaaaaaatagg	0.000													4	2	---	---	---	---	
C1orf201	90529	broad.mit.edu	37	1	24692287	24692288	+	Intron	INS	-	G	G	rs71589761		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24692287_24692288insG	uc001bjc.2	-						C1orf201_uc010oej.1_Intron|C1orf201_uc001bja.2_Intron|C1orf201_uc001bjb.2_Intron|C1orf201_uc001bjd.2_Intron|C1orf201_uc001bje.1_Intron			Q5TH74	CA201_HUMAN	RecName: Full=UPF0490 protein C1orf201;											ovary(1)|breast(1)	2		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.0191)|all_lung(284;0.0251)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.056)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.48e-25)|Colorectal(126;7.29e-08)|COAD - Colon adenocarcinoma(152;3.85e-06)|GBM - Glioblastoma multiforme(114;0.000399)|BRCA - Breast invasive adenocarcinoma(304;0.00107)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00393)|READ - Rectum adenocarcinoma(331;0.0672)|Lung(427;0.145)		ttgaacccactgggagttaagt	0.050													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	25828682	25828683	+	IGR	INS	-	CGT	CGT	rs146841318	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25828682_25828683insCGT								TMEM57 (1986 upstream) : LDLRAP1 (41393 downstream)																							CCCATCCTGAGCTGACTTTCCT	0.198													1	5	---	---	---	---	
EIF2C3	192669	broad.mit.edu	37	1	36437489	36437489	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36437489delA	uc001bzp.2	+						EIF2C3_uc001bzn.1_Intron|EIF2C3_uc001bzo.2_Intron|EIF2C3_uc001bzq.2_Intron	NM_024852	NP_079128	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TTTTATCTACAAAAAAAAATG	0.229													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37599323	37599324	+	IGR	DEL	GT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37599323_37599324delGT								GRIK3 (99479 upstream) : ZC3H12A (340795 downstream)																							gcacaggggagtgtgtgtgtgt	0.307													4	2	---	---	---	---	
SCMH1	22955	broad.mit.edu	37	1	41503454	41503454	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41503454delT	uc001cgo.2	-						SCMH1_uc010ojr.1_Intron|SCMH1_uc001cgp.2_Intron|SCMH1_uc001cgr.2_Intron|SCMH1_uc001cgs.2_Intron|SCMH1_uc001cgt.2_Intron|SCMH1_uc001cgq.2_Intron|SCMH1_uc010ojs.1_Intron	NM_001031694	NP_001026864	Q96GD3	SCMH1_HUMAN	sex comb on midleg 1 isoform 1						anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				tctttgaggctttttctggtc	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	61968340	61968340	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61968340delT								NFIA (39881 upstream) : TM2D1 (178379 downstream)																							GTTTTTCTGGTTAGTTGGCAG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	62853544	62853544	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62853544delT								KANK4 (68461 upstream) : USP1 (48431 downstream)																							AAGCAGAAAATTTTAGAATCT	0.353													4	2	---	---	---	---	
SLC44A5	204962	broad.mit.edu	37	1	75859539	75859539	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75859539delA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4						tgtttgaatgaagcaatttag	0.050													4	2	---	---	---	---	
SEP15	9403	broad.mit.edu	37	1	87329492	87329495	+	Intron	DEL	TCAT	-	-	rs112704469		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87329492_87329495delTCAT	uc010osi.1	-						SEP15_uc010osj.1_Intron	NM_004261	NP_004252	O60613	SEP15_HUMAN	15 kDa selenoprotein isoform 1 precursor						'de novo' posttranslational protein folding	endoplasmic reticulum lumen	selenium binding				0		Lung NSC(277;0.153)		all cancers(265;0.00744)|Epithelial(280;0.0333)		AAAAAAtcactcattcattcattc	0.132													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91339583	91339583	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91339583delT								BARHL2 (156789 upstream) : ZNF644 (41277 downstream)																							aatttactcatttttttcatg	0.000													4	2	---	---	---	---	
ZNF644	84146	broad.mit.edu	37	1	91448112	91448112	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91448112delC	uc001dnw.2	-						ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron|ZNF644_uc001dny.1_Intron	NM_201269	NP_958357	Q9H582	ZN644_HUMAN	zinc finger protein 644 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TTGCTAAGTGCCCCCCAACCT	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91512694	91512694	+	IGR	DEL	T	-	-	rs67116804		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91512694delT								ZNF644 (25023 upstream) : HFM1 (213630 downstream)																							cttctttctgttttttttttt	0.095													8	4	---	---	---	---	
RPAP2	79871	broad.mit.edu	37	1	92769332	92769332	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92769332delT	uc001dot.2	+						RPAP2_uc009wdh.2_Intron	NM_024813	NP_079089	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2							integral to membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		Taataataactttttttttga	0.144													4	2	---	---	---	---	
ALG14	199857	broad.mit.edu	37	1	95486900	95486900	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95486900delC	uc001dra.2	-							NM_144988	NP_659425	Q96F25	ALG14_HUMAN	asparagine-linked glycosylation 14 homolog						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity				0		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		tcaaggagttcacagtctGTA	0.164													4	2	---	---	---	---	
AMPD2	271	broad.mit.edu	37	1	110161398	110161399	+	5'Flank	DEL	TT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110161398_110161399delTT	uc009wfh.1	+						AMPD2_uc009wfg.1_5'Flank|AMPD2_uc001dyb.1_5'Flank|AMPD2_uc001dyc.1_5'Flank|AMPD2_uc010ovr.1_5'Flank	NM_004037	NP_004028	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2 (isoform L)						purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|breast(1)	3		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		AGAGGCCAAGTTTTTTTTAAGT	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	112615334	112615334	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112615334delA								KCND3 (83557 upstream) : CTTNBP2NL (323466 downstream)																							GACAAAAAGGAAAAAAAAAAA	0.194													4	2	---	---	---	---	
RPRD2	23248	broad.mit.edu	37	1	150436844	150436845	+	Intron	INS	-	TC	TC	rs111843239		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150436844_150436845insTC	uc009wlr.2	+						RPRD2_uc010pcc.1_Intron|RPRD2_uc001eup.3_Intron	NM_015203	NP_056018	Q5VT52	RPRD2_HUMAN	Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1						CAGGGTTTTTTTTTTTTTTTTT	0.248											OREG0013786	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	6	---	---	---	---	
GON4L	54856	broad.mit.edu	37	1	155822905	155822905	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155822905delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					ccgtctcaagaaaaaaaaaaa	0.184													5	3	---	---	---	---	
ARHGEF2	9181	broad.mit.edu	37	1	155933136	155933137	+	Intron	DEL	TT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155933136_155933137delTT	uc001fmt.2	-						ARHGEF2_uc001fmr.2_Intron|ARHGEF2_uc001fms.2_Intron|ARHGEF2_uc001fmu.2_Intron|ARHGEF2_uc010pgt.1_Intron|ARHGEF2_uc010pgu.1_Intron	NM_001162383	NP_001155855	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CAtttttatctttttttttttt	0.163													5	3	---	---	---	---	
NES	10763	broad.mit.edu	37	1	156650169	156650169	+	5'Flank	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156650169delA	uc001fpq.2	-							NM_006617	NP_006608	P48681	NEST_HUMAN	nestin						brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					agcaaaatagaaaaaaaaaac	0.000													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	172356004	172356004	+	Intron	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172356004delG	uc001gie.2	+						DNM3_uc001gif.2_Intron|DNM3_uc001gih.1_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						GCCCTGTTCTGGTGATGGCTG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	198913272	198913273	+	IGR	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198913272_198913273insT								MIR181A1 (84990 upstream) : None (None downstream)																							cagagaaacgattttttttttg	0.000													4	3	---	---	---	---	
CSRP1	1465	broad.mit.edu	37	1	201474639	201474640	+	Intron	DEL	TT	-	-	rs5780074		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201474639_201474640delTT	uc001gws.2	-						CSRP1_uc010ppr.1_Intron|CSRP1_uc010pps.1_Intron	NM_004078	NP_004069	P21291	CSRP1_HUMAN	cysteine and glycine-rich protein 1 isoform 1							nucleus	zinc ion binding			ovary(1)	1						CTCCTGCTTCTTCTTCCCCATA	0.510													4	2	---	---	---	---	
RABIF	5877	broad.mit.edu	37	1	202850536	202850536	+	Intron	DEL	T	-	-	rs111992348		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202850536delT	uc001gyl.2	-							NM_002871	NP_002862	P47224	MSS4_HUMAN	RAB-interacting factor						cellular membrane fusion|protein transport|small GTPase mediated signal transduction		guanyl-nucleotide exchange factor activity|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(75;0.166)			GCCCTGAttcttttttttttg	0.244													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	217315189	217315189	+	IGR	DEL	A	-	-	rs77024002		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217315189delA								ESRRG (4092 upstream) : GPATCH2 (288645 downstream)																							AAGAAAAAGGAAAAAAAAAAA	0.373													6	3	---	---	---	---	
NID1	4811	broad.mit.edu	37	1	236210042	236210042	+	Intron	DEL	C	-	-	rs3835671		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236210042delC	uc001hxo.2	-						NID1_uc009xgd.2_Intron	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)	AGGCATTTATCACCCAAGTGA	0.269													3	4	---	---	---	---	
TSSC1	7260	broad.mit.edu	37	2	3334491	3334492	+	Intron	DEL	AC	-	-	rs66488838		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3334491_3334492delAC	uc002qxj.2	-							NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		CACTCATGAGACAGTGTGAGCA	0.530													2	4	---	---	---	---	
DPYSL5	56896	broad.mit.edu	37	2	27163276	27163277	+	Intron	INS	-	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27163276_27163277insA	uc002rhu.3	+						DPYSL5_uc002rhv.3_Intron	NM_020134	NP_064519	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					aaaagtataagaaaaaaagaaa	0.054													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28485280	28485280	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28485280delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					accagggacctaaaaagacag	0.000													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28518370	28518370	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28518370delT	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron|BRE_uc002rlx.2_5'Flank	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					GTGAATAGGCttttttttttg	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	36204658	36204658	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36204658delT								None (None upstream) : CRIM1 (378739 downstream)																							agtcctgtggtttttcctgta	0.015													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41932156	41932156	+	IGR	DEL	A	-	-	rs72331805		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41932156delA								None (None upstream) : PKDCC (343005 downstream)																							TTTAATTGAGAAAAAAAAAAG	0.294													3	3	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43768645	43768645	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43768645delT	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_Intron|THADA_uc002rta.2_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TCATGCTAAGttttttttttt	0.174													4	3	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43798619	43798620	+	Intron	INS	-	A	A	rs113088849		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43798619_43798620insA	uc002rsw.3	-						THADA_uc010far.2_5'Flank|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_5'Flank|THADA_uc002rta.2_Intron|THADA_uc002rtb.1_Intron|THADA_uc002rtc.3_Intron|THADA_uc002rtd.2_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				ctgaactcctgaAAAAAAATGG	0.228													4	2	---	---	---	---	
PLEKHH2	130271	broad.mit.edu	37	2	43960108	43960109	+	Intron	INS	-	C	C	rs144735487	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43960108_43960109insC	uc010yny.1	+						PLEKHH2_uc002rtf.3_Intron	NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H							cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TTTGGTCACATCCCCCTCAAAC	0.347													4	2	---	---	---	---	
FBXO11	80204	broad.mit.edu	37	2	48047245	48047245	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48047245delA	uc010fbl.2	-						FBXO11_uc002rwe.2_Intron|FBXO11_uc002rwf.2_Intron|FBXO11_uc002rwg.1_Intron|FBXO11_uc010fbk.2_Intron	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1						ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGACTTTAATAAAAAGGTGTT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60975387	60975387	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60975387delA								BCL11A (194754 upstream) : PAPOLG (7996 downstream)																							TAATCTGCCGAAAAAAAGAAA	0.353													4	2	---	---	---	---	
SLC1A4	6509	broad.mit.edu	37	2	65224213	65224213	+	Intron	DEL	G	-	-	rs113097939	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65224213delG	uc010yqa.1	+						SLC1A4_uc010ypy.1_Intron|SLC1A4_uc010ypz.1_Intron|SLC1A4_uc010fcv.2_Intron|SLC1A4_uc002sdh.2_5'Flank	NM_003038	NP_003029	P43007	SATT_HUMAN	solute carrier family 1, member 4 isoform 1						cellular nitrogen compound metabolic process|cognition|synaptic transmission, glutamatergic	intermediate filament|melanosome	chloride channel activity|L-alanine transmembrane transporter activity|L-cystine transmembrane transporter activity|L-hydroxyproline transmembrane transporter activity|L-proline transmembrane transporter activity|L-serine transmembrane transporter activity|L-threonine transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(1)	1					L-Alanine(DB00160)	CCTTGCCCTTGGTGACAGCAG	0.517													4	2	---	---	---	---	
SLC4A5	57835	broad.mit.edu	37	2	74487059	74487059	+	Intron	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74487059delG	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9						tcaccaGGCTGTCTACTCTGG	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96607117	96607118	+	Intron	INS	-	TT	TT			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96607117_96607118insTT	uc002sva.1	-						uc010yug.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		GAAAAAAGAAACATAAAAACAA	0.252													6	3	---	---	---	---	
BUB1	699	broad.mit.edu	37	2	111427527	111427528	+	Intron	DEL	AA	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111427527_111427528delAA	uc002tgc.2	-						BUB1_uc010yxh.1_Intron|BUB1_uc010fkb.2_Intron|BUB1_uc002tgd.2_Intron	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1						apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		ATTTTGAATTAAAAAAAAATCC	0.287													4	2	---	---	---	---	
FBLN7	129804	broad.mit.edu	37	2	112907960	112907960	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112907960delA	uc002tho.1	+						FBLN7_uc002thn.2_Intron|FBLN7_uc010fki.1_Intron|FBLN7_uc010fkj.1_Intron	NM_153214	NP_694946	Q53RD9	FBLN7_HUMAN	fibulin 7 isoform 1						cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2						GTACCAGAAGAAAAAAAAAAT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126224541	126224542	+	IGR	DEL	CA	-	-	rs67061291		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126224541_126224542delCA								CNTNAP5 (551680 upstream) : None (None downstream)																							tgtagggaaccatagttgtgag	0.000													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132772269	132772269	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132772269delA								C2orf27B (213035 upstream) : NCRNA00164 (132895 downstream)																							AATACTATACAAAATCAAGAG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	171768836	171768836	+	IGR	DEL	T	-	-	rs67344897		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171768836delT								GAD1 (51179 upstream) : GORASP2 (16146 downstream)																							atttcttctatttttttttct	0.000													2	4	---	---	---	---	
UBE2E3	10477	broad.mit.edu	37	2	181918327	181918328	+	Intron	INS	-	CC	CC	rs142980607		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181918327_181918328insCC	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619	Q969T4	UB2E3_HUMAN	ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1						accccttgtatctctgcccctg	0.010													4	2	---	---	---	---	
SATB2	23314	broad.mit.edu	37	2	200332796	200332796	+	5'Flank	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200332796delT	uc002uva.1	-						FLJ32063_uc002uvd.1_5'Flank|FLJ32063_uc002uve.1_5'Flank	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2							cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1						tctctctctcttttttttttt	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201833365	201833365	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201833365delA								ORC2L (4955 upstream) : FAM126B (5077 downstream)																							aggattaattaaaaaaaaaag	0.000													4	2	---	---	---	---	
SPAG16	79582	broad.mit.edu	37	2	214751210	214751210	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214751210delC	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		actttctgatccccaacaCTG	0.114													4	2	---	---	---	---	
RNF25	64320	broad.mit.edu	37	2	219535989	219535990	+	Intron	INS	-	T	T	rs35556340		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219535989_219535990insT	uc002vit.2	-						STK36_uc002viu.2_5'Flank|STK36_uc002viv.2_5'Flank|RNF25_uc010fvw.2_Intron	NM_022453	NP_071898	Q96BH1	RNF25_HUMAN	ring finger protein 25						positive regulation of NF-kappaB transcription factor activity	cytosol|nucleus	NF-kappaB binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		gccacacccacttttttttttt	0.015													4	2	---	---	---	---	
GRM7	2917	broad.mit.edu	37	3	7478606	7478607	+	Intron	INS	-	ATC	ATC	rs139386106	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7478606_7478607insATC	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)	tcaggtcTTTTatcatcatcat	0.124													4	5	---	---	---	---	
SCN5A	6331	broad.mit.edu	37	3	38598922	38598923	+	Intron	INS	-	TGT	TGT			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38598922_38598923insTGT	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron|SCN5A_uc010hhj.1_Intron	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha						blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)	CAGCATCTAAATGCCTGGGTGG	0.535													6	3	---	---	---	---	
MYRIP	25924	broad.mit.edu	37	3	40052344	40052345	+	Intron	DEL	CT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40052344_40052345delCT	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc010hhx.1_Intron	NM_015460	NP_056275	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		TGAATCTTGCCTCTCTCTGCCT	0.450													4	2	---	---	---	---	
MITF	4286	broad.mit.edu	37	3	70001294	70001295	+	Intron	DEL	TC	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70001294_70001295delTC	uc003dnz.2	+						MITF_uc011bgb.1_Intron|MITF_uc003doa.2_Intron|MITF_uc003dob.2_Intron|MITF_uc003dod.2_Intron|MITF_uc003doe.2_Intron|MITF_uc003dof.2_Intron	NM_198159	NP_937802	O75030	MITF_HUMAN	microphthalmia-associated transcription factor						melanocyte differentiation|multicellular organismal development|protein complex assembly	nucleus|protein complex	DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			ovary(2)	2		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		GTAGTGGTTTTCTCTCTCTCTC	0.322			A		melanoma 		Waardenburg syndrome type 2|Tietz syndrome						4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75987251	75987252	+	IGR	INS	-	A	A	rs113554214		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75987251_75987252insA								ZNF717 (152581 upstream) : None (None downstream)																							GAAATTAAATGAAAAATGTGAT	0.317													4	3	---	---	---	---	
TBC1D23	55773	broad.mit.edu	37	3	100002217	100002218	+	Intron	DEL	AA	-	-	rs111909231		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100002217_100002218delAA	uc003dtt.2	+						TBC1D23_uc003dts.2_Intron	NM_018309	NP_060779	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23							intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2						actccgtctcaaaaaaaaaaaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	107162354	107162354	+	Intron	DEL	T	-	-	rs140177829		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107162354delT	uc003dwj.2	+											Homo sapiens cDNA clone IMAGE:5312582.																		ATTTGGAGTGTTTTTTTCTAT	0.194													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	110651449	110651449	+	IGR	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110651449delG								None (None upstream) : PVRL3 (139416 downstream)																							AAAAATTTAAGGGGAAAAAAC	0.383													4	2	---	---	---	---	
KIAA2018	205717	broad.mit.edu	37	3	113371901	113371901	+	3'UTR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113371901delA	uc003eam.2	-	7					KIAA2018_uc003eal.2_3'UTR	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717						regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						acagagtctcaaaaaaaaaag	0.289													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115200883	115200884	+	IGR	DEL	GT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115200883_115200884delGT								ZBTB20 (334756 upstream) : GAP43 (141267 downstream)																							gtgtgtgtgcgtgtgtgtgtgt	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	118370052	118370052	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118370052delA	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																		ATCATGTGCCAAAAAAAAAGG	0.338													4	3	---	---	---	---	
PLXNA1	5361	broad.mit.edu	37	3	126737999	126738000	+	Intron	INS	-	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126737999_126738000insG	uc003ejg.2	+							NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1						axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)		TCAGGGCTCTAGGGGGCAGATA	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	132714785	132714786	+	IGR	DEL	CT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132714785_132714786delCT								NCRNA00119 (121735 upstream) : TMEM108 (42385 downstream)																							TTCTCTCTTGCTCTCTCTCAGA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147775974	147775975	+	IGR	INS	-	T	T	rs139131398	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147775974_147775975insT								ZIC1 (641470 upstream) : AGTR1 (639683 downstream)																							attggtggagatttttttttaa	0.000													4	3	---	---	---	---	
GPR149	344758	broad.mit.edu	37	3	154072360	154072360	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154072360delT	uc003faa.2	-							NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTCCTTTTCCTTTTTTTTTTG	0.264													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165942083	165942083	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165942083delA								BCHE (386830 upstream) : None (None downstream)																							aacaaggaacaaaaaaaaaat	0.229													4	2	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	175437010	175437011	+	Intron	DEL	AA	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175437010_175437011delAA	uc003fit.2	+							NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		tgggggtTACAAAAAAAAAAAA	0.163													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187747475	187747475	+	IGR	DEL	A	-	-	rs80167772		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187747475delA								BCL6 (284000 upstream) : LPP (124244 downstream)																							AACCAAAACTAAAAAAAAAGT	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197838930	197838931	+	IGR	INS	-	C	C	rs143422750	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197838930_197838931insC								LOC348840 (31388 upstream) : FAM157A (40306 downstream)																							AATGGTAAGCTTTTTTGTAAAA	0.312													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197838931	197838932	+	IGR	INS	-	GCA	GCA	rs59815867		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197838931_197838932insGCA								LOC348840 (31389 upstream) : FAM157A (40305 downstream)																							ATGGTAAGCTTTTTTGTAAAAG	0.312													5	3	---	---	---	---	
NOP14	8602	broad.mit.edu	37	4	2958218	2958218	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2958218delA	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_5'Flank|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_Intron	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1						CTGAAAACTTAAAAAAAAAAC	0.229													8	4	---	---	---	---	
C1QTNF7	114905	broad.mit.edu	37	4	15432677	15432680	+	Intron	DEL	GATA	-	-	rs145320198		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15432677_15432680delGATA	uc011bxb.1	+						C1QTNF7_uc003gno.2_Intron|C1QTNF7_uc003gnp.2_Intron	NM_001135171	NP_001128643	Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7							collagen					0						atagatagatgatagatagataga	0.132													4	3	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21112915	21112916	+	Intron	INS	-	A	A	rs143846839	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21112915_21112916insA	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 4							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				GGCTCTGACGCGACAAAAGATT	0.406													1	5	---	---	---	---	
FAM114A1	92689	broad.mit.edu	37	4	38902626	38902626	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38902626delT	uc003gtn.2	+						FAM114A1_uc011byh.1_Intron	NM_138389	NP_612398	Q8IWE2	NXP20_HUMAN	hypothetical protein LOC92689							cytoplasm				ovary(1)	1						TATTATGGGATTTTTAAAAGT	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49160129	49160129	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49160129delC								CWH43 (96036 upstream) : None (None downstream)																							ccttttcaatctctggtttta	0.000													5	3	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54372594	54372595	+	Intron	DEL	AT	-	-	rs148914127		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54372594_54372595delAT	uc003haa.2	+						LNX1_uc003haf.3_Intron|LNX1_uc003hag.3_Intron|LNX1_uc003hah.3_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	TGGGGAAAACATATGGGATCTA	0.213			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58808645	58808655	+	IGR	DEL	TTCCCACTAAT	-	-	rs77033843		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58808645_58808655delTTCCCACTAAT								IGFBP7 (832106 upstream) : None (None downstream)																							GGAATTGGGATTCCCACTAATGTATCTGTAT	0.289													4	3	---	---	---	---	
LPHN3	23284	broad.mit.edu	37	4	62936764	62936764	+	3'UTR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62936764delT	uc010ihh.2	+	23					LPHN3_uc003hcq.3_3'UTR|LPHN3_uc003hct.2_3'UTR	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						ACTCTCAGACTTTTTTTTTTT	0.393													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	72557613	72557613	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72557613delC								SLC4A4 (119810 upstream) : GC (49800 downstream)																							CTCAGCTAAACCCCATGCCAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	76085249	76085250	+	IGR	INS	-	T	T	rs142482591	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76085249_76085250insT								PARM1 (109926 upstream) : RCHY1 (319105 downstream)																							CTCCAAGGTAGTTTTTTTTTTC	0.386													4	2	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79394956	79394957	+	Intron	INS	-	TA	TA	rs146146982	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79394956_79394957insTA	uc003hlb.2	+							NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						atgcatcatcttatataatact	0.059													6	8	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81526999	81527000	+	Intron	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81526999_81527000insT	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						TAACACTTAAGTTTTTTTTTTA	0.198													4	2	---	---	---	---	
HSD17B13	345275	broad.mit.edu	37	4	88226634	88226635	+	Intron	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88226634_88226635insT	uc003hqo.2	-						HSD17B13_uc010ikk.2_Intron	NM_178135	NP_835236	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13							extracellular region	binding|oxidoreductase activity				0		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)		CTTTCTTTTTCTTTTTTTTTTT	0.317													7	5	---	---	---	---	
TET2	54790	broad.mit.edu	37	4	106183185	106183185	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106183185delT	uc003hxk.2	+						TET2_uc011cez.1_Intron|TET2_uc003hxj.2_Intron	NM_001127208	NP_001120680	Q6N021	TET2_HUMAN	tet oncogene family member 2 isoform a						cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CAAAAGTACATTTTTTTTGTC	0.284			Mis N|F		MDS								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	135970705	135970705	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135970705delC								PABPC4L (847802 upstream) : None (None downstream)																							TTATAAATAACCACCTTAAGC	0.284													4	2	---	---	---	---	
ZNF827	152485	broad.mit.edu	37	4	146860159	146860160	+	5'Flank	DEL	CA	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146860159_146860160delCA	uc003ikn.2	-						ZNF827_uc003ikm.2_5'Flank|ZNF827_uc010iox.2_5'Flank	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)					cacacgcacgcacacacacaca	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	147469370	147469375	+	IGR	DEL	GAGTTT	-	-	rs3059768		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147469370_147469375delGAGTTT								SLC10A7 (26247 upstream) : POU4F2 (90670 downstream)																							aaggggcatagagtttgatgaaggag	0.000													4	2	---	---	---	---	
LRBA	987	broad.mit.edu	37	4	151224150	151224150	+	Intron	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151224150delG	uc010ipj.2	-						LRBA_uc010ipi.2_Intron|LRBA_uc003ils.3_Intron|LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron|LRBA_uc003ilr.3_Intron	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					taacatttttgaaaggcatgt	0.000													4	2	---	---	---	---	
LRBA	987	broad.mit.edu	37	4	151910937	151910937	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151910937delA	uc010ipj.2	-						LRBA_uc003ilu.3_Intron	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TAAAGGGGGTAAAAAAAAAAA	0.249													3	3	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154504164	154504164	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154504164delA	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron|KIAA0922_uc010ipq.2_Intron|KIAA0922_uc010ips.1_5'Flank	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				ATTAAAAAAGAAAAAAAAAAA	0.299													10	5	---	---	---	---	
GALNT7	51809	broad.mit.edu	37	4	174193369	174193369	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174193369delT	uc003isz.3	+							NM_017423	NP_059119	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		CATTTTTCTCTTTTTTTGTCT	0.413													4	2	---	---	---	---	
FAM92A3	403315	broad.mit.edu	37	4	183960484	183960484	+	RNA	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									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													4	2	---	---	---	---	
SNX25	83891	broad.mit.edu	37	4	186231584	186231585	+	Intron	INS	-	CT	CT	rs148164296	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									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													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188771561	188771562	+	IGR	DEL	CA	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188771561_188771562delCA								None (None upstream) : ZFP42 (145363 downstream)																							TATAATTGAGCACACACACACA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189164779	189164779	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189164779delT								TRIML1 (96130 upstream) : None (None downstream)																							TGCAGAGCAGTTTTTCTCCTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189241513	189241513	+	IGR	DEL	C	-	-	rs113069300		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189241513delC								TRIML1 (172864 upstream) : None (None downstream)																							aacccagcaaccctttatgat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190562403	190562403	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190562403delA								None (None upstream) : FRG1 (299571 downstream)																							GTATTGAATTAAAAATTCTTG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190569728	190569738	+	IGR	DEL	AAGTCGGAACT	-	-	rs67581894	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190569728_190569738delAAGTCGGAACT								None (None upstream) : FRG1 (292236 downstream)																							CAAAGGAGCGAAGTCGGAACTATTTTTGCTG	0.412													4	2	---	---	---	---	
ZDHHC11	79844	broad.mit.edu	37	5	834216	834216	+	Intron	DEL	A	-	-	rs74567234		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:834216delA	uc011cma.1	-						ZDHHC11_uc003jbj.2_Intron|ZDHHC11_uc010itd.1_Intron	NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			tcccactagcaaaaaaacgca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	73601632	73601632	+	IGR	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73601632delG								RGNEF (364219 upstream) : ENC1 (321603 downstream)																							CATGTCAAGTGCTCATTTTGT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	83720874	83720874	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83720874delA								EDIL3 (40263 upstream) : None (None downstream)																							CCTGCATTCTAATCTCTATGA	0.308													4	2	---	---	---	---	
GPR98	84059	broad.mit.edu	37	5	89918637	89918637	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89918637delA	uc003kju.2	+						GPR98_uc003kjt.2_Intron	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		agctcaatgcaacctctgcct	0.005													5	5	---	---	---	---	
MCTP1	79772	broad.mit.edu	37	5	94417702	94417703	+	Intron	INS	-	A	A	rs139816133	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94417702_94417703insA	uc003kkx.2	-						MCTP1_uc003kkv.2_5'Flank|MCTP1_uc003kkw.2_5'Flank|MCTP1_uc003kkz.2_5'Flank	NM_024717	NP_078993	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		GAAAGACATCTAAAAAAAAAAG	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116428929	116428929	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116428929delA								SEMA6A (518378 upstream) : None (None downstream)																							atacaaagggaaaaaaatcaa	0.035													4	2	---	---	---	---	
HSD17B4	3295	broad.mit.edu	37	5	118867264	118867265	+	Intron	DEL	GT	-	-	rs34403323		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118867264_118867265delGT	uc003ksj.2	+						HSD17B4_uc011cwg.1_Intron|HSD17B4_uc011cwh.1_Intron|HSD17B4_uc011cwi.1_Intron|HSD17B4_uc003ksk.3_Intron|HSD17B4_uc011cwj.1_Intron|HSD17B4_uc010jcn.1_Intron|HSD17B4_uc010jco.1_Intron	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)	CCAAAGGGGGgtgtgtgtgtgt	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119755302	119755302	+	IGR	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119755302delG								FAM170A (783786 upstream) : PRR16 (44717 downstream)																							TAGAAGCTGTGGTGCAGTGAG	0.249													4	2	---	---	---	---	
LMNB1	4001	broad.mit.edu	37	5	126135283	126135283	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126135283delA	uc003kud.1	+						LMNB1_uc003kuc.2_Intron|LMNB1_uc010jdb.1_Intron|LMNB1_uc011cxb.1_Intron	NM_005573	NP_005564	P20700	LMNB1_HUMAN	lamin B1						cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		AAAGGTACTGAGGGTCCAGAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139021227	139021227	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139021227delA								UBE2D2 (13211 upstream) : CXXC5 (7074 downstream)																							GGATCAGGGGATATGAAGGGG	0.468													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142273580	142273580	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142273580delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTAGAAAGCTTTTTTTTTGT	0.144													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	145088734	145088734	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145088734delC								None (None upstream) : PRELID2 (49848 downstream)																							CCTACAGAAGCCCACCCACTG	0.498													4	2	---	---	---	---	
STK32A	202374	broad.mit.edu	37	5	146677787	146677787	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146677787delT	uc010jgn.1	+						STK32A_uc003lol.3_Intron|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)			GATGGAGCAGTTAGAGGTGAA	0.368													4	2	---	---	---	---	
CSF1R	1436	broad.mit.edu	37	5	149471997	149471998	+	Intron	INS	-	T	T	rs148058086	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149471997_149471998insT	uc003lrm.2	-							NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor						cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity			haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	tatatgccatgtttttttccta	0.040													1	5	---	---	---	---	
GM2A	2760	broad.mit.edu	37	5	150647377	150647377	+	3'UTR	DEL	T	-	-	rs150406361		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150647377delT	uc003ltr.3	+	4					GM2A_uc011dcs.1_RNA|GM2A_uc011dcr.1_3'UTR|GM2A_uc003ltu.1_5'Flank	NM_000405	NP_000396	P17900	SAP3_HUMAN	GM2 ganglioside activator precursor							lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTTTCACTCTTTTTTTTTTT	0.393													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154387457	154387458	+	IGR	DEL	CT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154387457_154387458delCT								MRPL22 (38487 upstream) : KIF4B (5802 downstream)																							CTGTTTCATCCTCTCTCTCTCT	0.347													4	2	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156698150	156698151	+	Intron	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156698150_156698151insT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwp.2_Intron	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GATCGGTAAGATTTGAGAAGGG	0.460													4	2	---	---	---	---	
ADAM19	8728	broad.mit.edu	37	5	156898917	156898918	+	Intron	DEL	CA	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156898917_156898918delCA	uc003lww.1	-						NIPAL4_uc003lwx.3_Intron|NIPAL4_uc011ddq.1_Intron			Q9H013	ADA19_HUMAN	SubName: Full=cDNA FLJ34145 fis, clone FCBBF3011867, highly similar to ADAM 19 (EC 3.4.24.-);						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTGACCACCTCAGGTGCTGCCA	0.495											OREG0016979	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	13	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167557895	167557895	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167557895delA	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron|uc003lzs.1_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)		atcctgtctcaaaaaaaaTAC	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	168758316	168758317	+	IGR	DEL	TG	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168758316_168758317delTG								SLIT3 (30183 upstream) : CCDC99 (252321 downstream)																							AATGAGCATTTGTGTGTGTGTG	0.124													4	2	---	---	---	---	
CNOT6	57472	broad.mit.edu	37	5	179931503	179931503	+	Intron	DEL	G	-	-	rs71591486		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179931503delG	uc003mlx.2	+						CNOT6_uc010jld.2_Intron|CNOT6_uc010jle.2_Intron	NM_015455	NP_056270	Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	exonuclease activity|metal ion binding|protein binding|RNA binding				0	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		TTCCAAGAGCGGGGGCAGTAA	0.363													3	3	---	---	---	---	
F13A1	2162	broad.mit.edu	37	6	6264800	6264800	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6264800delT	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	tttatctatattttctcccta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27528844	27528844	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27528844delT								ZNF184 (87947 upstream) : HIST1H2BL (246414 downstream)																							cttttctttcttttttttttt	0.114													4	2	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32521955	32521956	+	Intron	INS	-	T	T	rs141382595		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32521955_32521956insT	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obm.1_Intron|HLA-DRB6_uc003obn.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CATCAAACTCATTCAAATATTA	0.248													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57447795	57447795	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57447795delC	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)		AACATACAGTCCTAAAAAGAT	0.229													4	2	---	---	---	---	
RRAGD	58528	broad.mit.edu	37	6	90088656	90088656	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90088656delT	uc003pnd.3	-						RRAGD_uc010kcc.2_Intron	NM_021244	NP_067067	Q9NQL2	RRAGD_HUMAN	Ras-related GTP binding D						cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade	lysosome|nucleus	GTP binding|protein heterodimerization activity			ovary(2)|central_nervous_system(1)	3		all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139)		BRCA - Breast invasive adenocarcinoma(108;0.0144)		agtttttacattttttttgta	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92014450	92014450	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92014450delT								MAP3K7 (717543 upstream) : None (None downstream)																							TGTTAAGCAATTTGAAGCATT	0.378													4	2	---	---	---	---	
CCNC	892	broad.mit.edu	37	6	100003881	100003883	+	Intron	DEL	TTC	-	-	rs67967832		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100003881_100003883delTTC	uc003pqe.2	-						uc003pqc.2_Intron|CCNC_uc003pqd.2_Intron|CCNC_uc010kcr.2_Intron|CCNC_uc010kcs.2_Intron|CCNC_uc011eah.1_Intron	NM_005190	NP_005181	P24863	CCNC_HUMAN	cyclin C isoform a						regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	DNA-directed RNA polymerase II, holoenzyme	protein kinase binding				0		all_cancers(76;8.46e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.064)		GGCTTGTTTGTTCTTCTTGCTGG	0.369													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100360525	100360525	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100360525delT								PRDM13 (297071 upstream) : MCHR2 (7261 downstream)																							AACAATCACATTTTTTTTTTC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	104163899	104163900	+	IGR	INS	-	T	T	rs77868789		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104163899_104163900insT								None (None upstream) : None (None downstream)																							CAGCTCCTAGATTTTTTTTTTC	0.356													3	3	---	---	---	---	
SNX3	8724	broad.mit.edu	37	6	108582834	108582834	+	5'Flank	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108582834delA	uc003psh.2	-						SNX3_uc003psi.2_5'Flank|SNX3_uc010kdi.2_5'Flank	NM_003795	NP_003786	O60493	SNX3_HUMAN	sorting nexin 3 isoform a						cell communication|endocytosis|protein transport	early endosome|endosome membrane	phosphatidylinositol-3-phosphate binding|protein phosphatase binding				0		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)		TGAAACCAGTAAAGTGGGGGA	0.433											OREG0003976	type=REGULATORY REGION|Gene=SNX3|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	4	2	---	---	---	---	
ARMC2	84071	broad.mit.edu	37	6	109285993	109285993	+	Intron	DEL	A	-	-	rs77214837		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109285993delA	uc003pss.3	+						ARMC2_uc011eao.1_Intron	NM_032131	NP_115507	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2								binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		actctgtctcaaaaaaaaaaa	0.114													6	6	---	---	---	---	
SESN1	27244	broad.mit.edu	37	6	109309010	109309010	+	Intron	DEL	T	-	-	rs35465901		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109309010delT	uc003pst.3	-						SESN1_uc003psu.2_Intron	NM_014454	NP_055269	Q9Y6P5	SESN1_HUMAN	sestrin 1						cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		AGCAGCTATCttttttttttt	0.169													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	113967189	113967189	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113967189delT								None (None upstream) : MARCKS (211338 downstream)																							TTCTTTTTAATTTTGGACTTA	0.343													4	2	---	---	---	---	
KPNA5	3841	broad.mit.edu	37	6	117038026	117038026	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117038026delA	uc003pxh.2	+							NM_002269	NP_002260	O15131	IMA5_HUMAN	karyopherin alpha 5						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		CTCTAGCACTAAGAGAAGTTT	0.313													4	2	---	---	---	---	
FAM184A	79632	broad.mit.edu	37	6	119417042	119417042	+	Intron	DEL	G	-	-	rs77840760	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119417042delG	uc003pyk.3	-						FAM184A_uc003pyl.3_Intron	NM_001100411	NP_001093881	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 2											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7						CTATTTTTTTGTGTGTGTGAA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	123396427	123396434	+	IGR	DEL	TTTCTTTC	-	-	rs72350422		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123396427_123396434delTTTCTTTC								CLVS2 (11364 upstream) : TRDN (141049 downstream)																							AGCTACCTCTtttctttctttctttctt	0.159													5	3	---	---	---	---	
CCDC28A	25901	broad.mit.edu	37	6	139113667	139113667	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139113667delA	uc003qie.2	+							NM_015439	NP_056254	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A												0				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		tctaaaatttaaaaaaaaaaa	0.149													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147202029	147202029	+	Intron	DEL	A	-	-	rs67976664		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147202029delA	uc003qls.1	-						uc003qlt.1_Intron|uc003qlu.1_Intron|uc003qlv.2_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																		TTTGAGTATTAAAAAAAAAAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148313559	148313559	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148313559delT								SAMD5 (422402 upstream) : SASH1 (350170 downstream)																							TTTCTTTTAATTTTTTTTTTG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148887891	148887891	+	IGR	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148887891delG								SASH1 (14707 upstream) : UST (180380 downstream)																							CATCCAGAGAGGCATCTAAAG	0.478													4	2	---	---	---	---	
SYNE1	23345	broad.mit.edu	37	6	152783641	152783641	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152783641delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qow.2_Intron|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTGGTTGTAGAAAAAAAAAAT	0.239										HNSCC(10;0.0054)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	153819749	153819749	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153819749delT								RGS17 (367360 upstream) : OPRM1 (511887 downstream)																							aagtatgtactttttttaatc	0.000													4	2	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162865696	162865697	+	Intron	INS	-	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162865696_162865697insA	uc003qtx.3	-						PARK2_uc010kkd.2_5'Flank|PARK2_uc003qtw.3_5'Flank|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		CTTCCTTATTCAGGGCACCAGT	0.193													4	2	---	---	---	---	
TNRC18	84629	broad.mit.edu	37	7	5399459	5399460	+	Intron	DEL	CA	-	-	rs35120436		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5399459_5399460delCA	uc003soi.3	-						TNRC18_uc003soj.2_5'Flank	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CGCGTACACTCACACACACACA	0.441													2	4	---	---	---	---	
CYTH3	9265	broad.mit.edu	37	7	6233795	6233795	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6233795delA	uc003spt.2	-							NM_004227	NP_004218	O43739	CYH3_HUMAN	cytohesin 3						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|membrane fraction|plasma membrane	1-phosphatidylinositol binding|ARF guanyl-nucleotide exchange factor activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity				0						aaacagacacaaaaaaGCAAA	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	10617608	10617608	+	IGR	DEL	T	-	-	rs75218527		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10617608delT								PER4 (942161 upstream) : NDUFA4 (355207 downstream)																							CTTCTCCAACTTTTCTTCAAT	0.373													3	3	---	---	---	---	
ABCB5	340273	broad.mit.edu	37	7	20691528	20691530	+	Intron	DEL	TTC	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20691528_20691530delTTC	uc003suw.3	+						ABCB5_uc010kuh.2_Intron|ABCB5_uc003suv.3_Intron|ABCB5_uc011jyi.1_Intron	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5						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						cccaagacaattcttctttcaat	0.089													2	4	---	---	---	---	
MPP6	51678	broad.mit.edu	37	7	24678965	24678965	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24678965delT	uc003swx.2	+						MPP6_uc003swy.2_Intron	NM_016447	NP_057531	Q9NZW5	MPP6_HUMAN	membrane protein, palmitoylated 6						protein complex assembly		protein binding				0						tcacttcacctttttttgcat	0.025													4	2	---	---	---	---	
PLEKHA8	84725	broad.mit.edu	37	7	30101797	30101797	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30101797delT	uc003tam.1	+						PLEKHA8_uc003tao.2_Intron|PLEKHA8_uc003tap.1_Intron|PLEKHA8_uc003tan.2_Intron	NM_032639	NP_116028	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4						TACCACCTTATTTTTTTTTTG	0.308											OREG0017934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	3	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34097444	34097445	+	Intron	DEL	AC	-	-	rs74446543		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34097444_34097445delAC	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						AGGAGGGGGAacacacacacac	0.312													4	3	---	---	---	---	
NPSR1	387129	broad.mit.edu	37	7	34853337	34853337	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34853337delT	uc003teg.1	+						AAA1_uc010kwq.1_Intron|AAA1_uc011kaq.1_Intron|NPSR1_uc003teh.1_Intron|NPSR1_uc010kwt.1_Intron|NPSR1_uc010kwu.1_Intron|NPSR1_uc010kwv.1_Intron|NPSR1_uc003tei.1_Intron|NPSR1_uc010kww.1_Intron|NPSR1_uc011kar.1_Intron|AAA1_uc010kwy.2_Intron|AAA1_uc003tek.3_Intron	NM_207172	NP_997055	Q6W5P4	NPSR1_HUMAN	G protein-coupled receptor for asthma							cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity			skin(3)|pancreas(1)	4					Halothane(DB01159)	AAACTTGACATTTGACCTCAC	0.348													4	2	---	---	---	---	
EEPD1	80820	broad.mit.edu	37	7	36286301	36286301	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36286301delT	uc003tfa.2	+							NM_030636	NP_085139	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0						CTGATAGGTGTTTTTTTTTTA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	42793955	42793955	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42793955delC								GLI3 (517337 upstream) : C7orf25 (154919 downstream)																							GTGACCCACTCCCCACCCACA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52639714	52639714	+	IGR	DEL	C	-	-	rs75437694		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52639714delC								None (None upstream) : POM121L12 (463635 downstream)																							ataagacactcccagttctat	0.119													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55944301	55944301	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55944301delT								SEPT14 (13819 upstream) : ZNF713 (10861 downstream)																							AATCGGtttcttttttttctt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61825815	61825815	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61825815delC								None (None upstream) : LOC643955 (925857 downstream)																							tgtctgacagctttgaagaga	0.000													4	2	---	---	---	---	
GTF2IRD2P1	401375	broad.mit.edu	37	7	72664015	72664016	+	5'UTR	INS	-	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72664015_72664016insG	uc003txs.1	-	11					FKBP6_uc003twz.2_Intron	NR_002164				RecName: Full=General transcription factor II-I repeat domain-containing protein 2B; AltName: Full=GTF2I repeat domain-containing protein 2B; AltName: Full=Transcription factor GTF2IRD2-beta;												0						ATACCACCCCCGGGGCATGCCA	0.505													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	72980019	72980019	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72980019delT								BCL7B (7995 upstream) : TBL2 (3260 downstream)																							TTTGGAACCATTAGTCCCTGG	0.289													4	2	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76626961	76626962	+	Intron	INS	-	TG	TG	rs140820337		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76626961_76626962insTG	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						ggaggtggggatgtggggtgtg	0.000													6	3	---	---	---	---	
PION	54103	broad.mit.edu	37	7	76982629	76982629	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76982629delA	uc003ugf.2	-						PION_uc003ugg.1_Intron	NM_017439	NP_059135	A4D1B5	GSAP_HUMAN	pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1						ATCTTACTGGAAAAAAAAATC	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	91289576	91289576	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91289576delA								FZD1 (391445 upstream) : MTERF (141884 downstream)																							CATGCCTTGCAGGTTCATCTA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	95315658	95315659	+	IGR	INS	-	T	T	rs150050309	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95315658_95315659insT								PDK4 (89733 upstream) : DYNC1I1 (86159 downstream)																							TCTTATGTTTCTTTTTTTATTT	0.421													3	4	---	---	---	---	
ZCWPW1	55063	broad.mit.edu	37	7	100004130	100004130	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100004130delA	uc003uut.2	-						ZCWPW1_uc011kjq.1_Intron|ZCWPW1_uc003uur.2_Intron|ZCWPW1_uc003uus.2_Intron|ZCWPW1_uc011kjr.1_Intron|ZCWPW1_uc003uuu.1_Intron|ZCWPW1_uc011kjp.1_Intron	NM_017984	NP_060454	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1								zinc ion binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AAGGGGACTGAAAAAAAAAAT	0.488													8	4	---	---	---	---	
CFTR	1080	broad.mit.edu	37	7	117171399	117171399	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117171399delT	uc003vjd.2	+						CFTR_uc011knq.1_Intron	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)	TCTGTTGTAGTTTTTTTTTTC	0.284									Cystic_Fibrosis				4	2	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135286492	135286492	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135286492delA	uc003vsw.2	+							NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						TTTTGTAGGTAAAGTGATCTT	0.303													4	2	---	---	---	---	
NUP205	23165	broad.mit.edu	37	7	135322456	135322457	+	Intron	INS	-	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135322456_135322457insA	uc003vsw.2	+						NUP205_uc003vsx.2_Intron	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						TTTATTGCTTTAAAAAAAAAGG	0.277													4	2	---	---	---	---	
TBXAS1	6916	broad.mit.edu	37	7	139683532	139683532	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139683532delT	uc011kqv.1	+						TBXAS1_uc003vvh.2_Intron|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Intron|TBXAS1_uc003vvi.2_Intron|TBXAS1_uc003vvj.2_Intron|TBXAS1_uc011kqw.1_Intron	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)					TCCGCACACATTTTTTTTTCT	0.423													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151964797	151964797	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151964797delC	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)		aacaatctttcaaaaatgtaa	0.000			N		medulloblastoma								4	2	---	---	---	---	
SGK223	157285	broad.mit.edu	37	8	8213518	8213518	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8213518delA	uc003wsh.3	-							NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin								ATP binding|non-membrane spanning protein tyrosine kinase activity				0						aggaactgggaaaaaatgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9810661	9810661	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9810661delA								MIR124-1 (49679 upstream) : MSRA (101169 downstream)																							ATTCACTTCTAGGAGAAGCCT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	16613249	16613250	+	IGR	INS	-	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16613249_16613250insC								MSR1 (562949 upstream) : FGF20 (237084 downstream)																							CTTCAACGCTTCCCCCCTTATA	0.366													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	25394136	25394136	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25394136delA	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		GTGACTAGGGAAACCCCCAGT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30821773	30821773	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30821773delT								TEX15 (75551 upstream) : PURG (31548 downstream)																							TTTAAGGTGGTTTTTTTTGAG	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	34717261	34717261	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34717261delT								None (None upstream) : UNC5D (375714 downstream)																							AAGCACtttatttttttcttt	0.179													4	2	---	---	---	---	
ADAM9	8754	broad.mit.edu	37	8	38871771	38871771	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38871771delT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron|ADAM9_uc003xmo.1_Intron|ADAM9_uc003xmp.2_3'UTR	NM_003816	NP_003807	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9 isoform 1						activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			GTAGTTAAGGTTTTTTTTTTA	0.303													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	68865795	68865795	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68865795delC	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron|PREX2_uc003xxt.2_3'UTR	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						CAATTCCATGCCCCCTTGGTC	0.408													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	69089202	69089202	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69089202delA	uc003xxv.1	+							NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						GACAATTGTTAAAAAAAAAAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	70188905	70188905	+	IGR	DEL	A	-	-	rs35739544		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70188905delA								C8orf34 (457649 upstream) : SULF1 (189954 downstream)																							AATGGTGGGGAAAAAAAACCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	73241148	73241148	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73241148delT	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																		TCTGTCTTGATTTTTTTTTTG	0.244													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	82414839	82414840	+	IGR	DEL	CA	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82414839_82414840delCA								FABP4 (19366 upstream) : FABP12 (22443 downstream)																							CTGCCCTCATCACATTCTAACT	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	110862925	110862925	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110862925delC								SYBU (158905 upstream) : KCNV1 (116310 downstream)																							gtgaagatgtcccattttgtc	0.000													4	2	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	113344529	113344531	+	Intron	DEL	AAG	-	-	rs141548591		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113344529_113344531delAAG	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc003ynw.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						TCAAATTATCAAGAAGTGGAGGA	0.300										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136425934	136425934	+	IGR	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136425934delG								LOC286094 (113975 upstream) : KHDRBS3 (43782 downstream)																							TCCTCCCCTAGGCTATACCAG	0.448													4	2	---	---	---	---	
ADAMTSL1	92949	broad.mit.edu	37	9	18696463	18696463	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18696463delT	uc003zne.3	+							NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)		aaagtttgtcttttttacctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33564702	33564702	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33564702delT								SUGT1P1 (53655 upstream) : ANXA2P2 (59521 downstream)																							tcaccagcacttttttttgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44118621	44118621	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44118621delA								FAM75A6 (487891 upstream) : FAM27C (871615 downstream)																							TCTACTCCACAATCCTCGATC	0.607													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44742109	44742110	+	IGR	INS	-	TG	TG	rs145005151	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44742109_44742110insTG								None (None upstream) : FAM27C (248126 downstream)																							tgtgtggattatgtgtgtgtat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66462280	66462281	+	Intron	INS	-	T	T	rs144579958	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66462280_66462281insT	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		aggtcctgggctttttgggggt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66462289	66462290	+	Intron	INS	-	A	A	rs60637301		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66462289_66462290insA	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																		gctttttgggggttggtaggct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69804754	69804754	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69804754delT								LOC100133920 (139805 upstream) : FOXD4L5 (370955 downstream)																							tcacataaccttttttttttt	0.000													5	3	---	---	---	---	
TMC1	117531	broad.mit.edu	37	9	75430881	75430881	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75430881delA	uc004aiz.1	+						TMC1_uc010moz.1_Intron|TMC1_uc004aja.1_Intron|TMC1_uc004ajb.1_Intron|TMC1_uc004ajc.1_Intron|TMC1_uc010mpa.1_Intron	NM_138691	NP_619636	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1						sensory perception of sound	integral to membrane				ovary(1)	1						CACTGTGTTTAAAAAAAAAAA	0.209													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81328094	81328094	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81328094delT								PSAT1 (383087 upstream) : TLE4 (858784 downstream)																							GTAGACCATCTTTAACCTTTC	0.373													4	2	---	---	---	---	
ZCCHC6	79670	broad.mit.edu	37	9	88937007	88937007	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88937007delT	uc004aoq.2	-						ZCCHC6_uc010mqe.2_5'Flank|ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2						taaaaaaaaaTTTTTTTTTAA	0.184													4	2	---	---	---	---	
SHC3	53358	broad.mit.edu	37	9	91693091	91693091	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91693091delT	uc004aqg.2	-							NM_016848	NP_058544	Q92529	SHC3_HUMAN	src homology 2 domain-containing transforming						central nervous system development|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	protein binding|signal transducer activity			lung(3)|skin(1)	4						AATGCTACACTTTTTTTTTTT	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107272851	107272851	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107272851delT								OR13F1 (5350 upstream) : OR13C4 (15685 downstream)																							tcttctctccttttttctttg	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	114622598	114622598	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114622598delT								C9orf84 (65375 upstream) : UGCG (36608 downstream)																							catcttcccatttcctctcct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	114723800	114723800	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114723800delT								UGCG (28369 upstream) : SUSD1 (79262 downstream)																							aagggcagagttttttttttt	0.124													4	2	---	---	---	---	
PAPPA	5069	broad.mit.edu	37	9	119136431	119136433	+	Intron	DEL	GTA	-	-	rs72208041		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119136431_119136433delGTA	uc004bjn.2	+						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						gatgatggtggtagtgttggtgg	0.039													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122527913	122527914	+	IGR	DEL	AC	-	-	rs112275053		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122527913_122527914delAC								DBC1 (396174 upstream) : MIR147 (479343 downstream)																							acacacgtgtacacacacacac	0.149													3	3	---	---	---	---	
CDK5RAP2	55755	broad.mit.edu	37	9	123282198	123282198	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123282198delA	uc004bkf.2	-						CDK5RAP2_uc004bkg.2_Intron|CDK5RAP2_uc011lxw.1_Intron|CDK5RAP2_uc011lxx.1_Intron|CDK5RAP2_uc011lxy.1_Intron|CDK5RAP2_uc011lxz.1_Intron|CDK5RAP2_uc011lya.1_Intron|CDK5RAP2_uc004bkh.1_Intron|CDK5RAP2_uc004bki.2_Intron	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2						brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4						TCATTTGGAGAAAAAAAAAAA	0.328													5	3	---	---	---	---	
BAT2L1	84726	broad.mit.edu	37	9	134317530	134317530	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134317530delT	uc004can.3	+						BAT2L1_uc004cam.1_Intron	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like								protein binding				0						tgtttgtttgtttttttttag	0.154													4	2	---	---	---	---	
TSC1	7248	broad.mit.edu	37	9	135798260	135798260	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135798260delA	uc004cca.2	-						TSC1_uc004ccb.3_Intron|TSC1_uc011mcq.1_Intron|TSC1_uc011mcr.1_Intron|TSC1_uc011mcs.1_Intron|TSC1_uc004ccc.1_Intron|TSC1_uc004ccd.2_Intron|TSC1_uc004cce.1_Intron	NM_000368	NP_000359	Q92574	TSC1_HUMAN	tuberous sclerosis 1 protein isoform 1						activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding			lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1)	14				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CCGATAGGGGAAAAAAAAAAA	0.448			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	316958	316962	+	IGR	DEL	CCTCT	-	-	rs67232603		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:316958_316962delCCTCT								ZMYND11 (16382 upstream) : DIP2C (3170 downstream)																							TCAGGGTGAACCTCTCCTAAGCTGT	0.493													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3837253	3837253	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3837253delC								KLF6 (9780 upstream) : LOC100216001 (784191 downstream)																							TGAGCAGCATCCCCCCTCGCT	0.582													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	7588434	7588434	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7588434delC								SFMBT2 (134984 upstream) : ITIH5 (13202 downstream)																							CAAGTCACCACCACATCGCTC	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8476830	8476831	+	IGR	DEL	TT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8476830_8476831delTT								GATA3 (359668 upstream) : None (None downstream)																							agtgctgggattacagatgcaa	0.109													4	2	---	---	---	---	
CACNB2	783	broad.mit.edu	37	10	18766823	18766823	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18766823delT	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron|CACNB2_uc009xkb.1_Intron|CACNB2_uc010qcm.1_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.2_Intron|CACNB2_uc010qcn.1_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	ttcagcttcatttttttttct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36995404	36995404	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36995404delA								None (None upstream) : ANKRD30A (419381 downstream)																							TCTGAAAGTGAAAAAAAAAAT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45736261	45736261	+	IGR	DEL	A	-	-	rs35312527		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45736261delA								LOC100133308 (86217 upstream) : OR13A1 (61841 downstream)																							AGGCAGTGAGAAAAAAAAATA	0.373													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46104061	46104061	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46104061delA								MARCH8 (13707 upstream) : ANUBL1 (6979 downstream)																							TGAGCTTCACAAAAAAAAGAA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64549839	64549840	+	IGR	DEL	CA	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64549839_64549840delCA								ZNF365 (118068 upstream) : ADO (14676 downstream)																							CAGGAAGGAGCAAAGACTCGCG	0.550													4	2	---	---	---	---	
REEP3	221035	broad.mit.edu	37	10	65376759	65376759	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65376759delT	uc001jmt.2	+							NM_001001330	NP_001001330	Q6NUK4	REEP3_HUMAN	receptor accessory protein 3							integral to membrane					0	Prostate(12;0.0119)|all_hematologic(501;0.191)					TATATGTACATTTTTTTTTTC	0.199													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65533624	65533624	+	IGR	DEL	T	-	-	rs34328042		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65533624delT								REEP3 (151653 upstream) : None (None downstream)																							TGTTGCTTGATTTTTTTTTTC	0.323													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80355731	80355731	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80355731delC								RPS24 (539161 upstream) : LOC283050 (347353 downstream)																							ggagaatgctcagggcagaag	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85582468	85582468	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85582468delA								NRG3 (835533 upstream) : GHITM (316717 downstream)																							aaacaacaacaaaaaAAACTT	0.353													4	2	---	---	---	---	
OPN4	94233	broad.mit.edu	37	10	88423774	88423775	+	Intron	DEL	TG	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88423774_88423775delTG	uc001kdq.2	+						LDB3_uc010qml.1_5'Flank|OPN4_uc001kdp.2_Intron|OPN4_uc010qmk.1_Intron|OPN4_uc009xsx.1_3'UTR	NM_033282	NP_150598	Q9UHM6	OPN4_HUMAN	opsin 4 isoform 1						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity			ovary(1)	1						GGTCTGCACATGTGTGTGTGTG	0.530													4	3	---	---	---	---	
LIPF	8513	broad.mit.edu	37	10	90426739	90426739	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90426739delT	uc001kfg.1	+						LIPF_uc009xtk.2_Intron|LIPF_uc001kfh.1_Intron|LIPF_uc010qmt.1_Intron|LIPF_uc010qmu.1_Intron	NM_004190	NP_004181	P07098	LIPG_HUMAN	lipase, gastric precursor						lipid catabolic process|triglyceride metabolic process	extracellular region	lipid binding|triglyceride lipase activity				0		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)		AATTAGAGGCTTTTTTTTTTT	0.353													4	2	---	---	---	---	
DNTT	1791	broad.mit.edu	37	10	98078825	98078825	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98078825delT	uc001kmf.2	+						DNTT_uc001kmg.2_Intron	NM_004088	NP_004079	P04053	TDT_HUMAN	terminal deoxynucleotidyltransferase isoform 1						DNA modification	nucleus	DNA binding|DNA nucleotidylexotransferase activity|DNA-directed DNA polymerase activity|metal ion binding			ovary(1)	1		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)		GGTCTTTTCATTTTTTTTTCT	0.279													4	2	---	---	---	---	
SH3PXD2A	9644	broad.mit.edu	37	10	105476966	105476967	+	Intron	INS	-	T	T	rs145596434	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105476966_105476967insT	uc001kxj.1	-						SH3PXD2A_uc010qqu.1_Intron	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1						cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		CTCTGCTCCCCGAGGTGGGCAG	0.243													9	7	---	---	---	---	
SORCS3	22986	broad.mit.edu	37	10	107012961	107012962	+	Intron	DEL	AG	-	-	rs72158485		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107012961_107012962delAG	uc001kyi.1	+							NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GGGGAGCAGCagagagagagag	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	115279339	115279341	+	IGR	DEL	GAT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115279339_115279341delGAT								TCF7L2 (351905 upstream) : HABP2 (33437 downstream)																							TTATCCtgaggatgatgatgatg	0.236													4	2	---	---	---	---	
TACC2	10579	broad.mit.edu	37	10	123755269	123755269	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123755269delT	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing							microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				tgccaggatcttttctttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	2276522	2276522	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2276522delA								TH (83487 upstream) : ASCL2 (13207 downstream)																							cagatgtaacaaaaaaagtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	2364543	2364543	+	Intron	DEL	T	-	-	rs143161828	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2364543delT	uc001lwe.2	-											Homo sapiens, clone IMAGE:4940779, mRNA.																		tcctatgagattaggacccac	0.005													4	2	---	---	---	---	
SBF2	81846	broad.mit.edu	37	11	10003422	10003422	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10003422delA	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		AATCGTAATGAAAAAAAATCA	0.333													4	2	---	---	---	---	
NELL1	4745	broad.mit.edu	37	11	21251153	21251153	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21251153delA	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3						TGCGTCAGGGAAAAAGAAAAA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	25567435	25567435	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25567435delT								LUZP2 (463253 upstream) : ANO3 (643394 downstream)																							AGCAGTCTAATTTTTTTTTCT	0.363													4	2	---	---	---	---	
BDNFOS	497258	broad.mit.edu	37	11	27668068	27668068	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27668068delT	uc001mrm.2	+						BDNFOS_uc009yij.2_Intron|BDNFOS_uc009yik.2_Intron|BDNFOS_uc009yil.2_Intron|BDNFOS_uc001mrp.2_Intron|BDNFOS_uc009yim.2_Intron|BDNFOS_uc009yin.2_Intron|BDNFOS_uc009yio.2_Intron|BDNFOS_uc009yip.2_Intron|BDNFOS_uc001mrn.2_Intron|BDNFOS_uc009yiq.2_Intron|BDNFOS_uc001mro.2_Intron|BDNFOS_uc009yir.2_Intron|BDNFOS_uc009yis.2_Intron|BDNFOS_uc009yit.2_Intron|BDNFOS_uc009yiu.2_Intron|BDNFOS_uc009yiv.2_Intron|BDNFOS_uc009yiw.2_Intron|BDNFOS_uc009yix.2_Intron|BDNFOS_uc009yiy.2_Intron|BDNFOS_uc009yiz.2_Intron|BDNFOS_uc001mrq.3_Intron|BDNFOS_uc001mrr.3_Intron|BDNFOS_uc009yja.2_Intron|BDNFOS_uc009yjb.2_Intron	NR_002832				Homo sapiens non-coding transcript BT2C (BDNF) mRNA, complete sequence; alternatively spliced.												0						ACATGGATTGTTTTTTTTTCT	0.368													4	2	---	---	---	---	
QSER1	79832	broad.mit.edu	37	11	32953094	32953094	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32953094delA	uc001mty.2	+						QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_5'Flank	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					cctgtctcttaaaaaaaaaag	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	34621015	34621015	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34621015delT								ELF5 (85685 upstream) : EHF (21653 downstream)																							CTGGAAGCCATTCTAACAAAC	0.493													4	2	---	---	---	---	
C2CD3	26005	broad.mit.edu	37	11	73750932	73750932	+	Intron	DEL	A	-	-	rs77278331		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73750932delA	uc001ouu.2	-						C2CD3_uc001out.2_Intron	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3							centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					TGAATGACCCAAAAAAATACA	0.274													4	2	---	---	---	---	
PPME1	51400	broad.mit.edu	37	11	73899810	73899810	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73899810delT	uc001ouw.2	+							NM_016147	NP_057231	Q9Y570	PPME1_HUMAN	protein phosphatase methylesterase 1						protein demethylation		carboxylesterase activity|protein C-terminal methylesterase activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity				0	Breast(11;3.29e-05)					ttttcagttcttttttttcct	0.025													4	2	---	---	---	---	
ME3	10873	broad.mit.edu	37	11	86195932	86195933	+	Intron	INS	-	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86195932_86195933insA	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)	ttctcttgcataaaatgggaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91738691	91738691	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91738691delT								None (None upstream) : FAT3 (346571 downstream)																							aaattgttccttttttttcct	0.005													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114188316	114188316	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114188316delT								NNMT (5078 upstream) : C11orf71 (73854 downstream)																							AAATGCTAGATTTTTTTTTTG	0.303											OREG0021349	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
REXO2	25996	broad.mit.edu	37	11	114315095	114315095	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114315095delA	uc001poy.2	+						REXO2_uc001poz.2_Intron	NM_015523	NP_056338	Q9Y3B8	ORN_HUMAN	small fragment nuclease precursor						nucleotide metabolic process	mitochondrion|nucleus	3'-5' exonuclease activity|nucleic acid binding				0		all_cancers(61;5.06e-12)|all_epithelial(67;5.3e-06)|all_hematologic(158;7.68e-05)|Acute lymphoblastic leukemia(157;0.000966)|Melanoma(852;0.00153)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.0818)|Prostate(24;0.104)		BRCA - Breast invasive adenocarcinoma(274;2.65e-06)|Epithelial(105;6.09e-05)|all cancers(92;0.000494)		ATTCTTGAAGAAAAAAAAATG	0.348													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	123138647	123138647	+	IGR	DEL	T	-	-	rs111237244		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123138647delT								ASAM (72640 upstream) : GRAMD1B (257881 downstream)																							AATGCTAAAATTTTTTTTTTT	0.343													3	4	---	---	---	---	
ZBTB44	29068	broad.mit.edu	37	11	130155186	130155186	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130155186delT	uc001qga.2	-						ZBTB44_uc001qgb.3_Intron|ZBTB44_uc001qfx.2_Intron|ZBTB44_uc001qgc.1_Intron	NM_014155	NP_054874	Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)		tcttgttttcttttttttttt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134609011	134609012	+	IGR	DEL	TG	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134609011_134609012delTG								B3GAT1 (327199 upstream) : None (None downstream)																							tgtgtatgtctgtgtgtgtgtg	0.025													4	3	---	---	---	---	
DYRK4	8798	broad.mit.edu	37	12	4689964	4689964	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4689964delT	uc009zeh.1	+							NM_003845	NP_003836	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation							Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)			CACTTAGGGATTTTTTTTTTT	0.463													5	6	---	---	---	---	
DDX12	440081	broad.mit.edu	37	12	9586446	9586460	+	Intron	DEL	CTCCCCAGGAGAGGA	-	-	rs68134972		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9586446_9586460delCTCCCCAGGAGAGGA	uc010sgs.1	-						DDX12_uc009zgq.1_Intron	NM_004400	NP_004391			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12												0						CAGGAAAGGTCTCCCCAGGAGAGGACTCCCCAGGC	0.642													7	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	24800082	24800083	+	IGR	DEL	AC	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24800082_24800083delAC								SOX5 (84702 upstream) : BCAT1 (164198 downstream)																							atggtatactacaaaaacaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	24951833	24951833	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24951833delT								SOX5 (236453 upstream) : BCAT1 (12448 downstream)																							GAGGAAAGTATTTTTTTAAGA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31289315	31289315	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31289315delT	uc010sjy.1	-											RecName: Full=Ovostatin homolog 1; Flags: Precursor;																		TAAACGCCACTTTTTTTTTTA	0.294													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34128091	34128091	+	IGR	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34128091delG								SYT10 (535337 upstream) : ALG10 (47125 downstream)																							GAGGCGCGATGGCGTGGACAG	0.408													4	2	---	---	---	---	
CPNE8	144402	broad.mit.edu	37	12	39164126	39164126	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39164126delC	uc001rls.1	-							NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN	copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				gatcctttatccagtccacca	0.000													4	2	---	---	---	---	
SLC2A13	114134	broad.mit.edu	37	12	40424513	40424514	+	Intron	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40424513_40424514insT	uc010skm.1	-						SLC2A13_uc001rmf.2_Intron	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)				ATTTTTACAAGTTTTTTTTTAA	0.228										HNSCC(50;0.14)			4	2	---	---	---	---	
PDZRN4	29951	broad.mit.edu	37	12	41687459	41687459	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41687459delA	uc010skn.1	+							NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TCATCCTGGCAAAAGGAAATC	0.403													4	2	---	---	---	---	
GALNT6	11226	broad.mit.edu	37	12	51749934	51749935	+	Intron	DEL	AT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51749934_51749935delAT	uc001ryk.2	-						GALNT6_uc009zma.1_Intron|GALNT6_uc001ryl.1_Intron|GALNT6_uc001ryj.1_Intron	NM_007210	NP_009141	Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6						protein O-linked glycosylation	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2						TTTtatatacatatatatatat	0.208													4	2	---	---	---	---	
LEMD3	23592	broad.mit.edu	37	12	65636924	65636925	+	Intron	INS	-	T	T	rs140937501	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65636924_65636925insT	uc001ssl.1	+						LEMD3_uc009zqo.1_Intron	NM_014319	NP_055134	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3						negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		gctttttgtactttttttttta	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68791420	68791420	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68791420delT								MDM1 (65259 upstream) : RAP1B (213232 downstream)																							tccaacaacctctcccacact	0.000													4	2	---	---	---	---	
PTPRQ	374462	broad.mit.edu	37	12	80936282	80936282	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80936282delT	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0						ACTTTGTTGATTTTTTTTTGC	0.308													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89397118	89397118	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89397118delT								KITLG (422880 upstream) : DUSP6 (344721 downstream)																							tttgcttgtatttccatcatt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92897701	92897701	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92897701delA								CLLU1 (20245 upstream) : C12orf74 (199139 downstream)																							ATTTGGTTGTAAAGTGAGGCC	0.418													4	2	---	---	---	---	
CCDC38	120935	broad.mit.edu	37	12	96289187	96289188	+	Intron	INS	-	T	T	rs143968981	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96289187_96289188insT	uc001tek.1	-							NM_182496	NP_872302	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38											skin(1)	1						CTTGTTTATTATTCTGTAGGAA	0.252													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102729580	102729580	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102729580delA								PMCH (137966 upstream) : IGF1 (60065 downstream)																							ctatcaggataatcctggata	0.000													4	2	---	---	---	---	
CORO1C	23603	broad.mit.edu	37	12	109056094	109056094	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109056094delT	uc001tnj.2	-						CORO1C_uc009zva.2_Intron|CORO1C_uc010sxf.1_Intron	NM_014325	NP_055140	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C isoform 1						actin cytoskeleton organization|phagocytosis|signal transduction	actin cytoskeleton	actin filament binding			skin(3)	3						TGTTAGGCGgttttttttttg	0.194													8	4	---	---	---	---	
MSI1	4440	broad.mit.edu	37	12	120809497	120809498	+	5'Flank	DEL	AA	-	-	rs112962110		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120809497_120809498delAA	uc001tye.1	-							NM_002442	NP_002433	O43347	MSI1H_HUMAN	musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATTTTGGATTAAAAAAAAAAAA	0.401													5	3	---	---	---	---	
SPPL3	121665	broad.mit.edu	37	12	121274366	121274366	+	Intron	DEL	T	-	-	rs34331497		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121274366delT	uc001tzd.2	-						SPPL3_uc009zwz.2_Intron	NM_139015	NP_620584	Q8TCT6	PSL4_HUMAN	signal peptide peptidase 3							integral to membrane	aspartic-type endopeptidase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					actgagcccctgcccaaatgc	0.000													1	5	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129676326	129676327	+	Intron	DEL	AC	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129676326_129676327delAC	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		acacacacatacacacacacac	0.114													4	2	---	---	---	---	
IFT88	8100	broad.mit.edu	37	13	21170193	21170194	+	Intron	INS	-	TAAAA	TAAAA	rs149283826	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21170193_21170194insTAAAA	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron|IFT88_uc001unk.2_5'Flank	NM_175605	NP_783195	Q13099	IFT88_HUMAN	intraflagellar transport 88 homolog isoform 1						cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		gaccttgtctgtaaaataaaat	0.094													5	7	---	---	---	---	
ELF1	1997	broad.mit.edu	37	13	41522877	41522877	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41522877delA	uc001uxs.2	-						ELF1_uc010tfc.1_Intron|ELF1_uc010acd.2_Intron	NM_172373	NP_758961	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		AACACATCCTAAAATACTCCT	0.393													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	54743699	54743699	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54743699delT								None (None upstream) : MIR1297 (142408 downstream)																							ttagtttatgttttaaagctc	0.055													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102885417	102885418	+	Intron	DEL	CA	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102885417_102885418delCA	uc001vpf.2	-							NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ggtcccacctcacaccattccc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105501488	105501488	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105501488delA								None (None upstream) : DAOA (616728 downstream)																							catagaactgaaaaaaatgct	0.000													4	2	---	---	---	---	
SUPT16H	11198	broad.mit.edu	37	14	21833520	21833521	+	Intron	INS	-	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21833520_21833521insC	uc001wao.2	-							NM_007192	NP_009123	Q9Y5B9	SP16H_HUMAN	chromatin-specific transcription elongation						DNA repair|DNA replication|nucleosome disassembly|positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|nucleoplasm	GTP binding				0	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		CTAATTGATTATATCGAGCCTT	0.351													7	4	---	---	---	---	
GPR137C	283554	broad.mit.edu	37	14	53074767	53074767	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53074767delT	uc001wzu.3	+						GPR137C_uc001wzt.3_Intron	NM_001099652	NP_001093122	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C							integral to membrane					0	Breast(41;0.0716)					ttagatcatgttttttaatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20135576	20135577	+	IGR	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20135576_20135577insT								None (None upstream) : GOLGA6L6 (601517 downstream)																							CATTTTCTCTATTTATTTTCCC	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20139627	20139627	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20139627delT								None (None upstream) : GOLGA6L6 (597467 downstream)																							tgattttctgtcacttatttt	0.065													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20522432	20522433	+	IGR	INS	-	GAC	GAC	rs111940997		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20522432_20522433insGAC								None (None upstream) : GOLGA6L6 (214661 downstream)																							tgagaagaaatgagatgaaatg	0.000													2	4	---	---	---	---	
LOC646214	646214	broad.mit.edu	37	15	21934828	21934828	+	RNA	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21934828delG	uc010tzj.1	-	1		c.5912delC				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						TAGATATAGTGGGAATAAAAT	0.279													4	2	---	---	---	---	
NF1P1	440225	broad.mit.edu	37	15	22146377	22146378	+	5'Flank	DEL	GT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22146377_22146378delGT	uc010tzs.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0						tTGAgtgtgggtgtgtgtgtgt	0.233													4	2	---	---	---	---	
GOLGA9P	283796	broad.mit.edu	37	15	23258265	23258268	+	Intron	DEL	TCTC	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23258265_23258268delTCTC	uc001yvh.1	+						uc001yvi.2_5'Flank	NR_024074				RecName: Full=Putative golgin subfamily A member 6-like protein 11;												0						TAATGATTGTTCTCTCTACCTCTC	0.603													9	4	---	---	---	---	
MAGEL2	54551	broad.mit.edu	37	15	23891981	23891982	+	5'Flank	INS	-	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23891981_23891982insG	uc001ywj.3	-							NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		GTGCTCCTGAAGCTGGAGGCTG	0.658													4	3	---	---	---	---	
MAGEL2	54551	broad.mit.edu	37	15	23891985	23891985	+	5'Flank	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23891985delG	uc001ywj.3	-							NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		TCCTGAAGCTGGAGGCTGGGT	0.662													4	3	---	---	---	---	
SCG5	6447	broad.mit.edu	37	15	32938021	32938022	+	Intron	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32938021_32938022insT	uc001zha.2	+						SCG5_uc001zgz.2_Intron	NM_001144757	NP_001138229	P05408	7B2_HUMAN	secretogranin V isoform 1						intracellular protein transport|neuropeptide signaling pathway|peptide hormone processing|regulation of hormone secretion	extracellular region|stored secretory granule	enzyme inhibitor activity|GTP binding|unfolded protein binding				0		all_lung(180;7.32e-08)		all cancers(64;6.48e-17)|Epithelial(43;1.23e-11)|GBM - Glioblastoma multiforme(186;1.39e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0212)		TAACATAGCAAtttttttttct	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39770776	39770776	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39770776delC								C15orf54 (223728 upstream) : THBS1 (102504 downstream)																							aacaggaacgccctccttagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39835824	39835824	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39835824delC								C15orf54 (288776 upstream) : THBS1 (37456 downstream)																							AATTCTTAATCCCAGCaaatc	0.184													4	2	---	---	---	---	
INO80	54617	broad.mit.edu	37	15	41361532	41361532	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41361532delT	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1						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						gcccggctaattttttttttg	0.000													6	3	---	---	---	---	
CAPN3	825	broad.mit.edu	37	15	42682468	42682468	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42682468delA	uc001zpn.1	+						CAPN3_uc001zpk.1_Intron|CAPN3_uc001zpl.1_Intron|CAPN3_uc010udf.1_Intron|CAPN3_uc010udg.1_Intron|CAPN3_uc001zpo.1_Intron|CAPN3_uc001zpp.1_Intron	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a						muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AAGAGGGTGCAAGAACCAGGA	0.522													4	2	---	---	---	---	
SEMA6D	80031	broad.mit.edu	37	15	47563619	47563620	+	Intron	DEL	GT	-	-	rs62014043		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47563619_47563620delGT	uc001zvw.2	+							NM_020858	NP_065909	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		gtaaataaaagtgtgtgtgtgt	0.040													4	2	---	---	---	---	
GABPB1	2553	broad.mit.edu	37	15	50581308	50581308	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50581308delA	uc001zyb.2	-						GABPB1_uc001zya.2_Intron|GABPB1_uc010ufg.1_Intron|GABPB1_uc001zyc.2_Intron|GABPB1_uc001zyd.2_Intron|GABPB1_uc001zye.2_Intron|GABPB1_uc001zyf.2_Intron	NM_005254	NP_005245	Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta						positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)	1						GAATTGCATTAAATGATCTAG	0.239													4	2	---	---	---	---	
WDR72	256764	broad.mit.edu	37	15	53906143	53906144	+	Intron	INS	-	TTAT	TTAT	rs138717914	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53906143_53906144insTTAT	uc002acj.2	-							NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		CACCTAAAATCTTATTTATTTA	0.307													3	5	---	---	---	---	
LIPC	3990	broad.mit.edu	37	15	58852850	58852869	+	Intron	DEL	ACAATATAAGTCCTGAATAG	-	-	rs142136988		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58852850_58852869delACAATATAAGTCCTGAATAG	uc010bga.1	+						LIPC_uc010bfz.1_Intron|LIPC_uc002afa.1_Intron|LIPC_uc010bgb.1_Intron|LIPC_uc010ugy.1_Intron	NM_000236	NP_000227	P11150	LIPC_HUMAN	lipase C precursor						cholesterol homeostasis|chylomicron remnant clearance|fatty acid biosynthetic process|high-density lipoprotein particle remodeling|intermediate-density lipoprotein particle remodeling|low-density lipoprotein particle remodeling|phosphatidylcholine catabolic process|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle	apolipoprotein binding|heparin binding|low-density lipoprotein particle binding|phospholipase activity|triglyceride lipase activity			ovary(1)	1		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		CATTACAAACACAATATAAGTCCTGAATAGACATTTAGGA	0.327													5	4	---	---	---	---	
GOLGA6A	342096	broad.mit.edu	37	15	74364482	74364482	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74364482delA	uc002axa.1	-						uc010ulg.1_5'Flank	NM_001038640	NP_001033729	Q9NYA3	GOG6A_HUMAN	golgi autoantigen, golgin subfamily a, 6												0						AGAAGGTGGGAAAACCAAGAG	0.617													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95707650	95707650	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95707650delA								MCTP2 (680470 upstream) : LOC145820 (268672 downstream)																							TCTCCTCTTTAAAAAAAAAAT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	14439284	14439284	+	IGR	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14439284delG								MIR365-1 (36056 upstream) : PARN (90275 downstream)																							tgtattttttgtagacacagg	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32410463	32410463	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32410463delT								HERC2P4 (246589 upstream) : TP53TG3B (274378 downstream)																							gcttggtagatttttttccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33946421	33946422	+	IGR	INS	-	A	A	rs112464617		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33946421_33946422insA								None (None upstream) : MIR1826 (19086 downstream)																							caaacagcatcacatgctacag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46460668	46460669	+	IGR	DEL	TT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46460668_46460669delTT								None (None upstream) : ANKRD26P1 (42580 downstream)																							tttctttctctttctttcttga	0.084													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	47818360	47818361	+	IGR	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47818360_47818361insT								PHKB (82927 upstream) : ABCC12 (298523 downstream)																							AATTTTTGAAGTTTTTTTTTTA	0.342													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55377964	55377964	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55377964delT								IRX6 (13293 upstream) : MMP2 (135117 downstream)																							ACAGTTTGCCTTttttacagg	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66126368	66126368	+	IGR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66126368delC								LOC283867 (516165 upstream) : CDH5 (274157 downstream)																							tcttcccactcccctacagag	0.025													4	2	---	---	---	---	
TMCO7	79613	broad.mit.edu	37	16	69050988	69050989	+	Intron	INS	-	A	A			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69050988_69050989insA	uc002ewi.3	+							NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7							integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)		AGGGAGTAGTGAAAAAAAAATG	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72613367	72613367	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72613367delA								PMFBP1 (407018 upstream) : ZFHX3 (203421 downstream)																							ATTTTAACTGAAAGGAATATT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	87114736	87114737	+	IGR	DEL	TC	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87114736_87114737delTC								FOXL1 (499433 upstream) : FBXO31 (248207 downstream)																							tatgtctccatctctctctctc	0.015													4	2	---	---	---	---	
ZC3H18	124245	broad.mit.edu	37	16	88666538	88666538	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88666538delC	uc002fky.2	+						ZC3H18_uc010voy.1_Intron|ZC3H18_uc010voz.1_Intron	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18							nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CAGTTTTTTGCTTCTAGGAAG	0.562													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	90185350	90185351	+	Intron	INS	-	G	G			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90185350_90185351insG	uc002fqr.2	+											Homo sapiens cDNA FLJ35239 fis, clone PROST2002212.																		GAGTATAATGtttttttttttt	0.074													18	8	---	---	---	---	
INPP5K	51763	broad.mit.edu	37	17	1398611	1398611	+	3'UTR	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1398611delC	uc002fsr.2	-	12					MYO1C_uc002fsp.2_5'Flank|INPP5K_uc002fss.2_3'UTR|INPP5K_uc002fsq.2_3'UTR|INPP5K_uc010cjr.2_3'UTR|INPP5K_uc010vql.1_3'UTR|INPP5K_uc010vqm.1_3'UTR	NM_016532	NP_057616	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K isoform						actin cytoskeleton organization	cytosol|endoplasmic reticulum|membrane fraction|neuron projection|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol bisphosphate phosphatase activity|inositol bisphosphate phosphatase activity|inositol trisphosphate phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|lipid phosphatase activity|protein binding				0						AAGCAGAAATCCCAGACCCTC	0.532													4	2	---	---	---	---	
ZZEF1	23140	broad.mit.edu	37	17	3920345	3920346	+	Intron	DEL	GT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3920345_3920346delGT	uc002fxe.2	-						ZZEF1_uc002fxg.1_5'UTR	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CATGGACTGCGTGTGTGTGTGT	0.530													4	2	---	---	---	---	
GAS7	8522	broad.mit.edu	37	17	9968076	9968078	+	Intron	DEL	TTT	-	-	rs10549742		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9968076_9968078delTTT	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						acactgtttgtttaagccacttg	0.000			T	MLL	AML*								4	2	---	---	---	---	
DNAH9	1770	broad.mit.edu	37	17	11854256	11854256	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11854256delC	uc002gne.2	+						DNAH9_uc010coo.2_Intron|DNAH9_uc002gnf.2_Intron	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GTCCAGTGTACCGCCAGCAGT	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20656957	20656957	+	IGR	DEL	T	-	-	rs113405636		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20656957delT								LGALS9B (286109 upstream) : CCDC144NL (109753 downstream)																							CAGTAACCAATTTTTTTTTTT	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21333424	21333424	+	IGR	DEL	C	-	-	rs111937714		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21333424delC								KCNJ12 (10245 upstream) : C17orf51 (98148 downstream)																							taaccacagaccttttcacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25298950	25298950	+	IGR	DEL	A	-	-	rs77602219		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25298950delA								None (None upstream) : WSB1 (322156 downstream)																							gttgataaatatttttcttgg	0.000													5	3	---	---	---	---	
LRRC37B	114659	broad.mit.edu	37	17	30375152	30375152	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30375152delA	uc002hgu.2	+						LRRC37B_uc010wbx.1_Intron|LRRC37B_uc010csu.2_Intron	NM_052888	NP_443120	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B precursor							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				CAAATATTTGAAAAAAAAATT	0.403													4	2	---	---	---	---	
ZNF207	7756	broad.mit.edu	37	17	30677557	30677558	+	Intron	DEL	TG	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30677557_30677558delTG	uc002hhh.3	+						ZNF207_uc002hhj.3_Intron|ZNF207_uc002hhi.3_Intron|ZNF207_uc010csz.2_Intron|ZNF207_uc002hhk.1_Intron	NM_003457	NP_003448	O43670	ZN207_HUMAN	zinc finger protein 207 isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			CGTGTGACTCTGTGACTCAGGA	0.594													14	7	---	---	---	---	
KRT27	342574	broad.mit.edu	37	17	38938140	38938149	+	Intron	DEL	TATTAGAATT	-	-	rs71827328		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38938140_38938149delTATTAGAATT	uc002hvg.2	-							NM_181537	NP_853515	Q7Z3Y8	K1C27_HUMAN	keratin 27							cytoplasm|intermediate filament	structural molecule activity				0		Breast(137;0.000812)				CATGTTCaaatattagaatttattagaaat	0.295													3	4	---	---	---	---	
NSF	4905	broad.mit.edu	37	17	44687433	44687433	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44687433delC	uc002iku.2	+						NSF_uc010wke.1_Intron|NSF_uc010wkf.1_Intron	NM_006178	NP_006169	P46459	NSF_HUMAN	vesicle-fusing ATPase						protein transport|synaptic transmission	cytosol	ATP binding|metal ion binding			ovary(1)	1		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		ttctttctttcctttctttcc	0.000													4	2	---	---	---	---	
ERN1	2081	broad.mit.edu	37	17	62160211	62160211	+	Intron	DEL	T	-	-	rs71768299		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62160211delT	uc002jdz.2	-							NM_001433	NP_001424	O75460	ERN1_HUMAN	endoplasmic reticulum to nucleus signalling 1						activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to endoplasmic reticulum membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1)	9						AGAACTGTGATTTTTTTTTTC	0.418													3	4	---	---	---	---	
SLC39A11	201266	broad.mit.edu	37	17	71083867	71083867	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71083867delC	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1						GGCTGTGGGGCCATGACAGTG	0.522													4	2	---	---	---	---	
ICT1	3396	broad.mit.edu	37	17	73013403	73013403	+	Intron	DEL	A	-	-	rs113430634		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73013403delA	uc002jmm.2	+							NM_001545	NP_001536	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1 precursor						mitochondrial translational termination	mitochondrial large ribosomal subunit	aminoacyl-tRNA hydrolase activity|translation release factor activity, codon nonspecific			ovary(1)|central_nervous_system(1)	2	all_lung(278;0.226)					attaaaaattaaaaaaaaaaa	0.025													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22477185	22477186	+	IGR	INS	-	AAATG	AAATG	rs143943786	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22477185_22477186insAAATG								HRH4 (417265 upstream) : ZNF521 (164702 downstream)																							GATTGCTATGAaaatgaaatga	0.257													4	2	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34255310	34255310	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34255310delT	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				AGTTGGCATCTTTTTTTTTTT	0.507													4	2	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34255317	34255318	+	Intron	INS	-	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34255317_34255318insC	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				ATCTTTTTTTTTTTCTCCCTAC	0.500													4	2	---	---	---	---	
SLC14A1	6563	broad.mit.edu	37	18	43301569	43301569	+	5'Flank	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43301569delC	uc010xcn.1	+						SLC14A1_uc010dnk.2_5'Flank|SLC14A1_uc002lbf.3_5'Flank|SLC14A1_uc002lbg.3_5'Flank|SLC14A1_uc010xco.1_5'Flank|SLC14A1_uc002lbh.3_5'Flank|SLC14A1_uc002lbi.3_5'Flank	NM_001146036	NP_001139508	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter),							integral to plasma membrane	urea transmembrane transporter activity			central_nervous_system(1)|pancreas(1)	2						TGTGATTGTTCCAGGCAGAGA	0.483													4	2	---	---	---	---	
ATP5A1	498	broad.mit.edu	37	18	43677280	43677280	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43677280delA	uc002lbr.1	-						ATP5A1_uc010dnl.1_Intron|ATP5A1_uc002lbs.1_Intron|ATP5A1_uc002lbt.1_Intron|ATP5A1_uc010dnm.1_Intron	NM_004046	NP_004037	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1						ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0						CTTTTAGAACAAAAAAAAAGT	0.348													4	2	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50915650	50915652	+	Intron	DEL	AAG	-	-	rs146354389	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50915650_50915652delAAG	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AGGAAGAGAAAAGAAAAAAGTTC	0.291													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	56058215	56058215	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56058215delT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpn.2_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						AAGGCTGCTCTTTTTTTTTTT	0.353													6	3	---	---	---	---	
ZNF532	55205	broad.mit.edu	37	18	56650988	56650989	+	Intron	INS	-	T	T	rs143271933	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56650988_56650989insT	uc002lho.2	+						ZNF532_uc002lhp.2_Intron|ZNF532_uc010xeg.1_Intron|ZNF532_uc002lhr.2_Intron|ZNF532_uc002lhs.2_Intron|ZNF532_uc010xeh.1_Intron	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2						gccccactggcagagcaatgcc	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	4044821	4044821	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4044821delT								PIAS4 (6756 upstream) : ZBTB7A (397 downstream)																							TCAAATATCATTTTTTTTTGT	0.343													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	20441860	20441860	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20441860delT								LOC284441 (71357 upstream) : ZNF826 (9218 downstream)																							ATTCATGttattttttttttt	0.164													4	3	---	---	---	---	
RHPN2	85415	broad.mit.edu	37	19	33479119	33479119	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33479119delA	uc002nuf.2	-						RHPN2_uc010xro.1_Intron|RHPN2_uc002nue.2_Intron	NM_033103	NP_149094	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2						signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)					caacaacaacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
FAM187B	148109	broad.mit.edu	37	19	35716084	35716084	+	Frame_Shift_Del	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35716084delG	uc002nyk.1	-	2	799	c.754delC	c.(754-756)CTGfs	p.L252fs		NM_152481	NP_689694	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	252	Extracellular (Potential).					integral to membrane				ovary(2)	2						TCCCACGTCAGGGGGGTGTCG	0.657													4	2	---	---	---	---	
ATP4A	495	broad.mit.edu	37	19	36051928	36051929	+	Intron	DEL	TT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36051928_36051929delTT	uc002oal.1	-							NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A						ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding			ovary(1)	1	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)	GTTTTCTTGGTTTTCCCCATGC	0.604													19	13	---	---	---	---	
FPR2	2358	broad.mit.edu	37	19	52273095	52273095	+	3'UTR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52273095delT	uc002pxr.2	+	2					FPR2_uc002pxs.3_3'UTR|FPR2_uc010epf.2_3'UTR	NM_001005738	NP_001005738	P25090	FPR2_HUMAN	formyl peptide receptor-like 1						cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			lung(3)|ovary(1)	4						GGAAAAATGCTTTTGTGTCCC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57172646	57172647	+	IGR	INS	-	C	C	rs138763827	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57172646_57172647insC								ZNF71 (37104 upstream) : ZNF835 (2308 downstream)																							TAGGGCTGGTGTGGGATGTTCA	0.163													1	5	---	---	---	---	
RASSF2	9770	broad.mit.edu	37	20	4798258	4798258	+	5'Flank	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4798258delA	uc002wld.2	-						RASSF2_uc002wle.2_Intron|RASSF2_uc002wlf.2_Intron	NM_170774	NP_739580	P50749	RASF2_HUMAN	Ras association domain family 2						cell cycle|signal transduction	nucleus	protein binding			ovary(3)|lung(2)|large_intestine(1)	6						CATCCGTTCCAAAAAAAACCA	0.483													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	11810014	11810015	+	IGR	INS	-	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11810014_11810015insC								None (None upstream) : BTBD3 (61462 downstream)																							TTCTCCTCTCACCCCCATTCTG	0.312													4	2	---	---	---	---	
C20orf7	79133	broad.mit.edu	37	20	13789832	13789832	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13789832delA	uc002wom.2	+						C20orf7_uc002won.2_Intron|C20orf7_uc002woo.2_Intron	NM_024120	NP_077025	Q5TEU4	CT007_HUMAN	hypothetical protein LOC79133 isoform 1						mitochondrial respiratory chain complex I assembly	extrinsic to mitochondrial inner membrane	methyltransferase activity				0		Myeloproliferative disorder(85;0.00878)				GGCTGTTTGTAAAAAGATGGC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37920476	37920476	+	IGR	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37920476delT								LOC339568 (67085 upstream) : None (None downstream)																							atctttgagcttttttatacc	0.000													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41044865	41044865	+	Intron	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41044865delG	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						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)				ggcagagactggggtgatgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44728843	44728843	+	IGR	DEL	A	-	-	rs112043390		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44728843delA								NCOA5 (10263 upstream) : CD40 (18063 downstream)																							GAGACAAGAGAAAAaaaaaat	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46473849	46473849	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46473849delA								SULF2 (58489 upstream) : LOC284749 (514805 downstream)																							tagctaatgcatttagcacag	0.139													42	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50195399	50195400	+	IGR	INS	-	C	C			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50195399_50195400insC								NFATC2 (16231 upstream) : ATP9A (17914 downstream)																							ACAGAACAGGGCCCCCCACTGC	0.584													4	2	---	---	---	---	
STX16	8675	broad.mit.edu	37	20	57246492	57246493	+	Intron	DEL	GG	-	-	rs35720492		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57246492_57246493delGG	uc002xzi.2	+						STX16_uc010zzq.1_Intron|STX16_uc002xzk.2_Intron|STX16_uc002xzm.2_Intron|STX16_uc002xzj.2_Intron|STX16_uc002xzl.2_Intron	NM_001001433	NP_001001433	O14662	STX16_HUMAN	syntaxin 16 isoform a						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|microsome|SNARE complex	SNAP receptor activity			ovary(1)	1	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			Atgtgtgtgtgggtgtgtgtgt	0.223													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9856378	9856380	+	IGR	DEL	CTC	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9856378_9856380delCTC								None (None upstream) : None (None downstream)																							CCTCTGCCTTCTCCTCCAGGGCA	0.581													4	3	---	---	---	---	
APP	351	broad.mit.edu	37	21	27339517	27339517	+	Intron	DEL	T	-	-	rs75712508		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27339517delT	uc002ylz.2	-						APP_uc011acg.1_Intron|APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron	NM_000484	NP_000475	P05067	A4_HUMAN	amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)				ACTGCCAACATTTTTTTTTTG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29962739	29962740	+	IGR	INS	-	A	A	rs149220489	by1000genomes	TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29962739_29962740insA								NCRNA00161 (50063 upstream) : N6AMT1 (281773 downstream)																							taatgaaaaataaaaaaaaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	33551752	33551753	+	IGR	DEL	CA	-	-	rs66502934		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33551752_33551753delCA								NCRNA00159 (22936 upstream) : C21orf45 (88779 downstream)																							TGcacacatgcacacacacaca	0.401													4	4	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36831826	36831826	+	Intron	DEL	C	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36831826delC	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						tacacttacaccagcacaaat	0.000			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	42058101	42058102	+	Intron	DEL	AT	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42058101_42058102delAT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				acacacacacatacagagcaca	0.054													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44915898	44915899	+	IGR	DEL	CA	-	-	rs67294815		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44915898_44915899delCA								C21orf84 (17795 upstream) : HSF2BP (33174 downstream)																							Aacacacgtgcacacacacaca	0.386													3	3	---	---	---	---	
ADARB1	104	broad.mit.edu	37	21	46644986	46644990	+	3'UTR	DEL	TTGTT	-	-	rs6487		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46644986_46644990delTTGTT	uc002zgy.2	+	12					ADARB1_uc002zgr.2_Intron|ADARB1_uc002zgs.2_Intron|ADARB1_uc002zgw.2_Intron|ADARB1_uc002zgv.2_Intron|ADARB1_uc002zgt.2_3'UTR|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_Intron|ADARB1_uc002zgu.2_Intron	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2						adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)		AGGGCTTCTGttgttttgttttgtt	0.366													6	4	---	---	---	---	
CECR2	27443	broad.mit.edu	37	22	17942645	17942645	+	Intron	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17942645delG	uc010gqv.1	+							NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		tactgagactggggagttaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23387245	23387245	+	IGR	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23387245delA								LOC96610 (122163 upstream) : RTDR1 (14349 downstream)																							gctctaaaccaaaaaaaaaca	0.000													4	2	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33720915	33720915	+	Intron	DEL	T	-	-	rs34010231		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33720915delT	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				tggggagagcttttgcaggtt	0.060													2	5	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2237134	2237134	+	Intron	DEL	T	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2237134delT	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				aaacagtgggttaaaaaaaat	0.154													4	2	---	---	---	---	
ZNF182	7569	broad.mit.edu	37	X	47842981	47842981	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47842981delA	uc004dir.2	-						ZNF182_uc004dis.2_Intron|ZNF182_uc004dit.2_Intron|ZNF182_uc011mlu.1_Intron|ZNF630_uc010nhz.1_Intron	NM_006962	NP_008893	P17025	ZN182_HUMAN	zinc finger protein 21 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3						AATCATGGTTAAAAAAAAACT	0.204													4	2	---	---	---	---	
KIAA1210	57481	broad.mit.edu	37	X	118215668	118215668	+	Intron	DEL	G	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118215668delG	uc004era.3	-							NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481											ovary(4)|skin(1)	5						GTATGTCAAAGGGGTAAAATC	0.498													4	3	---	---	---	---	
FGF13	2258	broad.mit.edu	37	X	137821189	137821189	+	Intron	DEL	A	-	-			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137821189delA	uc004faq.2	-						FGF13_uc004fan.2_Intron|FGF13_uc011mwi.1_Intron|FGF13_uc004far.2_Intron|FGF13_uc011mwj.1_Intron|FGF13_uc011mwk.1_Intron	NM_001139502	NP_001132974	Q92913	FGF13_HUMAN	fibroblast growth factor 13 isoform 3						cell-cell signaling|MAPKKK cascade|nervous system development	cytoplasm|nucleus	growth factor activity|protein kinase activator activity			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)					TTCCTCCCAGAAAAAAAAAAA	0.328													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9960883	9960883	+	IGR	DEL	A	-	-	rs146746526		TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9960883delA								TTTY22 (310029 upstream) : None (None downstream)																							TTGGCTAAACAAGATGTTTGC	0.473													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13401240	13401241	+	IGR	INS	-	T	T			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13401240_13401241insT								None (None upstream) : None (None downstream)																							cttttttcatgtttttttaagt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58975687	58975688	+	IGR	INS	-	ATTCC	ATTCC			TCGA-A3-3387-01A-01D-1534-10	TCGA-A3-3387-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58975687_58975688insATTCC								None (None upstream) : None (None downstream)																							gaatccattctattccattcca	0.000													4	2	---	---	---	---	
