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
SLC2A5	6518	broad.mit.edu	37	1	9129703	9129703	+	5'UTR	SNP	A	C	C	rs143295336	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9129703A>C	uc001apo.2	-	1					SLC2A5_uc010nzz.1_5'Flank|SLC2A5_uc010oaa.1_5'UTR|SLC2A5_uc010oab.1_Intron|SLC2A5_uc010oac.1_5'Flank|SLC2A5_uc001app.3_5'UTR	NM_003039	NP_003030	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated						carbohydrate metabolic process	integral to membrane|plasma membrane	fructose transmembrane transporter activity|glucose transmembrane transporter activity			pancreas(2)|ovary(1)	3	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		ATGCCAAATAACAGCCAATAG	0.458													8	29	---	---	---	---	PASS
HDAC1	3065	broad.mit.edu	37	1	32782361	32782361	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32782361G>C	uc001bvb.1	+	3	321	c.258G>C	c.(256-258)GAG>GAC	p.E86D	HDAC1_uc010ohd.1_Missense_Mutation_p.E86D|HDAC1_uc010ohe.1_Missense_Mutation_p.E23D|HDAC1_uc010ohf.1_Missense_Mutation_p.E57D	NM_004964	NP_004955	Q13547	HDAC1_HUMAN	histone deacetylase 1	86	Histone deacetylase.				anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	ACATGTCGGAGTACAGCAAGC	0.507													32	78	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62228715	62228715	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62228715G>A	uc001dab.2	+	3	167	c.53G>A	c.(52-54)CGC>CAC	p.R18H	INADL_uc009waf.1_Missense_Mutation_p.R18H|INADL_uc001daa.2_Missense_Mutation_p.R18H	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	18	L27.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						GTACTTGATCGCCTGAAAATG	0.373													42	84	---	---	---	---	PASS
MTF2	22823	broad.mit.edu	37	1	93583952	93583952	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93583952A>G	uc009wdj.2	+	7	975	c.683A>G	c.(682-684)GAG>GGG	p.E228G	MTF2_uc001dph.2_Missense_Mutation_p.E126G|MTF2_uc010oth.1_Missense_Mutation_p.E126G|MTF2_uc009wdk.2_Missense_Mutation_p.E228G|MTF2_uc001dpi.3_5'UTR|MTF2_uc010oti.1_Missense_Mutation_p.E126G|MTF2_uc001dpj.3_Missense_Mutation_p.E126G|MTF2_uc001dpl.3_Missense_Mutation_p.E126G	NM_007358	NP_031384	Q9Y483	MTF2_HUMAN	metal response element binding transcription	228	PHD-type 2.					nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)		TGGTTTCATGAGGCTTGTGTG	0.368													6	273	---	---	---	---	PASS
CD160	11126	broad.mit.edu	37	1	145698819	145698819	+	Intron	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145698819G>A	uc001eol.1	-						NBPF10_uc001emp.3_Intron|CD160_uc001eom.1_Silent_p.G115G	NM_007053	NP_008984	O95971	BY55_HUMAN	CD160 antigen precursor						cell proliferation|cell surface receptor linked signaling pathway|cellular defense response|regulation of immune response	anchored to plasma membrane	MHC class I receptor activity|receptor binding				0	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			CCTGTGGATAGCCAGGGCTTG	0.438													3	10	---	---	---	---	PASS
SPRR3	6707	broad.mit.edu	37	1	152976022	152976022	+	3'UTR	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152976022A>G	uc001fax.3	+	3					SPRR3_uc001faz.3_3'UTR|SPRR3_uc001fay.2_3'UTR	NM_005416	NP_005407	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3						keratinization|peptide cross-linking|wound healing	cytoplasm	protein binding|structural molecule activity			skin(1)	1	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGCACAGACAAGCCCTTGAGA	0.507													4	60	---	---	---	---	PASS
BAT2L2	23215	broad.mit.edu	37	1	171526993	171526993	+	Silent	SNP	A	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171526993A>C	uc010pmg.1	+	19	6002	c.5736A>C	c.(5734-5736)CCA>CCC	p.P1912P	BAT2L2_uc010pmh.1_Silent_p.P889P|BAT2L2_uc010pmi.1_5'UTR	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	1912	Ala-rich.						protein C-terminus binding				0						cttcagccccagccccagccc	0.149													11	103	---	---	---	---	PASS
ABL2	27	broad.mit.edu	37	1	179079801	179079801	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179079801T>G	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_3'UTR|ABL2_uc001gmg.3_Intron|ABL2_uc001gmi.3_Intron|ABL2_uc001gmh.3_Intron|ABL2_uc010pne.1_Intron	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	gtggcaggggttctcattgct	0.000			T	ETV6	AML								14	134	---	---	---	---	PASS
KDM5B	10765	broad.mit.edu	37	1	202718126	202718126	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202718126T>C	uc001gyf.2	-	14	2079	c.1963A>G	c.(1963-1965)ATG>GTG	p.M655V	KDM5B_uc009xag.2_Missense_Mutation_p.M691V|KDM5B_uc001gyg.1_Missense_Mutation_p.M497V	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B	655					negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5						ATAATGGCCATGTCTTTCTGA	0.393													5	125	---	---	---	---	PASS
CR1	1378	broad.mit.edu	37	1	207751242	207751242	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207751242C>A	uc001hfy.2	+	21	3420	c.3280C>A	c.(3280-3282)CGC>AGC	p.R1094S	CR1_uc009xcl.1_Missense_Mutation_p.R644S|CR1_uc001hfx.2_Missense_Mutation_p.R1544S	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1094	Extracellular (Potential).|Sushi 17.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3						GGTGACCTACCGCTGCAATCT	0.502													6	287	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214830403	214830403	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214830403T>C	uc001hkm.2	+	18	8787	c.8613T>C	c.(8611-8613)CAT>CAC	p.H2871H		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2967	Potential.|Sufficient for nuclear localization.|Sufficient for centromere localization.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		TTATAAGCCATGAAAAGTTAG	0.393													87	212	---	---	---	---	PASS
MARK1	4139	broad.mit.edu	37	1	220773196	220773196	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220773196G>A	uc001hmn.3	+	5	1012	c.415G>A	c.(415-417)GCG>ACG	p.A139T	MARK1_uc009xdw.2_Missense_Mutation_p.A139T|MARK1_uc010pun.1_Missense_Mutation_p.A139T|MARK1_uc001hmm.3_Intron	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	139	Protein kinase.				intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)		CATGGAATACGCGAGTGGGGG	0.333													4	218	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237796991	237796991	+	Silent	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237796991A>G	uc001hyl.1	+	43	6789	c.6669A>G	c.(6667-6669)GAA>GAG	p.E2223E		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2223	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATTTACTGGAAAACAGCAGTG	0.294													130	246	---	---	---	---	PASS
CENPO	79172	broad.mit.edu	37	2	25040566	25040566	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25040566A>G	uc002rfo.1	+	7	983	c.794A>G	c.(793-795)GAG>GGG	p.E265G	CENPO_uc002rfp.1_Missense_Mutation_p.E259G|CENPO_uc002rfq.1_Missense_Mutation_p.E265G	NM_024322	NP_077298	Q9BU64	CENPO_HUMAN	centromere protein O	265					cell division|CenH3-containing nucleosome assembly at centromere|chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					ACTTCATGGGAGGAGCAACGA	0.428													6	238	---	---	---	---	PASS
CAPN13	92291	broad.mit.edu	37	2	30964652	30964652	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30964652T>G	uc002rnn.2	-						CAPN13_uc002rnm.2_Intron|CAPN13_uc002rno.2_3'UTR	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					GAGAGGCAGGTAAAATAGTCC	0.582													11	16	---	---	---	---	PASS
DDX18	8886	broad.mit.edu	37	2	118583851	118583851	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118583851A>G	uc002tlh.1	+	11	1627	c.1528A>G	c.(1528-1530)ATT>GTT	p.I510V		NM_006773	NP_006764	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	510	Helicase C-terminal.						ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|ovary(1)|lung(1)	4						AAAGGAATATATTCATCGTGT	0.458													26	98	---	---	---	---	PASS
CNTNAP5	129684	broad.mit.edu	37	2	124979361	124979361	+	Silent	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124979361C>T	uc002tno.2	+	2	526	c.162C>T	c.(160-162)AGC>AGT	p.S54S	CNTNAP5_uc010flu.2_Silent_p.S54S	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	54	F5/8 type C.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCACTCACAGCCCAGCTCAAC	0.478													4	222	---	---	---	---	PASS
SAP130	79595	broad.mit.edu	37	2	128707772	128707772	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128707772T>C	uc002tpp.2	-	16	2738	c.2606A>G	c.(2605-2607)AAG>AGG	p.K869R	SAP130_uc002tpn.2_Missense_Mutation_p.K629R|SAP130_uc002tpo.2_Missense_Mutation_p.K649R|SAP130_uc010fmd.2_Missense_Mutation_p.K904R	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa isoform b	869	Interactions with SIN3A and HDAC1.				histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)|skin(2)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CTTCTCAGCCTTCACCAGAAG	0.473													6	258	---	---	---	---	PASS
MIR663B	100302269	broad.mit.edu	37	2	133015485	133015485	+	5'Flank	SNP	C	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133015485C>A	hsa-mir-663b|MI0006336	-						NCRNA00164_uc002ttj.3_RNA																	0						AACCCACACACAACCTGTCGG	0.697													3	25	---	---	---	---	PASS
MIR663B	100302269	broad.mit.edu	37	2	133015522	133015522	+	5'Flank	SNP	C	A	A	rs142087763	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133015522C>A	hsa-mir-663b|MI0006336	-						NCRNA00164_uc002ttj.3_RNA																	0						CCTCGGCGGCCGGCCGGCGCA	0.682													3	16	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141032036	141032036	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141032036C>T	uc002tvj.1	-	85	14071	c.13099G>A	c.(13099-13101)GGG>AGG	p.G4367R		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4367	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATGCAGTGCCCCCCATGGCAC	0.418										TSP Lung(27;0.18)			4	285	---	---	---	---	PASS
PPIG	9360	broad.mit.edu	37	2	170492924	170492924	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170492924A>G	uc002uez.2	+	14	1376	c.1156A>G	c.(1156-1158)AGT>GGT	p.S386G	PPIG_uc010fpx.2_Missense_Mutation_p.S371G|PPIG_uc010fpy.2_Missense_Mutation_p.S379G|PPIG_uc002ufb.2_Missense_Mutation_p.S386G|PPIG_uc002ufd.2_Missense_Mutation_p.S383G	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	386					protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	ATTTTTTAGGAGTGAGTTGAA	0.294													5	137	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179501393	179501393	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179501393T>C	uc010zfg.1	-	174	33581	c.33357A>G	c.(33355-33357)AAA>AAG	p.K11119K	TTN_uc010zfh.1_Silent_p.K4814K|TTN_uc010zfi.1_Silent_p.K4747K|TTN_uc010zfj.1_Silent_p.K4622K|TTN_uc010fre.1_Silent_p.K980K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12046							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTGATTTCTTTCACAAACT	0.463													5	167	---	---	---	---	PASS
CDK15	65061	broad.mit.edu	37	2	202687539	202687539	+	Silent	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202687539C>T	uc002uyt.2	+	5	505	c.456C>T	c.(454-456)CTC>CTT	p.L152L	CDK15_uc010ftm.2_Silent_p.L17L|CDK15_uc002uys.2_Silent_p.L101L|CDK15_uc010ftn.1_Silent_p.L101L|CDK15_uc010fto.1_Silent_p.L152L	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2	152	Protein kinase.						ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)	TAGCTTCTCTCCTGAAGGGTT	0.343													99	180	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47161848	47161848	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47161848T>C	uc003cqs.2	-	3	4331	c.4278A>G	c.(4276-4278)AAA>AAG	p.K1426K	SETD2_uc003cqv.2_Silent_p.K1415K	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1426					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CCACTCTAACTTTCTTTCTGT	0.473			N|F|S|Mis		clear cell renal carcinoma								9	767	---	---	---	---	PASS
MBD4	8930	broad.mit.edu	37	3	129150269	129150269	+	3'UTR	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129150269T>G	uc003emh.1	-	8					uc003emg.2_5'Flank|MBD4_uc003emi.1_3'UTR|MBD4_uc003emj.1_3'UTR|MBD4_uc003emk.1_3'UTR	NM_003925	NP_003916	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4						depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2						GCTGGAAAGGTGGTTGGTTGT	0.373								BER_DNA_glycosylases					21	163	---	---	---	---	PASS
CLDN18	51208	broad.mit.edu	37	3	137717737	137717737	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137717737G>T	uc003ero.1	+	1	80	c.27G>T	c.(25-27)TTG>TTT	p.L9F		NM_001002026	NP_001002026	P56856	CLD18_HUMAN	claudin 18 isoform 2	9	Helical; (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity			upper_aerodigestive_tract(1)|ovary(1)	2						GTCAGGGCTTGGGGTTCGTGG	0.567													41	23	---	---	---	---	PASS
ZBBX	79740	broad.mit.edu	37	3	167000259	167000259	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167000259G>C	uc003fep.2	-	19	2227	c.1904C>G	c.(1903-1905)ACA>AGA	p.T635R	ZBBX_uc011bpc.1_Missense_Mutation_p.T674R|ZBBX_uc003feq.2_Missense_Mutation_p.T606R	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	635						intracellular	zinc ion binding			ovary(2)	2						AAAATTTGCTGTTGAAGGTCT	0.338													75	248	---	---	---	---	PASS
NLGN1	22871	broad.mit.edu	37	3	173322301	173322301	+	5'UTR	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173322301A>G	uc003fio.1	+	3					NLGN1_uc010hww.1_5'UTR|NLGN1_uc003fip.1_5'UTR	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			AATCGGAGGTATATTCTACCA	0.423													4	75	---	---	---	---	PASS
ATP11B	23200	broad.mit.edu	37	3	182631843	182631843	+	Intron	SNP	A	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182631843A>C	uc003flb.2	+						ATP11B_uc003flc.2_3'UTR|ATP11B_uc010hxg.2_Intron	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B						aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			AACAGGATGAACCTGCCGCTC	0.428													10	25	---	---	---	---	PASS
EIF4G1	1981	broad.mit.edu	37	3	184042850	184042850	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184042850T>C	uc003fnp.2	+	18	3002	c.2804T>C	c.(2803-2805)CTT>CCT	p.L935P	EIF4G1_uc003fno.1_Missense_Mutation_p.L876P|EIF4G1_uc010hxw.1_Missense_Mutation_p.L771P|EIF4G1_uc003fnt.2_Missense_Mutation_p.L646P|EIF4G1_uc003fnq.2_Missense_Mutation_p.L848P|EIF4G1_uc003fnr.2_Missense_Mutation_p.L771P|EIF4G1_uc010hxx.2_Missense_Mutation_p.L942P|EIF4G1_uc003fns.2_Missense_Mutation_p.L895P|EIF4G1_uc010hxy.2_Missense_Mutation_p.L942P|EIF4G1_uc003fnv.3_Missense_Mutation_p.L936P|EIF4G1_uc003fnu.3_Missense_Mutation_p.L935P|EIF4G1_uc003fnw.2_Missense_Mutation_p.L942P|EIF4G1_uc003fnx.2_Missense_Mutation_p.L740P|EIF4G1_uc003fny.3_Missense_Mutation_p.L739P|SNORD66_uc003fnz.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	935	eIF3/EIF4A-binding.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTTGAGTGCCTTTGTCGTCTG	0.473													5	178	---	---	---	---	PASS
CCDC149	91050	broad.mit.edu	37	4	24832922	24832922	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24832922T>G	uc011bxr.1	-						CCDC149_uc003grc.2_Intron|CCDC149_uc003grb.2_Intron|CCDC149_uc003grd.2_Intron|CCDC149_uc003gre.2_3'UTR|CCDC149_uc011bxq.1_Intron	NM_173463	NP_775734	B4DZG3	B4DZG3_HUMAN	coiled-coil domain containing 149 isoform 1												0		Breast(46;0.173)				GTATGGCTGGTACCCTTTCCT	0.433													5	4	---	---	---	---	PASS
PDS5A	23244	broad.mit.edu	37	4	39875925	39875925	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39875925A>G	uc003guv.3	-	20	2801	c.2261T>C	c.(2260-2262)CTT>CCT	p.L754P	PDS5A_uc010ifo.2_Missense_Mutation_p.L714P	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog	754					cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						AATCTGTGCAAGCTGGACTTC	0.343													7	486	---	---	---	---	PASS
POLR2B	5431	broad.mit.edu	37	4	57876368	57876368	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57876368T>G	uc003hcl.1	+						POLR2B_uc011cae.1_Intron|POLR2B_uc011caf.1_Intron|POLR2B_uc003hcm.1_5'UTR	NM_000938	NP_000929	P30876	RPB2_HUMAN	DNA directed RNA polymerase II polypeptide B						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)					AAGTGGCAGGTAAGTTAAAGT	0.308													5	5	---	---	---	---	PASS
RCHY1	25898	broad.mit.edu	37	4	76419490	76419490	+	Intron	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76419490T>C	uc003hik.2	-						RCHY1_uc010iio.2_5'UTR|RCHY1_uc003hij.2_Intron|RCHY1_uc003hil.2_Intron|RCHY1_uc010iip.2_Intron|RCHY1_uc010iiq.2_Intron|RCHY1_uc010iir.2_Intron	NM_015436	NP_056251	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain						positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein autoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nuclear speck|ubiquitin ligase complex	electron carrier activity|p53 binding|protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AAAAAAAATTTCCAGCCACAA	0.358													14	49	---	---	---	---	PASS
C4orf26	152816	broad.mit.edu	37	4	76489658	76489658	+	3'UTR	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76489658A>G	uc003hip.1	+	2					C4orf26_uc011cbn.1_RNA|C4orf26_uc011cbo.1_Missense_Mutation_p.E149G	NM_178497	NP_848592	Q17RF5	CD026_HUMAN	hypothetical protein LOC152816 precursor							extracellular region					0			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GAGAGGGAAGAGAAACCCAAA	0.383													5	82	---	---	---	---	PASS
ARHGAP24	83478	broad.mit.edu	37	4	86852017	86852017	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86852017T>G	uc003hpk.2	+						ARHGAP24_uc003hpj.2_Intron|ARHGAP24_uc003hpl.2_Intron|ARHGAP24_uc010ikf.2_Intron|ARHGAP24_uc003hpm.2_5'UTR	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		GGAGTGGCTGTTGGGTTTCGC	0.488													6	8	---	---	---	---	PASS
SLC10A7	84068	broad.mit.edu	37	4	147179987	147179987	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147179987T>C	uc010ioz.2	-	11	1104	c.850A>G	c.(850-852)ATT>GTT	p.I284V	SLC10A7_uc003ikr.2_Missense_Mutation_p.I284V|SLC10A7_uc010ipa.2_Missense_Mutation_p.I271V|SLC10A7_uc003iks.2_RNA	NM_001029998	NP_001025169	Q0GE19	NTCP7_HUMAN	solute carrier family 10 (sodium/bile acid	284	Helical; (Potential).					integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)					AGCATCGGAATTCCTGTTGAA	0.398													5	147	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151604748	151604748	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151604748T>C	uc010ipj.2	-	37	6350	c.5876A>G	c.(5875-5877)AAC>AGC	p.N1959S	LRBA_uc003ilt.3_Missense_Mutation_p.N618S|LRBA_uc003ilu.3_Missense_Mutation_p.N1959S	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1959						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TGTGAGAATGTTGATAATTTT	0.418													231	488	---	---	---	---	PASS
KIAA0922	23240	broad.mit.edu	37	4	154506692	154506692	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154506692C>T	uc003inm.3	+	13	1289	c.1237C>T	c.(1237-1239)CGC>TGC	p.R413C	KIAA0922_uc010ipp.2_Missense_Mutation_p.R414C|KIAA0922_uc010ipq.2_Missense_Mutation_p.R266C|KIAA0922_uc010ips.1_Missense_Mutation_p.R25C	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	413	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				AATATGGTACCGCAACCATTT	0.388													4	239	---	---	---	---	PASS
DHX29	54505	broad.mit.edu	37	5	54579287	54579287	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54579287T>C	uc003jpx.2	-	11	1829	c.1709A>G	c.(1708-1710)CAA>CGA	p.Q570R	DHX29_uc010ivw.2_RNA	NM_019030	NP_061903	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	570							ATP binding|ATP-dependent helicase activity|translation initiation factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)				AGGTAGCTGTTGTCTTTCCTT	0.403													50	97	---	---	---	---	PASS
PAM	5066	broad.mit.edu	37	5	102326008	102326008	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102326008G>A	uc003knw.2	+	15	1889	c.1516G>A	c.(1516-1518)GGA>AGA	p.G506R	PAM_uc003kns.2_Missense_Mutation_p.G399R|PAM_uc003knt.2_Missense_Mutation_p.G506R|PAM_uc003knu.2_Missense_Mutation_p.G506R|PAM_uc003knv.2_Missense_Mutation_p.G506R|PAM_uc011cuz.1_Missense_Mutation_p.G409R|PAM_uc003knx.1_Missense_Mutation_p.G109R	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	506	Peptidyl-alpha-hydroxyglycine alpha- amidating lyase (By similarity).|NHL 1.|Intragranular (Potential).				peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	GGATTGGCCTGGAGTATACTT	0.438													46	110	---	---	---	---	PASS
WDR36	134430	broad.mit.edu	37	5	110428209	110428209	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110428209G>T	uc003kpd.2	+	1	340	c.223G>T	c.(223-225)GCC>TCC	p.A75S	WDR36_uc010jbu.2_RNA	NM_139281	NP_644810	Q8NI36	WDR36_HUMAN	WD repeat domain 36	75					response to stimulus|rRNA processing|visual perception	small-subunit processome				ovary(1)|skin(1)	2		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		GGGGTTCCGGGCCTTGGGACT	0.602													4	17	---	---	---	---	PASS
MEGF10	84466	broad.mit.edu	37	5	126793028	126793028	+	3'UTR	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126793028G>T	uc003kuh.3	+	26					MEGF10_uc003kui.3_3'UTR	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GGACCGCTTGGTAGCCACTGG	0.418													10	40	---	---	---	---	PASS
MIR1289-2	100302134	broad.mit.edu	37	5	132763378	132763378	+	RNA	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132763378C>T	hsa-mir-1289-2|MI0006351	-			c.21C>T			FSTL4_uc003kyn.1_Intron																	0						taggaatgtgcctttttaact	0.318													4	194	---	---	---	---	PASS
TCF7	6932	broad.mit.edu	37	5	133481533	133481533	+	Intron	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133481533G>A	uc003kyt.2	+						TCF7_uc003kyu.1_3'UTR|TCF7_uc003kyv.2_Intron|TCF7_uc003kyw.2_Intron|TCF7_uc003kyx.2_Intron|TCF7_uc003kyy.2_Intron|TCF7_uc003kyz.2_Intron|TCF7_uc003kza.2_Intron|TCF7_uc003kzb.2_Intron|TCF7_uc010jdu.2_Intron	NM_003202	NP_003193	P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific,						cellular response to interleukin-4|immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription regulatory region DNA binding				0		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCTGGGCAAGGAAGCCATAGG	0.552											OREG0016787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	67	---	---	---	---	PASS
MIR886	100126299	broad.mit.edu	37	5	135416289	135416289	+	RNA	SNP	G	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135416289G>C	hsa-mir-886|MI0005527	-			c.9G>C																				0						TCCGACCCGGGTAGGAGTGTG	0.592													34	37	---	---	---	---	PASS
SERPINB6	5269	broad.mit.edu	37	6	2955630	2955630	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2955630T>G	uc003muk.2	-						SERPINB6_uc003mui.2_5'UTR|SERPINB6_uc003muj.2_Intron|SERPINB6_uc003mul.2_Intron|SERPINB6_uc003mum.2_Intron|SERPINB6_uc003mun.2_Intron|SERPINB6_uc003muo.2_Intron	NM_004568	NP_004559	P35237	SPB6_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	centrosome|cytosol|protein complex	protease binding|serine-type endopeptidase inhibitor activity				0	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	TATTGGCAGGTGAAAAGAAAT	0.448													7	12	---	---	---	---	PASS
DSP	1832	broad.mit.edu	37	6	7567609	7567609	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7567609C>T	uc003mxp.1	+	9	1346	c.1067C>T	c.(1066-1068)ACG>ATG	p.T356M	DSP_uc003mxq.1_Missense_Mutation_p.T356M	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	356	Globular 1.|Spectrin 1.|Interacts with plakophilin 1 and junction plakoglobin.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		ACTCTGCAGACGCAGTGGAGT	0.408													7	395	---	---	---	---	PASS
DSP	1832	broad.mit.edu	37	6	7583844	7583844	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7583844G>T	uc003mxp.1	+	24	6628	c.6349G>T	c.(6349-6351)GAT>TAT	p.D2117Y	DSP_uc003mxq.1_Missense_Mutation_p.D1518Y	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	2117	Globular 2.|Plectin 3.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AAATTTGATTGATAGAGAAAC	0.443													26	61	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56394387	56394387	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56394387C>A	uc003pdf.2	-	60	11125	c.11097G>T	c.(11095-11097)CAG>CAT	p.Q3699H	DST_uc003pcz.3_Missense_Mutation_p.Q3521H|DST_uc011dxj.1_Missense_Mutation_p.Q3550H|DST_uc011dxk.1_Missense_Mutation_p.Q3561H|DST_uc003pcy.3_Missense_Mutation_p.Q3195H	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5607					cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TACATAAGGCCTGCTGGAGGA	0.428													117	254	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56394388	56394388	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56394388T>A	uc003pdf.2	-	60	11124	c.11096A>T	c.(11095-11097)CAG>CTG	p.Q3699L	DST_uc003pcz.3_Missense_Mutation_p.Q3521L|DST_uc011dxj.1_Missense_Mutation_p.Q3550L|DST_uc011dxk.1_Missense_Mutation_p.Q3561L|DST_uc003pcy.3_Missense_Mutation_p.Q3195L	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	5607					cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACATAAGGCCTGCTGGAGGAG	0.428													114	255	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70916883	70916883	+	Missense_Mutation	SNP	G	T	T	rs141812196	byFrequency	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70916883G>T	uc003pfc.1	+	51	3451	c.3334G>T	c.(3334-3336)GGC>TGC	p.G1112C		NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	1112					cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						AGGTGCCCCAGGCCCACAGGG	0.537													12	26	---	---	---	---	PASS
PHIP	55023	broad.mit.edu	37	6	79655053	79655053	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79655053A>G	uc003pir.2	-	39	5018	c.4792T>C	c.(4792-4794)TCC>CCC	p.S1598P	PHIP_uc003piq.2_Missense_Mutation_p.S622P|PHIP_uc011dyp.1_Missense_Mutation_p.S1597P|IRAK1BP1_uc010kbg.1_Intron|PHIP_uc003pio.3_Missense_Mutation_p.S484P	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1598					insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		GAAAGAGTGGACGCCTTTGGG	0.363													7	583	---	---	---	---	PASS
KIAA1009	22832	broad.mit.edu	37	6	84862656	84862656	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84862656T>C	uc010kbp.2	-	23	3334	c.3237A>G	c.(3235-3237)GAA>GAG	p.E1079E	KIAA1009_uc003pkj.3_Silent_p.E1003E|KIAA1009_uc003pki.3_Silent_p.E465E	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	1079	Potential.				cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		CATGAGCCTGTTCCACCTGGA	0.368													7	567	---	---	---	---	PASS
RSPO3	84870	broad.mit.edu	37	6	127517220	127517220	+	3'UTR	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127517220C>T	uc003qar.2	+	5					RSPO3_uc003qas.1_Intron	NM_032784	NP_116173	Q9BXY4	RSPO3_HUMAN	R-spondin 3 precursor							extracellular region	heparin binding				0				GBM - Glioblastoma multiforme(226;0.0555)		GACAGGTGCTCTAGCCATTAG	0.418													25	149	---	---	---	---	PASS
PDE7B	27115	broad.mit.edu	37	6	136500189	136500189	+	Silent	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136500189G>A	uc003qgp.2	+	10	1161	c.858G>A	c.(856-858)AGG>AGA	p.R286R	uc003qgq.1_Intron|PDE7B_uc003qgr.2_Silent_p.R338R	NM_018945	NP_061818	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	286	Catalytic (By similarity).				signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)	ACATCAACAGGCAGAATGAAT	0.428													114	186	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5396761	5396761	+	Silent	SNP	C	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5396761C>A	uc003soi.3	-	16	5329	c.4980G>T	c.(4978-4980)GGG>GGT	p.G1660G	TNRC18_uc003soj.2_Silent_p.G42G	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1660							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TGCCGCAGCCCCCGCTAGTTT	0.582													37	41	---	---	---	---	PASS
NDUFA4	4697	broad.mit.edu	37	7	10973217	10973217	+	3'UTR	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10973217C>T	uc003srx.1	-	4						NM_002489	NP_002480	O00483	NDUA4_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0				UCEC - Uterine corpus endometrioid carcinoma (126;0.177)	NADH(DB00157)	GATGTGGCTTCTGGAAGACCT	0.378													11	116	---	---	---	---	PASS
ITGB8	3696	broad.mit.edu	37	7	20431039	20431039	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20431039T>C	uc003suu.2	+	7	1679	c.974T>C	c.(973-975)CTA>CCA	p.L325P	ITGB8_uc011jyh.1_Missense_Mutation_p.L190P|ITGB8_uc003sut.2_Missense_Mutation_p.L325P	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor	325	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(3)	3						CACCCCTCACTAGGCCAACTT	0.308													5	366	---	---	---	---	PASS
GRB10	2887	broad.mit.edu	37	7	50680508	50680508	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50680508T>C	uc003tpi.2	-	10	1155	c.1124A>G	c.(1123-1125)GAG>GGG	p.E375G	GRB10_uc003tph.3_Missense_Mutation_p.E317G|GRB10_uc003tpj.2_Missense_Mutation_p.E329G|GRB10_uc003tpk.2_Missense_Mutation_p.E375G|GRB10_uc010kzb.2_Missense_Mutation_p.E317G|GRB10_uc003tpl.2_Missense_Mutation_p.E369G|GRB10_uc003tpm.2_Missense_Mutation_p.E317G|GRB10_uc003tpn.2_Missense_Mutation_p.E317G	NM_005311	NP_005302	Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10 isoform	375	PH.				insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)					CAACCTCAGCTCTTTAGTTTC	0.483									Russell-Silver_syndrome				6	371	---	---	---	---	PASS
KIAA1324L	222223	broad.mit.edu	37	7	86567448	86567448	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86567448T>C	uc011kha.1	-	8	1268	c.1083A>G	c.(1081-1083)GAA>GAG	p.E361E	KIAA1324L_uc003uif.1_Silent_p.E121E|KIAA1324L_uc011kgz.1_Silent_p.E247E|KIAA1324L_uc003uie.2_Silent_p.E194E	NM_001142749	NP_001136221	A8MWY0	K132L_HUMAN	hypothetical protein LOC222223 isoform 1	361	Extracellular (Potential).					integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)					GTACCTTTCCTTCTTCATCAC	0.418													7	516	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91670307	91670307	+	Intron	SNP	A	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91670307A>T	uc003ulg.2	+						AKAP9_uc003ule.2_3'UTR|AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGTATTTTTTATGTAGCCATA	0.348			T	BRAF	papillary thyroid								6	40	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91670309	91670309	+	Intron	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91670309G>T	uc003ulg.2	+						AKAP9_uc003ule.2_3'UTR|AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATTTTTTATGTAGCCATAAT	0.343			T	BRAF	papillary thyroid								11	37	---	---	---	---	PASS
ATXN7L1	222255	broad.mit.edu	37	7	105305526	105305526	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105305526T>C	uc003vde.2	-	4	592	c.565A>G	c.(565-567)AGG>GGG	p.R189G	ATXN7L1_uc003vdf.2_Missense_Mutation_p.R65G|ATXN7L1_uc003vdh.3_5'UTR|ATXN7L1_uc011klr.1_Missense_Mutation_p.R65G	NM_020725	NP_065776	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1 isoform 1	189											0						GGTTTATCCCTTGATCCTTTC	0.512													7	519	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116422132	116422132	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116422132T>G	uc003vij.2	+	18	3800	c.3613T>G	c.(3613-3615)TTG>GTG	p.L1205V	MET_uc010lkh.2_Missense_Mutation_p.L1223V|MET_uc011knj.1_Missense_Mutation_p.L775V	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	1205	Protein kinase.|Cytoplasmic (Potential).				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CCACAGAGACTTGGCTGCAAG	0.393			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				80	106	---	---	---	---	PASS
AASS	10157	broad.mit.edu	37	7	121716436	121716436	+	3'UTR	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121716436A>G	uc003vka.2	-	23					AASS_uc011knu.1_RNA|AASS_uc011knv.1_RNA|AASS_uc003vkb.2_3'UTR|AASS_uc011knw.1_3'UTR	NM_005763	NP_005754	Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase precursor						protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)	GTTAACCAAAACATATTATGC	0.294													5	119	---	---	---	---	PASS
KCP	375616	broad.mit.edu	37	7	128519646	128519646	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128519646A>T	uc011kor.1	-	35	3744	c.3701T>A	c.(3700-3702)CTG>CAG	p.L1234Q	KCP_uc003vob.1_RNA	NM_001135914	NP_001129386	Q6ZWJ8	KCP_HUMAN	cysteine rich BMP regulator 2 isoform 1	1234	VWFD.					extracellular region				central_nervous_system(1)	1						CGGCTCCTGCAGGAAGGGCAA	0.657													8	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142149173	142149173	+	Intron	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142149173G>A	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc010lnw.1_Missense_Mutation_p.T33M					SubName: Full=V_segment translation product; Flags: Fragment;																		CTGTCCTCTCGTTTTGATCAG	0.552													5	254	---	---	---	---	PASS
NEFM	4741	broad.mit.edu	37	8	24775663	24775663	+	Silent	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24775663G>A	uc003xed.3	+	3	2328	c.2295G>A	c.(2293-2295)GGG>GGA	p.G765G	NEFM_uc011lac.1_Intron|NEFM_uc010lue.2_Silent_p.G389G	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	765	Tail.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		aagaagaggggaagccactgc	0.189													7	72	---	---	---	---	PASS
MTDH	92140	broad.mit.edu	37	8	98712004	98712004	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98712004T>C	uc003yhz.2	+	7	1399	c.1071T>C	c.(1069-1071)TCT>TCC	p.S357S	MTDH_uc010mbf.2_Intron	NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin	357	Cytoplasmic (Potential).				lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			AGCCAGTTTCTCAGTCTACCA	0.338													8	724	---	---	---	---	PASS
C8orf31	286122	broad.mit.edu	37	8	144124475	144124475	+	Silent	SNP	C	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144124475C>G	uc003yxp.1	+	2	409	c.57C>G	c.(55-57)ACC>ACG	p.T19T	C8orf31_uc003yxq.1_RNA|C8orf31_uc003yxr.1_Intron	NM_173687	NP_775958	Q8N9H6	CH031_HUMAN	hypothetical protein LOC286122	19										ovary(1)	1	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCTTCAAAACCAAGCAGCTGG	0.612													23	38	---	---	---	---	PASS
ZNF7	7553	broad.mit.edu	37	8	146067912	146067912	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146067912T>C	uc003zeg.3	+	5	1557	c.1420T>C	c.(1420-1422)TGT>CGT	p.C474R	ZNF7_uc010mge.2_Missense_Mutation_p.C485R|ZNF7_uc011lln.1_Missense_Mutation_p.C378R|ZNF7_uc003zeh.2_Intron|ZNF7_uc003zek.3_Missense_Mutation_p.C378R|COMMD5_uc003zel.1_Intron	NM_003416	NP_003407	P17097	ZNF7_HUMAN	zinc finger protein 7	474	C2H2-type 9.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		ATGTGATGAGTGTGGCAAAGG	0.428													20	48	---	---	---	---	PASS
JAK2	3717	broad.mit.edu	37	9	5054568	5054568	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5054568A>G	uc010mhm.2	+	6	733	c.620A>G	c.(619-621)AAG>AGG	p.K207R	JAK2_uc003ziw.2_Missense_Mutation_p.K207R	NM_004972	NP_004963	O60674	JAK2_HUMAN	Janus kinase 2	207	Interaction with cytokine/interferon/growth hormone receptors (By similarity).|FERM.				actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)		CCTAGCTACAAGACATTCTTA	0.313		1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				5	173	---	---	---	---	PASS
FAM154A	158297	broad.mit.edu	37	9	18928830	18928830	+	Silent	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18928830G>A	uc003zni.1	-	4	923	c.645C>T	c.(643-645)CCC>CCT	p.P215P	FAM154A_uc010mip.1_Silent_p.P23P	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297	215										pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)		GCTTCTCCACGGGGTGGGCCA	0.502													4	187	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	66466172	66466172	+	RNA	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66466172T>C	uc004aec.2	+	3		c.805T>C								Homo sapiens, clone IMAGE:5213378, mRNA.																		GAATTGTACATGGTCCtgtga	0.179													3	4	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68414462	68414462	+	RNA	SNP	A	G	G	rs149255248		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-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													5	9	---	---	---	---	PASS
C9orf85	138241	broad.mit.edu	37	9	74587742	74587742	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74587742A>G	uc004ain.2	+	4	686	c.458A>G	c.(457-459)GAC>GGC	p.D153G	C9orf85_uc004aio.2_RNA|C9orf85_uc010mou.2_Intron|C9orf85_uc010mov.2_Intron	NM_182505	NP_872311	Q96MD7	CI085_HUMAN	hypothetical protein LOC138241	Error:Variant_position_missing_in_Q96MD7_after_alignment											0						ACAGGAGGAGACCATCAAATG	0.209													6	356	---	---	---	---	PASS
FIBCD1	84929	broad.mit.edu	37	9	133799697	133799697	+	Silent	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133799697C>T	uc004bzz.2	-	3	884	c.639G>A	c.(637-639)CTG>CTA	p.L213L	FIBCD1_uc011mcc.1_Silent_p.L213L	NM_032843	NP_116232	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	213	Extracellular (Potential).				signal transduction	extracellular space|integral to membrane	chitin binding|metal ion binding|receptor binding				0	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		GGGGCCGGCCCAGCCCCCGGT	0.701													2	2	---	---	---	---	PASS
TSC1	7248	broad.mit.edu	37	9	135778072	135778072	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135778072T>C	uc004cca.2	-	18	2545	c.2311A>G	c.(2311-2313)ATG>GTG	p.M771V	TSC1_uc004ccb.3_Missense_Mutation_p.M770V|TSC1_uc011mcq.1_Missense_Mutation_p.M720V|TSC1_uc011mcr.1_Intron	NM_000368	NP_000359	Q92574	TSC1_HUMAN	tuberous sclerosis 1 protein isoform 1	771	Potential.				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	p.?(1)		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)		TTGGTTACCATAGTGTCACGC	0.478			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis		OREG0019577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	286	---	---	---	---	PASS
TUBB2C	10383	broad.mit.edu	37	9	140137360	140137360	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140137360T>C	uc004cmh.1	+	4	792	c.690T>C	c.(688-690)TCT>TCC	p.S230S	TUBB2C_uc004cmg.1_Silent_p.S84S	NM_006088	NP_006079	P68371	TBB2C_HUMAN	tubulin, beta, 2	230					'de novo' posttranslational protein folding|cellular component movement|G2/M transition of mitotic cell cycle|microtubule-based movement|natural killer cell mediated cytotoxicity|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|MHC class I protein binding|structural molecule activity|unfolded protein binding			ovary(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		ACCTGGTGTCTGCTACCATGA	0.572													6	20	---	---	---	---	PASS
MAPK8	5599	broad.mit.edu	37	10	49632608	49632608	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49632608T>C	uc009xnz.2	+	7	892	c.668T>C	c.(667-669)GTT>GCT	p.V223A	MAPK8_uc001jgl.2_Missense_Mutation_p.V223A|MAPK8_uc001jgm.2_Missense_Mutation_p.V223A|MAPK8_uc001jgo.2_Missense_Mutation_p.V223A|MAPK8_uc009xoa.2_Intron|MAPK8_uc001jgn.2_Missense_Mutation_p.V223A|MAPK8_uc010qgk.1_Missense_Mutation_p.V223A|MAPK8_uc001jgp.2_Intron|MAPK8_uc001jgq.2_Intron	NM_139047	NP_620635	P45983	MK08_HUMAN	mitogen-activated protein kinase 8 isoform JNK1	223	Protein kinase.				activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		AAAGGTGGTGTTTTGTTCCCA	0.348													7	730	---	---	---	---	PASS
C10orf4	118924	broad.mit.edu	37	10	95459948	95459948	+	Intron	SNP	A	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95459948A>C	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron|C10orf4_uc001kjb.1_5'UTR|C10orf4_uc009xuh.1_Intron	NM_145246	NP_660289	Q70Z53	F10C1_HUMAN	FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)				gttatcttaaacagccacaat	0.149													22	54	---	---	---	---	PASS
EXOSC1	51013	broad.mit.edu	37	10	99196108	99196108	+	3'UTR	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99196108T>G	uc001kni.2	-	8					EXOSC1_uc009xvp.1_RNA	NM_016046	NP_057130	Q9Y3B2	EXOS1_HUMAN	exosomal core protein CSL4						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	protein binding|RNA binding				0		Renal(717;0.000147)|Colorectal(252;0.00205)|Ovarian(717;0.00965)		all cancers(201;8.29e-42)|Epithelial(162;5.7e-33)|BRCA - Breast invasive adenocarcinoma(275;0.000315)|Kidney(138;0.000832)|KIRC - Kidney renal clear cell carcinoma(50;0.00269)|STAD - Stomach adenocarcinoma(243;0.202)		GAAGTGGCTGTTGGCCGACGC	0.423													5	17	---	---	---	---	PASS
TRUB1	142940	broad.mit.edu	37	10	116710867	116710867	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116710867A>G	uc001lcd.2	+	3	461	c.400A>G	c.(400-402)AGC>GGC	p.S134G	TRUB1_uc010qsl.1_Missense_Mutation_p.S36G	NM_139169	NP_631908	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase homolog 1	134					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding				0		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		TGGAATTGGAAGCGGAACAAA	0.303													8	816	---	---	---	---	PASS
CYP2E1	1571	broad.mit.edu	37	10	135372523	135372523	+	3'UTR	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135372523T>C	uc001lnl.1	+	6					SYCE1_uc001lnm.2_5'UTR|SYCE1_uc009ybn.2_Intron|SYCE1_uc001lnn.2_Intron|SYCE1_uc001lno.2_Intron			P05181	CP2E1_HUMAN	SubName: Full=Cytochrome P450, family 2, subfamily E, polypeptide 1 variant; Flags: Fragment;						drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)	GTGACATTTCTCATTTGCCTT	0.413									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				5	135	---	---	---	---	PASS
OLFML1	283298	broad.mit.edu	37	11	7530679	7530679	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7530679A>G	uc001mfi.2	+	3	821	c.469A>G	c.(469-471)ATG>GTG	p.M157V	OLFML1_uc010raz.1_Missense_Mutation_p.M21V|OLFML1_uc010rba.1_Missense_Mutation_p.M157V	NM_198474	NP_940876	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1 precursor	157	Olfactomedin-like.					extracellular region				ovary(2)	2				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		AGTGAAGAAGATGATGGACAC	0.398													5	180	---	---	---	---	PASS
LDHC	3948	broad.mit.edu	37	11	18467864	18467864	+	Missense_Mutation	SNP	T	C	C	rs144032917		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18467864T>C	uc001mon.3	+	7	930	c.818T>C	c.(817-819)GTT>GCT	p.V273A	LDHC_uc001mom.3_Missense_Mutation_p.V273A|LDHC_uc009yhp.2_Intron|LDHC_uc001moo.3_Missense_Mutation_p.V157A|LDHC_uc009yhq.2_RNA|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144	P07864	LDHC_HUMAN	L-lactate dehydrogenase C	273					glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)	GTGCACCCAGTTTCCACCATG	0.279													6	453	---	---	---	---	PASS
ANO5	203859	broad.mit.edu	37	11	22301426	22301426	+	3'UTR	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22301426T>C	uc001mqi.2	+	22					ANO5_uc001mqj.2_3'UTR	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a							chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4						tttttttttcttttttttttt	0.368													3	7	---	---	---	---	PASS
NXF1	10482	broad.mit.edu	37	11	62569057	62569057	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62569057A>G	uc001nvf.1	-	7	822	c.686T>C	c.(685-687)CTC>CCC	p.L229P	NXF1_uc001nvg.1_Missense_Mutation_p.L229P|NXF1_uc009yog.1_Missense_Mutation_p.L272P|NXF1_uc010rmh.1_Missense_Mutation_p.L92P	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1	229	Interaction with THOC4.				gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3						GAGGCCTTTGAGGTCAAGGGC	0.512													7	436	---	---	---	---	PASS
CCDC88B	283234	broad.mit.edu	37	11	64124415	64124415	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64124415T>G	uc001nzy.2	+						CCDC88B_uc001oaa.2_Intron|CCDC88B_uc001oab.1_3'UTR|CCDC88B_uc001oac.2_Intron|RPS6KA4_uc001oad.2_5'Flank|RPS6KA4_uc001oae.2_5'Flank|RPS6KA4_uc010rnl.1_5'Flank|RPS6KA4_uc001oaf.2_5'Flank|RPS6KA4_uc009ypp.2_5'Flank	NM_032251	NP_115627	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88						microtubule cytoskeleton organization	cytoplasm	microtubule binding			ovary(3)|skin(1)	4						TATTGGCAGGTCGGGGGTGGG	0.483													5	9	---	---	---	---	PASS
RELT	84957	broad.mit.edu	37	11	73105299	73105299	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73105299A>G	uc001otv.2	+	8	890	c.725A>G	c.(724-726)GAG>GGG	p.E242G	RELT_uc001otw.2_Missense_Mutation_p.E242G|RELT_uc001otx.2_RNA	NM_152222	NP_689408	Q969Z4	TR19L_HUMAN	RELT tumor necrosis factor receptor precursor	242	Cytoplasmic (Potential).					cytoplasm|integral to membrane|plasma membrane	binding|receptor activity			upper_aerodigestive_tract(1)	1						GCGGCCCTGGAGGAGCTGCTG	0.612											OREG0021216	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	20	49	---	---	---	---	PASS
PICALM	8301	broad.mit.edu	37	11	85723393	85723393	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85723393A>G	uc001pbm.2	-	6	875	c.589T>C	c.(589-591)TTC>CTC	p.F197L	PICALM_uc001pbl.2_Missense_Mutation_p.F197L|PICALM_uc001pbn.2_Missense_Mutation_p.F197L|PICALM_uc010rtl.1_Missense_Mutation_p.F146L	NM_007166	NP_009097	Q13492	PICAL_HUMAN	phosphatidylinositol-binding clathrin assembly	197					clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				AGGAGCATGAAGGCAGCATTT	0.323			T	MLLT10|MLL	TALL|AML|								8	594	---	---	---	---	PASS
C11orf1	64776	broad.mit.edu	37	11	111750302	111750302	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111750302T>C	uc001pmd.2	+	1	355	c.18T>C	c.(16-18)TGT>TGC	p.C6C	ALG9_uc010rwo.1_5'Flank|FDXACB1_uc009yyi.2_5'Flank|FDXACB1_uc001pmc.3_5'Flank|C11orf1_uc001pme.2_5'Flank	NM_022761	NP_073598	Q9H5F2	CK001_HUMAN	hypothetical protein LOC64776	6						nucleus					0		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)		CCTCCCAGTGTCTCTGCTGCT	0.368													5	207	---	---	---	---	PASS
APOC3	345	broad.mit.edu	37	11	116703621	116703621	+	3'UTR	SNP	A	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116703621A>C	uc001ppt.1	+	4						NM_000040	NP_000031	P02656	APOC3_HUMAN	apolipoprotein C-III precursor						Cdc42 protein signal transduction|cholesterol efflux|cholesterol homeostasis|chylomicron remnant clearance|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol import|negative regulation of fatty acid biosynthetic process|negative regulation of high-density lipoprotein particle clearance|negative regulation of lipoprotein lipase activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor-mediated endocytosis|negative regulation of triglyceride catabolic process|negative regulation of very-low-density lipoprotein particle clearance|negative regulation of very-low-density lipoprotein particle remodeling|phospholipid efflux|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle assembly	chylomicron|intermediate-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	high-density lipoprotein particle receptor binding|lipase inhibitor activity|phospholipid binding				0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		CCCCAAGTCCACCTGCCTATC	0.557													6	15	---	---	---	---	PASS
IFT46	56912	broad.mit.edu	37	11	118430578	118430578	+	5'UTR	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118430578T>C	uc001ptp.1	-	3					IFT46_uc001pto.1_5'UTR|IFT46_uc009zaf.1_5'UTR	NM_020153	NP_064538	Q9NQC8	IFT46_HUMAN	IFT46						flagellum assembly|intraflagellar transport|protein stabilization	microtubule basal body|microtubule-based flagellum|nucleus	protein C-terminus binding				0						AACGAGGAAGTCCTTAGAAAA	0.303													93	209	---	---	---	---	PASS
SLC37A4	2542	broad.mit.edu	37	11	118899051	118899051	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118899051C>G	uc010rys.1	-	4	991	c.234G>C	c.(232-234)TGG>TGC	p.W78C	SLC37A4_uc009zam.2_RNA|SLC37A4_uc009zan.2_RNA|SLC37A4_uc010ryr.1_Missense_Mutation_p.W78C|SLC37A4_uc010ryt.1_Missense_Mutation_p.W5C|SLC37A4_uc001pus.2_Missense_Mutation_p.W78C	NM_001164277	NP_001157749	O43826	G6PT1_HUMAN	solute carrier family 37 (glucose-6-phosphate	78					glucose homeostasis|glucose metabolic process	endoplasmic reticulum membrane|integral to endoplasmic reticulum membrane|integral to membrane	glucose-6-phosphate transmembrane transporter activity|glucose-6-phosphate transmembrane transporter activity			large_intestine(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		AAGAGAAGAGCCAGCGAGCAC	0.542									Glycogen_Storage_Disease_type_Ib				33	76	---	---	---	---	PASS
ST14	6768	broad.mit.edu	37	11	130058115	130058115	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130058115T>C	uc001qfw.2	+	2	381	c.188T>C	c.(187-189)ATC>ACC	p.I63T	ST14_uc010sca.1_5'Flank	NM_021978	NP_068813	Q9Y5Y6	ST14_HUMAN	matriptase	63	Helical; Signal-anchor for type II membrane protein; (Potential).				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(2)|skin(2)|central_nervous_system(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	GCCGTGCTGATCGGCCTCCTC	0.617													24	56	---	---	---	---	PASS
PARP11	57097	broad.mit.edu	37	12	3921218	3921218	+	3'UTR	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3921218G>A	uc001qmk.1	-	7					PARP11_uc001qml.2_3'UTR|PARP11_uc009zef.2_RNA|PARP11_uc001qmm.2_3'UTR|PARP11_uc001qmn.2_3'UTR	NM_020367	NP_065100	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11								NAD+ ADP-ribosyltransferase activity			ovary(1)|central_nervous_system(1)	2			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			TTAGTGGCTAGATGACTGAAG	0.348													10	48	---	---	---	---	PASS
PLBD1	79887	broad.mit.edu	37	12	14706277	14706277	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14706277T>C	uc001rcc.1	-	2	346	c.185A>G	c.(184-186)AAG>AGG	p.K62R		NM_024829	NP_079105	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	62					lipid catabolic process	extracellular region	hydrolase activity				0						GTCCCCATTCTTGTCCATTAC	0.448													5	153	---	---	---	---	PASS
HOXC6	3223	broad.mit.edu	37	12	54422514	54422514	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54422514A>G	uc001sev.2	+	1	321	c.209A>G	c.(208-210)TAT>TGT	p.Y70C	HOXC6_uc001ses.2_5'UTR|HOXC5_uc001set.2_Intron|HOXC4_uc001seu.2_Intron	NM_004503	NP_004494	P09630	HXC6_HUMAN	homeobox C6 isoform 1	70					regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|upper_aerodigestive_tract(1)	3						CGGGGGCCGTATGACTATGGA	0.498													31	71	---	---	---	---	PASS
STAB2	55576	broad.mit.edu	37	12	103984690	103984690	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103984690A>G	uc001tjw.2	+	2	283	c.97A>G	c.(97-99)AGG>GGG	p.R33G		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	33	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						AAGATGTGATAGGAAGTCTCT	0.433													5	235	---	---	---	---	PASS
PARP4	143	broad.mit.edu	37	13	25023891	25023891	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25023891A>G	uc001upl.2	-	25	3185	c.3079T>C	c.(3079-3081)TTT>CTT	p.F1027L		NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1027	VWFA.				cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TTTGCATTAAAATATTCAAAT	0.333													5	142	---	---	---	---	PASS
KL	9365	broad.mit.edu	37	13	33635592	33635592	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33635592T>C	uc001uus.2	+	4	2384	c.2376T>C	c.(2374-2376)GAT>GAC	p.D792D	KL_uc001uur.1_3'UTR	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor	792	Glycosyl hydrolase-1 2.|Extracellular (Potential).				aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TCACTGAAGATGAAAAAAAGC	0.403													73	130	---	---	---	---	PASS
ESD	2098	broad.mit.edu	37	13	47351447	47351447	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47351447T>G	uc001vbn.2	-						ESD_uc001vbo.2_Intron|ESD_uc001vbp.1_3'UTR	NM_001984	NP_001975	P10768	ESTD_HUMAN	esterase D/formylglutathione hydrolase							cytoplasmic membrane-bounded vesicle	carboxylesterase activity|S-formylglutathione hydrolase activity			ovary(1)	1		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	TATAGGCAGGTTTTCACTTCA	0.244													6	6	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106714625	106714625	+	RNA	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106714625G>T	uc010tyt.1	-	645		c.18980C>A								Parts of antibodies, mostly variable regions.												0						CCCCCAGGCTGTACCAAGCCT	0.582													3	17	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106926267	106926267	+	RNA	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106926267T>C	uc010tyt.1	-	235		c.10288A>G			uc010tyu.1_Intron					Parts of antibodies, mostly variable regions.												0						TTTGCTGTTGTCTCTGGAGAT	0.498													5	160	---	---	---	---	PASS
LOC646214	646214	broad.mit.edu	37	15	21937109	21937109	+	RNA	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21937109T>C	uc010tzj.1	-	1		c.3631A>G				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						CAATCTGTGCTTCATCCATGC	0.443													8	757	---	---	---	---	PASS
ADAL	161823	broad.mit.edu	37	15	43644189	43644189	+	3'UTR	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43644189T>C	uc010udo.1	+	12					ADAL_uc001zri.1_3'UTR	NM_001159280	NP_001152752	Q6DHV7	ADAL_HUMAN	adenosine deaminase-like isoform 1						adenosine catabolic process|inosine biosynthetic process|purine ribonucleoside monophosphate biosynthetic process		adenosine deaminase activity|metal ion binding				0		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		TCAATCAAGTTCCTGCCATAT	0.353													7	38	---	---	---	---	PASS
SLC24A5	283652	broad.mit.edu	37	15	48428782	48428782	+	Intron	SNP	C	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48428782C>A	uc001zwe.2	+						SLC24A5_uc010bel.2_Intron|uc001zwf.1_RNA	NM_205850	NP_995322	Q71RS6	NCKX5_HUMAN	solute carrier family 24, member 5 precursor						response to stimulus	integral to membrane|melanosome|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity				0		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TCTATGGCTACTTTTGTTAGA	0.279													6	77	---	---	---	---	PASS
OSTBETA	123264	broad.mit.edu	37	15	65342250	65342250	+	5'UTR	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65342250C>T	uc002aog.2	+	2					OSTBETA_uc002aoh.2_5'Flank	NM_178859	NP_849190	Q86UW2	OSTB_HUMAN	organic solute transporter beta							integral to membrane|plasma membrane					0						TTCACGGCTTCTCTGCCCAGG	0.602													7	22	---	---	---	---	PASS
CLPX	10845	broad.mit.edu	37	15	65449219	65449219	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65449219T>C	uc002aom.2	-	9	1181	c.1109A>G	c.(1108-1110)CAT>CGT	p.H370R	CLPX_uc010uiu.1_RNA|CLPX_uc010bhg.1_Missense_Mutation_p.H370R	NM_006660	NP_006651	O76031	CLPX_HUMAN	ClpX caseinolytic protease X homolog precursor	370					protein folding|proteolysis involved in cellular protein catabolic process	mitochondrial endopeptidase Clp complex|mitochondrial inner membrane|mitochondrial nucleoid	ATP binding|ATPase activity|metal ion binding|peptidase activator activity|unfolded protein binding				0						CCGTAATTGATGAATGCCTGG	0.378													92	261	---	---	---	---	PASS
DENND4A	10260	broad.mit.edu	37	15	65957694	65957694	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65957694C>T	uc002aph.2	-	29	5594	c.5216G>A	c.(5215-5217)TGG>TAG	p.W1739*	DENND4A_uc002api.2_Nonsense_Mutation_p.W1782*	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2	1739					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						GTGTGCATTCCAGAGAATGTA	0.368													94	195	---	---	---	---	PASS
CT62	196993	broad.mit.edu	37	15	71403498	71403498	+	Silent	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71403498T>G	uc002ata.2	-	4	916	c.403A>C	c.(403-405)AGG>CGG	p.R135R		NM_001102658	NP_001096128	P0C5K7	CT62_HUMAN	cancer/testis antigen 62	135											0						TCCTATCTCCTCTGACCAGAT	0.438													141	307	---	---	---	---	PASS
LRRC28	123355	broad.mit.edu	37	15	99926442	99926442	+	3'UTR	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99926442A>G	uc002bva.1	+	10					LRRC28_uc002bvb.1_3'UTR|LRRC28_uc010urt.1_3'UTR|LRRC28_uc002bvc.1_3'UTR|LRRC28_uc010uru.1_3'UTR|LRRC28_uc002bvd.1_3'UTR	NM_144598	NP_653199	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28												0	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			ATTGAGCTTCAGAGCTAAAAT	0.473													15	30	---	---	---	---	PASS
PCSK6	5046	broad.mit.edu	37	15	101847520	101847520	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101847520T>C	uc002bwy.2	-	22	3024	c.2710A>G	c.(2710-2712)AAC>GAC	p.N904D	PCSK6_uc010bpd.2_Missense_Mutation_p.N700D|PCSK6_uc010bpe.2_Missense_Mutation_p.N891D	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4	904	CRM (Cys-rich motif).				glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CTCAAGCAGTTCTCGTCACAC	0.597													4	83	---	---	---	---	PASS
ERN2	10595	broad.mit.edu	37	16	23702118	23702118	+	3'UTR	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23702118G>A	uc002dma.3	-	22					ERN2_uc010bxp.2_3'UTR	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2						apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		CAGTGAGCCAGCACGGAGACC	0.453													5	20	---	---	---	---	PASS
MYLK3	91807	broad.mit.edu	37	16	46761073	46761073	+	Intron	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46761073G>A	uc002eei.3	-						MYLK3_uc010vge.1_Intron|MYLK3_uc002eej.1_3'UTR	NM_182493	NP_872299	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3						cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis	cytosol	ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	7		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				tctgTGGATAGAGCTCTCAAT	0.323													5	8	---	---	---	---	PASS
CLEC18B	497190	broad.mit.edu	37	16	74444645	74444645	+	Intron	SNP	C	T	T	rs144170380	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74444645C>T	uc002fct.2	-						CLEC18B_uc002fcu.2_Intron|CLEC18B_uc010vmu.1_3'UTR	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						CCTGGGCCCTCCCCGGGAAAG	0.682													7	168	---	---	---	---	PASS
ABR	29	broad.mit.edu	37	17	915255	915255	+	Intron	SNP	G	C	C	rs113364180		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:915255G>C	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqf.1_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron|ABR_uc002fsf.2_Missense_Mutation_p.C181W	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						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	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		TGGGTGGAGGGCAGCCCCCAC	0.662													9	50	---	---	---	---	PASS
ABR	29	broad.mit.edu	37	17	986770	986770	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:986770T>C	uc002fsd.2	-	5	739	c.629A>G	c.(628-630)AAG>AGG	p.K210R	ABR_uc002fse.2_Missense_Mutation_p.K164R|ABR_uc002fsg.2_Missense_Mutation_p.K173R|ABR_uc002fsh.1_Missense_Mutation_p.K94R	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related	210	DH.				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	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CTCTGAGATCTTCTGGAACTG	0.577													6	381	---	---	---	---	PASS
KCNH4	23415	broad.mit.edu	37	17	40327691	40327691	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40327691C>T	uc002hzb.2	-	6	1226	c.893G>A	c.(892-894)CGT>CAT	p.R298H		NM_012285	NP_036417	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H,	298	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	two-component sensor activity|voltage-gated potassium channel activity			large_intestine(1)	1		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GCCAATGGAACGAGGAGCAGA	0.547													6	387	---	---	---	---	PASS
PSME3	10197	broad.mit.edu	37	17	40986168	40986168	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40986168T>G	uc002ibr.2	+						PSME3_uc002ibp.2_Intron|PSME3_uc002ibq.2_Intron|PSME3_uc002ibs.2_5'UTR|PSME3_uc010whd.1_Intron	NM_005789	NP_005780	P61289	PSME3_HUMAN	proteasome activator subunit 3 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		GACAGGCAGGTGCTGTCCTCA	0.468													10	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	45105705	45105705	+	RNA	SNP	A	G	G	rs147936028	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45105705A>G	uc010wki.1	+	5		c.1307A>G								Homo sapiens cDNA FLJ42521 fis, clone BRACE3000973.																		GCCTGGCACGAAATGCAGTTT	0.303													6	462	---	---	---	---	PASS
UTP18	51096	broad.mit.edu	37	17	49371362	49371362	+	Silent	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49371362A>G	uc002its.2	+	12	1651	c.1602A>G	c.(1600-1602)GGA>GGG	p.G534G		NM_016001	NP_057085	Q9Y5J1	UTP18_HUMAN	UTP18, small subunit processome component	534					rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			CGAGAAGTGGATACTTTGCCT	0.358													6	361	---	---	---	---	PASS
TEX14	56155	broad.mit.edu	37	17	56738589	56738589	+	Intron	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56738589G>T	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron|TEX14_uc010wnz.1_Silent_p.A124A	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GCTCAAACTCGGCCACACGAT	0.478													4	206	---	---	---	---	PASS
LOC642597	642597	broad.mit.edu	37	18	5197060	5197060	+	5'UTR	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5197060T>C	uc010wzc.1	-	1						NM_001145194	NP_001138666	P0CW23	CR042_HUMAN	hypothetical protein LOC642597												0						CATGATTTCTTCCAGCCGCTA	0.537													8	46	---	---	---	---	PASS
ANKRD12	23253	broad.mit.edu	37	18	9255150	9255150	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9255150C>T	uc002knv.2	+	9	2142	c.1885C>T	c.(1885-1887)CAT>TAT	p.H629Y	ANKRD12_uc002knw.2_Missense_Mutation_p.H606Y|ANKRD12_uc002knx.2_Missense_Mutation_p.H606Y|ANKRD12_uc010dkx.1_Missense_Mutation_p.H336Y	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1	629						nucleus				ovary(2)|central_nervous_system(1)	3						GGATGAAGATCATAGTCCAAC	0.174													4	72	---	---	---	---	PASS
DSG4	147409	broad.mit.edu	37	18	28991165	28991165	+	Intron	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28991165G>T	uc002kwq.2	+						DSG4_uc002kwr.2_Silent_p.A722A	NM_177986	NP_817123	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 2 preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CAACTCCAGCGCTGTTAAACC	0.587													9	95	---	---	---	---	PASS
CELF4	56853	broad.mit.edu	37	18	34846493	34846493	+	Intron	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34846493A>G	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron|CELF4_uc002lah.1_Nonstop_Mutation_p.*115Q	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2						CGTGGATACTAACGACCTGCA	0.662													21	46	---	---	---	---	PASS
MYO5B	4645	broad.mit.edu	37	18	47581640	47581640	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47581640T>C	uc002leb.2	-	2	424	c.136A>G	c.(136-138)ACG>GCG	p.T46A	MYO5B_uc002lec.1_Missense_Mutation_p.T45A	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	46	Myosin head-like.				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		ACTCTTACCGTTTCATCCTCC	0.567													5	171	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56246350	56246350	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56246350A>G	uc002lhj.3	-	4	1872	c.1658T>C	c.(1657-1659)CTG>CCG	p.L553P		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	553							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						ACTTTCTCTCAGGTTGGCATT	0.517											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	77	116	---	---	---	---	PASS
CIRBP	1153	broad.mit.edu	37	19	1271824	1271824	+	Intron	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1271824T>G	uc002lrr.3	+						C19orf23_uc010xgk.1_5'Flank|CIRBP_uc010dsg.1_3'UTR|CIRBP_uc002lrt.2_Intron|CIRBP_uc010xgl.1_Intron|CIRBP_uc002lrv.3_Intron|CIRBP_uc002lru.2_Intron	NM_001280	NP_001271	Q14011	CIRBP_HUMAN	cold inducible RNA binding protein						mRNA stabilization|positive regulation of translation|response to cold|response to UV|stress granule assembly	nucleoplasm|stress granule	mRNA 3'-UTR binding|nucleotide binding|protein binding|SSU rRNA binding|translation repressor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GACAGGCTGGTGGAGATTTTG	0.627													7	12	---	---	---	---	PASS
ZNF700	90592	broad.mit.edu	37	19	12060408	12060408	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12060408T>C	uc002msu.2	+	4	1695	c.1569T>C	c.(1567-1569)TTT>TTC	p.F523F	ZNF700_uc010xme.1_Silent_p.F541F|ZNF763_uc010xmf.1_Intron	NM_144566	NP_653167	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	523	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CCAAGTCATTTCAAACACATG	0.368													39	65	---	---	---	---	PASS
ZNF799	90576	broad.mit.edu	37	19	12501081	12501081	+	3'UTR	SNP	G	T	T	rs147184220	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12501081G>T	uc010dyt.2	-	4					ZNF799_uc002mts.3_Intron	NM_001080821	NP_001074290	Q96GE5	ZN799_HUMAN	zinc finger protein 799						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6						aaaagggactggacatggctc	0.070													3	12	---	---	---	---	PASS
ZNF799	90576	broad.mit.edu	37	19	12501094	12501094	+	3'UTR	SNP	G	A	A	rs140533828	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12501094G>A	uc010dyt.2	-	4					ZNF799_uc002mts.3_Intron	NM_001080821	NP_001074290	Q96GE5	ZN799_HUMAN	zinc finger protein 799						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6						catggctcacggagtgctgga	0.104													3	9	---	---	---	---	PASS
PALM3	342979	broad.mit.edu	37	19	14165032	14165032	+	Silent	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14165032T>C	uc010xnk.1	-	6	1407	c.1407A>G	c.(1405-1407)GAA>GAG	p.E469E		NM_001145028	NP_001138500	A6NDB9	PALM3_HUMAN	hypothetical protein LOC342979	469	Glu-rich.				negative regulation of cytokine-mediated signaling pathway|response to lipopolysaccharide|Toll signaling pathway	cytoplasm|plasma membrane	ATP binding|protein binding			pancreas(1)	1						cctcatctccttccttctcTG	0.239													6	360	---	---	---	---	PASS
KIAA0355	9710	broad.mit.edu	37	19	34832722	34832722	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34832722A>G	uc002nvd.3	+	10	2742	c.1883A>G	c.(1882-1884)CAT>CGT	p.H628R		NM_014686	NP_055501	O15063	K0355_HUMAN	hypothetical protein LOC9710	628										ovary(1)	1	Esophageal squamous(110;0.162)					AACTTCCTGCATGGAGATGAC	0.478													15	28	---	---	---	---	PASS
WDR87	83889	broad.mit.edu	37	19	38385920	38385920	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38385920T>G	uc010efu.2	-	4	531	c.306A>C	c.(304-306)AAA>AAC	p.K102N	WDR87_uc002ohj.2_Missense_Mutation_p.K141N	NM_031951	NP_114157	Q6ZQQ6	WDR87_HUMAN	NYD-SP11 protein	102											0						TACCCAGGGGTTTGAATGCCC	0.557													11	82	---	---	---	---	PASS
PAF1	54623	broad.mit.edu	37	19	39880360	39880360	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39880360T>C	uc002old.2	-	4	387	c.212A>G	c.(211-213)AAA>AGA	p.K71R	PAF1_uc002ole.1_Missense_Mutation_p.K61R|PAF1_uc010xuv.1_Intron|MED29_uc010xuw.1_5'Flank|MED29_uc002olf.2_5'Flank|MED29_uc010xux.1_5'Flank	NM_019088	NP_061961	Q8N7H5	PAF1_HUMAN	Paf1, RNA polymerase II associated factor,	71					histone H2B ubiquitination|histone monoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			pancreas(1)	1	all_cancers(60;9.14e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			GAGGTCATGTTTGTGCTGTTT	0.552													5	163	---	---	---	---	PASS
CYTH2	9266	broad.mit.edu	37	19	48984369	48984369	+	3'UTR	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48984369A>G	uc002pjj.3	+	13					CYTH2_uc002pji.2_RNA	NM_017457	NP_059431	Q99418	CYH2_HUMAN	cytohesin 2 isoform 1						actin cytoskeleton organization|endocytosis|regulation of ARF protein signal transduction|regulation of cell adhesion	cytoplasm|membrane fraction|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						cagggagaataatttggaggc	0.000													2	0	---	---	---	---	PASS
LAIR2	3904	broad.mit.edu	37	19	55019314	55019314	+	Silent	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55019314A>G	uc002qgc.2	+	3	401	c.279A>G	c.(277-279)GAA>GAG	p.E93E	LAIR2_uc002qga.1_RNA|LAIR2_uc002qgb.1_RNA|LAIR2_uc002qgd.2_Silent_p.E93E|LAIR2_uc010erl.2_Intron	NM_002288	NP_002279	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like	93	Ig-like C2-type.					extracellular region	receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		CAGTAAGTGAAGGAAATGCCG	0.488													5	148	---	---	---	---	PASS
PTPRH	5794	broad.mit.edu	37	19	55713578	55713578	+	Silent	SNP	C	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55713578C>T	uc002qjq.2	-	6	1072	c.999G>A	c.(997-999)GAG>GAA	p.E333E	PTPRH_uc010esv.2_Silent_p.E155E|PTPRH_uc002qjs.2_Silent_p.E340E	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	333	Extracellular (Potential).|Fibronectin type-III 4.				apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CTCCAGTGTACTCAACCCCGT	0.567													51	78	---	---	---	---	PASS
NLRP9	338321	broad.mit.edu	37	19	56244335	56244335	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56244335G>A	uc002qly.2	-	2	890	c.862C>T	c.(862-864)CGG>TGG	p.R288W		NM_176820	NP_789790	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	288	NACHT.					cytoplasm	ATP binding			skin(4)|ovary(2)|breast(1)	7		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		TTTGGATGCCGCAACATAAAA	0.378													4	136	---	---	---	---	PASS
NOP56	10528	broad.mit.edu	37	20	2637468	2637468	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2637468A>G	uc002wgh.2	+	10	1261	c.1208A>G	c.(1207-1209)GAG>GGG	p.E403G	NOP56_uc010zpy.1_RNA|NOP56_uc002wgi.2_Missense_Mutation_p.E237G|NOP56_uc002wgm.1_Missense_Mutation_p.E150G|SNORD57_uc002wgo.1_5'Flank	NM_006392	NP_006383	O00567	NOP56_HUMAN	nucleolar protein 5A	403	Nop.				rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding			ovary(1)|pancreas(1)	2						CAAGTTGAAGAGCGACTGTCC	0.512													6	315	---	---	---	---	PASS
KCNB1	3745	broad.mit.edu	37	20	47989458	47989458	+	3'UTR	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47989458T>G	uc002xur.1	-	2					KCNB1_uc002xus.1_3'UTR	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related						energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CTGTGGCAGGTAAGCTGAACA	0.532													7	18	---	---	---	---	PASS
DSCR4	10281	broad.mit.edu	37	21	39426752	39426752	+	3'UTR	SNP	T	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39426752T>G	uc002ywp.2	-	3						NM_005867	NP_005858	P56555	DSCR4_HUMAN	Down syndrome critical region protein 4											ovary(1)	1						ATTATGGCTGTTGTTTTTCCA	0.398													9	21	---	---	---	---	PASS
CABIN1	23523	broad.mit.edu	37	22	24437602	24437602	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24437602G>A	uc002zzi.1	+	5	353	c.226G>A	c.(226-228)GAT>AAT	p.D76N	CABIN1_uc002zzj.1_Missense_Mutation_p.D76N|CABIN1_uc002zzl.1_Missense_Mutation_p.D76N|CABIN1_uc010guk.1_Intron|CABIN1_uc002zzk.1_Intron	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	76					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5						TTCATCCGGTGATGAGAAAGA	0.522													48	134	---	---	---	---	PASS
SEC14L4	284904	broad.mit.edu	37	22	30885908	30885908	+	3'UTR	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30885908G>T	uc003aid.2	-	12					SEC14L4_uc011akz.1_Intron|SEC14L4_uc003aie.2_3'UTR|SEC14L4_uc003aif.2_3'UTR	NM_174977	NP_777637	Q9UDX3	S14L4_HUMAN	SEC14p-like protein TAP3 isoform a							integral to membrane|intracellular	lipid binding|transporter activity			skin(1)	1					Vitamin E(DB00163)	CTTCAGCATGGGCTATGCACT	0.547													61	96	---	---	---	---	PASS
SEC14L4	284904	broad.mit.edu	37	22	30885909	30885909	+	3'UTR	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30885909G>T	uc003aid.2	-	12					SEC14L4_uc011akz.1_Intron|SEC14L4_uc003aie.2_3'UTR|SEC14L4_uc003aif.2_3'UTR	NM_174977	NP_777637	Q9UDX3	S14L4_HUMAN	SEC14p-like protein TAP3 isoform a							integral to membrane|intracellular	lipid binding|transporter activity			skin(1)	1					Vitamin E(DB00163)	TTCAGCATGGGCTATGCACTG	0.552													61	95	---	---	---	---	PASS
NOL12	79159	broad.mit.edu	37	22	38084989	38084989	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38084989C>G	uc003atp.2	+	4	427	c.371C>G	c.(370-372)ACC>AGC	p.T124S	NOL12_uc011anm.1_Missense_Mutation_p.T124S|NOL12_uc003ato.1_RNA|TRIOBP_uc003atq.1_5'UTR	NM_024313	NP_077289	Q9UGY1	NOL12_HUMAN	nucleolar protein 12	124						nucleolus	rRNA binding				0	Melanoma(58;0.0574)					CTCGGGCTGACCCCACCTGAG	0.647													7	16	---	---	---	---	PASS
RBX1	9978	broad.mit.edu	37	22	41368620	41368620	+	3'UTR	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41368620G>T	uc003azk.2	+	5						NM_014248	NP_055063	P62877	RBX1_HUMAN	ring-box 1						DNA repair|interspecies interaction between organisms|protein neddylation|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	Cul3-RING ubiquitin ligase complex|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytosol|nucleus|SCF ubiquitin ligase complex	NEDD8 ligase activity|protein binding|zinc ion binding			skin(1)	1						TGCTGTTTCTGTAGCCATATT	0.348													28	231	---	---	---	---	PASS
DACH2	117154	broad.mit.edu	37	X	86069820	86069820	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86069820G>T	uc004eew.2	+	10	1837	c.1667G>T	c.(1666-1668)GGC>GTC	p.G556V	DACH2_uc004eex.2_Missense_Mutation_p.G543V|DACH2_uc010nmq.2_Missense_Mutation_p.G422V|DACH2_uc011mra.1_Missense_Mutation_p.G389V|DACH2_uc010nmr.2_Missense_Mutation_p.G337V|DACH2_uc004eey.2_Missense_Mutation_p.G249V|DACH2_uc004eez.2_Missense_Mutation_p.G239V	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	556					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						AGTGACAGTGGCCTGAGGATG	0.363													14	313	---	---	---	---	PASS
BCORL1	63035	broad.mit.edu	37	X	129150165	129150165	+	Silent	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129150165G>A	uc004evb.1	+	4	3531	c.3417G>A	c.(3415-3417)GTG>GTA	p.V1139V	BCORL1_uc010nrd.1_Silent_p.V1041V	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	1139					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						CCAAGGCCGTGGTCCGGAGTT	0.587													3	8	---	---	---	---	PASS
CSAG1	158511	broad.mit.edu	37	X	151909357	151909357	+	3'UTR	SNP	G	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151909357G>C	uc004fge.2	+	5					CSAG1_uc004fgf.2_3'UTR|CSAG1_uc004fgd.2_RNA	NM_153478	NP_705611	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1 precursor											ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					GCTTCCTTGGGCAGCCAGTAA	0.527													16	134	---	---	---	---	PASS
F8	2157	broad.mit.edu	37	X	154132580	154132580	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154132580G>A	uc004fmt.2	-	17	5977	c.5806C>T	c.(5806-5808)CGC>TGC	p.R1936C	F8_uc010nvi.1_Missense_Mutation_p.R95C	NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	1936	F5/8 type A 3.|Plastocyanin-like 6.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CCATGGAAGCGATAATTCTCT	0.388													5	391	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14799	14799	+	5'UTR	SNP	T	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14799T>C	uc004coy.2	+	1					uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		TAACCACTCATTCATCGACCT	0.443													6	92	---	---	---	---	PASS
NPHP4	261734	broad.mit.edu	37	1	5944229	5944229	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5944229delC	uc001alq.1	-						NPHP4_uc001als.1_Intron|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin						actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGGTTACACCCGCACCAAC	0.552													4	2	---	---	---	---	
DNAJC11	55735	broad.mit.edu	37	1	6734788	6734788	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6734788delA	uc001aof.2	-						DNAJC11_uc010nzt.1_Intron|DNAJC11_uc001aog.2_Intron|DNAJC11_uc010nzu.1_Intron	NM_018198	NP_060668	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11						protein folding		heat shock protein binding|unfolded protein binding			ovary(1)|skin(1)	2	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		actctgtctcaaaaaaaaaaa	0.184													3	4	---	---	---	---	
RERE	473	broad.mit.edu	37	1	8686437	8686437	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8686437delC	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TTCCTACATACCACATTTCAT	0.279													4	2	---	---	---	---	
UBE4B	10277	broad.mit.edu	37	1	10121971	10121971	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10121971delT	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1						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)		ttcttttttcttttttttttt	0.124													3	4	---	---	---	---	
AKR7A3	22977	broad.mit.edu	37	1	19610328	19610328	+	Intron	DEL	A	-	-	rs11581031		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19610328delA	uc001bbv.1	-							NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3						cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ctgtccccccaaaaaaaaaac	0.149													4	2	---	---	---	---	
NBPF3	84224	broad.mit.edu	37	1	21793229	21793229	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21793229delA	uc001ber.2	+						NBPF3_uc001bes.2_Intron|NBPF3_uc009vqb.2_Intron|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3							cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CACAAAAACCAAAAAAAAAAA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	27310571	27310571	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27310571delA								C1orf172 (23674 upstream) : TRNP1 (9624 downstream)																							CGAAAACTGCAAaaaaaaaag	0.224													4	2	---	---	---	---	
CSMD2	114784	broad.mit.edu	37	1	34235137	34235137	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34235137delA	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AACCTAAATTAAAAAAAGACT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35517133	35517133	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35517133delA								ZMYM6 (19564 upstream) : ZMYM1 (27839 downstream)																							ctgtagctttaaaaaaaaatt	0.005													4	2	---	---	---	---	
ZNF691	51058	broad.mit.edu	37	1	43313142	43313142	+	5'Flank	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43313142delC	uc001cih.2	+						ZNF691_uc001cig.2_Intron|ZNF691_uc009vwm.2_Intron	NM_015911	NP_056995	Q5VV52	ZN691_HUMAN	zinc finger protein 691							nucleus	DNA binding|zinc ion binding			ovary(2)	2	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GACCCCTTTTCCCCCCAGATC	0.527													4	2	---	---	---	---	
KLF17	128209	broad.mit.edu	37	1	44553662	44553662	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44553662delA	uc009vxf.1	+							NM_173484	NP_775755	Q5JT82	KLF17_HUMAN	zinc finger protein 393						regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)					GACCACCATCAAACAGAAGAG	0.502													4	2	---	---	---	---	
RNF220	55182	broad.mit.edu	37	1	45029873	45029874	+	Intron	INS	-	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45029873_45029874insC	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2						tttctcaaattcccccctccct	0.000													4	2	---	---	---	---	
CMPK1	51727	broad.mit.edu	37	1	47841169	47841170	+	Intron	INS	-	A	A	rs138058309	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47841169_47841170insA	uc001cri.2	+						CMPK1_uc010omp.1_Intron|CMPK1_uc010omq.1_Intron	NM_016308	NP_057392	P30085	KCY_HUMAN	UMP-CMP kinase 1 isoform a						nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleus	ATP binding|cytidylate kinase activity|nucleoside phosphate kinase activity|uridine kinase activity			ovary(1)	1					Gemcitabine(DB00441)	ctctgtctcttaaaaaaaaaag	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	47958068	47958068	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47958068delA								FOXD2 (51706 upstream) : SKINTL (609319 downstream)																							agtgactgttaaaaaaaagta	0.000													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49331226	49331227	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49331226_49331227insT	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		GGCAGTGCTGATTTTTTTTTCA	0.401													4	2	---	---	---	---	
ELAVL4	1996	broad.mit.edu	37	1	50640161	50640162	+	Intron	DEL	TT	-	-	rs75902711		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50640161_50640162delTT	uc001csb.2	+						ELAVL4_uc001cry.3_Intron|ELAVL4_uc001crz.3_Intron|ELAVL4_uc001csa.3_Intron|ELAVL4_uc001csc.3_Intron|ELAVL4_uc009vyu.2_Intron|ELAVL4_uc010omz.1_Intron	NM_021952	NP_068771	P26378	ELAV4_HUMAN	ELAV-like 4 isoform 1						mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2						TTTTTGTTTGTTTTTTTTTTTT	0.327													4	2	---	---	---	---	
C1orf185	284546	broad.mit.edu	37	1	51578489	51578489	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51578489delT	uc001csh.2	+							NM_001136508	NP_001129980	Q5T7R7	CA185_HUMAN	hypothetical protein LOC284546							integral to membrane					0						Ctttcttttcttttttttttt	0.144													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56434726	56434726	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56434726delC								USP24 (753964 upstream) : PPAP2B (525707 downstream)																							gatagtggttcccggtgtaat	0.020													4	2	---	---	---	---	
FGGY	55277	broad.mit.edu	37	1	60220053	60220053	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60220053delT	uc001czi.3	+						FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron|FGGY_uc001czm.3_Intron	NM_018291	NP_060761	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)					aatcctttccttttttttttg	0.000													4	2	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64477996	64477996	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64477996delC	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						CTATGAAGCACCTTGGGCCAT	0.438													4	2	---	---	---	---	
JAK1	3716	broad.mit.edu	37	1	65310861	65310861	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65310861delC	uc001dbu.1	-						JAK1_uc009wam.1_Intron|JAK1_uc009wal.1_Intron	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		ggtgagcactcCACACGTCAG	0.254			Mis		ALL								4	2	---	---	---	---	
LRRC40	55631	broad.mit.edu	37	1	70656745	70656745	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70656745delA	uc001der.1	-							NM_017768	NP_060238	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40											ovary(1)	1						ATTTACTGACAAAAAAGCAGC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	73434298	73434298	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73434298delA								NEGR1 (685893 upstream) : None (None downstream)																							ATGAGACACTAAAAAACACTT	0.313													4	2	---	---	---	---	
GIPC2	54810	broad.mit.edu	37	1	78584742	78584742	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78584742delT	uc001dik.2	+							NM_017655	NP_060125	Q8TF65	GIPC2_HUMAN	PDZ domain protein GIPC2							cytoplasm				ovary(1)	1						ATTCTTTCCCTTTTTTTGTGA	0.279													4	2	---	---	---	---	
ZNF644	84146	broad.mit.edu	37	1	91453722	91453723	+	Intron	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91453722_91453723insG	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)		taaattttcaagaaaaaaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	94446390	94446390	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94446390delA								GCLM (71378 upstream) : ABCA4 (12006 downstream)																							gacagcgtggaggggcaatgc	0.000													4	2	---	---	---	---	
ABCA4	24	broad.mit.edu	37	1	94558364	94558365	+	Intron	INS	-	G	G	rs147486359	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94558364_94558365insG	uc001dqh.2	-						ABCA4_uc010otn.1_Intron	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4						phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TCTCCTAGTCTGGGGGGGTCTG	0.426													4	2	---	---	---	---	
ABCA4	24	broad.mit.edu	37	1	94581816	94581816	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94581816delT	uc001dqh.2	-						ABCA4_uc010otn.1_Intron	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4						phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		AATTAGGCTGTTTTTTTTTGC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102239245	102239245	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102239245delA								S1PR1 (532169 upstream) : OLFM3 (28882 downstream)																							GATTGTTTGGAAAAACAAGGT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	111069745	111069746	+	IGR	INS	-	TA	TA	rs146886375	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111069745_111069746insTA								KCNA10 (7948 upstream) : KCNA2 (66457 downstream)																							GGGCTGAGCTGAACACTCTCCA	0.599													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	114596717	114596718	+	IGR	INS	-	GT	GT	rs145683629	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114596717_114596718insGT								OLFML3 (71841 upstream) : SYT6 (35197 downstream)																							TGGCTTGAGAGgtgtgtgtgtg	0.238													4	2	---	---	---	---	
VTCN1	79679	broad.mit.edu	37	1	117741031	117741031	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117741031delA	uc001ehb.2	-						VTCN1_uc001ehc.2_Intron|VTCN1_uc009whf.1_Intron	NM_024626	NP_078902	Q7Z7D3	VTCN1_HUMAN	V-set domain containing T cell activation							integral to membrane|plasma membrane					0	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)		GTAAAACAAGAAAAAAAGGCA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	119138701	119138702	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119138701_119138702insA								SPAG17 (410853 upstream) : TBX15 (286964 downstream)																							ttactgatgttaaaaacttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121140484	121140485	+	IGR	DEL	AA	-	-	rs111761276		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121140484_121140485delAA								FCGR1B (204540 upstream) : LOC647121 (120425 downstream)																							tgatggggttaaaaaaaaaaaa	0.020													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143181181	143181181	+	Intron	DEL	C	-	-	rs71237956		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143181181delC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		atgacccaagctgtacctgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143394172	143394173	+	IGR	INS	-	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143394172_143394173insC								None (None upstream) : LOC100286793 (253466 downstream)																							CCTACTTCAAACCTCAGACTTC	0.371													3	4	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145007452	145007453	+	Intron	INS	-	T	T	rs141963263		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145007452_145007453insT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CATACAttttcttttttttgtt	0.139			T	PDGFRB	MPD								3	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145030486	145030486	+	Intron	DEL	T	-	-	rs66508015		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145030486delT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGCGTATTTCTTTTTTTTTTC	0.338			T	PDGFRB	MPD								4	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145189953	145189953	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145189953delC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						ttctctttctccttgctcctc	0.035													8	4	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145737007	145737007	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145737007delT	uc001emp.3	+						PDZK1_uc001eon.1_Intron|PDZK1_uc001eoo.1_Intron|PDZK1_uc010oza.1_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CTTTATCATATTTTTTTCTAC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152072739	152072739	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152072739delT								TCHHL1 (11199 upstream) : TCHH (6054 downstream)																							ttttagttagttttttttttt	0.000													4	2	---	---	---	---	
PGLYRP4	57115	broad.mit.edu	37	1	153318955	153318956	+	Intron	DEL	AA	-	-	rs67489315		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153318955_153318956delAA	uc001fbo.2	-						PGLYRP4_uc001fbp.2_Intron	NM_020393	NP_065126	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein-I-beta						defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(3)|skin(1)	4	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			ATTGGCGGGGAAAAAAAAAAAA	0.436													2	4	---	---	---	---	
NUP210L	91181	broad.mit.edu	37	1	154097046	154097046	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154097046delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			ttacaacagtaaaaaaaatgg	0.070													4	2	---	---	---	---	
DCST1	149095	broad.mit.edu	37	1	155007527	155007528	+	Intron	INS	-	ATTC	ATTC	rs147557352	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155007527_155007528insATTC	uc001fgn.1	+						DCST2_uc001fgm.2_5'Flank|DCST2_uc009wpb.2_5'Flank|DCST1_uc010per.1_Intron|DCST1_uc010pes.1_Intron	NM_152494	NP_689707	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1 isoform 1							integral to membrane	zinc ion binding			ovary(1)|skin(1)	2	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			TAAGAAATTAAattcattcatt	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	155538619	155538624	+	IGR	DEL	TTTTTC	-	-	rs7413821		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155538619_155538624delTTTTTC								LOC645676 (4887 upstream) : MSTO1 (41383 downstream)																							CCCCGGCCTTtttttctttttctttt	0.126													4	2	---	---	---	---	
GON4L	54856	broad.mit.edu	37	1	155733854	155733854	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155733854delA	uc001flz.2	-						GON4L_uc009wrg.1_Intron|GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmb.3_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)					AAAACAAGACAAAAAAAAGAA	0.254													4	2	---	---	---	---	
ARHGEF11	9826	broad.mit.edu	37	1	156958183	156958184	+	Intron	INS	-	CTA	CTA			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156958183_156958184insCTA	uc001fqo.2	-						ARHGEF11_uc001fqn.2_Intron	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11						actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACATGTTCTGCCTACTTTATTC	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165677450	165677451	+	Intron	DEL	TC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165677450_165677451delTC	uc001gdi.2	+											Homo sapiens carbonic anhydrase XIV (CA14) pseudogene, mRNA (cDNA clone IMAGE:4643256).																		tctctccccgtctctctctctG	0.307													4	2	---	---	---	---	
DCAF6	55827	broad.mit.edu	37	1	168033254	168033254	+	Intron	DEL	T	-	-	rs66652521		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168033254delT	uc001gew.2	+						DCAF6_uc001gev.2_Intron|DCAF6_uc001gex.2_Intron|DCAF6_uc010plk.1_Intron|DCAF6_uc001gey.2_Intron|DCAF6_uc001gez.2_Intron	NM_001017977	NP_001017977	Q58WW2	DCAF6_HUMAN	IQ motif and WD repeats 1 isoform b						positive regulation of transcription from RNA polymerase II promoter	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						ATTGCTTTTGTTTTTTTTTTT	0.239													3	3	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	172115633	172115633	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172115633delC	uc001gie.2	+						DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron|MIR199A2_hsa-mir-199a-2|MI0000281_5'Flank	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						ACTTTTGCTTCCATATTTGTG	0.388													4	2	---	---	---	---	
C1orf49	84066	broad.mit.edu	37	1	178491785	178491786	+	Intron	INS	-	T	T	rs151133039	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178491785_178491786insT	uc001glw.1	+						C1orf49_uc001glv.1_Intron	NM_032126	NP_115502	Q5T0J7	CA049_HUMAN	hypothetical protein LOC84066							microtubule cytoskeleton					0						TGGCCAAGTTCTTTTTTTTTGG	0.203													4	2	---	---	---	---	
C1orf21	81563	broad.mit.edu	37	1	184430483	184430483	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184430483delA	uc001gqv.1	+							NM_030806	NP_110433	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)		TAAGCATACCAAATAAGCAGC	0.463													4	2	---	---	---	---	
KDM5B	10765	broad.mit.edu	37	1	202710193	202710193	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202710193delA	uc001gyf.2	-						KDM5B_uc009xag.2_Intron|KDM5B_uc001gyg.1_Intron	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B						negative regulation of transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5						ACCTATTTGTAAATATTTTCC	0.338													4	2	---	---	---	---	
RABIF	5877	broad.mit.edu	37	1	202850536	202850536	+	Intron	DEL	T	-	-	rs111992348		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-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													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	206483310	206483310	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206483310delT								CTSE (151207 upstream) : SRGAP2 (32890 downstream)																							AATAGTTTTGTTTTTTAAGGC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208026935	208026935	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208026935delA								LOC148696 (30995 upstream) : CD34 (32948 downstream)																							GCTGCTCTTTAAAAAGAGCCC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208883625	208883625	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208883625delT								PLXNA2 (465960 upstream) : LOC642587 (718543 downstream)																							cctctttttcttttTTTTTTT	0.010													4	2	---	---	---	---	
NSL1	25936	broad.mit.edu	37	1	212905370	212905371	+	3'UTR	INS	-	T	T	rs11392084		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212905370_212905371insT	uc001hjn.2	-	6					NSL1_uc001hjm.2_3'UTR|NSL1_uc010pti.1_3'UTR	NM_015471	NP_056286	Q96IY1	NSL1_HUMAN	NSL1, MIND kinetochore complex component isoform						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)		AACTGTCCCAATTTTTTTTTTT	0.228													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213705323	213705323	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213705323delC								RPS6KC1 (258516 upstream) : PROX1 (455963 downstream)																							AGTGTCATCTCCCCCTACCCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214431048	214431049	+	IGR	INS	-	GA	GA			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214431048_214431049insGA								PROX1 (221288 upstream) : SMYD2 (23516 downstream)																							AGAAAGCCCCCGAGAGAGAGAA	0.371													4	2	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	215946855	215946856	+	Intron	DEL	TC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215946855_215946856delTC	uc001hku.1	-							NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		tctctctctgtctctctctctc	0.000										HNSCC(13;0.011)			6	3	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	217008496	217008498	+	Intron	DEL	ATC	-	-	rs145716421		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217008496_217008498delATC	uc001hky.1	-						ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CCAACTGATAATCAGAGTTGAAT	0.256													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	226520860	226520860	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226520860delA								LIN9 (23290 upstream) : PARP1 (27533 downstream)																							aaaatatgagaaaaaaaaaaG	0.104													5	5	---	---	---	---	
SLC35F3	148641	broad.mit.edu	37	1	234381366	234381366	+	Intron	DEL	T	-	-	rs57446896		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234381366delT	uc001hwa.1	+						SLC35F3_uc001hvy.1_Intron	NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			gcttttcccctgctccatgat	0.020													4	2	---	---	---	---	
LYST	1130	broad.mit.edu	37	1	235850457	235850457	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235850457delT	uc001hxj.2	-						LYST_uc001hxi.2_Intron	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			CTGACAACTATTTTTTTTAAC	0.249									Chediak-Higashi_syndrome				5	3	---	---	---	---	
HEATR1	55127	broad.mit.edu	37	1	236766893	236766893	+	Intron	DEL	T	-	-	rs34038039		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236766893delT	uc001hyd.1	-						HEATR1_uc001hye.1_Intron	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			CAGGGAACACTTTTTTTTTTT	0.323													5	3	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237354719	237354720	+	Intron	DEL	TT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237354719_237354720delTT	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			attttatgggtttttttttttt	0.069													4	2	---	---	---	---	
GREM2	64388	broad.mit.edu	37	1	240696873	240696873	+	Intron	DEL	C	-	-	rs5782152		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240696873delC	uc001hys.2	-							NM_022469	NP_071914	Q9H772	GREM2_HUMAN	gremlin 2 precursor						BMP signaling pathway	extracellular space	cytokine activity				0		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)			ACAACTGGGACAAGGGGAGTA	0.428													1	5	---	---	---	---	
CEP170	9859	broad.mit.edu	37	1	243336368	243336368	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243336368delT	uc001hzs.2	-						CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha							centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GTAATTATCCttttttttttt	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	249240249	249240250	+	IGR	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249240249_249240250insG								PGBD2 (26905 upstream) : None (None downstream)																							ggttagggttagggttaggggt	0.000													5	3	---	---	---	---	
PXDN	7837	broad.mit.edu	37	2	1683594	1683595	+	Intron	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1683594_1683595delGT	uc002qxa.2	-						PXDN_uc002qxb.1_Intron|PXDN_uc002qxc.1_Intron	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor						extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		tgtgtaaatggtgtgtgtgtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2647461	2647461	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2647461delG								MYT1L (312416 upstream) : TSSC1 (545280 downstream)																							CAGCTGGACTGGGGCCTCCTC	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2707776	2707776	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2707776delC								MYT1L (372731 upstream) : TSSC1 (484965 downstream)																							CACTCGTCCTCCACCCTGTCT	0.478													4	2	---	---	---	---	
ROCK2	9475	broad.mit.edu	37	2	11472593	11472593	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11472593delC	uc002rbd.1	-							NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CCAAATTAGGCCACACTCATG	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	26955926	26955926	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26955926delG								KCNK3 (1860 upstream) : C2orf18 (31216 downstream)																							TCCAGATGATGCCATCCCCAC	0.502													4	2	---	---	---	---	
LTBP1	4052	broad.mit.edu	37	2	33369536	33369536	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33369536delA	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GCCTTCTGGCAAGGGTAAAAG	0.438													4	2	---	---	---	---	
TTC7A	57217	broad.mit.edu	37	2	47250848	47250848	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47250848delG	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron|TTC7A_uc002rvq.2_Intron|TTC7A_uc002rvr.2_Intron	NM_020458	NP_065191	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			CCAGGGCTCAGGGGTCtaaaa	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	59960033	59960033	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59960033delA								None (None upstream) : BCL11A (718270 downstream)																							TTCAAAAGACAAAAAAAAATT	0.353													3	3	---	---	---	---	
CD207	50489	broad.mit.edu	37	2	71058341	71058341	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71058341delG	uc002shg.2	-							NM_015717	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 antigen, langerin						defense response to virus	endocytic vesicle|integral to membrane	mannose binding			ovary(1)|lung(1)	2						CCTACCAAGAGCGGGGAAAAA	0.443													189	104	---	---	---	---	
C2orf3	6936	broad.mit.edu	37	2	75926634	75926634	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75926634delC	uc002sno.2	-						C2orf3_uc010ffs.2_Intron|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						GGACTTTTAACCCCAAGTACA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	78230573	78230573	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78230573delA								SNAR-H (48421 upstream) : None (None downstream)																							AAGTAAACATAAAAAAAAACT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	78759652	78759652	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78759652delA	uc002snv.3	-											Homo sapiens cytochrome c, somatic pseudogene 6, mRNA (cDNA clone IMAGE:4815768).																		GAAAAGACTGAAAAAAAAAGA	0.338													4	2	---	---	---	---	
CTNNA2	1496	broad.mit.edu	37	2	80576711	80576711	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80576711delT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysi.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						AGGTCTCCCCTCAGTTTGTCT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91738373	91738375	+	IGR	DEL	TCA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91738373_91738375delTCA								None (None upstream) : LOC654342 (66817 downstream)																							tcatttcatctcatcatttcttc	0.000													6	4	---	---	---	---	
TMEM131	23505	broad.mit.edu	37	2	98460442	98460443	+	Intron	DEL	AG	-	-	rs144504477		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98460442_98460443delAG	uc002syh.3	-						TMEM131_uc010yvg.1_Intron	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6						TGATTTGAATAGAGATATTGAA	0.287													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	112490326	112490326	+	IGR	DEL	T	-	-	rs10707606		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112490326delT								LOC541471 (237634 upstream) : ANAPC1 (36315 downstream)																							AGAGTTGTTGTTTTTTTTTTT	0.418													3	3	---	---	---	---	
ACTR3	10096	broad.mit.edu	37	2	114686708	114686708	+	Intron	DEL	T	-	-	rs138322996		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114686708delT	uc002tkx.1	+						ACTR3_uc010yyc.1_Intron|ACTR3_uc010yyd.1_Intron	NM_005721	NP_005712	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog						cellular component movement|cilium morphogenesis	Arp2/3 protein complex	actin binding|ATP binding			skin(1)	1						gctatttttgttttttttttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121316867	121316867	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121316867delC								LOC84931 (92942 upstream) : GLI2 (176332 downstream)																							gtgagaccctcccagaccacc	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121400589	121400590	+	IGR	INS	-	AA	AA	rs55864136		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121400589_121400590insAA								LOC84931 (176664 upstream) : GLI2 (92609 downstream)																							atgtcccagagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
CNTNAP5	129684	broad.mit.edu	37	2	124800360	124800361	+	Intron	INS	-	ATCT	ATCT	rs148779365	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124800360_124800361insATCT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)		AACTCtctatcatctatctatc	0.257													4	3	---	---	---	---	
IWS1	55677	broad.mit.edu	37	2	128240608	128240608	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128240608delA	uc002ton.2	-							NM_017969	NP_060439	Q96ST2	IWS1_HUMAN	IWS1 homolog						transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		ATGTCGCTTGAAAAAAAAACA	0.204													4	2	---	---	---	---	
WDR33	55339	broad.mit.edu	37	2	128527021	128527021	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128527021delA	uc002tpg.1	-						WDR33_uc002tph.1_Intron|WDR33_uc002tpi.1_Intron	NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1						postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		acaaacaaacaaaaaaaaaaC	0.214													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129335882	129335882	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129335882delA								HS6ST1 (259711 upstream) : None (None downstream)																							ACATCCATATAAAAAGCAAGA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133021069	133021070	+	IGR	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133021069_133021070insG								NCRNA00164 (5527 upstream) : GPR39 (153077 downstream)																							ATTGGATAATAGAAAAAAACAC	0.312													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133052910	133052911	+	IGR	INS	-	T	T	rs138624541	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133052910_133052911insT								NCRNA00164 (37368 upstream) : GPR39 (121236 downstream)																							actagtccttatttaaaaaaaa	0.069													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133086349	133086350	+	IGR	INS	-	A	A	rs145771742	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133086349_133086350insA								NCRNA00164 (70807 upstream) : GPR39 (87797 downstream)																							GAACACAAAACAAACAAAACTG	0.243													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	135546994	135546995	+	IGR	DEL	GT	-	-	rs10554305		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135546994_135546995delGT								TMEM163 (21660 upstream) : ACMSD (49191 downstream)																							acagggaagggtgaggaatggg	0.168													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139425974	139425975	+	IGR	DEL	AA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139425974_139425975delAA								SPOPL (95171 upstream) : NXPH2 (754 downstream)																							cctgtctgtcaaaaaagaggat	0.139													4	2	---	---	---	---	
ZEB2	9839	broad.mit.edu	37	2	145260422	145260422	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145260422delT	uc002tvu.2	-						ZEB2_uc002tvv.2_Intron|ZEB2_uc010zbm.1_Intron|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Intron|ZEB2_uc002tvw.2_Intron|ZEB2_uc002tvx.1_Intron	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b							cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		ACTCCCTTGATTTTTTTTTTT	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	147137777	147137777	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147137777delT								None (None upstream) : PABPC1P2 (206848 downstream)																							TTGTGGCGACTTTCCACTTTC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	147559637	147559638	+	IGR	DEL	CA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147559637_147559638delCA								PABPC1P2 (211080 upstream) : None (None downstream)																							gttacaggaccacaggtttgca	0.000													4	2	---	---	---	---	
CACNB4	785	broad.mit.edu	37	2	152893250	152893250	+	Intron	DEL	A	-	-	rs34291403		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152893250delA	uc002tya.2	-						CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron	NM_000726	NP_000717	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)	tttctgggttactttaggcta	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	156931350	156931350	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156931350delC	uc002tyw.2	-											Homo sapiens cDNA clone IMAGE:5209417.																		cctagttgctcgtgactgata	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	169181380	169181380	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169181380delT								STK39 (77275 upstream) : LASS6 (131455 downstream)																							ataggtctgcttttttttgag	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177358193	177358193	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177358193delG								MTX2 (155442 upstream) : MIR1246 (107515 downstream)																							TTGGTGGAGTGGGAGGAGGCT	0.453													4	2	---	---	---	---	
PDE11A	50940	broad.mit.edu	37	2	178845619	178845620	+	Intron	INS	-	CTC	CTC	rs150555612	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178845619_178845620insCTC	uc002ulq.2	-						PDE11A_uc002ulr.2_Intron|PDE11A_uc002ult.1_Intron	NM_016953	NP_058649	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)			CAAGAGCAATTCTTTAAATAGA	0.371									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				5	3	---	---	---	---	
SESTD1	91404	broad.mit.edu	37	2	179974274	179974274	+	3'UTR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179974274delT	uc002uni.3	-	18					SESTD1_uc002unh.3_3'UTR	NM_178123	NP_835224	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1						regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			GAAGGGCAACTTTTTTTTTTC	0.333													4	2	---	---	---	---	
ANKAR	150709	broad.mit.edu	37	2	190538771	190538771	+	5'Flank	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190538771delA	uc002uqw.1	+						ANKAR_uc002uqu.2_5'Flank|ANKAR_uc002uqv.1_5'Flank	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			ctcggaggggaaaagggcact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	202839223	202839223	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202839223delT								CDK15 (80960 upstream) : FZD7 (60087 downstream)																							CTTACATAGGTTGTTTTGGAG	0.423													4	2	---	---	---	---	
PARD3B	117583	broad.mit.edu	37	2	206478768	206478768	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206478768delA	uc002var.1	+						PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron|uc010fuc.1_5'Flank	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		GGGGAGTGGCAAAAAAATGGG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	212072521	212072521	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212072521delT								CPS1 (528692 upstream) : ERBB4 (167921 downstream)																							TATTTTTTTCTTTTTTTGACA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220549300	220549300	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220549300delT								SLC4A3 (42599 upstream) : None (None downstream)																							TAATTGTCACTTTTTTTTTTT	0.388													4	4	---	---	---	---	
DNER	92737	broad.mit.edu	37	2	230492628	230492628	+	Intron	DEL	A	-	-	rs147171567		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230492628delA	uc002vpv.2	-							NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		aacatggcgcaacaatggttc	0.184													1	5	---	---	---	---	
DIS3L2	129563	broad.mit.edu	37	2	233134465	233134466	+	Intron	INS	-	GAGG	GAGG	rs77399752		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233134465_233134466insGAGG	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vso.2_Intron	NM_152383	NP_689596	Q8IYB7	DI3L2_HUMAN	DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		TGTAGGGTGCAGAGAGAGAGAG	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239637045	239637045	+	IGR	DEL	A	-	-	rs34331796		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239637045delA								ASB1 (276155 upstream) : TWIST2 (119628 downstream)																							TTCTCTCATTAAAAAAAAAAA	0.423													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	242513670	242513670	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242513670delT								BOK (119 upstream) : THAP4 (10151 downstream)																							GATGGGAgggttcctggaatt	0.234													4	2	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2224515	2224515	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2224515delT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TCAGCACAGGTTTTTTTTTTT	0.343													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	3318369	3318369	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3318369delA								CRBN (96979 upstream) : SUMF1 (504667 downstream)																							cctttatgataacactgcctc	0.134													4	2	---	---	---	---	
SRGAP3	9901	broad.mit.edu	37	3	9229230	9229230	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9229230delC	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron|SRGAP3_uc003brk.2_Intron	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		TGGGCCTCTTCCCCCGGGAAG	0.522			T	RAF1	pilocytic astrocytoma								4	2	---	---	---	---	
ATG7	10533	broad.mit.edu	37	3	11371438	11371438	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11371438delT	uc003bwc.2	+						ATG7_uc003bwd.2_Intron|ATG7_uc011aum.1_Intron	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a						autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1						ctttctttgattttttttgat	0.000													4	2	---	---	---	---	
COLQ	8292	broad.mit.edu	37	3	15553297	15553297	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15553297delC	uc003bzx.2	-						HACL1_uc011avr.1_Intron|COLQ_uc003bzz.2_Intron|COLQ_uc010heo.2_Intron|COLQ_uc003cae.1_Intron|COLQ_uc003cad.1_Intron	NM_005677	NP_005668	Q9Y215	COLQ_HUMAN	acetylcholinesterase collagen-like tail subunit						acetylcholine catabolic process in synaptic cleft|asymmetric protein localization	basal lamina|cell junction|collagen|extracellular space|synaptic cleft					0						GGGGGCCACTCCATGAGGTCC	0.527													4	2	---	---	---	---	
RFTN1	23180	broad.mit.edu	37	3	16457508	16457509	+	Intron	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16457508_16457509insA	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4						TTGGCTCCTTGAAAAAAAAAAA	0.351													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	18066133	18066133	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18066133delT	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																		TGGCACTAAGTTTAACAAATA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23030790	23030790	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23030790delT								ZNF385D (616667 upstream) : UBE2E2 (213863 downstream)																							CAATTTAATATTTCCAGTCAC	0.209													4	2	---	---	---	---	
UBE2E1	7324	broad.mit.edu	37	3	23877081	23877082	+	Intron	INS	-	AATGTATACTTTTA	AATGTATACTTTTA	rs145680197	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23877081_23877082insAATGTATACTTTTA	uc003cch.2	+						UBE2E1_uc003cci.2_Intron|UBE2E1_uc011awh.1_Intron	NM_003341	NP_003332	P51965	UB2E1_HUMAN	ubiquitin-conjugating enzyme E2E 1 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|histone H2B ubiquitination|histone monoubiquitination|ISG15-protein conjugation|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination	cytosol|nucleoplasm|ubiquitin ligase complex	ATP binding|ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity				0						accaAGGAAGTAATGTATACTT	0.144													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	26604459	26604459	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26604459delT								OXSM (768435 upstream) : LRRC3B (59841 downstream)																							attattattatttttttttta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	38887106	38887106	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38887106delA								SCN10A (51605 upstream) : SCN11A (154 downstream)																							tgaatgctataaagcatggct	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	39457613	39457613	+	IGR	DEL	G	-	-	rs35714292		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39457613delG								RPSA (3583 upstream) : MOBP (51457 downstream)																							AGTTGGGACTGGGTCTGGTCT	0.507													4	4	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41862103	41862104	+	Intron	DEL	CT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41862103_41862104delCT	uc003ckv.3	-						ULK4_uc003ckw.2_Intron	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		acaaaagacactagagactaca	0.000													4	2	---	---	---	---	
TRAK1	22906	broad.mit.edu	37	3	42179234	42179234	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42179234delA	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1						CTTTATAGTGAAGCTTTTCTT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	42515926	42515927	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42515926_42515927insT								LYZL4 (63861 upstream) : VIPR1 (28177 downstream)																							CAAATCTCACCTCCCACATATG	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	43199885	43199885	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43199885delG								C3orf39 (52320 upstream) : SNRK (128119 downstream)																							cagagaggaagggacttgctg	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	47595249	47595249	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47595249delT								C3orf75 (40050 upstream) : CSPG5 (8480 downstream)																							tttctttttcttttttttttt	0.000													3	4	---	---	---	---	
DHX30	22907	broad.mit.edu	37	3	47885203	47885203	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47885203delT	uc003cru.2	+						DHX30_uc003crt.2_Intron|DHX30_uc010hjr.1_Intron	NM_138615	NP_619520	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 30							mitochondrial nucleoid	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)	4				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		ggcagttctcttttttttgag	0.000													4	2	---	---	---	---	
MAP4	4134	broad.mit.edu	37	3	47963013	47963013	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47963013delA	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc011bbf.1_Intron|MAP4_uc003csf.3_Intron	NM_002375	NP_002366	P27816	MAP4_HUMAN	microtubule-associated protein 4 isoform 1						negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)		ctcacctctcaaaaaaaaaat	0.000													4	2	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54575615	54575616	+	Intron	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54575615_54575616insG	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		ttgttatggcagcccttggaca	0.208													4	2	---	---	---	---	
FLNB	2317	broad.mit.edu	37	3	58037413	58037413	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58037413delT	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		tttttttgggtttttttttta	0.139													4	2	---	---	---	---	
FLNB	2317	broad.mit.edu	37	3	58047882	58047882	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58047882delC	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		AGCCCATCTTCCACCATCAGC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	59619419	59619422	+	IGR	DEL	TGTG	-	-	rs34918960		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59619419_59619422delTGTG								C3orf67 (583661 upstream) : FHIT (115616 downstream)																							CTCCTAAGCAtgtgtgtgtgtgtg	0.363													4	2	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	60380913	60380914	+	Intron	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60380913_60380914delTG	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003	P49789	FHIT_HUMAN	fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		GGTGGTGCTTTGTGAAGCTGAT	0.366			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	2	---	---	---	---	
FHIT	2272	broad.mit.edu	37	3	61066506	61066506	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61066506delA	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003	P49789	FHIT_HUMAN	fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		CCACAGCAGGAAAAAAAAAAA	0.448			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	61263773	61263773	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61263773delG								FHIT (26640 upstream) : PTPRG (283470 downstream)																							GGAAGCAGGTGGGTGGGAAGC	0.517													4	2	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	62180479	62180480	+	Intron	INS	-	A	A	rs112680245	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62180479_62180480insA	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		ttcatctcaataaaaaaaaaaa	0.183													4	2	---	---	---	---	
PRICKLE2	166336	broad.mit.edu	37	3	64116482	64116482	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64116482delG	uc003dmf.2	-							NM_198859	NP_942559	Q7Z3G6	PRIC2_HUMAN	prickle-like 2							cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		tcttgggggtggggtccaggt	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	64933275	64933276	+	Intron	DEL	CA	-	-	rs34693641		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64933275_64933276delCA	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																		GTAGTCCATGCACACACACACA	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	70111888	70111891	+	IGR	DEL	CTGG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70111888_70111891delCTGG								MITF (94402 upstream) : FOXP1 (892846 downstream)																							ACGTTCAGGCCTGGCTGGCTGTTT	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	71854126	71854126	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71854126delG								PROK2 (19769 upstream) : RYBP (569625 downstream)																							AATCTCTCCTGGGGCCTCAAT	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72773735	72773736	+	IGR	INS	-	T	T	rs72085457		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72773735_72773736insT								RYBP (277961 upstream) : SHQ1 (24694 downstream)																							TTCTAAACttgttttttttttt	0.223													3	3	---	---	---	---	
ROBO1	6091	broad.mit.edu	37	3	78924696	78924697	+	Intron	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78924696_78924697insA	uc003dqe.2	-						ROBO1_uc003dqb.2_Intron|ROBO1_uc003dqc.2_Intron|ROBO1_uc003dqd.2_Intron	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		AGCTAGAATAGAAAAAAAAATC	0.312													4	2	---	---	---	---	
GBE1	2632	broad.mit.edu	37	3	81801901	81801901	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81801901delA	uc003dqg.2	-							NM_000158	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		TCCTACTAACAAAAAAAAAGA	0.343									Glycogen_Storage_Disease_type_IV				6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	88057333	88057334	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88057333_88057334insA								HTR1F (14414 upstream) : CGGBP1 (43772 downstream)																							GAGTTCCTTTCAAAAAAAAAAA	0.144													4	2	---	---	---	---	
LOC152225	152225	broad.mit.edu	37	3	101668516	101668516	+	Intron	DEL	T	-	-	rs34818757		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101668516delT	uc003dvr.1	+							NR_026934				Homo sapiens cDNA FLJ33269 fis, clone ASTRO2007578.												0						TCTTCTGGTCTATCTTCCTCC	0.194													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	102223540	102223541	+	IGR	INS	-	GA	GA	rs144708663	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102223540_102223541insGA								ZPLD1 (24855 upstream) : None (None downstream)																							CATTGCCAGGGAAAAAAAAACA	0.386													3	4	---	---	---	---	
PHLDB2	90102	broad.mit.edu	37	3	111632040	111632050	+	Intron	DEL	GCCAAGTGTTT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111632040_111632050delGCCAAGTGTTT	uc010hqa.2	+						PHLDB2_uc003dyc.2_Intron|PHLDB2_uc003dyd.2_Intron|PHLDB2_uc003dyg.2_Intron|PHLDB2_uc003dyh.2_Intron|PHLDB2_uc003dyi.2_Intron|PHLDB2_uc003dyf.3_Intron	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6						ATCATCACCAGCCAAGTGTTTGTGGGTTTAT	0.431													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112169323	112169324	+	IGR	INS	-	G	G	rs142022192	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112169323_112169324insG								CD200 (87667 upstream) : BTLA (13491 downstream)																							ttcagagcaaaggaaggcatgc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112465049	112465049	+	IGR	DEL	C	-	-	rs113423276		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112465049delC								CCDC80 (105072 upstream) : CD200R1L (69507 downstream)																							ATCCAAGAGGCttttttttgt	0.085													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	113976275	113976275	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113976275delT								ZNF80 (19850 upstream) : TIGIT (36600 downstream)																							tctttctctctttttttttga	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117817824	117817824	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117817824delT								None (None upstream) : IGSF11 (801657 downstream)																							AGTGCACTACTTTTTGCCAGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	120252063	120252064	+	IGR	INS	-	T	T	rs149554271	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120252063_120252064insT								FSTL1 (82145 upstream) : NDUFB4 (63064 downstream)																							tctttaaatacttttttttgtg	0.000													4	2	---	---	---	---	
CASR	846	broad.mit.edu	37	3	121973644	121973644	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121973644delT	uc003eev.3	+						CASR_uc003eew.3_Intron	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor						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)	ACTCtttttcttttttttctt	0.338													4	2	---	---	---	---	
SEMA5B	54437	broad.mit.edu	37	3	122696163	122696163	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122696163delA	uc003efz.1	-						SEMA5B_uc011bju.1_Intron|SEMA5B_uc003ega.1_Intron|SEMA5B_uc003egb.1_Intron|SEMA5B_uc010hro.1_Intron|SEMA5B_uc010hrp.1_Intron	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1						cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)		CTGTTGCAGGATCGCTGAATA	0.075													4	2	---	---	---	---	
KALRN	8997	broad.mit.edu	37	3	124440025	124440025	+	3'UTR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124440025delT	uc003ehg.2	+	60					KALRN_uc003ehk.2_3'UTR	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						AATCATCATCTTTTTTTTTCC	0.303													4	2	---	---	---	---	
CHCHD6	84303	broad.mit.edu	37	3	126534684	126534684	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126534684delC	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719	Q9BRQ6	CHCH6_HUMAN	coiled-coil-helix-coiled-coil-helix domain												0						CCTCTGCTGGCCTCATCCTAG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127107214	127107214	+	Intron	DEL	T	-	-	rs11337613		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127107214delT	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																		gagttgcaaataaaaaggtca	0.254													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127141008	127141008	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127141008delA								PLXNA1 (384780 upstream) : TPRA1 (150900 downstream)																							TGGTTAGTCCAAAAAAACAGA	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	128249673	128249673	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128249673delT								LOC90246 (20246 upstream) : C3orf27 (41171 downstream)																							tctcatcttctttttttttgg	0.000													4	2	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131850415	131850415	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131850415delT	uc003eom.2	-							NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						GTCACTTAGATTTTTTTTTAT	0.254													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140440740	140440741	+	IGR	DEL	AC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140440740_140440741delAC								TRIM42 (20749 upstream) : SLC25A36 (219921 downstream)																							acatacacatacacacacacac	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144014868	144014868	+	IGR	DEL	T	-	-	rs72367514		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144014868delT								C3orf58 (303659 upstream) : None (None downstream)																							catcatctcattttttttttt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	148819796	148819796	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148819796delT								HLTF (15455 upstream) : HPS3 (27575 downstream)																							caaccctgacttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149442090	149442090	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149442090delT								WWTR1 (20975 upstream) : COMMD2 (14170 downstream)																							ctccttcacCTGAATTTCAGC	0.214													4	2	---	---	---	---	
C3orf16	389161	broad.mit.edu	37	3	149509829	149509830	+	Intron	INS	-	TT	TT			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149509829_149509830insTT	uc003exl.2	-						C3orf16_uc011bnt.1_Intron|C3orf16_uc003exm.2_5'Flank	NM_001144960	NP_001138432	E9PHT4	E9PHT4_HUMAN	hypothetical protein LOC389161												0						AGAAGTCAGACTTTTTTTTTTT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	150375090	150375091	+	IGR	DEL	AA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150375090_150375091delAA								SELT (26858 upstream) : FAM194A (2586 downstream)																							GATAGAAGCTAAAAGTTTACTC	0.302													4	2	---	---	---	---	
GMPS	8833	broad.mit.edu	37	3	155629773	155629774	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155629773_155629774insT	uc003faq.2	+						GMPS_uc011bom.1_Intron	NM_003875	NP_003866	P49915	GUAA_HUMAN	guanine monophosphate synthetase						glutamine metabolic process|purine base biosynthetic process	cytosol	ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity			ovary(2)|lung(1)	3			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	AGATTCTATACTTTTTTTTTAA	0.327			T	MLL	AML								4	2	---	---	---	---	
KCNAB1	7881	broad.mit.edu	37	3	155908001	155908001	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155908001delC	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TCCGCCTGCTCCCCCAGTGCC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	167574161	167574161	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167574161delC								SERPINI1 (30805 upstream) : GOLIM4 (153493 downstream)																							GCAGTGTGGTCCCGAGACTTT	0.478													4	2	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	168953273	168953274	+	Intron	DEL	AC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168953273_168953274delAC	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						GCACATGCATACACACACACAC	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179845944	179845944	+	IGR	DEL	A	-	-	rs111428181		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179845944delA								PEX5L (91427 upstream) : TTC14 (473974 downstream)																							acacccccccaaaaaaaagca	0.000													4	2	---	---	---	---	
ECE2	9718	broad.mit.edu	37	3	183972965	183972965	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183972965delG	uc003fni.3	+						ECE2_uc003fnh.3_Intron	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A						brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGTCAGGTGTGGGGGTAATGA	0.483													4	2	---	---	---	---	
LIPH	200879	broad.mit.edu	37	3	185241592	185241592	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185241592delC	uc003fpm.2	-						LIPH_uc010hyh.2_Intron	NM_139248	NP_640341	Q8WWY8	LIPH_HUMAN	lipase, member H precursor						lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			ctcaccgcaacctctgtctcc	0.015													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187163438	187163439	+	IGR	DEL	CT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187163438_187163439delCT								RTP4 (74071 upstream) : SST (223257 downstream)																							AGGCCAATGGCTCTCAGGAGAG	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	188647669	188647669	+	IGR	DEL	C	-	-	rs11923468	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188647669delC								LPP (50228 upstream) : TPRG1 (17334 downstream)																							CACAGTGCCTCCCCCAGAAGA	0.617													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193456116	193456116	+	IGR	DEL	T	-	-	rs77483905		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193456116delT								OPA1 (40517 upstream) : LOC100128023 (254768 downstream)																							TCTAGACATCTTTTTTTTTTt	0.229													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194230861	194230862	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194230861_194230862insT	uc003fua.1	+											Homo sapiens cDNA FLJ34208 fis, clone FCBBF3020232.																		ctgatctgttgtttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195641869	195641870	+	IGR	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195641869_195641870insG								TNK2 (3053 upstream) : SDHAP1 (44922 downstream)																							GGAGCTGCCAAGGGGGCTGTGC	0.594											OREG0016003	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
PIGZ	80235	broad.mit.edu	37	3	196674754	196674755	+	Frame_Shift_Ins	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196674754_196674755insT	uc003fxh.2	-	3	1160_1161	c.1013_1014insA	c.(1012-1014)TGGfs	p.W338fs		NM_025163	NP_079439	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	338					GPI anchor biosynthetic process	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			ovary(3)	3	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		GCAGCCGTTGCCACGCAGCCTG	0.668													41	41	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	197150689	197150690	+	IGR	INS	-	T	T	rs145869557	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197150689_197150690insT								DLG1 (124546 upstream) : BDH1 (85965 downstream)																							cagtcagaagctggaggagatg	0.188													5	3	---	---	---	---	
LOC348840	348840	broad.mit.edu	37	3	197803398	197803398	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197803398delA	uc003fyx.3	-						LOC348840_uc010iat.2_Intron	NR_003291				Homo sapiens hypothetical protein LOC348840, mRNA (cDNA clone IMAGE:5167648), partial cds.												0						ACGTAATTAGAAAAAAAAATA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	16871	16871	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16871delT								None (None upstream) : ZNF595 (36356 downstream)																							acgttaattctttTTTTTTTC	0.060													4	2	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	57746	57746	+	Intron	DEL	A	-	-	rs111852468		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57746delA	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		CTGGAAAAACAAAAGGGTTTT	0.303													4	4	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	77663	77663	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77663delA	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		ggcctgagacaaaaaaaaatc	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11540277	11540277	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11540277delA								HS3ST1 (109740 upstream) : None (None downstream)																							ATGTCAAACTATCCCATCTCA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	13732419	13732419	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13732419delG	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																		gtgcctatgtggtaactgatc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14341338	14341338	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14341338delT								BOD1L (712010 upstream) : CPEB2 (664184 downstream)																							AATTGCATACTTTTTTTGGTG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24250112	24250112	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24250112delA								PPARGC1A (358412 upstream) : MIR573 (271703 downstream)																							CCACCTCTGGAAAAAAAAAAG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	31210868	31210869	+	IGR	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31210868_31210869delTG								PCDH7 (62447 upstream) : None (None downstream)																							tatatgtttatgtgtgtgtgtg	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	35175572	35175572	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35175572delT								None (None upstream) : ARAP2 (774272 downstream)																							tctccaatgataacagtatca	0.005													4	2	---	---	---	---	
ARAP2	116984	broad.mit.edu	37	4	36168282	36168282	+	Intron	DEL	A	-	-	rs34197719		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36168282delA	uc003gsq.1	-						ARAP2_uc003gsr.1_Intron	NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						ACATATTTTCAAAAAAAAAAC	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42678606	42678606	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42678606delA								ATP8A1 (19484 upstream) : GRXCR1 (216678 downstream)																							ccactcagggaaagggaaccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	44829308	44829308	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44829308delT								GNPDA2 (100696 upstream) : None (None downstream)																							ctttcctctctctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	44829310	44829310	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44829310delT								GNPDA2 (100698 upstream) : None (None downstream)																							ttcctctctctctctctctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49237605	49237606	+	5'Flank	DEL	AT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49237605_49237606delAT	uc003gyy.2	-											DQ587539																		CTGAACTGACATGTGTATATAC	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49275069	49275069	+	IGR	DEL	G	-	-	rs71253582		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49275069delG								CWH43 (210976 upstream) : None (None downstream)																							agccatctatgacaaacccac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58171913	58171913	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58171913delT								IGFBP7 (195374 upstream) : None (None downstream)																							tttttctttcttttttttttt	0.164													2	4	---	---	---	---	
SLC4A4	8671	broad.mit.edu	37	4	72106383	72106383	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72106383delA	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			CAGGAAAAGTAAAAAAAGTAT	0.214													4	2	---	---	---	---	
EREG	2069	broad.mit.edu	37	4	75228167	75228168	+	5'Flank	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75228167_75228168insT	uc003hie.1	+						EREG_uc003hid.2_5'Flank	NM_001432	NP_001423	O14944	EREG_HUMAN	epiregulin preproprotein						angiogenesis|cell-cell signaling|cytokine-mediated signaling pathway|epidermal growth factor receptor signaling pathway|female meiosis|keratinocyte differentiation|keratinocyte proliferation|luteinizing hormone signaling pathway|mRNA transcription|negative regulation of epithelial cell proliferation|negative regulation of smooth muscle cell differentiation|negative regulation of transcription, DNA-dependent|oocyte maturation|organ morphogenesis|ovarian cumulus expansion|ovulation|positive regulation of cell division|positive regulation of cytokine production|positive regulation of DNA replication|positive regulation of epidermal growth factor receptor activity|positive regulation of fibroblast proliferation|positive regulation of innate immune response|positive regulation of interleukin-6 biosynthetic process|positive regulation of mitosis|positive regulation of phosphorylation|positive regulation of smooth muscle cell proliferation|primary follicle stage|wound healing	extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|growth factor activity			breast(1)|skin(1)	2			Lung(101;0.196)			GTTCCCAATTATTTAAAAAAAA	0.282													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	81986059	81986059	+	IGR	DEL	T	-	-	rs72509642		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81986059delT								BMP3 (7375 upstream) : PRKG2 (23778 downstream)																							TTAAAAAAAATTTTTTTTTAG	0.348													4	2	---	---	---	---	
PRKG2	5593	broad.mit.edu	37	4	82043766	82043766	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82043766delT	uc003hmh.2	-						PRKG2_uc011ccf.1_Intron|PRKG2_uc011ccg.1_Intron|PRKG2_uc011cch.1_Intron	NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II						platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7						TATTTAGGCCTTTTTTTTCCT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	89506802	89506802	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89506802delT								PIGY (61847 upstream) : HERC3 (6845 downstream)																							GGAAACTTTATTTTTGGCAGG	0.343													4	2	---	---	---	---	
BMPR1B	658	broad.mit.edu	37	4	95869015	95869015	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95869015delT	uc003htm.3	+							NM_001203	NP_001194	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB						BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(4)|skin(2)|stomach(1)|breast(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		TGGCCTTACATTTACCTAGCA	0.428													4	2	---	---	---	---	
ADH5	128	broad.mit.edu	37	4	99996365	99996365	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99996365delT	uc003hui.2	-						ADH5_uc003huj.2_Intron	NM_000671	NP_000662	P11766	ADHX_HUMAN	class III alcohol dehydrogenase, chi subunit						ethanol oxidation|response to redox state		alcohol dehydrogenase (NAD) activity|electron carrier activity|fatty acid binding|formaldehyde dehydrogenase activity|S-(hydroxymethyl)glutathione dehydrogenase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)	NADH(DB00157)	TATATTTTAAttttttttgtt	0.144													4	2	---	---	---	---	
SYNPO2	171024	broad.mit.edu	37	4	119816190	119816190	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119816190delT	uc003icm.3	+						SYNPO2_uc010ina.2_Intron|SYNPO2_uc010inb.2_Intron|SYNPO2_uc011cgh.1_Intron	NM_001128933	NP_001122405	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform b							nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2						ATGTAAATGATTttttttaag	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	132999015	132999015	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132999015delA								None (None upstream) : None (None downstream)																							caaaaggtttaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	133003289	133003290	+	IGR	INS	-	T	T	rs150744811	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133003289_133003290insT								None (None upstream) : None (None downstream)																							AATTTAAGGGATTTTTTTTTCA	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	146532059	146532060	+	IGR	INS	-	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146532059_146532060insC								SMAD1 (51736 upstream) : MMAA (8480 downstream)																							ttgaatgtgttccccaaagtta	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153191231	153191231	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153191231delC								PET112L (509085 upstream) : FBXW7 (51180 downstream)																							AAATATCTGGCCTTGAACTAG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	165338669	165338669	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165338669delA								MARCH1 (33467 upstream) : TRIM61 (536931 downstream)																							TCCAAATGACAAAAAAATCAC	0.279													4	2	---	---	---	---	
SPOCK3	50859	broad.mit.edu	37	4	168036073	168036073	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168036073delA	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron|SPOCK3_uc003irk.3_Intron|SPOCK3_uc011cjw.1_Intron	NM_016950	NP_058646	Q9BQ16	TICN3_HUMAN	testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)		ggactaagagaaaaaaaaaca	0.000													4	2	---	---	---	---	
GPM6A	2823	broad.mit.edu	37	4	176895018	176895018	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176895018delT	uc003iug.2	-						GPM6A_uc003iuh.2_Intron	NM_005277	NP_005268	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 1							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		TTATGCTGACTTTTTTTTCAC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189324744	189324745	+	Intron	INS	-	T	T	rs147477880	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189324744_189324745insT	uc003izo.1	+											Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																		gttttttgttgtttttttttgt	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190664836	190664836	+	IGR	DEL	G	-	-	rs2318576		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190664836delG								None (None upstream) : FRG1 (197138 downstream)																							ctgaaaaaaagagacaaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190859672	190859672	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190859672delG	uc003izq.2	-						FRG1_uc003izs.2_5'Flank					Homo sapiens cDNA clone IMAGE:30384438.																		TTTTCAAAAAGCAAAGACTCT	0.264													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6777349	6777349	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6777349delG								PAPD7 (20188 upstream) : ADCY2 (618994 downstream)																							TAGGAAAATTGCTCTGAAACA	0.403													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22430503	22430503	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22430503delA	uc003jgk.2	-							NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						AAAACAGAGTAAAAAAAAAAT	0.289										HNSCC(59;0.17)			4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22493768	22493768	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22493768delT	uc003jgk.2	-							NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						ttccaggtaattatgaataaa	0.035										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23492402	23492402	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23492402delG								CDH12 (638671 upstream) : PRDM9 (15322 downstream)																							aacatggtgtgggggaggttg	0.000													4	2	---	---	---	---	
MTMR12	54545	broad.mit.edu	37	5	32233576	32233579	+	Intron	DEL	ACAA	-	-	rs35760638		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32233576_32233579delACAA	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1						acacacacacacaaacacacacac	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42253597	42253597	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42253597delA								FBXO4 (311934 upstream) : GHR (170429 downstream)																							aTCCTTAAGGAAAAAAAAAAA	0.149													4	2	---	---	---	---	
EMB	133418	broad.mit.edu	37	5	49730755	49730755	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49730755delT	uc003jom.2	-						EMB_uc010ivr.2_Intron	NM_198449	NP_940851	Q6PCB8	EMB_HUMAN	embigin precursor							integral to membrane					0	Lung SC(58;0.218)	Lung NSC(810;0.0795)				AACGTTCACCTTATATTGTGC	0.323													4	2	---	---	---	---	
SLC38A9	153129	broad.mit.edu	37	5	54968743	54968743	+	Intron	DEL	T	-	-	rs5867996		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54968743delT	uc003jqf.2	-						SLC38A9_uc003jqd.2_Intron|SLC38A9_uc010ivx.2_Intron|SLC38A9_uc003jqe.2_Intron|SLC38A9_uc010ivy.2_Intron	NM_173514	NP_775785	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9						amino acid transport|sodium ion transport	integral to membrane					0		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				TTAAGCACACTTTTTTTGTAA	0.303													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	58151918	58151918	+	5'Flank	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58151918delT	uc003jrq.2	+											Homo sapiens primary neuroblastoma cDNA, clone:Nbla00158, full insert sequence.																		ACACTGATACTTTTTTTTAAG	0.388													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71315622	71315623	+	IGR	INS	-	CA	CA			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71315622_71315623insCA								CARTPT (298750 upstream) : MAP1B (87495 downstream)																							CACAGATACATcacacacacac	0.287													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	72545227	72545227	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72545227delG								TMEM174 (74259 upstream) : FOXD1 (196860 downstream)																							ATGAACTCTTGGAGGCAAGAG	0.468													4	2	---	---	---	---	
AP3B1	8546	broad.mit.edu	37	5	77458455	77458455	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77458455delA	uc003kfj.2	-							NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		CTATTTTACTAAAAAAAAAAG	0.294									Hermansky-Pudlak_syndrome				3	3	---	---	---	---	
AP3B1	8546	broad.mit.edu	37	5	77563270	77563271	+	Intron	DEL	TA	-	-	rs146975881		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77563270_77563271delTA	uc003kfj.2	-							NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		AACGtatttttatatatatata	0.277									Hermansky-Pudlak_syndrome				6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	99925166	99925166	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99925166delT								FAM174A (2726 upstream) : ST8SIA4 (217474 downstream)																							CCTCTATGTCTTTTTTTAATG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	107162282	107162282	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107162282delC								EFNA5 (155686 upstream) : FBXL17 (32458 downstream)																							CACAGCAGGACCCTGAATTCC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	109273026	109273026	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109273026delA								MAN2A1 (69597 upstream) : TMEM232 (351908 downstream)																							CACACAGCAGAAATAGATGAG	0.478													4	2	---	---	---	---	
TMEM232	642987	broad.mit.edu	37	5	109942071	109942072	+	Intron	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109942071_109942072insG	uc011cvh.1	-						TMEM232_uc003kow.1_Intron|TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;							integral to membrane					0						AAAATGAAATAGGTCAGAGGAA	0.282													31	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	116471461	116471461	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116471461delT								SEMA6A (560910 upstream) : None (None downstream)																							TCACCTGGTCTTTTTTTCCCT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117077514	117077514	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117077514delT								None (None upstream) : None (None downstream)																							CCTACATTACTCCCTTTCTGG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119399103	119399103	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119399103delT								FAM170A (427587 upstream) : PRR16 (400916 downstream)																							GCTTATTTTCTTTTTTTTAAC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	131844956	131844956	+	IGR	DEL	T	-	-	rs74367688		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131844956delT								IRF1 (13697 upstream) : IL5 (32180 downstream)																							atattgggaatttttttttta	0.000													6	3	---	---	---	---	
GDF9	2661	broad.mit.edu	37	5	132198374	132198374	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132198374delA	uc003kxz.1	-						GDF9_uc011cxj.1_Intron	NM_005260	NP_005251	O60383	GDF9_HUMAN	growth differentiation factor 9 precursor						female gamete generation|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			skin(1)	1		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCAAGCCTCAAAAAAAAAAA	0.363													5	3	---	---	---	---	
PPP2CA	5515	broad.mit.edu	37	5	133535113	133535113	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133535113delT	uc003kze.2	-							NM_002715	NP_002706	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha						ceramide metabolic process|inactivation of MAPK activity|induction of apoptosis|meiosis|negative regulation of cell growth|negative regulation of epithelial to mesenchymal transition|negative regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of protein serine/threonine kinase activity|protein dephosphorylation|regulation of cell adhesion|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction|spindle pole	metal ion binding|phosphoprotein phosphatase activity			ovary(2)|lung(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Vitamin E(DB00163)	ACAAAACTTGTTTTTTTTTTA	0.299													8	4	---	---	---	---	
CTNNA1	1495	broad.mit.edu	37	5	138093601	138093602	+	Intron	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138093601_138093602insA	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GAACCATCTACAGCCCATTCTT	0.401													4	2	---	---	---	---	
SIL1	64374	broad.mit.edu	37	5	138310106	138310107	+	Intron	DEL	GA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138310106_138310107delGA	uc003ldm.2	-						SIL1_uc003ldn.2_Intron|SIL1_uc003ldo.2_Intron|SIL1_uc003ldp.2_Intron|SIL1_uc003ldq.1_Intron	NM_022464	NP_071909	Q9H173	SIL1_HUMAN	SIL1 protein precursor						intracellular protein transport|protein folding|transmembrane transport	endoplasmic reticulum lumen	unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTGTGCAACTGAGAACAACAGG	0.500									Marinesco-Sj_gren_syndrome				4	2	---	---	---	---	
PPP2R2B	5521	broad.mit.edu	37	5	146189352	146189352	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146189352delA	uc003loe.2	-						PPP2R2B_uc010jgm.2_Intron|PPP2R2B_uc003log.3_Intron|PPP2R2B_uc003lof.3_Intron|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_004576	NP_004567	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			cactctagctaaagtgtgaag	0.000													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148354743	148354743	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148354743delA	uc003lpp.1	-							NM_024577		Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACATTCACTGAGGATGGCATG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	149094514	149094514	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149094514delC								ARHGEF37 (79987 upstream) : PPARGC1B (15350 downstream)																							tagtatttgtccaggGcaaaa	0.129													4	2	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153769852	153769853	+	Intron	INS	-	C	C	rs145987985	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153769852_153769853insC	uc003lvh.2	+						GALNT10_uc010jic.2_Intron|GALNT10_uc010jid.2_Intron|uc003lvi.2_RNA	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			ctgagtcactaattccatcaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	158920056	158920056	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158920056delG								LOC285627 (26772 upstream) : ADRA1B (423684 downstream)																							tttctgGGCTGGACAAATGCA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	159427274	159427274	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159427274delT								ADRA1B (27257 upstream) : TTC1 (8906 downstream)																							GAAGCTATTCTTTTTTTTTTT	0.343													1	5	---	---	---	---	
C1QTNF2	114898	broad.mit.edu	37	5	159795213	159795213	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159795213delA	uc003lyd.2	-							NM_031908	NP_114114	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2							collagen				skin(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TATTTGCTTGAAAAAATATTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165941193	165941193	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165941193delT								None (None upstream) : ODZ2 (770650 downstream)																							TGGTACAATATTTTTTTAAAT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166510020	166510020	+	IGR	DEL	A	-	-	rs34839213		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166510020delA								None (None upstream) : ODZ2 (201823 downstream)																							TGAAATTGGCAAAAAAAAAAG	0.348													2	4	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167069538	167069539	+	Intron	DEL	AC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167069538_167069539delAC	uc010jjd.2	+							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)		GTTTTTTTATACACACACACAC	0.356													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168503106	168503107	+	Intron	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168503106_168503107insG	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAGGACCCTCAGGGGGGTTTCA	0.550													4	2	---	---	---	---	
RANBP17	64901	broad.mit.edu	37	5	170448971	170448971	+	Intron	DEL	G	-	-	rs10475972	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170448971delG	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_Intron	NM_022897	NP_075048	Q9H2T7	RBP17_HUMAN	RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ggacttttttgttgttgttgt	0.000			T	TRD@	ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172150952	172150953	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172150952_172150953insA								NEURL1B (32421 upstream) : DUSP1 (44149 downstream)																							aatgaagagggaaaaatgggtt	0.000													4	2	---	---	---	---	
CPEB4	80315	broad.mit.edu	37	5	173352088	173352089	+	Intron	INS	-	AG	AG	rs150952648	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173352088_173352089insAG	uc003mcs.3	+						CPEB4_uc010jju.1_Intron|CPEB4_uc010jjv.2_Intron|CPEB4_uc011dfg.1_Intron|CPEB4_uc003mct.3_Intron|CPEB4_uc003mcu.3_Intron	NM_030627	NP_085130	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CATTGAGGGGCAGAGAGAGAGA	0.540													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	176205654	176205654	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176205654delC								TSPAN17 (119596 upstream) : UNC5A (31906 downstream)																							CCCCTGGccacccctccccaa	0.224													4	2	---	---	---	---	
PRELID1	27166	broad.mit.edu	37	5	176732201	176732201	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176732201delT	uc003mfx.2	+						RAB24_uc003mfu.2_5'Flank|RAB24_uc003mfv.2_5'Flank|RAB24_uc003mfw.2_5'Flank|PRELID1_uc003mfy.2_Intron	NM_013237	NP_037369	Q9Y255	PRLD1_HUMAN	PRELI domain containing 1 precursor						immune response|multicellular organismal development	mitochondrion|nucleus					0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGTGCTTTTCTTttttttttt	0.219													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	178510272	178510273	+	IGR	DEL	AT	-	-	rs147516432		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178510272_178510273delAT								ZNF354C (2583 upstream) : ADAMTS2 (30578 downstream)																							tgggtagtagataatgtggtat	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	4384751	4384751	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4384751delA								PECI (248920 upstream) : CDYL (321642 downstream)																							ttgaaaaaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9607090	9607090	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9607090delC								HULC (953013 upstream) : TFAP2A (789827 downstream)																							TATCCCCTGGCCCTGGGTAAG	0.259													4	2	---	---	---	---	
C6orf105	84830	broad.mit.edu	37	6	11714379	11714380	+	3'UTR	INS	-	CT	CT			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11714379_11714380insCT	uc003nab.2	-	6					C6orf105_uc003naa.2_RNA|C6orf105_uc011dip.1_3'UTR	NM_032744	NP_116133	Q96IZ2	CF105_HUMAN	hypothetical protein LOC84830 isoform 2							integral to membrane					0	Ovarian(93;0.0848)|Breast(50;0.0871)	all_hematologic(90;0.135)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.193)			actctaagttcctctctctctc	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	13982337	13982337	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13982337delT								RNF182 (2104 upstream) : CD83 (135528 downstream)																							tgagaacaacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28620036	28620036	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28620036delA								SCAND3 (64924 upstream) : TRIM27 (250744 downstream)																							GAAGCTAGAGAAATGCAAGTT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	33307389	33307389	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33307389delT								DAXX (16596 upstream) : LYPLA2P1 (25126 downstream)																							GCTTTGCCTCTTTTTTTTTTT	0.368													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	42114938	42114938	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42114938delA								C6orf132 (42449 upstream) : GUCA1A (8206 downstream)																							actccgtttcaaaaaaaaaaa	0.169													3	3	---	---	---	---	
TRERF1	55809	broad.mit.edu	37	6	42263738	42263739	+	Intron	INS	-	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42263738_42263739insC	uc003osd.2	-						TRERF1_uc003osb.2_Intron|TRERF1_uc003osc.2_Intron|TRERF1_uc003ose.2_Intron|TRERF1_uc010jxu.1_Intron	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			ACGACCCTTCTCCCCCAGCCCC	0.490													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	45731134	45731134	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45731134delA								RUNX2 (212316 upstream) : CLIC5 (135056 downstream)																							acactgaaagaaaaaaaaaat	0.000													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57380824	57380825	+	Intron	INS	-	TT	TT	rs145567229		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57380824_57380825insTT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		gtcagcaaggcttatattcctt	0.000													4	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57390643	57390644	+	Intron	DEL	CA	-	-	rs141634742		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57390643_57390644delCA	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)		TTTAATGCTCCACACATTGCCT	0.401													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57391940	57391941	+	Intron	INS	-	T	T	rs139175265		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57391940_57391941insT	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)		GGGCGCGTCTCTTCCCTGGCTA	0.411													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57502970	57502971	+	Intron	DEL	TT	-	-	rs5876658		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57502970_57502971delTT	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)		CAAAACACAATTTTTTTTAAAT	0.337													0	6	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57503445	57503445	+	Intron	DEL	C	-	-	rs11343070		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57503445delC	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)		aagagcttcacaaaatgagtt	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	64145920	64145920	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64145920delT								LGSN (116038 upstream) : PTP4A1 (85731 downstream)																							cttttttgtgtttttttaaat	0.030													4	2	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69914650	69914650	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69914650delT	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				TCTTTTTTTCTTTTTtttagc	0.189													4	2	---	---	---	---	
LMBRD1	55788	broad.mit.edu	37	6	70386648	70386648	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70386648delA	uc003pfa.2	-						LMBRD1_uc003pey.2_Intron|LMBRD1_uc003pez.2_Intron|LMBRD1_uc010kal.2_Intron|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838	Q9NUN5	LMBD1_HUMAN	liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1						ATGACATATTAAAAAAAAAAT	0.169													4	2	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70797606	70797606	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70797606delG	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						TTCTAACCTCGCCAGCAATGG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82509897	82509898	+	IGR	DEL	TT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82509897_82509898delTT								FAM46A (47469 upstream) : IBTK (370058 downstream)																							ttatcattgctttttggtatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	126528471	126528471	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126528471delC								TRMT11 (168053 upstream) : CENPW (132782 downstream)																							GAAGACAAATCAGGCAACAAG	0.473													4	2	---	---	---	---	
ARHGAP18	93663	broad.mit.edu	37	6	129981131	129981132	+	Intron	INS	-	G	G	rs144740136	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129981131_129981132insG	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050	Q8N392	RHG18_HUMAN	Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		gcatggacagtgggtttagaga	0.124													3	3	---	---	---	---	
VNN1	8876	broad.mit.edu	37	6	133032457	133032458	+	Intron	INS	-	T	T	rs141293420	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133032457_133032458insT	uc003qdo.2	-							NM_004666	NP_004657	O95497	VNN1_HUMAN	vanin 1 precursor						acute inflammatory response|anti-apoptosis|cell-cell adhesion|cellular component movement|chronic inflammatory response|innate immune response|pantothenate metabolic process|positive regulation of T cell differentiation in thymus|response to oxidative stress	anchored to membrane|integral to membrane|plasma membrane	GPI anchor binding|pantetheine hydrolase activity			ovary(3)	3	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		ACTTTAAGGACTTTACTACATT	0.347													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	137920189	137920189	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137920189delC								OLIG3 (104658 upstream) : TNFAIP3 (268392 downstream)																							CTTGAGACCGCCCCACTCCTG	0.428													4	2	---	---	---	---	
NHSL1	57224	broad.mit.edu	37	6	138892679	138892679	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138892679delT	uc003qhx.2	-							NM_020464	NP_065197	Q5SYE7	NHSL1_HUMAN	NHS-like 1 isoform 1												0						AGGAAGAGCATTTTTATTTTA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141224438	141224438	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141224438delA								None (None upstream) : None (None downstream)																							ggtgagagggaaaggaacgta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145840080	145840083	+	IGR	DEL	GAGA	-	-	rs113264279		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145840080_145840083delGAGA								UTRN (665912 upstream) : EPM2A (106363 downstream)																							GAGAAGCAGTGAGAGAGAAAGAGT	0.451													2	4	---	---	---	---	
EPM2A	7957	broad.mit.edu	37	6	146011773	146011773	+	Intron	DEL	A	-	-	rs79330527		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146011773delA	uc003qkw.2	-						EPM2A_uc003qkv.2_Intron|EPM2A_uc010khr.2_Intron|EPM2A_uc003qkx.2_Intron	NM_005670	NP_005661	O95278	EPM2A_HUMAN	laforin isoform a						glycogen metabolic process	cytosol|endoplasmic reticulum|nucleus|plasma membrane|polysome	carbohydrate binding|identical protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		aactaaatggaaaaaaaaaaa	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157035609	157035609	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157035609delT								MIR1202 (767596 upstream) : ARID1B (63477 downstream)																							ACTTCTTCAGTTTCCAGATCT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168086738	168086739	+	5'Flank	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168086738_168086739delTG	uc010kkq.1	-						uc003qvy.1_Intron					Homo sapiens cDNA FLJ32038 fis, clone NTONG2000583.																		TGAGCGTGTCTGTGTGTGTGTG	0.347													4	2	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945259	945260	+	Intron	INS	-	A	A	rs145893866		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945259_945260insA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						aaggagaaagggaaaggagaaa	0.000													6	3	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	945285	945286	+	Intron	INS	-	A	A	rs141647614	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:945285_945286insA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						aaggagaaagggaaaggagaaa	0.000													4	4	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3823720	3823720	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3823720delT	uc003smx.2	+							NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		cttttctttgttttttttttt	0.000													4	3	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	4051074	4051074	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4051074delC	uc003smx.2	+						SDK1_uc010kso.2_Intron	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TCTTTGTCCACCCCACTGCCG	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	7969013	7969013	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7969013delA								RPA3 (210775 upstream) : GLCCI1 (39410 downstream)																							atctgggctgaaaaagtaaat	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	9160301	9160301	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9160301delA								NXPH1 (367709 upstream) : PER4 (513599 downstream)																							CCTAGATTTTAAACCAGGAGT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12557905	12557905	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12557905delT								VWDE (114053 upstream) : SCIN (38282 downstream)																							atacctgtcctttagccccct	0.000													4	2	---	---	---	---	
MGC87042	256227	broad.mit.edu	37	7	22478569	22478569	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22478569delA	uc003svh.2	-						MGC87042_uc010kum.1_Intron			Q6NZ63	STEAL_HUMAN	SubName: Full=cDNA FLJ60218, highly similar to Six transmembrane epithelial antigen ofprostate 1;							integral to membrane	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0						tgaataaaacaaaaaaaagtg	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24256978	24256978	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24256978delA								STK31 (312613 upstream) : NPY (66831 downstream)																							GGGATGATAGAAAAAAAAAAA	0.299													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25357639	25357641	+	IGR	DEL	TGG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25357639_25357641delTGG								NPVF (89534 upstream) : MIR148A (631898 downstream)																							TAGGATTTACTGGTGGTAATAAG	0.394													4	2	---	---	---	---	
CPVL	54504	broad.mit.edu	37	7	29108006	29108006	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29108006delA	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601	Q9H3G5	CPVL_HUMAN	serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2						GCCAAGAATGAAAAGGGTTAT	0.303													4	2	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	34010735	34010735	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34010735delT	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						tgtttttttgttttttttttt	0.383													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	34197578	34197579	+	IGR	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34197578_34197579delTG								BMPER (3467 upstream) : AAA1 (192456 downstream)																							tgtgtgtgcatgtgtgtgtgtg	0.287													3	5	---	---	---	---	
TBX20	57057	broad.mit.edu	37	7	35291570	35291571	+	Intron	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35291570_35291571delTG	uc011kas.1	-							NM_001077653	NP_001071121	Q9UMR3	TBX20_HUMAN	T-box transcription factor TBX20							nucleus	DNA binding			central_nervous_system(1)	1						AGTGCCTATATGTGTGTGTGGG	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35357489	35357490	+	IGR	INS	-	C	C	rs143995099	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35357489_35357490insC								TBX20 (64247 upstream) : HERPUD2 (314782 downstream)																							atggaaatgtaccccctaaaag	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	38399067	38399067	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38399067delG	uc003tgp.1	+						uc003tgr.2_5'Flank					Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																		CCTCTGATTAGGGCCCGGAAC	0.537													4	2	---	---	---	---	
POU6F2	11281	broad.mit.edu	37	7	39389803	39389803	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39389803delT	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1						TAGAGATTCCTTTTTTTTTTT	0.423													4	3	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40637554	40637554	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40637554delA	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						AGTTTCTCCGAAAAAAAAAAT	0.244													4	3	---	---	---	---	
GLI3	2737	broad.mit.edu	37	7	42143341	42143342	+	Intron	INS	-	G	G	rs139157487	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42143341_42143342insG	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						tcacctatccaagagcacccaa	0.094									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46464258	46464259	+	IGR	DEL	AG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46464258_46464259delAG								IGFBP3 (503387 upstream) : TNS3 (850494 downstream)																							ggagagagaaagagagagagag	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46792620	46792621	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46792620_46792621insA								IGFBP3 (831749 upstream) : TNS3 (522132 downstream)																							TGCACAGAAAGAAAAAAAAAAC	0.347													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46847704	46847705	+	IGR	INS	-	A	A	rs115645461		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46847704_46847705insA								IGFBP3 (886833 upstream) : TNS3 (467048 downstream)																							agaaaaaaaagaaaaaaGCAAT	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	51072330	51072331	+	IGR	DEL	GA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51072330_51072331delGA								GRB10 (211171 upstream) : COBL (11579 downstream)																							ctgtggggatgagagagaggga	0.144													4	2	---	---	---	---	
COBL	23242	broad.mit.edu	37	7	51330475	51330475	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51330475delG	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)					AGTGAGTGCTGGGATACAAGG	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54695478	54695479	+	IGR	INS	-	C	C	rs142611747	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54695478_54695479insC								VSTM2A (57291 upstream) : SEC61G (124462 downstream)																							ccatgcagcctcccccaatgca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61661760	61661761	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61661760_61661761insA								None (None upstream) : None (None downstream)																							AATTATATCACACATGATAGTT	0.317													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61824040	61824040	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61824040delA								None (None upstream) : LOC643955 (927632 downstream)																							TTAAAAAAGGAGGGAAGGTGT	0.254													4	2	---	---	---	---	
ZNF679	168417	broad.mit.edu	37	7	63721651	63721651	+	Intron	DEL	T	-	-	rs145025661		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63721651delT	uc003tsx.2	+							NM_153363	NP_699194	Q8IYX0	ZN679_HUMAN	zinc finger protein 679						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						CCATTAAAAATTTTTTTTTGC	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68291660	68291660	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68291660delA								None (None upstream) : AUTS2 (772245 downstream)																							aggttgcactaatttaTTtac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	69027065	69027065	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69027065delA								None (None upstream) : AUTS2 (36840 downstream)																							ctctaaaatgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70251990	70251990	+	Intron	DEL	A	-	-	rs66464728		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70251990delA	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron|AUTS2_uc011keg.1_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		TTTTAAAAAGAAAAAAAAAAG	0.393													4	3	---	---	---	---	
ELN	2006	broad.mit.edu	37	7	73461431	73461431	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73461431delA	uc003tzw.2	+						RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_Intron|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Intron|ELN_uc003tzz.2_Intron|ELN_uc003tzo.2_Intron|ELN_uc003tzp.2_Intron|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_Intron|ELN_uc003tzt.2_Intron|ELN_uc003tzu.2_Intron|ELN_uc003tzv.2_Intron|ELN_uc003tzx.2_Intron|ELN_uc011kff.1_Intron|ELN_uc003tzy.2_Intron	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor						blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)	gaaaaagaagaaaaaaaaaaT	0.264			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	77850425	77850425	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77850425delG	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GAGCCTTCCTGGATTCTTGAG	0.443													4	2	---	---	---	---	
STEAP2	261729	broad.mit.edu	37	7	89859613	89859613	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89859613delA	uc003ujz.2	+						STEAP2_uc010len.2_Intron|STEAP2_uc003uka.2_Intron|STEAP2_uc003ukb.2_Intron|STEAP2_uc003ukc.2_Intron|STEAP2_uc003ukd.2_Intron	NM_152999	NP_694544	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the						electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)					CTTAAAAGAGAAAAAAAAAAT	0.289													4	2	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	91972215	91972215	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91972215delT	uc003ulw.2	+							NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CAGTTACTACTTTTATATACT	0.259													26	22	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	92000490	92000490	+	Intron	DEL	T	-	-	rs67457943		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92000490delT	uc003ulw.2	+						ANKIB1_uc010lew.1_5'Flank	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AATATGTTGCttttttttttt	0.279													1	8	---	---	---	---	
PILRB	29990	broad.mit.edu	37	7	99957995	99957996	+	Intron	DEL	GA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99957995_99957996delGA	uc003uuk.2	+						PILRB_uc003uul.2_Intron|PILRB_uc003uun.2_Intron	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta						activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGGGTGGGAGGAGAGAGAGGTA	0.267													3	3	---	---	---	---	
PILRB	29990	broad.mit.edu	37	7	99965329	99965329	+	3'UTR	DEL	A	-	-	rs11284139		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99965329delA	uc003uuk.2	+	18					PILRB_uc003uul.2_3'UTR|PILRB_uc003uun.2_3'UTR	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta						activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CCAAGGATGGAAAAATACAAT	0.279													4	3	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101801507	101801507	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101801507delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						tttctccctctttttttcaga	0.000													4	2	---	---	---	---	
FBXL13	222235	broad.mit.edu	37	7	102511085	102511085	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102511085delT	uc003vaq.2	-						FBXL13_uc010liq.1_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron	NM_145032	NP_659469	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13 isoform												0						atttggcttgtttgcagagct	0.035													4	2	---	---	---	---	
RELN	5649	broad.mit.edu	37	7	103230631	103230631	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103230631delG	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ACCATAAGATGGAGAAGCAGC	0.443													4	2	---	---	---	---	
SRPK2	6733	broad.mit.edu	37	7	104845630	104845630	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104845630delA	uc003vct.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcv.2_Intron|SRPK2_uc003vcw.1_Intron	NM_182691	NP_872633	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6						GCTTGCCAACAAAAAAACCCA	0.502													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111780658	111780658	+	Intron	DEL	A	-	-	rs35430125		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111780658delA	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				GCTCCCCGACAAAAAAAAAAA	0.279													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	112990542	112990542	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112990542delT								LOC401397 (231905 upstream) : PPP1R3A (526340 downstream)																							TGCATAAAACTTTTTTTTTAG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117892429	117892429	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117892429delT								ANKRD7 (9647 upstream) : None (None downstream)																							aattattgaatttttttctgc	0.000													4	2	---	---	---	---	
KCND2	3751	broad.mit.edu	37	7	120100612	120100613	+	Intron	INS	-	T	T	rs72451808		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120100612_120100613insT	uc003vjj.1	+							NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)					CCACCACGGCCttttttttttt	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	121806971	121806971	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121806971delT								AASS (22627 upstream) : FEZF1 (134478 downstream)																							TACAGGAAGATTTTTTTTTTT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124185763	124185764	+	IGR	DEL	TT	-	-	rs74357177		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124185763_124185764delTT								TMEM229A (512240 upstream) : GPR37 (200352 downstream)																							GAAATCTTCCTTTTTTTTTTTG	0.312													3	3	---	---	---	---	
METTL2B	55798	broad.mit.edu	37	7	128127855	128127858	+	Intron	DEL	CAAG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128127855_128127858delCAAG	uc003vnf.2	+						METTL2B_uc003vng.2_Intron|METTL2B_uc011kop.1_Intron	NM_018396	NP_060866	Q6P1Q9	MTL2B_HUMAN	methyltransferase like 2B								methyltransferase activity			skin(1)	1						GTGGTGCTATCAAGCAAGGCTTCA	0.422													4	4	---	---	---	---	
KCP	375616	broad.mit.edu	37	7	128516423	128516424	+	Intron	INS	-	TGTGTGTTTCTG	TGTGTGTTTCTG	rs147644069	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128516423_128516424insTGTGTGTTTCTG	uc003vob.1	-									Q6ZWJ8	KCP_HUMAN	Homo sapiens cDNA FLJ33365 fis, clone BRACE2005460, moderately similar to Xenopus laevis mRNA for Kielin.							extracellular region				central_nervous_system(1)	1						TTTCTGAGGGATGTGTGTTTCT	0.540													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	129171668	129171668	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129171668delC								FAM40B (43431 upstream) : NRF1 (79887 downstream)																							ACCTGGCCCACCCCACTCCTT	0.637													4	2	---	---	---	---	
EXOC4	60412	broad.mit.edu	37	7	132995995	132995996	+	Intron	INS	-	C	C	rs2345066	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132995995_132995996insC	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vri.2_Intron|EXOC4_uc003vrj.2_Intron	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				GGGAGGTTATGAGGGGGGCATT	0.312													4	2	---	---	---	---	
AGBL3	340351	broad.mit.edu	37	7	134719869	134719883	+	Intron	DEL	TAACCTCCCCTTAAA	-	-	rs72283959		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134719869_134719883delTAACCTCCCCTTAAA	uc011kpw.1	+							NM_178563	NP_848658	Q8NEM8	CBPC3_HUMAN	carboxypeptidase 3, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding				0						CTGGATTCACTAACCTCCCCTTAAATAACCTCCCC	0.344													6	5	---	---	---	---	
CNOT4	4850	broad.mit.edu	37	7	135065845	135065845	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135065845delA	uc011kpy.1	-						CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_Intron|CNOT4_uc003vst.2_Intron	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4						nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0						TGGTTCCTTCAAAAAAAAATT	0.338													4	2	---	---	---	---	
AKR1D1	6718	broad.mit.edu	37	7	137792595	137792595	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137792595delT	uc003vtz.2	+						AKR1D1_uc011kqe.1_Intron|AKR1D1_uc011kqf.1_Intron|AKR1D1_uc010lmy.1_Intron	NM_005989	NP_005980	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1						TTGTTTTAAATTttttttttg	0.144													4	2	---	---	---	---	
SVOPL	136306	broad.mit.edu	37	7	138298430	138298430	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138298430delA	uc011kqh.1	-						SVOPL_uc003vue.2_Intron	NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1							integral to membrane	transmembrane transporter activity				0						ccaaagcactaatcacaatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	138799353	138799353	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138799353delT								ZC3HAV1 (4888 upstream) : TTC26 (19137 downstream)																							tacccacatattaagctagcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	139961518	139961519	+	IGR	DEL	TC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139961518_139961519delTC								LOC100134229 (82079 upstream) : SLC37A3 (72035 downstream)																							cctctctctttctctctctctc	0.000													4	2	---	---	---	---	
OR6B1	135946	broad.mit.edu	37	7	143700867	143700868	+	5'Flank	DEL	CA	-	-	rs10665770		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143700867_143700868delCA	uc003wdt.1	+							NM_001005281	NP_001005281	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.0783)					cagatacaatcacacacacaca	0.000													3	3	---	---	---	---	
TPK1	27010	broad.mit.edu	37	7	144215223	144215223	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144215223delG	uc003weq.2	-						TPK1_uc003weo.2_Intron|TPK1_uc003wep.2_Intron|TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)	CAGTTCCAGTGGAAATATCCT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148609785	148609785	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148609785delT								EZH2 (28371 upstream) : MIR1975 (28795 downstream)																							TTGTGTGTTGTTTTTTTTTTA	0.279													9	6	---	---	---	---	
SMARCD3	6604	broad.mit.edu	37	7	150961796	150961797	+	Intron	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150961796_150961797insA	uc003wjt.2	-						SMARCD3_uc003wju.2_Intron	NM_001003802	NP_001003802	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin						cellular lipid metabolic process|chromatin modification|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	nuclear hormone receptor binding|protein binding|transcription coactivator activity|transcription factor binding			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGCTGGGCCCAAGCCTCTGCT	0.644													4	3	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151504031	151504031	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151504031delA	uc003wkj.2	-						PRKAG2_uc003wkk.2_Intron|PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron|uc003wkn.2_Frame_Shift_Del_p.E17fs	NM_001040633	NP_001035723	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		cagcctgggGAAAAAAAAAAG	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	152140121	152140121	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152140121delT								FABP5L3 (23 upstream) : LOC100128822 (21088 downstream)																							TGTTTCTTTCTTTTTTTTTTC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	154858672	154858673	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154858672_154858673insT								LOC202781 (61260 upstream) : HTR5A (3873 downstream)																							ttcaaacactgtggtctcagga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155120549	155120550	+	IGR	INS	-	CT	CT			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155120549_155120550insCT								INSIG1 (18607 upstream) : EN2 (130274 downstream)																							CTCATCTCTCCCTCCCCAAAGA	0.559													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155609333	155609333	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155609333delG								SHH (4366 upstream) : C7orf4 (723852 downstream)																							GCCTGCCTTTGTTGAGTCACT	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	156388484	156388484	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156388484delA								C7orf4 (54689 upstream) : C7orf13 (42578 downstream)																							AAGCTCATACAAAAAAATCCT	0.363													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158320619	158320622	+	Intron	DEL	ACCT	-	-	rs3032743		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158320619_158320622delACCT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		AGCAGGGACCACCTACCTGTGTTG	0.569													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	6968907	6968907	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6968907delG								DEFA5 (54648 upstream) : LOC349196 (149235 downstream)																							GGTGCTGAGTGGAGTCAGGCT	0.448													4	2	---	---	---	---	
BMP1	649	broad.mit.edu	37	8	22043090	22043090	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22043090delC	uc003xbg.2	+						BMP1_uc003xba.2_Intron|BMP1_uc003xbb.2_Intron|BMP1_uc003xbe.2_Intron|BMP1_uc003xbc.2_Intron|BMP1_uc003xbd.2_Intron|BMP1_uc003xbf.2_Intron|BMP1_uc011kzc.1_Intron|BMP1_uc003xbh.2_Intron|BMP1_uc003xbi.2_Intron	NM_006129	NP_006120	P13497	BMP1_HUMAN	bone morphogenetic protein 1 isoform 3						cartilage condensation|cell differentiation|lipid metabolic process|lipoprotein metabolic process|ossification|positive regulation of cartilage development|proteolysis	extracellular space	calcium ion binding|cytokine activity|growth factor activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)	3				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		CGCCCTCATTCCCATCCCTGC	0.323													4	2	---	---	---	---	
PEBP4	157310	broad.mit.edu	37	8	22764406	22764406	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22764406delA	uc003xcn.1	-							NM_144962	NP_659399	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		caaaaaacgtaaaaaaaagaa	0.000													4	2	---	---	---	---	
RAB11FIP1	80223	broad.mit.edu	37	8	37727720	37727720	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37727720delA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_Intron|RAB11FIP1_uc003xko.1_3'UTR|RAB11FIP1_uc003xkp.1_3'UTR	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TGCTTGAGACAAAAAAAAAAA	0.224													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	38359762	38359763	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38359762_38359763insT								FGFR1 (33410 upstream) : C8orf86 (8589 downstream)																							AGTCTGTCTTCATGGGCTGAAG	0.614													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	53709813	53709813	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53709813delT								RB1CC1 (82787 upstream) : NPBWR1 (142655 downstream)																							gattcttgccttttttgttct	0.055													4	2	---	---	---	---	
TOX	9760	broad.mit.edu	37	8	60031708	60031708	+	5'UTR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60031708delA	uc003xtw.1	-	1					uc003xtx.1_5'Flank|uc003xty.1_5'Flank	NM_014729	NP_055544	O94900	TOX_HUMAN	thymus high mobility group box protein TOX							nucleus	DNA binding			kidney(2)|lung(1)|skin(1)	4		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				gaagaagaggaaaaaaaaaaa	0.488													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61819160	61819160	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61819160delA								CHD7 (39697 upstream) : CLVS1 (381365 downstream)																							TGTGTTCCTGAAAAAAAAAAA	0.388													2	4	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	69114652	69114652	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69114652delT	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						cctggaggacttaggaagcca	0.274													4	2	---	---	---	---	
RBM12B	389677	broad.mit.edu	37	8	94744338	94744338	+	3'UTR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94744338delC	uc003yfz.2	-	3						NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			ttaaaattggccccacgattt	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	97224492	97224492	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97224492delG								GDF6 (51472 upstream) : UQCRB (14818 downstream)																							ttgtttggctgggggacctta	0.000													4	2	---	---	---	---	
STK3	6788	broad.mit.edu	37	8	99777092	99777093	+	Intron	INS	-	T	T	rs138946366	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99777092_99777093insT	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		tagatggaacatgaaggacctt	0.000													2	4	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	102881505	102881506	+	Intron	DEL	AG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102881505_102881506delAG	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			gaatctttcaagagagagggag	0.000													4	2	---	---	---	---	
TNFRSF11B	4982	broad.mit.edu	37	8	119936331	119936331	+	3'UTR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119936331delT	uc003yon.3	-	5						NM_002546	NP_002537	O00300	TR11B_HUMAN	osteoprotegerin precursor						apoptosis|skeletal system development		cytokine activity|receptor activity			central_nervous_system(2)	2	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			TGGAGTCTAGTTTTTTTTTTT	0.318													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120021602	120021603	+	IGR	DEL	TC	-	-	rs147209307		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120021602_120021603delTC								TNFRSF11B (57219 upstream) : COLEC10 (57821 downstream)																							cagactaagttctctctctctc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	123516571	123516572	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123516571_123516572insA								HAS2AS (859638 upstream) : ZHX2 (277329 downstream)																							TCCTATAGCTTAAAAAAAAAGC	0.371													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124835002	124835002	+	IGR	DEL	G	-	-	rs5894677		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124835002delG								FAM91A1 (7314 upstream) : FER1L6 (29225 downstream)																							AGACCATTTAGAATACTCTAT	0.328													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	131769764	131769764	+	IGR	DEL	G	-	-	rs77193874		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131769764delG								ASAP1 (355548 upstream) : ADCY8 (22784 downstream)																							TTGAGAAAAAGAAAAAGTGTT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142578220	142578220	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142578220delG								FLJ43860 (60890 upstream) : MIR1302-7 (289383 downstream)																							cccacctcctggctgtgtgac	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142730202	142730203	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142730202_142730203insT								FLJ43860 (212872 upstream) : MIR1302-7 (137400 downstream)																							TGTATCTCTTCAAAGGCCCTCC	0.629													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143087692	143087692	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143087692delA								MIR1302-7 (220018 upstream) : NCRNA00051 (192025 downstream)																							TATCACGACTAAAACAGCAAG	0.493													4	2	---	---	---	---	
FAM83H	286077	broad.mit.edu	37	8	144817036	144817037	+	5'Flank	INS	-	TC	TC			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144817036_144817037insTC	uc003yzk.2	-						uc003yzl.1_Intron	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	FAM83H						biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			ACCACCCCGAGCTGCCCCTGGG	0.639													5	3	---	---	---	---	
FAM83H	286077	broad.mit.edu	37	8	144817046	144817051	+	5'Flank	DEL	GGTGCT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144817046_144817051delGGTGCT	uc003yzk.2	-						uc003yzl.1_Intron	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	FAM83H						biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			GCTGCCCCTGGGTGCTCCAGTCCCCC	0.660													3	3	---	---	---	---	
DOCK8	81704	broad.mit.edu	37	9	409107	409107	+	Intron	DEL	T	-	-	rs75365909		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:409107delT	uc003zgf.2	+						DOCK8_uc010mgu.2_Intron|DOCK8_uc010mgv.2_Intron|DOCK8_uc003zgk.2_Intron	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CAGCACTTCCTTTTTTTTTTT	0.423													2	4	---	---	---	---	
GLDC	2731	broad.mit.edu	37	9	6594772	6594772	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6594772delA	uc003zkc.2	-							NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	agcaagcaagaaaaaaagaaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	24049110	24049110	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24049110delT								ELAVL2 (223047 upstream) : None (None downstream)																							GGACCATTGCTTTTTTAGAAT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	27863838	27863838	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27863838delT								C9orf72 (289996 upstream) : LINGO2 (84690 downstream)																							GGGGAAAATCTTTAAAATAAC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	36741112	36741113	+	IGR	DEL	AC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36741112_36741113delAC								MELK (63434 upstream) : PAX5 (97418 downstream)																							AGAGCATTTTacacacacacac	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68490476	68490476	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68490476delA								FAM27B (696287 upstream) : MIR1299 (511763 downstream)																							TGAAAGGTTTAAAAATATAAT	0.209													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69804754	69804754	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69804754delT								LOC100133920 (139805 upstream) : FOXD4L5 (370955 downstream)																							tcacataaccttttttttttt	0.000													4	2	---	---	---	---	
TRPM6	140803	broad.mit.edu	37	9	77484533	77484533	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77484533delC	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajn.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,						response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						ACTATTTATTCCCTCTTCACC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	84194472	84194472	+	IGR	DEL	C	-	-	rs35931914		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84194472delC								None (None upstream) : TLE1 (4128 downstream)																							AGTAAACAATCCACGCACCCG	0.458													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	86272285	86272287	+	IGR	DEL	CTC	-	-	rs144194651		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86272285_86272287delCTC								C9orf103 (13247 upstream) : UBQLN1 (2592 downstream)																							tccactccttctcctgtctttct	0.000													5	6	---	---	---	---	
NTRK2	4915	broad.mit.edu	37	9	87324565	87324565	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87324565delG	uc004aoa.1	+						NTRK2_uc004anv.1_Intron|NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron|NTRK2_uc011lsz.1_Intron|NTRK2_uc011lta.1_Intron|NTRK2_uc004aob.1_Intron|NTRK2_uc011ltb.1_Intron	NM_001018064	NP_001018074	Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16						CTGTCTTCACGGAAATCTTAA	0.403										TSP Lung(25;0.17)			4	2	---	---	---	---	
DAPK1	1612	broad.mit.edu	37	9	90234142	90234142	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90234142delT	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2						ttttcctcactttttaggcgt	0.000									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	91801609	91801609	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91801609delA								SHC3 (7927 upstream) : CKS2 (124504 downstream)																							ATGAAGGGAGAAAAAAAACAC	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93887757	93887757	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93887757delA								SYK (226924 upstream) : AUH (88342 downstream)																							ACATTTCTTTAAAAAAAAATC	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	94740783	94740783	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94740783delG								ROR2 (28339 upstream) : SPTLC1 (52637 downstream)																							TACCCATGCTGGGATCGGAGG	0.552													4	2	---	---	---	---	
C9orf3	84909	broad.mit.edu	37	9	97533598	97533598	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97533598delC	uc004ava.2	+						C9orf3_uc011lui.1_Intron|C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		CCCCGCTTCACCAGCCCAATA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102383503	102383503	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102383503delA	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																		gctggggtttaaaaaaaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	103421098	103421099	+	IGR	INS	-	A	A	rs78612307		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103421098_103421099insA								MURC (70927 upstream) : LPPR1 (369932 downstream)																							ctcagaaaaagaaaaaaaaaaa	0.158													4	2	---	---	---	---	
SMC2	10592	broad.mit.edu	37	9	106888729	106888729	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106888729delT	uc004bbv.2	+						SMC2_uc004bbw.2_Intron|SMC2_uc011lvl.1_Intron|SMC2_uc004bbx.2_Intron|SMC2_uc004bby.2_5'Flank	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2						cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9						TTACACATACTTTTTTTTTTG	0.323													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	108790219	108790219	+	IGR	DEL	T	-	-	rs7866703	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108790219delT								TMEM38B (252775 upstream) : ZNF462 (835159 downstream)																							aatatgtctgttttttttcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110196933	110196933	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110196933delT								RAD23B (102464 upstream) : KLF4 (50202 downstream)																							TGACATATGATTTTTTTTTTT	0.269													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	111384098	111384098	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111384098delA								None (None upstream) : ACTL7B (232773 downstream)																							AAATGTACAGAAAAAGCTTTG	0.269													4	2	---	---	---	---	
PALM2	114299	broad.mit.edu	37	9	112453303	112453304	+	Intron	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112453303_112453304insG	uc004beg.2	+						PALM2_uc004bef.2_Intron	NM_001037293	NP_001032370	Q8IXS6	PALM2_HUMAN	paralemmin 2 isoform b						regulation of cell shape	plasma membrane				ovary(2)	2						AAGAAACAGAAGGGGGGAAGTT	0.386													4	2	---	---	---	---	
PALM2-AKAP2	445815	broad.mit.edu	37	9	112668307	112668310	+	Intron	DEL	TTCC	-	-	rs35354227		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112668307_112668310delTTCC	uc004bei.2	+						PALM2_uc004bef.2_Intron|PALM2_uc004beg.2_Intron|PALM2_uc004beh.3_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6						TACGTTGCATTTCCTTCTTTTCCT	0.353													4	3	---	---	---	---	
SNX30	401548	broad.mit.edu	37	9	115632451	115632451	+	3'UTR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115632451delT	uc004bgj.3	+	9					SNX30_uc004bgi.3_3'UTR	NM_001012994	NP_001013012	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30						cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0						CTTCCAACTCTTTTTTTTTTC	0.413													3	4	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	120165524	120165524	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120165524delC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						GGGAACTCTTCCACCTACAAA	0.323													4	2	---	---	---	---	
DBC1	1620	broad.mit.edu	37	9	122122805	122122806	+	Intron	INS	-	AC	AC	rs146485048	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122122805_122122806insAC	uc004bkc.2	-						DBC1_uc004bkd.2_Intron	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor						cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8						AGCTCCTGGGGACTCTAGGAAT	0.431													3	3	---	---	---	---	
C9orf45	81571	broad.mit.edu	37	9	125875319	125875319	+	3'UTR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125875319delG	uc004bnp.3	-	1					MIR600_hsa-mir-600|MI0003613_5'Flank	NR_026677				Homo sapiens GL012 mRNA, complete cds.												0						AAATAAAGGTGGGGTGCTCAC	0.453													4	2	---	---	---	---	
NUP214	8021	broad.mit.edu	37	9	134076793	134076793	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134076793delA	uc004cag.2	+						NUP214_uc004cah.2_Intron|NUP214_uc004cai.2_Intron|NUP214_uc010mzg.2_Intron|NUP214_uc011mcg.1_Intron	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa						carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		actccatctcaaaaaaaaaaa	0.000			T	DEK|SET|ABL1	AML|T-ALL								7	4	---	---	---	---	
BAT2L1	84726	broad.mit.edu	37	9	134309890	134309890	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134309890delG	uc004can.3	+						BAT2L1_uc004cam.1_Intron	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like								protein binding				0						GGTGGCAAGTGGGCCCACAAC	0.532													4	2	---	---	---	---	
NTNG2	84628	broad.mit.edu	37	9	135115093	135115093	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135115093delG	uc004cbh.2	+							NM_032536	NP_115925	Q96CW9	NTNG2_HUMAN	netrin G2 precursor						axonogenesis	anchored to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		TCCTCCTGCAGGGGCCCAGTT	0.403													4	2	---	---	---	---	
NACC2	138151	broad.mit.edu	37	9	138915939	138915940	+	Intron	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138915939_138915940delGT	uc004cgw.2	-						NACC2_uc010nbh.2_Intron	NM_144653	NP_653254	Q96BF6	NACC2_HUMAN	BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0						GAGGGCCAGAGTGTGTGTGTGT	0.485													6	3	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	687081	687082	+	Intron	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:687081_687082insG	uc001ifp.2	-							NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GCTAATTGCAAAAAAAAAAAAA	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	5670167	5670168	+	IGR	INS	-	A	A	rs142111241	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5670167_5670168insA								CALML3 (101942 upstream) : ASB13 (10652 downstream)																							AAAACAAAAACAACAAAAAAAA	0.317													4	2	---	---	---	---	
GDI2	2665	broad.mit.edu	37	10	5815772	5815773	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5815772_5815773insT	uc001iil.3	-						GDI2_uc001iim.3_Intron|GDI2_uc009xid.2_Intron	NM_001494	NP_001485	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2 isoform 1						protein transport|small GTPase mediated signal transduction	cell surface|cytosol|membrane	protein binding|Rab GDP-dissociation inhibitor activity				0						TCACAAGAACATAGTAATTTTT	0.302													383	187	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11131307	11131307	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11131307delA	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|uc001ikn.1_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						TTTGAAGGTGAAAAGGGTGTA	0.403													4	2	---	---	---	---	
PTF1A	256297	broad.mit.edu	37	10	23482410	23482410	+	Intron	DEL	A	-	-	rs74121766		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23482410delA	uc001irp.2	+							NM_178161	NP_835455	Q7RTS3	PTF1A_HUMAN	pancreas specific transcription factor, 1a						endocrine pancreas development|exocrine pancreas development|regulation of transcription, DNA-dependent|tissue development|transcription, DNA-dependent	cytoplasm|transcription factor complex				pancreas(1)|skin(1)	2						ttttttttttatttttCTGCC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35993103	35993104	+	IGR	DEL	AC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35993103_35993104delAC								FZD8 (62741 upstream) : None (None downstream)																							gtgcccaccaacacacacacac	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38597097	38597104	+	IGR	DEL	CCTCCCTC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38597097_38597104delCCTCCCTC								LOC100129055 (93825 upstream) : HSD17B7P2 (48204 downstream)																							TTTACAAACTCCTCCCTCCCTCCTAGAA	0.423													4	2	---	---	---	---	
RASGEF1A	221002	broad.mit.edu	37	10	43718452	43718452	+	Intron	DEL	T	-	-	rs112583979		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43718452delT	uc001jap.1	-						RASGEF1A_uc001jao.1_Intron	NM_145313	NP_660356	Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A						cell migration|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0						actttattggtttttttTTTA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46984899	46984899	+	IGR	DEL	T	-	-	rs10715133		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46984899delT								SYT15 (14298 upstream) : GPRIN2 (8647 downstream)																							AAATACAGTATTTTTTTTCTG	0.388													4	3	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53970097	53970097	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53970097delC	uc001jjm.2	+						PRKG1_uc001jjo.2_Intron|PRKG1_uc009xow.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CTCATGCACTCCAAcctctcc	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54364225	54364225	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54364225delT								DKK1 (286809 upstream) : MBL2 (160916 downstream)																							ACAAACTTCCTTGCTCTAGTT	0.194													4	2	---	---	---	---	
REEP3	221035	broad.mit.edu	37	10	65355344	65355344	+	Intron	DEL	T	-	-	rs72453049		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65355344delT	uc001jmt.2	+						REEP3_uc009xpl.1_Intron	NM_001001330	NP_001001330	Q6NUK4	REEP3_HUMAN	receptor accessory protein 3							integral to membrane					0	Prostate(12;0.0119)|all_hematologic(501;0.191)					Cttttttttcttttttttttt	0.169													4	2	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	69348176	69348177	+	Intron	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69348176_69348177delTG	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						tggctttgcttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	70006748	70006748	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70006748delA								ATOH7 (14893 upstream) : PBLD (35669 downstream)																							CTGAAAATTGAAAAAAAAAAT	0.343													4	2	---	---	---	---	
H2AFY2	55506	broad.mit.edu	37	10	71840036	71840036	+	Intron	DEL	A	-	-	rs111237495		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71840036delA	uc001jqm.2	+						H2AFY2_uc001jqn.2_Intron	NM_018649	NP_061119	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2						chromatin modification|dosage compensation|nucleosome assembly	Barr body|nucleosome	DNA binding			skin(1)	1						actccatctcaaaaaaaaaaa	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	77343462	77343462	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77343462delT								MIR606 (31151 upstream) : C10orf11 (199057 downstream)																							TCCTCTTGTATTTTTTTCAAT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81800217	81800219	+	IGR	DEL	AAC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81800217_81800219delAAC								MBL1P (89434 upstream) : LOC219347 (5772 downstream)																							CAATAAAGATAACAACCTTTGGA	0.271													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85686295	85686296	+	IGR	INS	-	CCC	CCC	rs142794081	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85686295_85686296insCCC								NRG3 (939360 upstream) : GHITM (212889 downstream)																							TGGCTTTATTTCCATTAACTCA	0.183													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	86761904	86761904	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86761904delT								FAM190B (483628 upstream) : GRID1 (597408 downstream)																							CCACATCTGATTTTTTTTTTG	0.398													4	5	---	---	---	---	
LIPA	3988	broad.mit.edu	37	10	90978930	90978930	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90978930delA	uc001kga.3	-						LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|LIPA_uc010qnf.1_Intron|LIPA_uc009xtq.2_Intron|LIPA_uc009xtr.1_Intron	NM_000235	NP_000226	P38571	LICH_HUMAN	lipase A precursor						lipid catabolic process	lysosome	lipase activity|sterol esterase activity				0		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		TCCTTTAAAGAAAAAAAAAAG	0.114													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	92919008	92919008	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92919008delT								NUDT9P1 (6171 upstream) : PCGF5 (3767 downstream)																							gaagtcataatttttttttgc	0.035													2	4	---	---	---	---	
LOC100188947	100188947	broad.mit.edu	37	10	93278596	93278596	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93278596delT	uc010qnl.1	-							NR_024467				Homo sapiens, clone IMAGE:6063621, mRNA.												0						tgtttttttgttttttttttt	0.174													4	3	---	---	---	---	
CNNM2	54805	broad.mit.edu	37	10	104680458	104680458	+	Intron	DEL	A	-	-	rs113496934		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104680458delA	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron|CNNM2_uc001kwl.2_Intron	NM_017649	NP_060119	Q9H8M5	CNNM2_HUMAN	cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		AAGTATCGCCAAAAAAAATCA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109426050	109426051	+	IGR	DEL	TC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109426050_109426051delTC								SORCS1 (501758 upstream) : None (None downstream)																							cttcttcctttctctctctctc	0.223													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	114591959	114591959	+	IGR	DEL	T	-	-	rs78700540		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114591959delT								VTI1A (13458 upstream) : LOC143188 (18714 downstream)																							AGGGGGTGTATTTTGATGTAG	0.498													3	4	---	---	---	---	
ATRNL1	26033	broad.mit.edu	37	10	117314127	117314128	+	Intron	DEL	AC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117314127_117314128delAC	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		AATAAGGCAGACACACACACAC	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122872101	122872102	+	IGR	INS	-	AC	AC	rs144848418	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122872101_122872102insAC								WDR11 (203066 upstream) : FGFR2 (365743 downstream)																							Gacacacacagacacacacaca	0.307													4	2	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127583238	127583239	+	Intron	INS	-	T	T	rs142355498		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127583238_127583239insT	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GACCTGCACTGTTGTTTCTTCT	0.302													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133280008	133280009	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133280008_133280009insT								TCERG1L (170024 upstream) : PPP2R2D (467951 downstream)																							GGGGACAGGGATTTTCTCTGTT	0.495													4	2	---	---	---	---	
PRAP1	118471	broad.mit.edu	37	10	135162745	135162746	+	Intron	DEL	CA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135162745_135162746delCA	uc001lmp.2	+						PRAP1_uc001lmr.2_Intron|PRAP1_uc001lmq.1_5'Flank	NM_145202	NP_660203	Q96NZ9	PRAP1_HUMAN	proline-rich acidic protein 1 isoform 1							extracellular region					0		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		all cancers(32;7.08e-06)|OV - Ovarian serous cystadenocarcinoma(35;7.88e-06)|Epithelial(32;9.48e-06)		gcacacacagcacacacacaca	0.079													4	4	---	---	---	---	
NLRP14	338323	broad.mit.edu	37	11	7057130	7057130	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7057130delA	uc001mfb.1	+							NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14						cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		AAGTGAAATTAaaaggcaatg	0.204													4	2	---	---	---	---	
ZNF143	7702	broad.mit.edu	37	11	9547156	9547156	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9547156delA	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433	P52747	ZN143_HUMAN	zinc finger protein 143						regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		TTATAGCAAGAAAAAAAACCT	0.398													3	3	---	---	---	---	
PARVA	55742	broad.mit.edu	37	11	12465635	12465635	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12465635delC	uc001mki.2	+						PARVA_uc001mkh.2_Intron|PARVA_uc010rck.1_Intron	NM_018222	NP_060692	Q9NVD7	PARVA_HUMAN	parvin, alpha						cell adhesion|cell junction assembly|cilium morphogenesis	actin cytoskeleton|cytosol|focal adhesion	actin binding			breast(3)	3				Epithelial(150;0.00624)		CAGCTTCCTACCCACCCCCTA	0.537													4	2	---	---	---	---	
PTPN5	84867	broad.mit.edu	37	11	18776462	18776462	+	Intron	DEL	C	-	-	rs71050630		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18776462delC	uc001mpd.2	-						PTPN5_uc001mpb.2_Intron|PTPN5_uc001mpc.2_Intron|PTPN5_uc001mpe.2_Intron|PTPN5_uc010rdj.1_Intron|PTPN5_uc001mpf.2_Intron|PTPN5_uc010rdk.1_Intron	NM_006906	NP_008837	P54829	PTN5_HUMAN	protein-tyrosine-phosphatase non-receptor 5							integral to membrane	phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(2)	2						aggtggccctcagtgaaccct	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28008292	28008292	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28008292delC								BDNF (264687 upstream) : KIF18A (33871 downstream)																							cacaccctttcctattcttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	39731409	39731409	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39731409delA								None (None upstream) : LRRC4C (404344 downstream)																							gaactactgtaaaaaaaactc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42250779	42250780	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42250779_42250780insA								LRRC4C (769456 upstream) : None (None downstream)																							acaaaggaaacagagtagttga	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42504685	42504685	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42504685delT								None (None upstream) : API5 (828820 downstream)																							TACTTCCTACTTTTTTTACCT	0.383													4	2	---	---	---	---	
CREB3L1	90993	broad.mit.edu	37	11	46320695	46320695	+	Intron	DEL	T	-	-	rs111258259		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46320695delT	uc001ncf.2	+							NM_052854	NP_443086	Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like						response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L1(6)	soft_tissue(6)|ovary(2)	8				GBM - Glioblastoma multiforme(35;0.0285)		tattttctacttttttttttc	0.000			T	FUS	myxofibrosarcoma								5	3	---	---	---	---	
AMBRA1	55626	broad.mit.edu	37	11	46450139	46450140	+	Intron	INS	-	T	T	rs142253407	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46450139_46450140insT	uc010rgu.1	-						AMBRA1_uc010rgt.1_Intron|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		tcttcttcttcttctttttttt	0.376													3	3	---	---	---	---	
MADD	8567	broad.mit.edu	37	11	47300933	47300933	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47300933delT	uc001ner.1	+						MADD_uc001neq.2_Intron|MADD_uc001nev.1_Intron|MADD_uc001nes.1_Intron|MADD_uc001net.1_Intron|MADD_uc009yln.1_Intron|MADD_uc001neu.1_Intron|MADD_uc001nex.2_Intron|MADD_uc001nez.2_Intron|MADD_uc001new.2_Intron	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing						activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)		TTTCTCAGTCttttttttttt	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48357273	48357273	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48357273delT								OR4C3 (9793 upstream) : OR4C45 (9629 downstream)																							attcttttcctttgtgggaaa	0.000													2	4	---	---	---	---	
MACROD1	28992	broad.mit.edu	37	11	63934264	63934264	+	5'Flank	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63934264delT	uc001nyh.2	-							NM_014067	NP_054786	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1												0						TGTCTGTGTGttttttttttt	0.259													3	3	---	---	---	---	
STIP1	10963	broad.mit.edu	37	11	63964257	63964257	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63964257delA	uc001nyk.1	+						STIP1_uc010rnb.1_Intron	NM_006819	NP_006810	P31948	STIP1_HUMAN	stress-induced-phosphoprotein 1						axon guidance|response to stress	Golgi apparatus|nucleus				ovary(2)|liver(1)	3						TCTCAGCTGGAAAAAGGCCCT	0.507													4	2	---	---	---	---	
PC	5091	broad.mit.edu	37	11	66685509	66685510	+	Intron	INS	-	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66685509_66685510insC	uc001ojo.1	-						PC_uc001ojp.1_Intron	NM_001040716	NP_001035806	P11498	PYC_HUMAN	pyruvate carboxylase precursor						gluconeogenesis|lipid biosynthetic process	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|pyruvate carboxylase activity			ovary(2)|lung(1)|kidney(1)	4		Melanoma(852;0.0525)		Lung(977;0.153)|LUSC - Lung squamous cell carcinoma(976;0.227)	Biotin(DB00121)|Pyruvic acid(DB00119)	CCAAGTCCTTTCCCCCACAGCA	0.421													4	2	---	---	---	---	
MRPL48	51642	broad.mit.edu	37	11	73561410	73561411	+	Intron	INS	-	CTCACAGATCATC	CTCACAGATCATC	rs143635170	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73561410_73561411insCTCACAGATCATC	uc001ouh.3	+						MRPL48_uc009ytt.2_Intron|MRPL48_uc010rri.1_Intron|MRPL48_uc009ytu.2_Intron	NM_016055	NP_057139	Q96GC5	RM48_HUMAN	mitochondrial ribosomal protein L48 precursor						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0						ACTGTTGTTGGCTCACAGATCA	0.361													4	2	---	---	---	---	
C2CD3	26005	broad.mit.edu	37	11	73841834	73841835	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73841834_73841835insT	uc001ouu.2	-						C2CD3_uc001ouv.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)					gtcctactttcttttttttcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	74132766	74132767	+	IGR	INS	-	AA	AA	rs138820245	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74132766_74132767insAA								PGM2L1 (23264 upstream) : KCNE3 (33121 downstream)																							gcctttccttcagacacctacc	0.069													3	3	---	---	---	---	
GRM5	2915	broad.mit.edu	37	11	88283195	88283195	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88283195delG	uc001pcq.2	-						GRM5_uc009yvm.2_Intron	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	atgactggttggatgtgaagg	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91822101	91822101	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91822101delT								None (None upstream) : FAT3 (263161 downstream)																							CAGTCCAGCATTTTTTAGAAC	0.403													4	2	---	---	---	---	
DLAT	1737	broad.mit.edu	37	11	111932774	111932774	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111932774delT	uc001pmo.2	+						DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Intron	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)	gtcagcatgcttttttttagt	0.144													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112409541	112409542	+	IGR	DEL	TC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112409541_112409542delTC								PTS (268864 upstream) : NCAM1 (422453 downstream)																							ATCTTTTCTGTCTCTCTCTCTG	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116529602	116529603	+	IGR	INS	-	G	G	rs139852443	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116529602_116529603insG								None (None upstream) : BUD13 (89285 downstream)																							CAAGGACCACAGTCGCCAGAAA	0.490													6	4	---	---	---	---	
KIRREL3	84623	broad.mit.edu	37	11	126619539	126619540	+	Intron	INS	-	A	A	rs144267247		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126619539_126619540insA	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AAGTCCCTCTTAAAAAAAAAAA	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127378242	127378242	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127378242delT								KIRREL3 (504887 upstream) : ETS1 (950414 downstream)																							actttgtctatttttttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	5141556	5141557	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5141556_5141557insT								KCNA1 (114136 upstream) : KCNA5 (11528 downstream)																							actttcccttcttTTTTTTTTT	0.173													4	2	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11178557	11178557	+	Intron	DEL	C	-	-	rs66541998		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11178557delC	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						GTGTTTTTGACTTTTGGAGTT	0.264										HNSCC(22;0.051)			3	3	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	14018581	14018581	+	Intron	DEL	A	-	-	rs74837716		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14018581delA	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						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)	agagagagagaaaaaaaaaGG	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16342393	16342396	+	IGR	DEL	ATTA	-	-	rs66881403		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16342393_16342396delATTA								DERA (152079 upstream) : MGST1 (157680 downstream)																							AAATTATTTTATTAATTCTAATGC	0.260													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16774067	16774067	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16774067delT								LMO3 (11309 upstream) : None (None downstream)																							TTAGTTTAGATTTTCTTTTAC	0.403													4	8	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	21242657	21242658	+	Intron	DEL	AT	-	-	rs67150063		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21242657_21242658delAT	uc010sil.1	+						LST-3TM12_uc010sim.1_Intron|LST-3TM12_uc010sin.1_Intron			Q9NPD5	SO1B3_HUMAN	SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					TTGCATTTAAATAAAAAAAAAA	0.124													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47364315	47364315	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47364315delA								SLC38A4 (144535 upstream) : AMIGO2 (105176 downstream)																							AATATTCACCAAAAAAAAAAA	0.284													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54990870	54990870	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54990870delT								PPP1R1A (8427 upstream) : GLYCAM1 (11101 downstream)																							ggagttaggcttttttttttt	0.114											OREG0021899	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
DNAJC14	85406	broad.mit.edu	37	12	56217486	56217487	+	Intron	DEL	TT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56217486_56217487delTT	uc001shx.1	-						DNAJC14_uc001shu.1_Intron|DNAJC14_uc009zob.1_Intron	NM_032364	NP_115740	Q6Y2X3	DJC14_HUMAN	dopamine receptor interacting protein						protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4						cttgaatatctttttttttttt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80092136	80092136	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80092136delC								PAWR (7346 upstream) : PPP1R12A (75208 downstream)																							tcctctcatacccccactcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	89622161	89622161	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89622161delT								KITLG (647923 upstream) : DUSP6 (119678 downstream)																							TCTCCAAATGTTTTTTAGCCC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97707791	97707791	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97707791delA								NEDD1 (360330 upstream) : RMST (151008 downstream)																							ttgaaaccacaaaaagggagg	0.000													4	2	---	---	---	---	
CRY1	1407	broad.mit.edu	37	12	107385795	107385796	+	Intron	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107385795_107385796insA	uc001tmi.3	-							NM_004075	NP_004066	Q16526	CRY1_HUMAN	cryptochrome 1 (photolyase-like)						DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3						ATTTAAGGGGGAAAAAAAAACT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108161601	108161602	+	IGR	INS	-	A	A	rs72517984		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108161601_108161602insA								PRDM4 (6580 upstream) : ASCL4 (6560 downstream)																							gacagagagagttctgttttct	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115401351	115401351	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115401351delG								TBX3 (279382 upstream) : MED13L (995032 downstream)																							cacttgggctggtctagagca	0.000													4	2	---	---	---	---	
MED13L	23389	broad.mit.edu	37	12	116558517	116558517	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116558517delA	uc001tvw.2	-							NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ATTCCAAAAGAAAAAAAAATA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	122923787	122923787	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122923787delC								CLIP1 (16671 upstream) : ZCCHC8 (33649 downstream)																							ACTGACTCCTCATTAGCATGT	0.214													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	129583252	129583253	+	Intron	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129583252_129583253delGT	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)		cctcgccaaagtgaccttatta	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	34886663	34886663	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34886663delT								RFC3 (345969 upstream) : NBEA (629793 downstream)																							ATGGGGTTGATTTTTTTTTCT	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35108523	35108523	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35108523delC								RFC3 (567829 upstream) : NBEA (407933 downstream)																							AGTTAATGGTCCCCACCACAT	0.388													4	2	---	---	---	---	
DCLK1	9201	broad.mit.edu	37	13	36606162	36606163	+	Intron	INS	-	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36606162_36606163insC	uc001uvf.2	-							NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CATTAATCTTTCTTTCACTCCC	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	47569181	47569181	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47569181delT								HTR2A (98131 upstream) : SUCLA2 (947611 downstream)																							GTGACAACTATTTTTTTTTCA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	56472510	56472510	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56472510delT								None (None upstream) : None (None downstream)																							AAAATATTCCTTTTTTTTTTC	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	60207402	60207402	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60207402delT								None (None upstream) : DIAPH3 (32323 downstream)																							gaatcttcccttttttcacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71022294	71022294	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71022294delA								ATXN8OS (308409 upstream) : DACH1 (989804 downstream)																							GTAAAGATGGAAAAAAAAGAT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	88267988	88267988	+	Intron	DEL	T	-	-	rs67899026		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88267988delT	uc001vlm.1	-											Homo sapiens clone IMAGE:32106, mRNA sequence.																		TTAATGGCAATTTTTTTTTCT	0.299													4	2	---	---	---	---	
FARP1	10160	broad.mit.edu	37	13	98883557	98883557	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98883557delA	uc001vnj.2	+						FARP1_uc001vnh.2_Intron|FARP1_uc001vni.2_Intron	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CAGAGGATGTAAAAAAAAAAT	0.438													4	2	---	---	---	---	
STK24	8428	broad.mit.edu	37	13	99170758	99170758	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99170758delT	uc001vnm.1	-						STK24_uc001vnn.1_Intron|STK24_uc010tim.1_Intron	NM_003576	NP_003567	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24 isoform a						cellular component disassembly involved in apoptosis|signal transduction	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			TAAAACCCCATTTTAAAGGTT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	99828477	99828478	+	IGR	INS	-	CGGTGC	CGGTGC	rs145524999	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99828477_99828478insCGGTGC								DOCK9 (89817 upstream) : UBAC2 (24201 downstream)																							agaggcatccacggtgcctgca	0.020											OREG0022481	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ITGBL1	9358	broad.mit.edu	37	13	102351632	102351632	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102351632delG	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AGGGTTGGATGGTGAGGCGAC	0.443													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102958768	102958769	+	Intron	INS	-	TTCC	TTCC	rs146435428	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102958768_102958769insTTCC	uc001vpf.2	-						uc001vph.1_Intron|uc001vpg.1_Intron	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)					agatgatggaggggaagacaaa	0.119													4	2	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109517337	109517338	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109517337_109517338insT	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			gtataatattcttTTTTTTAAA	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112621025	112621026	+	IGR	DEL	TT	-	-	rs67559399		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112621025_112621026delTT								C13orf16 (624432 upstream) : SOX1 (100887 downstream)																							AGGATAACtatttttttttttt	0.351													6	3	---	---	---	---	
UPF3A	65110	broad.mit.edu	37	13	115062913	115062913	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115062913delT	uc001vup.2	+						UPF3A_uc001vuq.2_Intron|UPF3A_uc001vus.2_Intron|UPF3A_uc001vur.2_Intron|UPF3A_uc001vut.2_Intron|UPF3A_uc001vuu.2_Intron	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A						mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		CTTTTAAAAATTTTTTTTTCC	0.294													4	2	---	---	---	---	
SLC7A8	23428	broad.mit.edu	37	14	23653814	23653814	+	5'Flank	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23653814delA	uc001wiz.2	-						SLC7A8_uc010akj.2_5'Flank	NM_012244	NP_036376	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (cationic amino acid						blood coagulation|cellular amino acid metabolic process|leukocyte migration|metal ion homeostasis|response to toxin	basolateral plasma membrane|cytoplasm|integral to plasma membrane	neutral amino acid transmembrane transporter activity|organic cation transmembrane transporter activity|peptide antigen binding|protein binding|toxin transporter activity			ovary(1)	1	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	CTGAAACATGAAAAAAAATGA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	43718316	43718316	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43718316delT								None (None upstream) : None (None downstream)																							gtcttgtgtatttttttttct	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49421890	49421890	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49421890delA								None (None upstream) : SDCCAG1 (611137 downstream)																							AACTTAGGGGAAAAAAAAGGA	0.323													4	3	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50244330	50244330	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50244330delA	uc010anj.1	-						KLHDC2_uc001wwx.2_Intron|KLHDC2_uc001wwy.2_Intron|KLHDC2_uc010anp.2_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		TGTGActatgaaaaaaaaaat	0.015													3	3	---	---	---	---	
SYNE2	23224	broad.mit.edu	37	14	64607928	64607929	+	Intron	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64607928_64607929delGT	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_5'Flank	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GGAAAAAGGGGTGTGTGTGTGT	0.193													8	4	---	---	---	---	
VTI1B	10490	broad.mit.edu	37	14	68128896	68128897	+	Intron	INS	-	A	A	rs56185554	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68128896_68128897insA	uc001xjt.2	-						VTI1B_uc010aqp.2_Intron|VTI1B_uc001xju.2_Intron	NM_006370	NP_006361	Q9UEU0	VTI1B_HUMAN	vesicle transport through interaction with						cell proliferation|cellular membrane fusion|intracellular protein transport|vesicle docking involved in exocytosis	endomembrane system|integral to membrane					0				all cancers(60;0.000344)|OV - Ovarian serous cystadenocarcinoma(108;0.00212)|BRCA - Breast invasive adenocarcinoma(234;0.00941)		acaacaacaacaaaaaaaaaaa	0.153													6	4	---	---	---	---	
KIAA0247	9766	broad.mit.edu	37	14	70159303	70159304	+	Intron	DEL	AA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70159303_70159304delAA	uc001xlk.2	+						KIAA0247_uc010aqz.2_Intron	NM_014734	NP_055549	Q92537	K0247_HUMAN	hypothetical protein LOC9766 precursor							integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		GATAAATGTTAATTCTCTTCCT	0.198													4	2	---	---	---	---	
NUMB	8650	broad.mit.edu	37	14	73861505	73861505	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73861505delT	uc001xny.1	-						NUMB_uc001xoa.1_Intron|NUMB_uc001xnz.1_Intron|NUMB_uc001xob.1_Intron|NUMB_uc001xod.1_Intron|NUMB_uc001xoc.1_Intron|NUMB_uc010ars.1_Intron|NUMB_uc001xof.1_Intron|NUMB_uc001xog.2_Intron|NUMB_uc001xoh.1_Intron	NM_001005743	NP_001005743	P49757	NUMB_HUMAN	numb homolog isoform 1						axon guidance|lateral ventricle development|neuroblast division in subventricular zone|positive regulation of neurogenesis	integral to plasma membrane				ovary(2)|central_nervous_system(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		ctgtcttttctttttttttgc	0.085													6	3	---	---	---	---	
SNW1	22938	broad.mit.edu	37	14	78185057	78185057	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78185057delT	uc001xuf.2	-						SNW1_uc010tvm.1_Intron|SNW1_uc010asu.2_Intron|SNW1_uc010tvn.1_Intron	NM_012245	NP_036377	Q13573	SNW1_HUMAN	SKI-interacting protein						negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|regulation of transcription from RNA polymerase II promoter	catalytic step 2 spliceosome|nucleoplasm	Notch binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CTTTGGAttcttttttttttt	0.154													4	3	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	78756982	78756982	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78756982delA	uc001xum.1	+									Q9Y4C0	NRX3A_HUMAN	Homo sapiens mRNA for KIAA0743 protein, partial cds.						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		accttgtctcaaaaaaaaaGG	0.234													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82147622	82147623	+	IGR	INS	-	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82147622_82147623insC								SEL1L (147417 upstream) : None (None downstream)																							ttattgcatttcccccaacaGA	0.188													4	2	---	---	---	---	
TRIP11	9321	broad.mit.edu	37	14	92505069	92505069	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92505069delT	uc001xzy.2	-						TRIP11_uc001xzz.3_Intron	NM_004239	NP_004230	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)		gaacagcccattatctccctg	0.030			T	PDGFRB	AML								4	2	---	---	---	---	
KIAA1409	57578	broad.mit.edu	37	14	94086789	94086790	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94086789_94086790insT	uc001ybv.1	+						KIAA1409_uc001ybs.1_Intron	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578							integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		ATAAAGGCAGATTTTTTTTTCT	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95807966	95807967	+	IGR	DEL	AA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95807966_95807967delAA								CLMN (21721 upstream) : C14orf139 (65639 downstream)																							taggaatggcaaatggcagagg	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20135710	20135710	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20135710delT								None (None upstream) : GOLGA6L6 (601384 downstream)																							AGTAATGATGTTTTCCCCTCC	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20515046	20515047	+	IGR	INS	-	AAATA	AAATA	rs140589410		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20515046_20515047insAAATA								None (None upstream) : GOLGA6L6 (222047 downstream)																							ctgatgaaatgaaataatgaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20527129	20527130	+	IGR	DEL	CT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20527129_20527130delCT								None (None upstream) : GOLGA6L6 (209964 downstream)																							GAATTATCCCCTGTTCATTGGG	0.277													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20607082	20607082	+	Intron	DEL	A	-	-	rs28755877		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20607082delA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		GTCAGCATTTAAAAAAAAAAA	0.328													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20851346	20851347	+	IGR	INS	-	T	T	rs71399680		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20851346_20851347insT								GOLGA8C (70320 upstream) : BCL8 (18709 downstream)																							ACTCATGGAGGGCACCACCAAG	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21968357	21968357	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21968357delA								LOC646214 (27618 upstream) : CXADRP2 (46063 downstream)																							AAGCGATGACAAAAAAAAATC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22538094	22538095	+	IGR	INS	-	C	C	rs7183041		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22538094_22538095insC								MIR1268 (24814 upstream) : GOLGA8DP (164190 downstream)																							ACAGGAACACATGGGGGGGCTT	0.386													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23167053	23167053	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23167053delA								NIPA1 (80210 upstream) : WHAMML1 (20678 downstream)																							GGGCAGAATGAAAAAAAAAAC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23461685	23461685	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23461685delG								GOLGA8E (13262 upstream) : MKRN3 (348769 downstream)																							acagagcaccgaaagttctag	0.000													4	3	---	---	---	---	
OCA2	4948	broad.mit.edu	37	15	28149457	28149457	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28149457delG	uc001zbh.3	-						OCA2_uc010ayv.2_Intron	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II						eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		GCTGTTGGCTGGGAGCGCTGG	0.607									Oculocutaneous_Albinism				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	33574563	33574563	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33574563delT								FMN1 (214478 upstream) : RYR3 (28614 downstream)																							TGAAGGAGCATTTTTTTTAAT	0.433													4	2	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33879028	33879028	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33879028delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ATATGGGGAGTTTTTTTTCCT	0.343													4	2	---	---	---	---	
ATPBD4	89978	broad.mit.edu	37	15	35742658	35742658	+	Intron	DEL	A	-	-	rs36117761		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35742658delA	uc001zja.2	-						ATPBD4_uc001ziz.2_Intron	NM_080650	NP_542381	Q7L8W6	ATBD4_HUMAN	ATP binding domain 4 isoform 1												0		all_epithelial(112;2.11e-09)|Lung NSC(122;2.38e-08)|all_lung(180;3.65e-07)		all cancers(64;9.9e-19)|GBM - Glioblastoma multiforme(113;2.01e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)		GTTATATGTTAAAAAAAAAAA	0.299													5	4	---	---	---	---	
C15orf41	84529	broad.mit.edu	37	15	37040189	37040189	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37040189delA	uc001zje.3	+						C15orf41_uc001zjd.2_Intron|C15orf41_uc010bbb.1_Intron|C15orf41_uc001zjf.2_Intron|C15orf41_uc010uci.1_Intron	NM_001130010	NP_001123482	Q9Y2V0	CO041_HUMAN	hypothetical protein LOC84529 isoform 1								protein binding			pancreas(1)	1		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		GAAGTTATTTAATCATTCGTT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	41902174	41902174	+	IGR	DEL	A	-	-	rs76119158		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41902174delA								TYRO3 (30648 upstream) : MGA (11590 downstream)																							AGAGAAACAGAAAAAAAAAAG	0.458													4	2	---	---	---	---	
VPS39	23339	broad.mit.edu	37	15	42470926	42470926	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42470926delA	uc001zpd.2	-						VPS39_uc001zpc.2_Intron	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39						protein transport	HOPS complex|late endosome membrane|lysosomal membrane	small GTPase regulator activity			ovary(1)|pancreas(1)|skin(1)	3		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		AGAAAGAAAGAAAAAAAAAAT	0.194													6	3	---	---	---	---	
SPATA5L1	79029	broad.mit.edu	37	15	45695555	45695555	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45695555delC	uc001zve.2	+	1	1037	c.928delC	c.(928-930)CCCfs	p.P310fs	uc001zvd.2_5'Flank|SPATA5L1_uc001zvf.2_RNA	NM_024063	NP_076968	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	310						cytoplasm	ATP binding|nucleoside-triphosphatase activity			ovary(3)|skin(1)	4		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		CGCCTTGTGTCCCCAGCGGGG	0.706													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46386265	46386265	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46386265delT								SQRDL (402787 upstream) : None (None downstream)																							ctcaatagcattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	46578087	46578087	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46578087delT								SQRDL (594609 upstream) : SEMA6D (898316 downstream)																							tattttattctttttttgtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	47259605	47259605	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47259605delG								None (None upstream) : SEMA6D (216798 downstream)																							gggaagagttgggggggctgc	0.000													4	2	---	---	---	---	
TNFAIP8L3	388121	broad.mit.edu	37	15	51392971	51392971	+	Intron	DEL	C	-	-	rs113070839		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51392971delC	uc001zyy.2	-							NM_207381	NP_997264	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein												0				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)		ggaaaaaaaacaaacaaacaa	0.100													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	52370816	52370816	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52370816delC								MAPK6 (12355 upstream) : BCL2L10 (31008 downstream)																							TGCTCTCCTGCCCCAGGTCCC	0.527											OREG0023127	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ARPP19	10776	broad.mit.edu	37	15	52839924	52839925	+	3'UTR	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52839924_52839925delGT	uc002acd.1	-	3					ARPP19_uc002ace.1_3'UTR	NM_006628	NP_006619	P56211	ARP19_HUMAN	cyclic AMP phosphoprotein, 19 kD						cell division|G2/M transition of mitotic cell cycle|mitosis|positive regulation of gluconeogenesis|positive regulation of glucose import	cytoplasm	potassium channel regulator activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity|receptor binding				0						AAGACTGGCAGTGTGTGCTGAG	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	54951182	54951182	+	IGR	DEL	A	-	-	rs79354205		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54951182delA								UNC13C (30377 upstream) : RSL24D1 (522339 downstream)																							GTCTCCTTTGAAAAAAAAAAA	0.408													7	4	---	---	---	---	
LIPC	3990	broad.mit.edu	37	15	58847422	58847422	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58847422delA	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)		ACAATTTAAGAAAAAGGGAAG	0.458													11	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62560823	62560823	+	IGR	DEL	A	-	-	rs34953481		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62560823delA								C2CD4B (103341 upstream) : MGC15885 (368548 downstream)																							TGATGGCTACAAAAAAAAAGG	0.318													10	5	---	---	---	---	
CA12	771	broad.mit.edu	37	15	63664033	63664034	+	Intron	INS	-	G	G	rs5813207		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63664033_63664034insG	uc002amc.2	-						CA12_uc002amd.2_Intron|CA12_uc002ame.2_Intron	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor						one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)	TGAACACACTAGGgtttttttt	0.322													5	3	---	---	---	---	
ITGA11	22801	broad.mit.edu	37	15	68668566	68668567	+	Intron	INS	-	T	T	rs141266701	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68668566_68668567insT	uc002ari.2	-						ITGA11_uc010bib.2_Intron	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)	GTTCTCCTCTCTTTTTTTTTTC	0.332													1	7	---	---	---	---	
THSD4	79875	broad.mit.edu	37	15	71742682	71742682	+	Intron	DEL	T	-	-	rs113018622		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71742682delT	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2						CAATTGAAGATTTTTTTTTTT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	83202832	83202832	+	5'Flank	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83202832delC	uc002bim.2	-											DQ574758																		ACCATGAGGTCCCACACTGTC	0.473													4	2	---	---	---	---	
NTRK3	4916	broad.mit.edu	37	15	88802148	88802148	+	5'Flank	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88802148delA	uc002bme.1	-						NTRK3_uc002bmh.2_5'Flank|NTRK3_uc002bmf.1_5'Flank|NTRK3_uc010bnh.1_5'Flank|NTRK3_uc002bmg.2_5'Flank	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)			AAAAACCTTTAAAAACCCCTC	0.348			T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			4	2	---	---	---	---	
MCTP2	55784	broad.mit.edu	37	15	94868771	94868773	+	Intron	DEL	GCC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94868771_94868773delGCC	uc002btj.2	+						MCTP2_uc010urg.1_Intron|MCTP2_uc002bti.2_Intron|MCTP2_uc010boj.2_Intron|MCTP2_uc010bok.2_Intron|MCTP2_uc002btg.3_Intron|MCTP2_uc002bth.3_Intron	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			TCCTCCCCCTGCCGCCACCACCA	0.419													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	96466283	96466284	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96466283_96466284insA								LOC145820 (415209 upstream) : NR2F2 (402873 downstream)																							CCACACCTTTTAAAAAAAAACA	0.322													4	2	---	---	---	---	
TARSL2	123283	broad.mit.edu	37	15	102211172	102211173	+	Intron	INS	-	G	G			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102211172_102211173insG	uc002bxm.2	-						TARSL2_uc002bxl.2_Intron|TARSL2_uc010usi.1_Intron	NM_152334	NP_689547	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2						threonyl-tRNA aminoacylation	cytoplasm	ATP binding|threonine-tRNA ligase activity			ovary(2)	2	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			cattaacggcagccaggggtta	0.074													4	2	---	---	---	---	
NPRL3	8131	broad.mit.edu	37	16	163086	163088	+	Intron	DEL	AAC	-	-	rs66730655		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:163086_163088delAAC	uc002cfr.2	-						NPRL3_uc010uua.1_Intron|NPRL3_uc002cfp.1_Intron|NPRL3_uc002cfq.2_Intron|NPRL3_uc010uub.1_Intron|NPRL3_uc010uuc.1_Intron|NPRL3_uc002cfs.1_Intron	NM_001077350	NP_001070818	Q12980	NPRL3_HUMAN	conserved gene telomeric to alpha globin cluster								protein binding			ovary(1)	1						CTTAAGGAAGAACAACAATGGTG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	1313150	1313151	+	IGR	INS	-	C	C	rs147596319	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1313150_1313151insC								TPSD1 (4656 upstream) : UBE2I (46029 downstream)																							TGGACATGGAGCCCCCCCAGGC	0.668													3	4	---	---	---	---	
IFT140	9742	broad.mit.edu	37	16	1627973	1627974	+	Intron	INS	-	AA	AA	rs140000457	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1627973_1627974insAA	uc002cmb.2	-						IFT140_uc002clz.2_Intron	NM_014714	NP_055529	Q96RY7	IF140_HUMAN	intraflagellar transport 140											ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)				ATGGCAGCAACAAGTGTGCTTG	0.554													2	5	---	---	---	---	
HAGH	3029	broad.mit.edu	37	16	1866254	1866254	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1866254delT	uc002cna.2	-						HAGH_uc002cmz.2_Intron|HAGH_uc010uvp.1_Intron|HAGH_uc002cnb.1_Intron	NM_005326	NP_005317	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase isoform 1						glutathione biosynthetic process	cytoplasm|mitochondrial matrix|mitochondrial matrix	hydroxyacylglutathione hydrolase activity|zinc ion binding			ovary(1)	1		Hepatocellular(780;0.00335)			Glutathione(DB00143)	ATTCATCTGATTTAGAGTTGG	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5279677	5279677	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5279677delA								FAM86A (131888 upstream) : A2BP1 (789455 downstream)																							AGAGAGAATGAAGGGGGTAAG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5844513	5844514	+	IGR	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5844513_5844514delGT								FAM86A (696724 upstream) : A2BP1 (224618 downstream)																							GCCAGCgtgcgtgtgtgtgtgt	0.322													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	10324599	10324600	+	IGR	INS	-	CTCT	CTCT	rs145614637	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10324599_10324600insCTCT								GRIN2A (47988 upstream) : ATF7IP2 (155312 downstream)																							gatgatgtttcctctctctctc	0.059													4	2	---	---	---	---	
GSPT1	2935	broad.mit.edu	37	16	11993188	11993188	+	5'Flank	DEL	T	-	-	rs36028471		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11993188delT	uc002dbr.2	-						GSPT1_uc002dbu.2_Intron|GSPT1_uc002dbt.2_Intron|GSPT1_uc010bux.2_Intron	NM_001130007	NP_001123479	P15170	ERF3A_HUMAN	G1 to S phase transition 1 isoform 3						G1/S transition of mitotic cell cycle|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation	intracellular	GTP binding|GTPase activity|protein binding|translation release factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						AATTGTTTTCTTTTTTTTTTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	12706705	12706706	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12706705_12706706insT								SNX29 (38560 upstream) : CPPED1 (46951 downstream)																							ggttctgtagcagtcattcctg	0.000													4	2	---	---	---	---	
SHISA9	729993	broad.mit.edu	37	16	13178859	13178859	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13178859delA	uc010uyy.1	+							NM_001145204	NP_001138676	B4DS77	SHSA9_HUMAN	shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0						GTTCTTTAATAAAAGGGAAGA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16682604	16682605	+	IGR	DEL	CA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16682604_16682605delCA								LOC339047 (238167 upstream) : XYLT1 (513578 downstream)																							GAAGAAAAATCACACACACACA	0.376													6	3	---	---	---	---	
XYLT1	64131	broad.mit.edu	37	16	17472947	17472947	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17472947delA	uc002dfa.2	-							NM_022166	NP_071449	Q86Y38	XYLT1_HUMAN	xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4						AAAAGGCAGGAAAAAAGTGCA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17909081	17909081	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17909081delT								XYLT1 (344343 upstream) : NOMO2 (602102 downstream)																							TACGTAACAATTTTAAAAATG	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20093455	20093456	+	IGR	INS	-	TG	TG	rs143615785	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20093455_20093456insTG								GPR139 (8355 upstream) : GP2 (228356 downstream)																							GGTTAGGAgtatgtgtgtgtgt	0.223													3	3	---	---	---	---	
NPIPL3	23117	broad.mit.edu	37	16	21458336	21458337	+	Intron	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21458336_21458337insA	uc002dix.1	-						uc002diq.3_Intron|LOC100271836_uc002diu.1_Intron	NM_130464	NP_569731	Q92617	NPPL3_HUMAN	nuclear pore complex interacting protein-like 3							integral to membrane					0						aaagcaaaatttaaaaaaAAAA	0.124													8	4	---	---	---	---	
SEZ6L2	26470	broad.mit.edu	37	16	29909744	29909745	+	Intron	INS	-	TC	TC	rs148845357	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29909744_29909745insTC	uc002duq.3	-						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Intron|SEZ6L2_uc002dur.3_Intron|SEZ6L2_uc002dus.3_Intron|SEZ6L2_uc010vec.1_Intron|SEZ6L2_uc010ved.1_Intron|ASPHD1_uc002dut.2_5'Flank|ASPHD1_uc002duu.3_5'Flank|ASPHD1_uc010bzi.2_5'Flank	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform							endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2						TGGCTGTCTTTtctctctctct	0.490													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32409562	32409562	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32409562delT								HERC2P4 (245688 upstream) : TP53TG3B (275279 downstream)																							cagcttttagtttcatttatc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32468824	32468825	+	IGR	INS	-	C	C	rs142220499	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32468824_32468825insC								HERC2P4 (304950 upstream) : TP53TG3B (216016 downstream)																							AGTTACTTTTTTTTTCCTTTAC	0.317													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33052524	33052524	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33052524delC								SLC6A10P (156061 upstream) : MIR1826 (912984 downstream)																							aacctgtgtactacattacta	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34973255	34973256	+	IGR	DEL	AA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34973255_34973256delAA								LOC146481 (258288 upstream) : None (None downstream)																							gggtgtaagtaaacaagttgcg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54606596	54606597	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54606596_54606597insT								IRX3 (286218 upstream) : IRX5 (358514 downstream)																							tgcACCCTGCATTTTTTTTTAC	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54684212	54684212	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54684212delT								IRX3 (363834 upstream) : IRX5 (280899 downstream)																							GAAGATTTGCTTTTTTTTTCT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55005968	55005968	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55005968delT								IRX5 (37575 upstream) : IRX6 (352503 downstream)																							tttcctttcctttccttcctt	0.000													4	2	---	---	---	---	
FAM192A	80011	broad.mit.edu	37	16	57197756	57197756	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57197756delA	uc010vhk.1	-						FAM192A_uc002ekz.3_Intron|FAM192A_uc002ekv.3_Intron|FAM192A_uc002ekw.3_Intron|FAM192A_uc002ekx.3_Intron|FAM192A_uc002eky.3_Intron	NM_024946	NP_079222	Q9GZU8	F192A_HUMAN	NEFA-interacting nuclear protein NIP30							nucleus					0						GCCTGGTAATAAAATCCTGCC	0.378													25	26	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	57611099	57611099	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57611099delA								GPR114 (1 upstream) : GPR56 (42551 downstream)																							agtgctcagtaaatggttact	0.184											OREG0023828	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	61433610	61433610	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61433610delA								None (None upstream) : CDH8 (253625 downstream)																							gaagaatctgaaaaaaagcag	0.000													4	2	---	---	---	---	
ATP6V0D1	9114	broad.mit.edu	37	16	67497479	67497479	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67497479delA	uc002ete.1	-						ATP6V0D1_uc010vjo.1_Intron	NM_004691	NP_004682	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal, V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)		GAAGAAGGGGaaaaaaaaaaa	0.244													2	4	---	---	---	---	
NFATC3	4775	broad.mit.edu	37	16	68134811	68134812	+	Intron	DEL	GT	-	-	rs34355254	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68134811_68134812delGT	uc002evo.1	+						NFATC3_uc010vkl.1_Intron|NFATC3_uc010vkm.1_Intron|NFATC3_uc010vkn.1_Intron|NFATC3_uc010vko.1_Intron|NFATC3_uc010vkp.1_Intron|NFATC3_uc010vkq.1_Intron|NFATC3_uc002evl.2_Intron|NFATC3_uc002evk.2_Intron|NFATC3_uc002evm.1_Intron|NFATC3_uc002evn.1_Intron|NFATC3_uc010vkr.1_Intron|NFATC3_uc010vks.1_Intron|NFATC3_uc010vkt.1_Intron|NFATC3_uc010vku.1_Intron|NFATC3_uc010vkv.1_Intron|NFATC3_uc010vkw.1_Intron|NFATC3_uc010vkx.1_Intron|NFATC3_uc010vky.1_Intron|NFATC3_uc010vkz.1_Intron|NFATC3_uc010vla.1_Intron|NFATC3_uc010vlb.1_Intron|NFATC3_uc010vlc.1_Intron	NM_173165	NP_775188	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells,						inflammatory response|transcription from RNA polymerase II promoter	nucleolus|plasma membrane	DNA binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		tgtgtgtggggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
TMCO7	79613	broad.mit.edu	37	16	69045299	69045299	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69045299delG	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)		TAGTGAATTAGGGGAATGATT	0.274													4	2	---	---	---	---	
CHTF8	54921	broad.mit.edu	37	16	69155575	69155575	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69155575delT	uc002ewn.1	-						CHTF8_uc002ewm.1_5'Flank|CHTF8_uc002ewo.1_Intron|CHTF8_uc002ewp.1_Intron	NM_001040146	NP_001035236	P0CG13	CTF8_HUMAN	chromosome transmission fidelity factor 8						cell cycle|DNA replication	nucleus	DNA binding				0						agagatggggttttttttttt	0.000													8	4	---	---	---	---	
IL34	146433	broad.mit.edu	37	16	70683628	70683628	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70683628delA	uc002ezh.1	+						IL34_uc002ezi.1_Intron	NM_152456	NP_689669	Q6ZMJ4	IL34_HUMAN	interleukin 34 precursor						positive regulation of cell proliferation|positive regulation of protein phosphorylation	extracellular space	cytokine activity|growth factor activity|macrophage colony-stimulating factor receptor binding			central_nervous_system(1)|skin(1)	2						CCAGGGAACCAGGAAGGGAGT	0.418													4	2	---	---	---	---	
DHODH	1723	broad.mit.edu	37	16	72058292	72058294	+	3'UTR	DEL	AAC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72058292_72058294delAAC	uc002fbp.2	+	9					DHODH_uc010cgk.2_RNA	NM_001361	NP_001352	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase precursor						'de novo' pyrimidine base biosynthetic process|pyrimidine nucleoside biosynthetic process|UMP biosynthetic process	integral to membrane|mitochondrial inner membrane	dihydroorotate oxidase activity				0		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)	TCAGACCATAAACTGCATTTTTG	0.463													8	6	---	---	---	---	
DHODH	1723	broad.mit.edu	37	16	72058296	72058312	+	3'UTR	DEL	GCATTTTTGATTCTTTG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72058296_72058312delGCATTTTTGATTCTTTG	uc002fbp.2	+	9					DHODH_uc010cgk.2_RNA	NM_001361	NP_001352	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase precursor						'de novo' pyrimidine base biosynthetic process|pyrimidine nucleoside biosynthetic process|UMP biosynthetic process	integral to membrane|mitochondrial inner membrane	dihydroorotate oxidase activity				0		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)	ACCATAAACTGCATTTTTGATTCTTTGTGGATTCAAA	0.456													8	6	---	---	---	---	
ZNRF1	84937	broad.mit.edu	37	16	75034759	75034759	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75034759delC	uc002fdk.2	+						ZNRF1_uc010vmz.1_Intron|ZNRF1_uc002fdl.1_Intron|ZNRF1_uc010cgr.1_Intron	NM_032268	NP_115644	Q8ND25	ZNRF1_HUMAN	zinc and ring finger protein 1							cell junction|endosome|lysosome|synaptic vesicle membrane	ligase activity|protein binding|zinc ion binding				0						GAGCCTGTCACGGTGGGGCAT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77148990	77148990	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77148990delA								CNTNAP4 (555855 upstream) : MON1B (75846 downstream)																							CAGCAGACATAAGGGGGAACT	0.408													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78474523	78474523	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78474523delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		tttttttttctttttttttga	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79844703	79844703	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79844703delA								MAF (210081 upstream) : DYNLRB2 (730151 downstream)																							TGTAAAAAGTAAAGGGCGGGA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80456562	80456562	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80456562delT								MAF (821940 upstream) : DYNLRB2 (118292 downstream)																							TAAGTAGATCTTTTTTTTTTT	0.423													0	6	---	---	---	---	
KCNG4	93107	broad.mit.edu	37	16	84263541	84263541	+	Intron	DEL	T	-	-	rs138369405	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84263541delT	uc010voc.1	-							NM_172347	NP_758857	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G,							voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(3)	3						AGCAGGCCAGTTTTTTAGGAA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	85463476	85463477	+	IGR	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85463476_85463477delTG								FAM92B (317362 upstream) : KIAA0182 (181552 downstream)																							tactcatggatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86526216	86526230	+	Intron	DEL	GTGGTGATGAAGATA	-	-	rs57451334	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86526216_86526230delGTGGTGATGAAGATA	uc002fjk.1	-											Homo sapiens cDNA FLJ34515 fis, clone HLUNG2006614.																		gatgacagtggtggtgatgaagataaCACTGCAGA	0.107													4	3	---	---	---	---	
JPH3	57338	broad.mit.edu	37	16	87675030	87675031	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87675030_87675031insT	uc002fkd.2	+						JPH3_uc010vou.1_Intron	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)		CCCCAAGCAGCTTTGGGGGTAC	0.431													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	90217102	90217102	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90217102delA								PRDM7 (74764 upstream) : None (None downstream)																							cctcatgtctaaaaaaaaatg	0.000													4	2	---	---	---	---	
RPA1	6117	broad.mit.edu	37	17	1764418	1764419	+	Intron	DEL	CA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1764418_1764419delCA	uc002fto.2	+							NM_002945	NP_002936	P27694	RFA1_HUMAN	replication protein A1						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding				0						agatcgtgtccacacacacaca	0.000								NER					3	3	---	---	---	---	
NLRP1	22861	broad.mit.edu	37	17	5452065	5452066	+	Intron	INS	-	CTTA	CTTA	rs139019919	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5452065_5452066insCTTA	uc002gci.2	-						NLRP1_uc002gcg.1_Intron|NLRP1_uc002gck.2_Intron|NLRP1_uc002gcj.2_Intron|NLRP1_uc002gcl.2_Intron|NLRP1_uc002gch.3_Intron|NLRP1_uc010clh.2_Intron	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1						defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)				tcagtccttatcttgacctccc	0.000													4	2	---	---	---	---	
PIK3R6	146850	broad.mit.edu	37	17	8732532	8732533	+	Intron	DEL	AC	-	-	rs138287023		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8732532_8732533delAC	uc002glq.1	-						PIK3R6_uc002glr.1_Intron|PIK3R6_uc002gls.1_Intron	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6						platelet activation	cytosol					0						acacacacagacacacacacag	0.005													4	2	---	---	---	---	
MYH13	8735	broad.mit.edu	37	17	10213264	10213264	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10213264delT	uc002gmk.1	-							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						taaatttaaattttttttttt	0.174													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13320638	13320638	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13320638delC								ELAC2 (399279 upstream) : HS3ST3A1 (78368 downstream)																							atgtccttttccaacaagaaa	0.005													4	2	---	---	---	---	
CCDC144A	9720	broad.mit.edu	37	17	16596641	16596641	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16596641delT	uc002gqk.1	+							NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A												0						tttttttttgttttttttttg	0.100													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	17744384	17744384	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17744384delC								MIR33B (27139 upstream) : TOM1L2 (2439 downstream)																							GAGGCTCACACCCATGTGGGC	0.567													4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21210741	21210741	+	Intron	DEL	G	-	-	rs66831346		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21210741delG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CAGATGCGGAGGCCTCTGCaa	0.264													5	3	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21216528	21216528	+	Intron	DEL	G	-	-	rs5819746		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21216528delG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GAGCATTGCAGCCCCATTTTG	0.463													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21227396	21227396	+	IGR	DEL	G	-	-	rs66676557		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21227396delG								MAP2K3 (8847 upstream) : KCNJ12 (52303 downstream)																							TGTAAGGGCCGTGGTTGATAC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21233115	21233115	+	IGR	DEL	A	-	-	rs113355841		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21233115delA								MAP2K3 (14566 upstream) : KCNJ12 (46584 downstream)																							atgcccagttaatttttgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25291422	25291422	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25291422delC								None (None upstream) : WSB1 (329684 downstream)																							acataaaatacactaatgcta	0.060													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27532511	27532512	+	IGR	DEL	AG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27532511_27532512delAG								MYO18A (25104 upstream) : CRYBA1 (41363 downstream)																							TAGGTAGGTCAGAGAGAGAGAG	0.500													4	2	---	---	---	---	
SLC6A4	6532	broad.mit.edu	37	17	28534291	28534292	+	Intron	INS	-	TTTG	TTTG			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28534291_28534292insTTTG	uc002hey.3	-						SLC6A4_uc010csg.2_Intron	NM_001045	NP_001036	P31645	SC6A4_HUMAN	solute carrier family 6 member 4						response to toxin|serotonin uptake|thalamus development	cytosol|endomembrane system|endosome membrane|membrane raft	actin filament binding|Rab GTPase binding|serotonin transmembrane transporter activity|serotonin:sodium symporter activity			skin(3)|ovary(1)	4					Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Doxepin(DB01142)|Duloxetine(DB00476)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Minaprine(DB00805)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phentermine(DB00191)|Protriptyline(DB00344)|Sertraline(DB01104)|Sibutramine(DB01105)|Tegaserod(DB01079)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Zimelidine(DB04832)	ctggtcatgtttttgtctcctg	0.000													4	3	---	---	---	---	
RNF135	84282	broad.mit.edu	37	17	29302175	29302175	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29302175delA	uc002hfz.2	+						RNF135_uc002hga.2_Intron|RNF135_uc010csm.2_Intron|RNF135_uc002hgb.2_Intron|DPRXP4_uc002hgc.2_5'Flank	NM_032322	NP_115698	Q8IUD6	RN135_HUMAN	ring finger protein 135 isoform 1						innate immune response|negative regulation of type I interferon production|positive regulation of interferon-beta production|regulation of innate immune response	cytosol	protein binding|ribonucleoprotein binding|ubiquitin-protein ligase activity|zinc ion binding	p.?(1)		skin(2)	2		all_cancers(10;8.65e-08)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Myeloproliferative disorder(56;0.0255)				agacccaatgaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29369598	29369599	+	IGR	DEL	CA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29369598_29369599delCA								RNF135 (42673 upstream) : NF1 (52396 downstream)																							cacttgcaagcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	30137165	30137165	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30137165delT								MIR365-2 (234625 upstream) : C17orf79 (41720 downstream)																							GCAATCAAACttttttttttt	0.020													3	3	---	---	---	---	
UTP6	55813	broad.mit.edu	37	17	30216089	30216089	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30216089delA	uc002hgr.2	-						UTP6_uc002hgq.2_5'Flank|UTP6_uc010cst.2_Intron|UTP6_uc010wbw.1_Intron	NM_018428	NP_060898	Q9NYH9	UTP6_HUMAN	hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				agactgtctcaaaaaaaaaaa	0.005													6	4	---	---	---	---	
TMEM98	26022	broad.mit.edu	37	17	31255961	31255964	+	Intron	DEL	CAAA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31255961_31255964delCAAA	uc002hhq.2	+						TMEM98_uc002hhr.2_Intron	NM_015544	NP_056359	Q9Y2Y6	TMM98_HUMAN	transmembrane protein 98							endoplasmic reticulum|integral to membrane					0		Ovarian(249;0.182)|Breast(31;0.244)	BRCA - Breast invasive adenocarcinoma(9;0.0769)			gaagcacactcaaacattcagttc	0.191													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33609678	33609678	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33609678delG								SLFN5 (14924 upstream) : SLFN11 (67653 downstream)																							ggattggagtggtaatctgag	0.000													4	2	---	---	---	---	
GGNBP2	79893	broad.mit.edu	37	17	34914602	34914602	+	Intron	DEL	T	-	-	rs79491251		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34914602delT	uc002hnb.2	+						GGNBP2_uc002hna.2_Intron	NM_024835	NP_079111	Q9H3C7	GGNB2_HUMAN	zinc finger protein 403						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		ggctgaggtcttttttttttt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	36581924	36581924	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36581924delA								SOCS7 (25907 upstream) : ARHGAP23 (31720 downstream)																							TCCAAACCCCAAAAAAATAGG	0.572													4	2	---	---	---	---	
ASB16	92591	broad.mit.edu	37	17	42249996	42249996	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42249996delT	uc002ifl.1	+						ASB16_uc002ifm.1_Intron	NM_080863	NP_543139	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box-containing protein						intracellular signal transduction		protein binding			kidney(2)	2		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		AACCTAGCTGtttttttttgt	0.189													4	2	---	---	---	---	
GFAP	2670	broad.mit.edu	37	17	42991734	42991735	+	Intron	DEL	CA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42991734_42991735delCA	uc002ihq.2	-						GFAP_uc002ihr.2_Intron|GFAP_uc010wjg.1_Intron	NM_002055	NP_002046	P14136	GFAP_HUMAN	glial fibrillary acidic protein isoform 1							cytoplasm|intermediate filament	structural constituent of cytoskeleton			ovary(1)|pancreas(1)	2		Prostate(33;0.0959)				CTCACTGTTGcacacacacaca	0.446													4	2	---	---	---	---	
LRRC37A2	474170	broad.mit.edu	37	17	44611564	44611564	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44611564delT	uc002ikn.1	+						ARL17A_uc002iko.3_Intron	NM_001006607	NP_001006608	A6NM11	L37A2_HUMAN	c114 SLIT-like testicular protein precursor							integral to membrane					0		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		tttgtTTTTGttttttttaat	0.005													4	2	---	---	---	---	
ANKFN1	162282	broad.mit.edu	37	17	54363371	54363371	+	Intron	DEL	A	-	-	rs141243681		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54363371delA	uc002iun.1	+							NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2						TTTCACTTTCAAAAAAAATGT	0.398													4	3	---	---	---	---	
ANKFN1	162282	broad.mit.edu	37	17	54473333	54473333	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54473333delA	uc002iun.1	+							NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2						taatagttccaaaaatagcta	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54833292	54833293	+	IGR	INS	-	G	G	rs141898804	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54833292_54833293insG								NOG (160341 upstream) : C17orf67 (35982 downstream)																							ATTTAGGAGgtggcccccaagc	0.203													4	2	---	---	---	---	
INTS2	57508	broad.mit.edu	37	17	59968674	59968674	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59968674delA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3						actccatctcaaaaaaaaaaG	0.124													7	8	---	---	---	---	
DDX42	11325	broad.mit.edu	37	17	61878276	61878276	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61878276delC	uc002jbu.2	+						DDX42_uc002jbv.2_Intron|DDX42_uc002jbw.1_Intron	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein						protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5						tcttttctttccttccttcct	0.070													4	2	---	---	---	---	
DDX42	11325	broad.mit.edu	37	17	61878283	61878284	+	Intron	DEL	TC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61878283_61878284delTC	uc002jbu.2	+						DDX42_uc002jbv.2_Intron|DDX42_uc002jbw.1_Intron	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein						protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5						tttccttccttcctttctttct	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63285492	63285492	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63285492delT								RGS9 (61673 upstream) : AXIN2 (239193 downstream)																							ctttcatctcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63320299	63320299	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63320299delA								RGS9 (96480 upstream) : AXIN2 (204386 downstream)																							actccatctcaaaaaaaaaaa	0.000													5	9	---	---	---	---	
ABCA8	10351	broad.mit.edu	37	17	66918080	66918080	+	Intron	DEL	A	-	-	rs4148020		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66918080delA	uc002jhp.2	-						ABCA8_uc002jhq.2_Intron|ABCA8_uc010wqq.1_Intron|ABCA8_uc010wqr.1_Intron|ABCA8_uc002jhr.2_Intron	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)					GAGTTTGTAGAAAAAAAAACC	0.279													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70572768	70572768	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70572768delT	uc002jix.2	-						uc002jiz.1_Intron					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																		GGGGAAGGAATTTTTTTTTCC	0.527													4	3	---	---	---	---	
PRPSAP1	5635	broad.mit.edu	37	17	74325828	74325828	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74325828delA	uc010wta.1	-						PRPSAP1_uc010wtb.1_Intron	NM_002766	NP_002757	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|identical protein binding|magnesium ion binding|ribose phosphate diphosphokinase activity			ovary(1)	1						aaaaaaaaacaaaaaaaaaaa	0.189													5	3	---	---	---	---	
RHBDF2	79651	broad.mit.edu	37	17	74492840	74492840	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74492840delT	uc002jrq.1	-						RHBDF2_uc002jrp.1_Intron	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1						negative regulation of protein secretion|protein transport|proteolysis	endoplasmic reticulum membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity				0						TCCAGAtctcttttttttttc	0.274													3	4	---	---	---	---	
C17orf101	79701	broad.mit.edu	37	17	80358802	80358802	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80358802delA	uc002keu.1	-						C17orf101_uc002ket.1_Intron|C17orf101_uc010dip.1_Intron	NM_024648	NP_078924	Q6PK18	CQ101_HUMAN	hypothetical protein LOC79701 isoform 1							integral to membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(1)	1						GGGGCCATGGAAGGAGCCGGG	0.517													4	2	---	---	---	---	
EMILIN2	84034	broad.mit.edu	37	18	2894626	2894626	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2894626delG	uc002kln.2	+							NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2 precursor						cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			skin(2)|ovary(1)	3				READ - Rectum adenocarcinoma(2;0.1)		AGTAGGAGTTGGGGGGTGAAT	0.413													4	2	---	---	---	---	
IMPA2	3613	broad.mit.edu	37	18	12012530	12012530	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12012530delC	uc002kqp.1	+						IMPA2_uc002kqo.1_Intron|IMPA2_uc010dlb.1_Intron|IMPA2_uc002kqq.1_Intron	NM_014214	NP_055029	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2						inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)	CTCCAGCTGACCCCTAGAGCG	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	13836398	13836398	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13836398delG								MC5R (9658 upstream) : MC2R (45645 downstream)																							aaaaaaAAAAGAAACATCTCT	0.294													4	2	---	---	---	---	
ROCK1	6093	broad.mit.edu	37	18	18566615	18566615	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18566615delT	uc002kte.2	-							NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)					TAATAAAGACTTTTTTTTTCT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	20416215	20416215	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20416215delG								CTAGE1 (418337 upstream) : RBBP8 (97080 downstream)																							ttctaaatatgacaaaactac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	24991252	24991252	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24991252delA	uc002kwf.1	-											Homo sapiens cDNA FLJ45994 fis, clone SKMUS2009557.																		CAAAACTCTGAAAAAAAAAAT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	27049055	27049055	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27049055delC								None (None upstream) : MIR302F (829821 downstream)																							tatccagtttccccacgtttg	0.000													4	2	---	---	---	---	
MEP1B	4225	broad.mit.edu	37	18	29793800	29793800	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29793800delT	uc002kxj.3	+							NM_005925	NP_005916	Q16820	MEP1B_HUMAN	meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2						gaagtgttggttttagagtct	0.179													4	2	---	---	---	---	
KC6	641516	broad.mit.edu	37	18	39074703	39074704	+	Intron	DEL	TC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39074703_39074704delTC	uc002lan.2	-							NR_002838				Homo sapiens KC6 mRNA, complete sequence.												0						ATTGTGGTTGtctctctctctc	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41483555	41483555	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41483555delA								SYT4 (625940 upstream) : SETBP1 (776583 downstream)																							tccaaatttcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	48869153	48869154	+	IGR	DEL	AT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48869153_48869154delAT								MEX3C (145463 upstream) : DCC (997417 downstream)																							GGTGAAAGGGATAAGGCTGGAA	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49682090	49682090	+	IGR	DEL	T	-	-	rs35103696		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49682090delT								MEX3C (958400 upstream) : DCC (184481 downstream)																							GTTATGTGCATTTTTTCACCT	0.313													2	4	---	---	---	---	
TCF4	6925	broad.mit.edu	37	18	52962987	52962987	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52962987delT	uc002lfz.2	-						TCF4_uc002lfw.3_Intron|TCF4_uc010xdu.1_Intron|TCF4_uc010xdv.1_Intron|TCF4_uc002lfx.2_Intron|TCF4_uc010xdw.1_Intron|TCF4_uc002lfy.2_Intron|TCF4_uc010xdx.1_Intron|TCF4_uc010dph.1_Intron|TCF4_uc010xdy.1_Intron|TCF4_uc002lga.2_Intron|TCF4_uc002lgb.1_Intron|TCF4_uc010dpi.2_Intron|TCF4_uc002lgc.3_Intron	NM_003199	NP_003190	P15884	ITF2_HUMAN	transcription factor 4 isoform b						positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		tctggcattctgaactacttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	54991518	54991518	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54991518delA								WDR7 (294482 upstream) : ST8SIA3 (28203 downstream)																							AGTACTGTTTAAAAAAAAACA	0.199													4	2	---	---	---	---	
NARS	4677	broad.mit.edu	37	18	55275102	55275102	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55275102delT	uc002lgs.2	-						NARS_uc002lgt.2_Intron|NARS_uc010xea.1_Intron|NARS_uc010xeb.1_Intron|NARS_uc010xec.1_Intron|NARS_uc010xed.1_Intron	NM_004539	NP_004530	O43776	SYNC_HUMAN	asparaginyl-tRNA synthetase						asparaginyl-tRNA aminoacylation	cytosol|soluble fraction	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding				0		Colorectal(73;0.227)			L-Asparagine(DB00174)	CACAAATATCttttttttttt	0.139													4	2	---	---	---	---	
CCBE1	147372	broad.mit.edu	37	18	57169927	57169928	+	Intron	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57169927_57169928insA	uc002lib.2	-							NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)				CCTCCCCCCGCAAAAAAAAAGG	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	64035525	64035526	+	IGR	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64035525_64035526delTG								CDH7 (487351 upstream) : CDH19 (135795 downstream)																							ggtgtaaatctgtgtaagttct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	2859211	2859218	+	IGR	DEL	GCGCAGGC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2859211_2859218delGCGCAGGC								ZNF555 (5005 upstream) : ZNF556 (8115 downstream)																							TCCATGAAGTGCGCAGGCGCACTTAGGC	0.601													4	3	---	---	---	---	
MPND	84954	broad.mit.edu	37	19	4348661	4348661	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4348661delT	uc002mae.2	+						MPND_uc010dtx.2_Intron|MPND_uc002mag.2_Intron|MPND_uc002maf.2_Intron|MPND_uc002mah.2_Intron|MPND_uc002mai.2_Intron	NM_032868	NP_116257	Q8N594	MPND_HUMAN	MPN domain containing isoform 1								peptidase activity			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		tgttgaattcttttttttttt	0.164													4	2	---	---	---	---	
SH3GL1	6455	broad.mit.edu	37	19	4367421	4367421	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4367421delA	uc002maj.2	-						SH3GL1_uc002mak.2_Intron|SH3GL1_uc010xig.1_Intron	NM_003025	NP_003016	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1						central nervous system development|endocytosis|signal transduction	early endosome membrane	lipid binding|protein binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		GGGTCTACTTAAAAAAAAAAA	0.547			T	MLL	AL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	8772479	8772479	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8772479delT								ADAMTS10 (96891 upstream) : ACTL9 (35272 downstream)																							ttctttttccttttttttttt	0.000													4	3	---	---	---	---	
TNPO2	30000	broad.mit.edu	37	19	12822681	12822681	+	Intron	DEL	T	-	-	rs35251364		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12822681delT	uc002muo.2	-						TNPO2_uc002mup.2_Intron|TNPO2_uc002muq.2_Intron|TNPO2_uc002mur.2_Intron	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)						intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1						CAGAGAAAGGttttttttttt	0.224													4	3	---	---	---	---	
ZSWIM4	65249	broad.mit.edu	37	19	13920085	13920085	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13920085delG	uc002mxh.1	+						ZSWIM4_uc010xng.1_Intron	NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4								zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			CGGCTCCCATGGGGGCTGGCC	0.493													4	2	---	---	---	---	
PKN1	5585	broad.mit.edu	37	19	14578331	14578331	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14578331delG	uc002myp.2	+						PKN1_uc002myq.2_Intron|PKN1_uc002myr.2_5'Flank	NM_002741	NP_002732	Q16512	PKN1_HUMAN	protein kinase N1 isoform 2						activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8						gtGGTTATGAGGGCATCTCTG	0.333													10	8	---	---	---	---	
PGPEP1	54858	broad.mit.edu	37	19	18470143	18470144	+	Intron	INS	-	C	C			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18470143_18470144insC	uc002nis.1	+						PGPEP1_uc002nir.1_Intron|PGPEP1_uc002nit.1_Intron|PGPEP1_uc010xqg.1_Intron	NM_017712	NP_060182	Q9NXJ5	PGPI_HUMAN	pyroglutamyl-peptidase I								cysteine-type peptidase activity				0						ctggcccttggcccgcctctcc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31240776	31240777	+	IGR	DEL	TT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31240776_31240777delTT								ZNF536 (191811 upstream) : DKFZp566F0947 (400006 downstream)																							tcctctgctctttcagtgttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	33314283	33314283	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33314283delT	uc002nts.1	+											Homo sapiens cDNA FLJ13072 fis, clone NT2RP3001844.																		CCCACACAGCTTTTTTTTGGG	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	40925161	40925162	+	IGR	DEL	GT	-	-	rs5028922	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40925161_40925162delGT								PRX (5890 upstream) : SERTAD1 (3249 downstream)																							GAGAGAGAGAgtgtgtgtgtgt	0.391													4	2	---	---	---	---	
POU2F2	5452	broad.mit.edu	37	19	42637797	42637798	+	5'Flank	DEL	CA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42637797_42637798delCA	uc002osn.2	-						POU2F2_uc002oso.2_5'Flank|POU2F2_uc002osp.2_5'Flank|POU2F2_uc002osq.2_5'Flank|POU2F2_uc002osr.1_5'Flank|uc002oss.2_Intron|hsa-mir-4323|MI0015853_5'Flank	NM_002698	NP_002689	P09086	PO2F2_HUMAN	POU domain, class 2, transcription factor 2						humoral immune response|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2		Prostate(69;0.059)				CACACGTGTGCACACACACGTG	0.540													4	2	---	---	---	---	
GLTSCR1	29998	broad.mit.edu	37	19	48123370	48123371	+	Intron	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48123370_48123371delGT	uc002phh.3	+							NM_015711	NP_056526	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1								protein binding			pancreas(3)	3		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		agggatgttggtgtgtgtgtat	0.149													4	2	---	---	---	---	
PLA2G4C	8605	broad.mit.edu	37	19	48591632	48591632	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48591632delA	uc002phx.2	-						PLA2G4C_uc002phw.2_Intron|PLA2G4C_uc010elr.2_Intron|PLA2G4C_uc010xzd.1_Intron	NM_003706	NP_003697	Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC isoform 1 precursor						arachidonic acid metabolic process|glycerophospholipid catabolic process|inflammatory response|intracellular signal transduction|parturition	cytosol|membrane	calcium-independent phospholipase A2 activity|phospholipid binding			ovary(1)|skin(1)	2		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		cggaaaaaagaaaaaaaaaac	0.000													3	4	---	---	---	---	
TEAD2	8463	broad.mit.edu	37	19	49845484	49845485	+	Intron	INS	-	CCACATCAGTT	CCACATCAGTT	rs149352076	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49845484_49845485insCCACATCAGTT	uc002pnj.2	-						uc002pnb.1_5'Flank|TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		TGACATCCCCACCCTGGGTGAA	0.327													4	2	---	---	---	---	
POLD1	5424	broad.mit.edu	37	19	50916022	50916023	+	Intron	DEL	TG	-	-	rs71707090		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50916022_50916023delTG	uc002psb.3	+						POLD1_uc002psc.3_Intron|POLD1_uc010enx.2_Intron|POLD1_uc010eny.2_Intron	NM_002691	NP_002682	P28340	DPOD1_HUMAN	DNA-directed DNA polymerase delta 1						base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|response to UV|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm|nucleotide-excision repair complex	3'-5'-exodeoxyribonuclease activity|chromatin binding|DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding|protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		TTTTTAGTTTTGTGTGTGTGTG	0.198								DNA_polymerases_(catalytic_subunits)					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53738106	53738106	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53738106delA								ZNF665 (41487 upstream) : ZNF677 (532 downstream)																							TAGTTTCTTTAAAAAAAAAAT	0.234													7	4	---	---	---	---	
CSNK2A1	1457	broad.mit.edu	37	20	508382	508383	+	Intron	DEL	CA	-	-	rs143479499		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:508382_508383delCA	uc002wdw.1	-						CSNK2A1_uc002wdx.1_Intron|CSNK2A1_uc002wdy.1_Intron	NM_177559	NP_808227	P68400	CSK21_HUMAN	casein kinase II alpha 1 subunit isoform a						axon guidance|Wnt receptor signaling pathway	cytosol|NuRD complex|plasma membrane|Sin3 complex	ATP binding|protein N-terminus binding|protein serine/threonine kinase activity			ovary(1)	1		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			CGTgtttcaccacactgcccag	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	663246	663246	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:663246delG								SRXN1 (6423 upstream) : C20orf54 (77479 downstream)																							TGTGGTGGCTGGGGGCATAGC	0.413													4	2	---	---	---	---	
C20orf46	55321	broad.mit.edu	37	20	1162840	1162840	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1162840delG	uc010gaa.1	-						C20orf46_uc002weq.1_Intron	NM_018354	NP_060824	Q9NUR3	CT046_HUMAN	hypothetical protein LOC55321							integral to membrane	protein binding			ovary(1)	1						GGGTGGGGGAGGGGGTAGAAA	0.229													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2183707	2183707	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2183707delA								STK35 (54511 upstream) : TGM3 (92906 downstream)																							AAATTTTTTTAAAAAGCAGTA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2436449	2436450	+	IGR	INS	-	A	A	rs72018550		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2436449_2436450insA								TGM6 (23050 upstream) : SNRPB (5831 downstream)																							ctgtgtctaccaaaaaaaaaag	0.079													4	2	---	---	---	---	
C20orf194	25943	broad.mit.edu	37	20	3277032	3277032	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3277032delT	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943												0						ACAtttttcgttttttttttt	0.323													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	3702676	3702677	+	IGR	INS	-	T	T	rs144163044	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3702676_3702677insT								SIGLEC1 (14901 upstream) : HSPA12B (10679 downstream)																							ATATGTTGAACTTTTTTTTTAA	0.337													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	3861166	3861166	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3861166delT								MAVS (4405 upstream) : PANK2 (8320 downstream)																							GCAAACCTACttttttttttt	0.244													4	2	---	---	---	---	
SLC23A2	9962	broad.mit.edu	37	20	4979985	4979988	+	Intron	DEL	TGGA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4979985_4979988delTGGA	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_Intron|SLC23A2_uc002wlj.1_Intron	NM_005116	NP_005107	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (nucleobase						L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2						GGTCACCAAGTGGATGGATGGATG	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6630104	6630104	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6630104delT								FERMT1 (525913 upstream) : BMP2 (118641 downstream)																							tgtaaagagatttttttttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7095686	7095686	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7095686delA								BMP2 (334776 upstream) : HAO1 (767945 downstream)																							tagtaaattgaagggattcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	8917496	8917496	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8917496delT								PLCB1 (51951 upstream) : PLCB4 (132205 downstream)																							TTTTCTTTTCTTTTTTTTTTT	0.388													5	3	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9422558	9422558	+	Intron	DEL	T	-	-	rs113280992		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9422558delT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						CCAACACGACTTTTTTTTTTT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	11318806	11318806	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11318806delC								JAG1 (664112 upstream) : BTBD3 (552671 downstream)																							tctcagctgaccccacaggga	0.000													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15743925	15743925	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15743925delC	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				AGTGGCAGAACCACCCGAGAT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16801725	16801725	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16801725delT								OTOR (68917 upstream) : PCSK2 (405027 downstream)																							TGAGCCTTGCTTTTTTtcaag	0.194													4	2	---	---	---	---	
BFSP1	631	broad.mit.edu	37	20	17488660	17488661	+	Intron	DEL	TT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17488660_17488661delTT	uc002wpo.2	-						BFSP1_uc002wpp.2_Intron|BFSP1_uc010zrn.1_Intron|BFSP1_uc010zro.1_Intron	NM_001195	NP_001186	Q12934	BFSP1_HUMAN	filensin isoform 1							cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1						TGGCTTCACATTTTTAGACAGA	0.252													4	2	---	---	---	---	
BANF2	140836	broad.mit.edu	37	20	17672225	17672225	+	5'Flank	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17672225delA	uc010zrs.1	+							NM_001159495	NP_001152967	Q9H503	BAFL_HUMAN	barrier to autointegration factor 2 isoform 2							cytoplasm|nucleus	DNA binding			skin(1)	1						ACTCTTCAACAAAAAAGCTTA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19731126	19731126	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19731126delA								SLC24A3 (27586 upstream) : RIN2 (139084 downstream)																							tctccaaaagaaaaaaaaaaT	0.169													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	21000142	21000143	+	IGR	INS	-	GT	GT	rs111402898		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21000142_21000143insGT								RALGAPA2 (306876 upstream) : PLK1S1 (106481 downstream)																							CCCTGCCGCGCGCGCGcacaca	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24436971	24436972	+	IGR	DEL	CA	-	-	rs57046153		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24436971_24436972delCA								GGTLC1 (467555 upstream) : TMEM90B (12863 downstream)																							ctctctctctcacacacacaca	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25118056	25118057	+	IGR	DEL	TG	-	-	rs34675343		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25118056_25118057delTG								VSX1 (55289 upstream) : LOC284798 (3377 downstream)																							TTGCAGTGTTTGTGTGTGTGTG	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29583385	29583385	+	IGR	DEL	T	-	-	rs112099758		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29583385delT								None (None upstream) : FRG1B (28494 downstream)																							AATGTTTTAATTTTTGTAAAG	0.279													3	3	---	---	---	---	
DEFB123	245936	broad.mit.edu	37	20	30026627	30026628	+	5'Flank	DEL	AA	-	-	rs142475288		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30026627_30026628delAA	uc002wvy.2	+							NM_153324	NP_697019	Q8N688	DB123_HUMAN	defensin, beta 123 precursor						defense response to bacterium	extracellular region					0	Lung NSC(7;0.000139)|all_lung(7;0.000197)|all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GCTTCAAAACAAGAGCAAAATT	0.485													3	7	---	---	---	---	
COX4I2	84701	broad.mit.edu	37	20	30228209	30228210	+	Intron	DEL	GG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30228209_30228210delGG	uc002wwj.1	+						COX4I2_uc002wwi.2_Intron	NM_032609	NP_115998	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2						cellular respiration		cytochrome-c oxidase activity			ovary(1)	1	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			catgtggctagggtgaggtgtg	0.000													4	2	---	---	---	---	
DUSP15	128853	broad.mit.edu	37	20	30436494	30436494	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30436494delC	uc002wwu.1	-									Q9H1R2	DUS15_HUMAN	RecName: Full=Dual specificity protein phosphatase 15;          EC=3.1.3.48;          EC=3.1.3.16; AltName: Full=Vaccinia virus VH1-related dual-specific protein phosphatase Y; AltName: Full=VH1-related member Y;							cytoplasm|plasma membrane	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GTCCTACAGACCCGAGGGTGC	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31142532	31142532	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31142532delG	uc002wxx.2	-											SubName: Full=LOC284804 protein; Flags: Fragment;																		CATTGGCTCTGGAGCTCAGGA	0.537													4	2	---	---	---	---	
ERGIC3	51614	broad.mit.edu	37	20	34133985	34133985	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34133985delA	uc002xct.2	+						ERGIC3_uc002xcr.1_Intron|ERGIC3_uc010zvg.1_Intron|ERGIC3_uc002xcs.2_Intron|ERGIC3_uc002xcu.2_Intron|ERGIC3_uc002xcv.2_Intron	NM_015966	NP_057050	Q9Y282	ERGI3_HUMAN	serologically defined breast cancer antigen 84						vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi apparatus|integral to membrane	protein binding			large_intestine(2)|ovary(1)	3	Lung NSC(9;0.00489)|all_lung(11;0.00729)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			atcaaagagcaaaaaaggaag	0.000													4	2	---	---	---	---	
RBM39	9584	broad.mit.edu	37	20	34296924	34296924	+	Intron	DEL	A	-	-	rs76254627		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34296924delA	uc002xeb.2	-						RBM39_uc002xdz.2_Intron|RBM39_uc002xea.2_Intron|RBM39_uc010gfn.2_Intron|RBM39_uc010zvm.1_Intron|RBM39_uc002xeg.2_Intron|RBM39_uc002xec.2_Intron|RBM39_uc002xed.2_Intron|RBM39_uc002xee.2_Intron|RBM39_uc002xef.2_Intron|RBM39_uc010zvn.1_Intron	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					AAACTAAAGCAAAAAAAAAAA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	34667450	34667450	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34667450delA								LOC647979 (28568 upstream) : EPB41L1 (11976 downstream)																							acttcgtctcaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	35377816	35377816	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35377816delT								NDRG3 (3335 upstream) : DSN1 (2379 downstream)																							TGCTTTATTCTTTTTTTTTTT	0.134													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36513496	36513496	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36513496delA								CTNNBL1 (12977 upstream) : VSTM2L (18003 downstream)																							GAGGCCTGAGAAAAAAGTCCA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37016686	37016687	+	IGR	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37016686_37016687insT								LBP (11033 upstream) : LOC388796 (32552 downstream)																							CTTAGAAAAAGTTTTTCATCCA	0.252													4	2	---	---	---	---	
ADIG	149685	broad.mit.edu	37	20	37216061	37216061	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37216061delC	uc002xjb.1	+							NM_001018082	NP_001018092	Q0VDE8	ADIG_HUMAN	small adipocyte factor 1						brown fat cell differentiation|positive regulation of fat cell differentiation|white fat cell differentiation	cytoplasm|integral to membrane|nucleus					0		Myeloproliferative disorder(115;0.00878)				GGGCCCTTTTCCCAGGAAAAC	0.348													2	4	---	---	---	---	
ZHX3	23051	broad.mit.edu	37	20	39822723	39822723	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39822723delT	uc002xjs.1	-						ZHX3_uc002xjq.1_Intron|ZHX3_uc002xjr.1_Intron|ZHX3_uc002xjt.1_Intron|ZHX3_uc002xju.1_Intron|ZHX3_uc010ggg.1_Intron	NM_015035	NP_055850	Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3						negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)				cttttatttattttttttgcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	40361477	40361477	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40361477delG								CHD6 (114344 upstream) : PTPRT (339916 downstream)																							tgacaggggtgggaaactttc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47159519	47159520	+	IGR	INS	-	A	A	rs138918505	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47159519_47159520insA								LOC284749 (160138 upstream) : PREX1 (81273 downstream)																							TGTGCCCTTCGAAGGTTCAAAC	0.545													4	6	---	---	---	---	
DDX27	55661	broad.mit.edu	37	20	47859880	47859880	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47859880delC	uc002xuh.2	+							NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27							nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			AATATGTTGTCCCACACCATT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48341677	48341677	+	IGR	DEL	G	-	-	rs11475573		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48341677delG								B4GALT5 (11256 upstream) : SLC9A8 (87573 downstream)																							agggaggggtggctccccgag	0.050													3	4	---	---	---	---	
SLC9A8	23315	broad.mit.edu	37	20	48459834	48459834	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48459834delT	uc002xuv.1	+						SLC9A8_uc010zym.1_Intron|SLC9A8_uc010zyj.1_Intron|SLC9A8_uc010zyk.1_Intron|SLC9A8_uc010zyl.1_Intron|SLC9A8_uc010gib.1_Intron	NM_015266	NP_056081	Q9Y2E8	SL9A8_HUMAN	sodium/hydrogen exchanger 8							Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			GCTCGGCTCATTTTTTTTCAC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51365359	51365359	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51365359delT								ZFP64 (556835 upstream) : TSHZ2 (223518 downstream)																							TTGTGTTTTGTTTTTTTTTTT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	52840830	52840830	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52840830delG								PFDN4 (4339 upstream) : DOK5 (251427 downstream)																							AAAAGTCAACGGACAAGAGGT	0.403													4	2	---	---	---	---	
AURKA	6790	broad.mit.edu	37	20	54945982	54945982	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54945982delC	uc002xxd.1	-						AURKA_uc002xxe.1_Intron|AURKA_uc002xxf.1_Intron|AURKA_uc002xxg.1_Intron|AURKA_uc002xxh.1_Intron|AURKA_uc002xxi.1_Intron|AURKA_uc002xxj.1_Intron|AURKA_uc002xxk.1_Intron|AURKA_uc010zzd.1_Intron	NM_198433	NP_940835	O14965	AURKA_HUMAN	serine/threonine protein kinase 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|phosphatidylinositol-mediated signaling|regulation of protein stability|spindle organization	cytosol|nucleus|perinuclear region of cytoplasm|spindle microtubule|spindle pole centrosome	ATP binding|protein kinase binding|protein serine/threonine kinase activity			lung(3)|ovary(2)|breast(1)|large_intestine(1)|skin(1)	8			Colorectal(105;0.202)			CTGAATGTATCACTACCATAT	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55341048	55341048	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55341048delC								TFAP2C (126712 upstream) : BMP7 (402761 downstream)																							tggtcatgtgcccattggtga	0.109													4	2	---	---	---	---	
PCK1	5105	broad.mit.edu	37	20	56139163	56139164	+	Intron	DEL	AA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56139163_56139164delAA	uc002xyn.3	+						PCK1_uc010zzm.1_Intron	NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1						gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			skin(1)	1	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GGCAATATATAAGAGTATATGT	0.391													36	40	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57667272	57667272	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57667272delT								SLMO2 (49371 upstream) : ZNF831 (98803 downstream)																							CAGCTGGGTCTTGGTGTTCAt	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	58947454	58947454	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58947454delT	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		GCTGGGACTGTTTTTTTTTTT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59623497	59623497	+	IGR	DEL	T	-	-	rs5842331		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59623497delT								MIR646 (739872 upstream) : CDH4 (204062 downstream)																							TATGGAGAGCTTTCTCAACTT	0.463													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59644956	59644956	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59644956delA								MIR646 (761331 upstream) : CDH4 (182603 downstream)																							GATTGGAGGTAAAGGGAGACA	0.209													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	59930760	59930761	+	Intron	DEL	TG	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59930760_59930761delTG	uc002ybn.1	+							NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CATGCACACCTGTGTGTGTGTG	0.500													4	3	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60209552	60209553	+	Intron	INS	-	G	G	rs151327936	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60209552_60209553insG	uc002ybn.1	+						CDH4_uc002ybo.1_Intron|CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			AAAGCAACAATCCCAGAGGCTG	0.594													3	4	---	---	---	---	
TAF4	6874	broad.mit.edu	37	20	60557124	60557124	+	Intron	DEL	C	-	-	rs112352725		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60557124delC	uc002ybs.2	-							NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			CAAACCCACACCCCACCCGAG	0.577													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10717006	10717007	+	IGR	DEL	AA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10717006_10717007delAA								None (None upstream) : TPTE (189736 downstream)																							cagattctacaaaaagagtgtc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10760890	10760891	+	IGR	DEL	AG	-	-	rs138985880		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10760890_10760891delAG								None (None upstream) : TPTE (145852 downstream)																							ttctacaaacagagagtttcaa	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10760918	10760919	+	IGR	INS	-	A	A	rs146573419		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10760918_10760919insA								None (None upstream) : TPTE (145824 downstream)																							tcaatcaaaagaaaggtttaac	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10868441	10868441	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10868441delG								None (None upstream) : TPTE (38302 downstream)																							CTGAGTGTGTGGGGGGGTCAT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14366259	14366259	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14366259delA								None (None upstream) : C21orf99 (44228 downstream)																							cagattctacaaaaaaagagg	0.000													4	2	---	---	---	---	
CXADR	1525	broad.mit.edu	37	21	18910671	18910673	+	Intron	DEL	GAT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18910671_18910673delGAT	uc002yki.2	+						CXADR_uc002ykh.1_Intron|CXADR_uc010gld.1_Intron|CXADR_uc010gle.1_Intron	NM_001338	NP_001329	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor						blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		tgatgatggagatgatgatggct	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26852872	26852872	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26852872delC								NCRNA00158 (48859 upstream) : MIR155HG (81585 downstream)																							agtaaacccacccccagcaaa	0.000													4	2	---	---	---	---	
TIAM1	7074	broad.mit.edu	37	21	32668608	32668608	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32668608delA	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						TACTCATTCCAAAAAAAAATA	0.294													4	2	---	---	---	---	
SFRS15	57466	broad.mit.edu	37	21	33058909	33058909	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33058909delT	uc002ypd.2	-						SFRS15_uc002ype.2_Intron|SFRS15_uc010glu.2_Intron|SFRS15_uc002ypf.1_Intron	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0						acgttagctatttttTTTTTT	0.015													6	3	---	---	---	---	
IL10RB	3588	broad.mit.edu	37	21	34649355	34649357	+	Intron	DEL	GTG	-	-	rs71868821		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34649355_34649357delGTG	uc002yrk.1	+						IL10RB_uc002yrh.1_Intron|IL10RB_uc002yri.1_Intron|IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0						AAGGATTCTTGTGGTGAATTTTC	0.384													2	4	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37218678	37218678	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37218678delT	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						ttggccaaaatttagttcaca	0.114			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
KCNJ6	3763	broad.mit.edu	37	21	39050258	39050258	+	Intron	DEL	T	-	-	rs67475873		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39050258delT	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	AAGGCAAGCATTTGGAATTGC	0.284													1	5	---	---	---	---	
BCR	613	broad.mit.edu	37	22	23623941	23623941	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23623941delG	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc010gtx.1_Intron|BCR_uc002zwy.1_5'Flank	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12						CGAGCCTCCCGGGCCTGCAGC	0.637			T	ABL1| FGFR1|JAK2 	CML|ALL|AML						OREG0026389	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26345298	26345298	+	Intron	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26345298delG	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						ACTCCAGCCTGGTAGATGGAG	0.373													4	2	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	33304077	33304077	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33304077delT	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						acCttttttcttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	33599737	33599737	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33599737delC								SYN3 (145360 upstream) : LARGE (69326 downstream)																							gaatgcttttcccacagactc	0.080													4	2	---	---	---	---	
TOM1	10043	broad.mit.edu	37	22	35702741	35702742	+	Intron	INS	-	C	C	rs142013402	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35702741_35702742insC	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						CATTCCTGGGACCCAGTCTAAG	0.317													1	6	---	---	---	---	
ADSL	158	broad.mit.edu	37	22	40756731	40756731	+	Intron	DEL	T	-	-	rs67833957		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40756731delT	uc003ayp.3	+						ADSL_uc003ays.3_Intron|ADSL_uc003ayq.3_Intron|ADSL_uc003ayr.3_Intron|ADSL_uc003ayt.3_Intron|ADSL_uc010gyb.1_Intron	NM_000026	NP_000017	P30566	PUR8_HUMAN	adenylosuccinate lyase isoform a						AMP biosynthetic process|protein tetramerization|purine base metabolic process	cytosol	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity			ovary(1)	1						TAAATTAATCttttttttttt	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41759125	41759126	+	IGR	INS	-	CT	CT	rs139230756	by1000genomes	TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41759125_41759126insCT								ZC3H7B (2975 upstream) : TEF (4266 downstream)																							CAGCTCTACACCTCTAGAGAAA	0.564													5	3	---	---	---	---	
NFAM1	150372	broad.mit.edu	37	22	42787437	42787438	+	Intron	INS	-	T	T			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42787437_42787438insT	uc003bcn.3	-							NM_145912	NP_666017	Q8NET5	NFAM1_HUMAN	NFAT activation molecule 1 precursor						B cell differentiation|inflammatory response|intracellular signal transduction|positive regulation of B cell receptor signaling pathway|positive regulation of cytokine production|positive regulation of sequence-specific DNA binding transcription factor activity	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity				0						gcaggactccaggcaagaaacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	43924101	43924101	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43924101delA								MPPED1 (21302 upstream) : EFCAB6 (553 downstream)																							TGGAGGAGACACCTGGCAGGG	0.438													4	2	---	---	---	---	
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45152748	45152748	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45152748delT	uc003bfd.2	+						PRR5-ARHGAP8_uc003bfc.2_Intron|PRR5-ARHGAP8_uc011aqi.1_Intron|PRR5-ARHGAP8_uc011aqj.1_Intron|ARHGAP8_uc003bfi.2_Intron|ARHGAP8_uc010gzv.2_Intron|ARHGAP8_uc003bfj.2_Intron|ARHGAP8_uc003bfk.2_Intron|PRR5-ARHGAP8_uc003bfg.1_Intron	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2						catccctcacttttttttccg	0.000													4	3	---	---	---	---	
TBC1D22A	25771	broad.mit.edu	37	22	47472584	47472584	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47472584delT	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		CTGACCTCCATTATTGGTCTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49410113	49410114	+	IGR	DEL	CA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49410113_49410114delCA								FAM19A5 (262371 upstream) : C22orf34 (398062 downstream)																							ATCTGACCTTCACAGAATATCT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	3142243	3142243	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3142243delT								ARSF (111496 upstream) : MXRA5 (84368 downstream)																							AAAGTAAGAATTTTTTTTTTG	0.378													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6383241	6383241	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6383241delA								NLGN4X (236535 upstream) : VCX3A (68419 downstream)																							ACGTTGACTGAAAAAATGACT	0.433													4	2	---	---	---	---	
GPR143	4935	broad.mit.edu	37	X	9698833	9698833	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9698833delC	uc004cst.1	-							NM_000273	NP_000264	P51810	GP143_HUMAN	G protein-coupled receptor 143						calcium-mediated signaling using intracellular calcium source|eye pigment biosynthetic process|melanosome organization|melanosome transport|phosphatidylinositol-mediated signaling|regulation of calcium-mediated signaling|visual perception	apical plasma membrane|Golgi apparatus|integral to membrane|lysosomal membrane|melanosome membrane|membrane fraction	dopamine binding|L-DOPA receptor activity|protein binding|tyrosine binding			ovary(1)	1		Hepatocellular(5;0.000888)				CCACTGAGTGCCCCAAAGGCT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	11070946	11070947	+	Intron	DEL	TT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11070946_11070947delTT	uc004cuh.2	-						uc004cui.1_Intron					Homo sapiens clone IMAGE:4081578, mRNA sequence.																		AGCAGAGTGATTACAGGGGCTT	0.129													4	2	---	---	---	---	
HCCS	3052	broad.mit.edu	37	X	11138715	11138715	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11138715delT	uc004cuk.2	+						HCCS_uc004cuj.2_Intron|HCCS_uc004cul.1_Intron	NM_005333	NP_005324	P53701	CCHL_HUMAN	holocytochrome c synthase						organ morphogenesis|oxidation-reduction process	mitochondrial inner membrane	holocytochrome-c synthase activity|metal ion binding				0						CTTGAGGCTGTTTTTTTTTTT	0.418													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	19006267	19006267	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19006267delA								PHKA2 (3787 upstream) : GPR64 (1160 downstream)																							aaaacaaaacaaaaaaaaacT	0.378													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	22341456	22341456	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22341456delA								ZNF645 (48882 upstream) : DDX53 (676631 downstream)																							AAAGAAAAACAAAAAAACCTG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	25238361	25238361	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25238361delA								ARX (204296 upstream) : MAGEB18 (918102 downstream)																							GGAATATTGCAGGCTGAGAAC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	28332721	28332721	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:28332721delC								DCAF8L1 (333155 upstream) : IL1RAPL1 (272960 downstream)																							aaatttaggacccagacgccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	34806472	34806473	+	IGR	DEL	TT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34806472_34806473delTT								TMEM47 (131067 upstream) : FAM47B (154458 downstream)																							tttttctttctttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	35569825	35569825	+	IGR	DEL	G	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35569825delG								FAM47B (606791 upstream) : MAGEB16 (246634 downstream)																							GAATCTGGGTGGGGAGCATCT	0.408													4	2	---	---	---	---	
CXorf22	170063	broad.mit.edu	37	X	35966903	35966904	+	Intron	INS	-	GT	GT	rs112888014		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35966903_35966904insGT	uc004ddj.2	+						CXorf22_uc010ngv.2_Intron	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063											large_intestine(1)|lung(1)|ovary(1)	3						TGTGATTTGGGgtgtgtgtgtg	0.223													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	39285697	39285699	+	IGR	DEL	TAC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39285697_39285699delTAC								MID1IP1 (619916 upstream) : BCOR (624802 downstream)																							GAGCATGCAATACTACTTCTCTG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	42930970	42930971	+	IGR	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42930970_42930971delGT								PPP1R2P9 (293484 upstream) : MAOA (584438 downstream)																							TTCTGGATAAGTGTGTGTGTGT	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	47628382	47628382	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47628382delT								LOC100133957 (108606 upstream) : ZNF81 (67919 downstream)																							ggccagcttgtttttttaagt	0.000													4	2	---	---	---	---	
CCNB3	85417	broad.mit.edu	37	X	49972000	49972000	+	Intron	DEL	A	-	-	rs67002520		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49972000delA	uc004dox.3	+							NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3						cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)					GTGAATTTATAAATTCACATA	0.333													4	5	---	---	---	---	
KLF8	11279	broad.mit.edu	37	X	56295626	56295626	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56295626delA	uc004dur.2	+						KLF8_uc010nkg.2_3'UTR|KLF8_uc011mop.1_Intron|KLF8_uc010nkh.2_Intron	NM_007250	NP_009181	O95600	KLF8_HUMAN	Kruppel-like factor 8 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						CCTGCTATGCAAAAAAAAAAA	0.333													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	57614838	57614838	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57614838delC								FAAH2 (99211 upstream) : ZXDB (3431 downstream)																							tggatactctcccccagtccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	57904689	57904689	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57904689delA								ZXDB (280783 upstream) : ZXDA (29509 downstream)																							ctctccaatcaaaaaaaaaaa	0.005													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	62345499	62345499	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62345499delT								None (None upstream) : SPIN4 (221609 downstream)																							attaaatccgtttttaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	68610801	68610801	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68610801delA								PJA1 (225461 upstream) : FAM155B (114277 downstream)																							CTCACCTTCCAAACCCCCCTG	0.537													4	2	---	---	---	---	
DLG3	1741	broad.mit.edu	37	X	69690874	69690874	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69690874delT	uc004dyi.1	+						DLG3_uc004dyj.1_Intron|DLG3_uc011mpn.1_Intron	NM_021120	NP_066943	Q92796	DLG3_HUMAN	synapse-associated protein 102 isoform a						axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)					TTTGTATTCCTTTTTTTTTTT	0.388													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	82311032	82311032	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82311032delA								None (None upstream) : POU3F4 (452237 downstream)																							gaaattgaacaaaaaaaagga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	82830583	82830584	+	IGR	INS	-	A	A			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82830583_82830584insA								POU3F4 (65808 upstream) : CYLC1 (285570 downstream)																							tctcaaaaaagaaaaaaaaaga	0.059													4	2	---	---	---	---	
NOX1	27035	broad.mit.edu	37	X	100101611	100101612	+	Intron	DEL	TC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100101611_100101612delTC	uc004egj.2	-						NOX1_uc004egl.3_Intron|NOX1_uc010nne.2_Intron	NM_007052	NP_008983	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1 isoform long						angiogenesis|cell migration|electron transport chain|FADH2 metabolic process|hydrogen peroxide metabolic process|inflammatory response|intracellular pH elevation|positive regulation of integrin biosynthetic process|positive regulation of smooth muscle cell proliferation|positive regulation vascular endothelial growth factor production|respiratory burst|response to pH|signal transduction|superoxide anion generation	cell junction|early endosome|invadopodium membrane|NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|Rac GTPase binding|superoxide-generating NADPH oxidase activity|voltage-gated proton channel activity			ovary(1)	1						CCCTCGCTAGtctctctctctc	0.317													2	4	---	---	---	---	
GUCY2F	2986	broad.mit.edu	37	X	108670903	108670903	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108670903delA	uc004eod.3	-						GUCY2F_uc011msq.1_Intron	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor						intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8						CTCCAGCTTCAAAAAAGCATT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	109133478	109133479	+	IGR	DEL	AA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109133478_109133479delAA								ACSL4 (156857 upstream) : TMEM164 (112384 downstream)																							CAGTTGTCTTAATTCCATTCAC	0.525													4	2	---	---	---	---	
PAK3	5063	broad.mit.edu	37	X	110440083	110440083	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110440083delT	uc004epa.2	+						PAK3_uc010npt.1_Intron|PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_Intron|PAK3_uc004eoz.2_Intron|PAK3_uc011mst.1_Intron|PAK3_uc010npv.1_Intron|PAK3_uc010npw.1_Intron	NM_001128173	NP_001121645	O75914	PAK3_HUMAN	p21-activated kinase 3 isoform d						multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10						tctttctttcttttttttttt	0.159										TSP Lung(19;0.15)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	113022773	113022773	+	IGR	DEL	A	-	-	rs10710299		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113022773delA								AMOT (938730 upstream) : HTR2C (795778 downstream)																							ctgtctctacaaaaaaaaaat	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	119548996	119548996	+	IGR	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119548996delC								ATP1B4 (32774 upstream) : LAMP2 (11008 downstream)																							cagatgaacaccattccacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	125158799	125158799	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125158799delT								None (None upstream) : DCAF12L2 (139715 downstream)																							tctgtttgtcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	130333249	130333249	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130333249delA								ARHGAP36 (109393 upstream) : IGSF1 (74234 downstream)																							AGCAGGGGAGAAAAAAAACCC	0.478													4	3	---	---	---	---	
ZIC3	7547	broad.mit.edu	37	X	136645954	136645954	+	5'Flank	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136645954delT	uc004fak.2	+							NM_003413	NP_003404	O60481	ZIC3_HUMAN	zinc finger protein of the cerebellum 3						cell differentiation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)					TCAAGACCCCTTCCCAAATAG	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	137568064	137568065	+	IGR	DEL	CC	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137568064_137568065delCC								ZIC3 (913807 upstream) : LOC158696 (128827 downstream)																							ACCTGCCCTTCCCCTGACACAG	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	144358364	144358364	+	IGR	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144358364delA								SPANXN1 (20636 upstream) : SLITRK2 (540983 downstream)																							tgttacaggtagttaggttgg	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	144589257	144589258	+	IGR	DEL	GT	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144589257_144589258delGT								SPANXN1 (251529 upstream) : SLITRK2 (310089 downstream)																							cttgaggctggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	145905385	145905385	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:145905385delT								CXorf51 (13461 upstream) : MIR513C (365837 downstream)																							CATCTTTTGGTTttttttaaa	0.119													4	2	---	---	---	---	
MTMR1	8776	broad.mit.edu	37	X	149860913	149860913	+	5'Flank	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149860913delA	uc004fei.2	+						MTMR1_uc011mya.1_5'Flank|MTMR1_uc004feg.1_5'Flank|MTMR1_uc004feh.1_5'Flank|MTMR1_uc004fej.2_5'Flank	NM_003828	NP_003819	Q13613	MTMR1_HUMAN	myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					tcggggcttcaggcatcatat	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	150482538	150482540	+	IGR	DEL	CCA	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150482538_150482540delCCA								GPR50 (132608 upstream) : VMA21 (83165 downstream)																							cacctcctccccaccaccaccac	0.271													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	151120856	151120856	+	IGR	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151120856delT								MAGEA4 (27216 upstream) : GABRE (741 downstream)																							CCACACTGCCTTTTTTCCTCC	0.353													4	2	---	---	---	---	
GABRA3	2556	broad.mit.edu	37	X	151480311	151480311	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151480311delA	uc010ntk.1	-							NM_000808	NP_000799	P34903	GBRA3_HUMAN	gamma-aminobutyric acid A receptor, alpha 3						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	tagagctgataaaaaaaaaaa	0.000													2	4	---	---	---	---	
GABRA3	2556	broad.mit.edu	37	X	151573315	151573315	+	Intron	DEL	T	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151573315delT	uc010ntk.1	-							NM_000808	NP_000799	P34903	GBRA3_HUMAN	gamma-aminobutyric acid A receptor, alpha 3						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	aaacacagacttcaatgacca	0.000													4	2	---	---	---	---	
MECP2	4204	broad.mit.edu	37	X	153322108	153322108	+	Intron	DEL	A	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153322108delA	uc004fjv.2	-						MECP2_uc004fjw.2_Intron	NM_004992	NP_004983	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					aaattcctagaaaaaaaaatt	0.179													4	2	---	---	---	---	
VBP1	7411	broad.mit.edu	37	X	154465817	154465817	+	Intron	DEL	C	-	-			TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154465817delC	uc004fnc.2	+						VBP1_uc004fnd.2_Intron	NM_003372	NP_003363	P61758	PFD3_HUMAN	von Hippel-Lindau binding protein 1						'de novo' posttranslational protein folding	nucleus|prefoldin complex	unfolded protein binding				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TTGTGAAGTGCCCCCAGCTTG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59014683	59014684	+	IGR	DEL	AT	-	-	rs10534960		TCGA-B0-5707-01A-11D-1534-10	TCGA-B0-5707-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59014683_59014684delAT								None (None upstream) : None (None downstream)																							acaaaacagaatgagagttccc	0.035													3	4	---	---	---	---	
