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
CCDC27	148870	broad.mit.edu	37	1	3669160	3669160	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3669160C>A	uc001akv.2	+	1	196	c.115C>A	c.(115-117)CTT>ATT	p.L39I		NM_152492	NP_689705	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	39										skin(1)	1	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		CTCACTTGGTCTTTGCATCCC	0.587													28	89	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11184589	11184589	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11184589C>G	uc001asd.2	-	47	6749	c.6628G>C	c.(6628-6630)GCC>CCC	p.A2210P	MTOR_uc001asc.2_Missense_Mutation_p.A415P	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2210	PI3K/PI4K.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						GGGTCATTGGCCAGAAGGGTG	0.463													66	232	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974182	16974182	+	RNA	SNP	C	A	A	rs144074313	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974182C>A	uc009vow.2	+	5		c.992C>A			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GAGCATATCCCGTGGAGTACC	0.672													4	24	---	---	---	---	PASS
OSCP1	127700	broad.mit.edu	37	1	36883842	36883842	+	Silent	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36883842G>A	uc001cap.2	-	11	1150	c.1068C>T	c.(1066-1068)AGC>AGT	p.S356S	OSCP1_uc001caq.2_Silent_p.S346S	NM_145047	NP_659484	Q8WVF1	OSCP1_HUMAN	oxidored-nitro domain-containing protein isoform	356					transport	basal plasma membrane				ovary(2)|central_nervous_system(1)|pancreas(1)	4						CCAGCTCCTCGCTCCGTTGCT	0.537													4	80	---	---	---	---	PASS
LRRC8B	23507	broad.mit.edu	37	1	90058482	90058482	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90058482T>C	uc001dni.2	+	8	2799	c.2292T>C	c.(2290-2292)CCT>CCC	p.P764P	LRRC8B_uc001dnh.2_Silent_p.P764P|LRRC8B_uc001dnj.2_Silent_p.P764P	NM_001134476	NP_001127948	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member	764	LRR 13.					integral to membrane				ovary(2)	2		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		AAACACTTCCTCCTGAACTAG	0.433													6	318	---	---	---	---	PASS
BRDT	676	broad.mit.edu	37	1	92428454	92428454	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92428454T>C	uc001dok.3	+	2	492	c.143T>C	c.(142-144)TTT>TCT	p.F48S	BRDT_uc001dol.3_Missense_Mutation_p.F48S|BRDT_uc010osz.1_Missense_Mutation_p.F48S|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Missense_Mutation_p.F48S|BRDT_uc010otb.1_Missense_Mutation_p.F48S|BRDT_uc001dom.3_Missense_Mutation_p.F48S	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein	48	Bromo 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		AAGCATAGTTTTTCATGGCCC	0.353													6	309	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103468818	103468818	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103468818G>A	uc001dul.2	-	21	2269	c.1951C>T	c.(1951-1953)CGA>TGA	p.R651*	COL11A1_uc001duk.2_Translation_Start_Site|COL11A1_uc001dum.2_Nonsense_Mutation_p.R663*|COL11A1_uc001dun.2_Nonsense_Mutation_p.R612*|COL11A1_uc009weh.2_Nonsense_Mutation_p.R535*	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	651	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		AGCAAACCTCGTGGGCCCTAG	0.418													37	139	---	---	---	---	PASS
LRIG2	9860	broad.mit.edu	37	1	113637004	113637004	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113637004T>A	uc001edf.1	+	5	757	c.559T>A	c.(559-561)TTC>ATC	p.F187I	LRIG2_uc009wgn.1_Missense_Mutation_p.F84I	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	187	LRR 5.|Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		GGCTGGTTGCTTCGATAATTT	0.323													7	268	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145293473	145293473	+	Missense_Mutation	SNP	C	A	A	rs57489144		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145293473C>A	uc001end.3	+	1	103	c.68C>A	c.(67-69)ACA>AAA	p.T23K	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.T23K|NOTCH2NL_uc010oyh.1_RNA|NBPF10_uc001emq.1_Missense_Mutation_p.T23K	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	23											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATCAACGAGACATTGCGCCCC	0.517													7	376	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145293535	145293535	+	Missense_Mutation	SNP	C	G	G	rs55936365	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145293535C>G	uc001end.3	+	1	165	c.130C>G	c.(130-132)CTA>GTA	p.L44V	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.L44V|NOTCH2NL_uc010oyh.1_RNA|NBPF10_uc001emq.1_Missense_Mutation_p.L44V	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	44											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAAATGTTTTCTAACTCAACT	0.443													7	297	---	---	---	---	PASS
TXNIP	10628	broad.mit.edu	37	1	145440928	145440928	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145440928C>G	uc001enn.3	+	7	1356	c.1015C>G	c.(1015-1017)CCT>GCT	p.P339A	NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_Intron|TXNIP_uc010oys.1_Missense_Mutation_p.P284A	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	339					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGATGTCATTCCTGAAGATCA	0.458													13	274	---	---	---	---	PASS
SMG5	23381	broad.mit.edu	37	1	156223280	156223280	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156223280C>T	uc001foc.3	-	17	2611	c.2462G>A	c.(2461-2463)CGG>CAG	p.R821Q	SMG5_uc009wrv.2_Missense_Mutation_p.R306Q	NM_015327	NP_056142	Q9UPR3	SMG5_HUMAN	SMG5 homolog nonsense mediated mRNA decay	821	Potential.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|nucleus	protein phosphatase 2A binding			ovary(2)|skin(2)|pancreas(1)	5	Hepatocellular(266;0.158)					GAGCCTGTTCCGACGAGCTTC	0.493													5	221	---	---	---	---	PASS
RABGAP1L	9910	broad.mit.edu	37	1	174671262	174671262	+	Silent	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174671262G>A	uc001gjx.2	+	17	2232	c.2037G>A	c.(2035-2037)CCG>CCA	p.P679P	RABGAP1L_uc001gkb.3_5'UTR|RABGAP1L_uc001gkc.3_5'UTR|RABGAP1L_uc001gkd.3_Silent_p.P5P	NM_014857	NP_055672	Q5R372	RBG1L_HUMAN	RAB GTPase activating protein 1-like isoform A	679	Rab-GAP TBC.				regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4						AACAGCTACCGGACCTGCATA	0.443													16	259	---	---	---	---	PASS
CDC42BPA	8476	broad.mit.edu	37	1	227441848	227441848	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227441848A>G	uc001hqr.2	-	2	1130	c.187T>C	c.(187-189)TTT>CTT	p.F63L	CDC42BPA_uc001hqs.2_Missense_Mutation_p.F63L|CDC42BPA_uc009xes.2_Missense_Mutation_p.F63L|CDC42BPA_uc010pvs.1_Missense_Mutation_p.F63L	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	63					actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)				TTAGAAGTAAATGGTTTAGCT	0.289													7	477	---	---	---	---	PASS
ARID4B	51742	broad.mit.edu	37	1	235377293	235377293	+	Silent	SNP	C	T	T	rs10588817		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235377293C>T	uc001hwq.2	-	17	2130	c.1632G>A	c.(1630-1632)GAG>GAA	p.E544E	ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwt.3_Silent_p.E225E	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	544	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			cctcctcctcctcttctgctt	0.224													7	374	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237824231	237824231	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237824231T>C	uc001hyl.1	+	56	8540	c.8420T>C	c.(8419-8421)ATT>ACT	p.I2807T		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2807	Modulator (Potential).|Cytoplasmic (By similarity).|3.|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)			ACTCGTCGTATTTCTCAGACA	0.368													7	301	---	---	---	---	PASS
OR2L13	284521	broad.mit.edu	37	1	248263200	248263200	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248263200C>T	uc001ids.2	+	3	860	c.523C>T	c.(523-525)CAT>TAT	p.H175Y		NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,	175	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			GGCTATTGACCATTTCTTCTG	0.458													6	451	---	---	---	---	PASS
FAM49A	81553	broad.mit.edu	37	2	16742257	16742257	+	Splice_Site	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16742257C>T	uc010exm.1	-	8	858	c.710_splice	c.e8+1	p.P237_splice	FAM49A_uc002rck.1_Splice_Site_p.P237_splice	NM_030797	NP_110424	Q9H0Q0	FA49A_HUMAN	family with sequence similarity 49, member A							intracellular					0	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)			ATTTAACTTACGGAGTTTCCA	0.408													127	352	---	---	---	---	PASS
SLC8A1	6546	broad.mit.edu	37	2	40366736	40366736	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40366736A>G	uc002rrx.2	-	9	2374	c.2350T>C	c.(2350-2352)TTC>CTC	p.F784L	uc002rrw.2_Intron|SLC8A1_uc002rry.2_Missense_Mutation_p.F779L|SLC8A1_uc002rrz.2_Missense_Mutation_p.F771L|SLC8A1_uc002rsa.2_Missense_Mutation_p.F748L|SLC8A1_uc002rsd.3_Missense_Mutation_p.F748L	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	784	Helical; (Potential).				cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	ACCTTCCAGAACACAGTCAGA	0.498													5	179	---	---	---	---	PASS
OXER1	165140	broad.mit.edu	37	2	42990368	42990368	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42990368A>G	uc002rss.2	-	1	1034	c.952T>C	c.(952-954)TCC>CCC	p.S318P		NM_148962	NP_683765	Q8TDS5	OXER1_HUMAN	G-protein coupled receptor TG1019	318	Extracellular (Potential).				regulation of cAMP biosynthetic process	integral to membrane|plasma membrane	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding|G-protein coupled receptor activity			breast(1)	1						GCCACCATGGAAGCCATGCCA	0.627													4	57	---	---	---	---	PASS
PLEK	5341	broad.mit.edu	37	2	68623036	68623036	+	3'UTR	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68623036G>T	uc002sen.3	+	9					PLEK_uc010fde.2_3'UTR	NM_002664	NP_002655	P08567	PLEK_HUMAN	pleckstrin						actin cytoskeleton reorganization|cortical actin cytoskeleton organization|hemopoietic progenitor cell differentiation|inhibition of phospholipase C activity involved in G-protein coupled receptor signaling pathway|integrin-mediated signaling pathway|negative regulation of calcium-mediated signaling|negative regulation of inositol phosphate biosynthetic process|phosphatidylinositol metabolic process|platelet aggregation|positive regulation of actin filament bundle assembly|positive regulation of actin filament depolymerization|positive regulation of inositol-polyphosphate 5-phosphatase activity|positive regulation of integrin activation|positive regulation of platelet activation|protein kinase C signaling cascade|protein secretion by platelet|regulation of cell diameter|ruffle organization|thrombin receptor signaling pathway|vesicle docking involved in exocytosis	cytosol|extracellular region|membrane fraction|ruffle membrane|soluble fraction	phosphatidylinositol-3,4-bisphosphate binding|protein homodimerization activity|protein kinase C binding			ovary(1)	1		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		ACAAATCAACGGGAAACAGCC	0.527													7	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96546357	96546357	+	RNA	SNP	G	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96546357G>C	uc002sva.1	-	38		c.1886C>G			uc002suz.1_Missense_Mutation_p.L155V|uc002svb.1_Missense_Mutation_p.L155V					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		AAGGTGGGCAGATTCTCAGGA	0.299													9	234	---	---	---	---	PASS
MGAT5	4249	broad.mit.edu	37	2	135107382	135107382	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135107382G>A	uc002ttv.1	+	9	1264	c.1119G>A	c.(1117-1119)ATG>ATA	p.M373I		NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V	373	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)		TCAGGTGCATGCTCCGAGTCC	0.408													66	197	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141135789	141135789	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141135789C>A	uc002tvj.1	-	68	11570	c.10598G>T	c.(10597-10599)TGG>TTG	p.W3533L		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3533	Extracellular (Potential).|LDL-receptor class A 26.				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)		TCCATCACACCAAAACCTTGA	0.398										TSP Lung(27;0.18)			94	325	---	---	---	---	PASS
ARHGAP15	55843	broad.mit.edu	37	2	144194521	144194521	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144194521T>C	uc002tvm.3	+	8	764	c.613T>C	c.(613-615)TTC>CTC	p.F205L	ARHGAP15_uc010zbl.1_Missense_Mutation_p.F205L|ARHGAP15_uc002tvn.2_5'UTR	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15	205					regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)		CCTGGAATTATTCAAAATCCA	0.338													7	326	---	---	---	---	PASS
SCN2A	6326	broad.mit.edu	37	2	166223836	166223836	+	Silent	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166223836C>T	uc002udc.2	+	19	3920	c.3630C>T	c.(3628-3630)TTC>TTT	p.F1210F	SCN2A_uc002udd.2_Silent_p.F1210F|SCN2A_uc002ude.2_Silent_p.F1210F	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1210	III.|Helical; Name=S1 of repeat III; (Potential).				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)	ACAATTGGTTCGAAACCTTCA	0.433													14	503	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179426187	179426187	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179426187C>T	uc010zfg.1	-	275	77192	c.76968G>A	c.(76966-76968)ATG>ATA	p.M25656I	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.M19351I|TTN_uc010zfi.1_Missense_Mutation_p.M19284I|TTN_uc010zfj.1_Missense_Mutation_p.M19159I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	26583							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)			GATACTCATACATCAGTCCTT	0.398													5	185	---	---	---	---	PASS
ZC3H15	55854	broad.mit.edu	37	2	187371486	187371486	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187371486T>C	uc002upo.2	+	9	1238	c.1013T>C	c.(1012-1014)ATC>ACC	p.I338T		NM_018471	NP_060941	Q8WU90	ZC3HF_HUMAN	erythropoietin 4 immediate early response	338						cytoplasm|nucleolus|plasma membrane	nucleic acid binding|zinc ion binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			AGCCTGTACATCCCAAGAGAT	0.323													6	395	---	---	---	---	PASS
CLK1	1195	broad.mit.edu	37	2	201721415	201721415	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201721415T>C	uc002uwe.2	-	9	1228	c.1047A>G	c.(1045-1047)GAA>GAG	p.E349E	CLK1_uc002uwd.2_Silent_p.E172E|CLK1_uc010zhi.1_Silent_p.E391E|CLK1_uc002uwf.2_Silent_p.E123E|CLK1_uc002uwg.2_Silent_p.E198E|CLK1_uc010fsv.2_RNA	NM_004071	NP_004062	P49759	CLK1_HUMAN	CDC-like kinase 1 isoform 1	349	Protein kinase.				cell proliferation	nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			pancreas(2)	2						CTAAAATAACTTCAGGTGCTC	0.323													85	344	---	---	---	---	PASS
NOP58	51602	broad.mit.edu	37	2	203157832	203157832	+	Intron	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203157832T>C	uc002uzb.2	+						SNORD11_uc002uzd.1_RNA	NM_015934	NP_057018	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein homolog						cell growth|rRNA processing|snRNP protein import into nucleus	box C/D snoRNP complex|Cajal body|cytoplasm|pre-snoRNP complex	protein binding|snoRNA binding				0						TGAAGGCATCTTTAGTCACTA	0.373													3	11	---	---	---	---	PASS
RPL37A	6168	broad.mit.edu	37	2	217364842	217364842	+	Intron	SNP	C	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217364842C>G	uc002vgf.2	+						RPL37A_uc002vgg.2_3'UTR	NM_000998	NP_000989	P61513	RL37A_HUMAN	ribosomal protein L37a						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	metal ion binding|protein binding|structural constituent of ribosome			ovary(1)	1		Renal(323;0.0458)		Epithelial(149;3.51e-06)|all cancers(144;0.000249)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGTTTTAACACTTTCTCAGGA	0.418													24	102	---	---	---	---	PASS
CCDC13	152206	broad.mit.edu	37	3	42781196	42781196	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42781196G>T	uc003cly.3	-	9	1178	c.1094C>A	c.(1093-1095)ACC>AAC	p.T365N		NM_144719	NP_653320	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	365	Potential.									ovary(1)	1						ACTCTTGAGGGTCTTCATCTC	0.562													58	109	---	---	---	---	PASS
FAM86D	692099	broad.mit.edu	37	3	75476735	75476735	+	Silent	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75476735C>T	uc003dpp.3	-	6	689	c.330G>A	c.(328-330)GAG>GAA	p.E110E	FAM86D_uc003dpo.3_Intron|FAM86D_uc003dps.3_Intron|FAM86D_uc003dpq.3_Silent_p.E18E|FAM86D_uc003dpr.3_Intron	NR_024241				RecName: Full=Protein FAM86B1;												0						CTCGGAGCTGCTCGAGGACCC	0.602													4	18	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132221273	132221273	+	Silent	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132221273A>G	uc003eor.2	+	40	4742	c.4677A>G	c.(4675-4677)GAA>GAG	p.E1559E		NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1559							heat shock protein binding			ovary(1)|breast(1)	2						ACACACTAGAAGAGAGTGGCA	0.368													7	442	---	---	---	---	PASS
CLSTN2	64084	broad.mit.edu	37	3	140281063	140281063	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140281063A>G	uc003etn.2	+	13	2315	c.2125A>G	c.(2125-2127)AGG>GGG	p.R709G		NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	709	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						CTTGGACCCAAGGCAGGAGTG	0.493										HNSCC(16;0.037)			6	305	---	---	---	---	PASS
SR140	23350	broad.mit.edu	37	3	142740327	142740327	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142740327A>T	uc003evh.1	+	10	881	c.782A>T	c.(781-783)TAC>TTC	p.Y261F	SR140_uc003evi.1_5'UTR|SR140_uc011bnj.1_Missense_Mutation_p.Y261F|SR140_uc003evj.1_RNA|SR140_uc003evk.1_Missense_Mutation_p.Y260F	NM_001080415	NP_001073884	O15042	SR140_HUMAN	U2-associated SR140 protein	261					RNA processing	nucleus	nucleotide binding|RNA binding				0						CTTGATGATTACGCACCTGGC	0.323													16	371	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	3	149700749	149700749	+	IGR	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149700749T>C								PFN2 (12008 upstream) : TSC22D2 (426039 downstream)																							CTTGCTTTTCTTTTTTCTGGA	0.498													6	281	---	---	---	---	PASS
PDCD10	11235	broad.mit.edu	37	3	167413409	167413409	+	Silent	SNP	T	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167413409T>G	uc003fex.2	-	6	768	c.370A>C	c.(370-372)AGA>CGA	p.R124R	PDCD10_uc003fez.2_Silent_p.R124R|PDCD10_uc003fey.2_Silent_p.R124R	NM_007217	NP_009148	Q9BUL8	PDC10_HUMAN	programmed cell death 10	124					angiogenesis|apoptosis|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of MAP kinase activity	cytosol|Golgi membrane|plasma membrane	protein homodimerization activity|protein N-terminus binding			lung(1)|central_nervous_system(1)	2						AACCTCACTCTGTCATTGATC	0.358									Familial_Cerebral_Cavernous_Angioma				25	715	---	---	---	---	PASS
SPATA16	83893	broad.mit.edu	37	3	172607298	172607298	+	3'UTR	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172607298G>A	uc003fin.3	-	11						NM_031955	NP_114161	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)			GGTGGGCATTGGAGTGGATGC	0.443													47	171	---	---	---	---	PASS
NOP14	8602	broad.mit.edu	37	4	2959398	2959398	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2959398C>T	uc003ggj.1	-	2	337	c.265G>A	c.(265-267)GGA>AGA	p.G89R	C4orf10_uc003ggi.1_Intron|NOP14_uc003ggk.3_Missense_Mutation_p.G89R|NOP14_uc003ggl.2_Missense_Mutation_p.G89R|NOP14_uc010icq.1_RNA	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14	89					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1						TTGTATTCTCCGAAGCGTTTA	0.418													6	747	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	4	9241928	9241928	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9241928G>C	uc011bwo.1	+	1	1073	c.821G>C	c.(820-822)AGC>ACC	p.S274T						RecName: Full=Ubiquitin carboxyl-terminal hydrolase 17-like protein 2;          EC=3.1.2.15; AltName: Full=Ubiquitin thioesterase 17-like protein 2; AltName: Full=Ubiquitin-specific-processing protease 17-like protein 2; AltName: Full=Deubiquitinating enzyme 17-like protein 2; AltName: Full=Deubiquitinating protein 3;          Short=DUB-3;																		ACCGCCGCTAGCATCACTTCT	0.488													5	16	---	---	---	---	PASS
PAICS	10606	broad.mit.edu	37	4	57318164	57318164	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57318164A>G	uc003hbs.1	+	8	1129	c.898A>G	c.(898-900)ACA>GCA	p.T300A	PAICS_uc011cac.1_Missense_Mutation_p.T300A|PAICS_uc003hbt.1_Missense_Mutation_p.T307A|PAICS_uc003hbu.1_Missense_Mutation_p.T300A|PAICS_uc010ihd.1_Missense_Mutation_p.T301A	NM_006452	NP_006443	P22234	PUR6_HUMAN	phosphoribosylaminoimidazole carboxylase,	300	AIR carboxylase.				'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|identical protein binding|phosphoribosylaminoimidazole carboxylase activity|phosphoribosylaminoimidazolesuccinocarboxamide synthase activity				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Aspartic Acid(DB00128)	ACTTCGAGTAACATCTGCGCA	0.403													7	348	---	---	---	---	PASS
ART3	419	broad.mit.edu	37	4	77003637	77003637	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77003637C>T	uc003hjo.2	+	3	849	c.730C>T	c.(730-732)CTT>TTT	p.L244F	ART3_uc003hji.2_Missense_Mutation_p.L244F|ART3_uc003hjj.2_Missense_Mutation_p.L244F|ART3_uc003hjk.2_Missense_Mutation_p.L244F|ART3_uc010ija.1_Missense_Mutation_p.L244F|ART3_uc003hjn.2_Missense_Mutation_p.L244F|ART3_uc003hjp.2_Intron|ART3_uc010ijb.2_Intron|ART3_uc003hjq.2_Intron|ART3_uc003hjr.2_Missense_Mutation_p.L214F|ART3_uc010ijc.2_Missense_Mutation_p.L214F|ART3_uc010ijd.2_Missense_Mutation_p.L214F	NM_001130016	NP_001123488	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3 isoform a	244					protein ADP-ribosylation	anchored to membrane|integral to plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity			ovary(2)	2			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TAACCTTATCCTTCAAAGCAT	0.418													72	220	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79391164	79391164	+	Silent	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79391164A>G	uc003hlb.2	+	51	7730	c.7290A>G	c.(7288-7290)GTA>GTG	p.V2430V		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	2429	CSPG 12.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						CGTTCCGAGTAGACATCCTCC	0.522													5	126	---	---	---	---	PASS
BMP2K	55589	broad.mit.edu	37	4	79831928	79831928	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79831928G>T	uc003hlk.2	+	16	2393	c.2227G>T	c.(2227-2229)GAT>TAT	p.D743Y	PAQR3_uc003hlm.2_Intron|PAQR3_uc003hln.2_Intron|uc010ijm.1_5'Flank	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a	743						nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1						ATCTGAAAGTGATTTTGAATC	0.423													24	103	---	---	---	---	PASS
NHEDC2	133308	broad.mit.edu	37	4	103971409	103971409	+	Silent	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103971409A>G	uc003hwx.3	-	5	1445	c.573T>C	c.(571-573)GGT>GGC	p.G191G	NHEDC2_uc010iln.1_Silent_p.G43G|NHEDC2_uc003hwy.2_Silent_p.G191G|NHEDC2_uc011cew.1_Silent_p.G134G|NHEDC2_uc011cex.1_Silent_p.G134G|NHEDC2_uc011cey.1_Silent_p.G134G	NM_178833	NP_849155	Q86UD5	NHDC2_HUMAN	Na+/H+ exchanger domain containing 2	191					sodium ion transport	integral to membrane|mitochondrial membrane	solute:hydrogen antiporter activity				0				OV - Ovarian serous cystadenocarcinoma(123;2.3e-08)		TTGAATCCAGACCAAGGCCAG	0.383													28	143	---	---	---	---	PASS
ANKRD50	57182	broad.mit.edu	37	4	125590855	125590855	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125590855T>C	uc003ifg.3	-	3	3843	c.3577A>G	c.(3577-3579)AGA>GGA	p.R1193G	ANKRD50_uc011cgo.1_Missense_Mutation_p.R1014G|ANKRD50_uc010inw.2_Missense_Mutation_p.R1193G	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1193	Ser-rich.									central_nervous_system(1)	1						GAAGTAGTTCTCAAAGATGAA	0.393													27	76	---	---	---	---	PASS
ELMOD2	255520	broad.mit.edu	37	4	141446698	141446698	+	Missense_Mutation	SNP	T	C	C	rs150922490	byFrequency	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141446698T>C	uc003iik.2	+	2	208	c.116T>C	c.(115-117)GTA>GCA	p.V39A		NM_153702	NP_714913	Q8IZ81	ELMD2_HUMAN	ELMO/CED-12 domain containing 2	39					phagocytosis|regulation of defense response to virus|response to virus	cytoskeleton	GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)					GATACCTATGTAGGTGCACAA	0.378													6	516	---	---	---	---	PASS
NEK1	4750	broad.mit.edu	37	4	170510619	170510619	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170510619C>T	uc003isb.1	-	6	935	c.443G>A	c.(442-444)GGA>GAA	p.G148E	NEK1_uc003isc.1_Missense_Mutation_p.G148E|NEK1_uc003isd.1_Missense_Mutation_p.G148E|NEK1_uc003ise.1_Missense_Mutation_p.G148E|NEK1_uc003isf.1_Missense_Mutation_p.G148E|NEK1_uc003isg.1_Missense_Mutation_p.G69E	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	148	Protein kinase.				cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TCTAGCAATTCCAAAATCTCC	0.289													65	251	---	---	---	---	PASS
ZDHHC11	79844	broad.mit.edu	37	5	850746	850746	+	5'UTR	SNP	G	A	A	rs111620039		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:850746G>A	uc011cma.1	-	1						NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GAGGACCTGCGCCGTCAGATC	0.627													7	39	---	---	---	---	PASS
NIPBL	25836	broad.mit.edu	37	5	37024687	37024687	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37024687G>T	uc003jkl.3	+	30	6074	c.5575G>T	c.(5575-5577)GAT>TAT	p.D1859Y	NIPBL_uc003jkk.3_Missense_Mutation_p.D1859Y	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1859	HEAT 2.				brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CTGTTTTTAGGATACTGGTAT	0.299													9	263	---	---	---	---	PASS
ITGA2	3673	broad.mit.edu	37	5	52376411	52376411	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52376411A>G	uc003joy.2	+	25	3142	c.2999A>G	c.(2998-3000)AAG>AGG	p.K1000R	ITGA2_uc011cqa.1_RNA|ITGA2_uc011cqb.1_RNA|ITGA2_uc011cqc.1_Missense_Mutation_p.K924R|ITGA2_uc011cqd.1_RNA|ITGA2_uc011cqe.1_RNA	NM_002203	NP_002194	P17301	ITA2_HUMAN	integrin alpha 2 precursor	1000	Extracellular (Potential).				axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				ACCAAAGAAAAGAACCCACTG	0.378													6	337	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469483	75469483	+	Intron	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469483G>A	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		GACTTTTTGCGAGCCTTCCCA	0.393													14	407	---	---	---	---	PASS
POLR3G	10622	broad.mit.edu	37	5	89783892	89783892	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89783892A>G	uc003kjq.2	+	3	393	c.193A>G	c.(193-195)AGA>GGA	p.R65G	POLR3G_uc011cuc.1_Missense_Mutation_p.R65G	NM_006467	NP_006458	O15318	RPC7_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	65					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|regulation of transcription from RNA polymerase III promoter|response to virus	DNA-directed RNA polymerase III complex	DNA-directed RNA polymerase activity				0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;2.74e-31)|Epithelial(54;8.2e-26)|all cancers(79;3.86e-22)		ACAGGAGTTGAGAGAAACAAT	0.343													7	468	---	---	---	---	PASS
NCRNA00219	114915	broad.mit.edu	37	5	111496885	111496885	+	3'UTR	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111496885T>C	uc003kpq.1	+	1					EPB41L4A_uc003kpp.1_Intron|NCRNA00219_uc003kps.2_RNA|SNORA13_uc003kpt.1_5'Flank					RecName: Full=Putative uncharacterized protein TIGA1;												0						ACCGTATAACTGACTTTATGC	0.478													5	18	---	---	---	---	PASS
SHROOM1	134549	broad.mit.edu	37	5	132158628	132158628	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132158628C>T	uc003kxx.2	-	10	3224	c.2419G>A	c.(2419-2421)GAC>AAC	p.D807N	SHROOM1_uc003kxy.1_Missense_Mutation_p.D802N	NM_133456	NP_597713	Q2M3G4	SHRM1_HUMAN	shroom family member 1	807	ASD2.				actin filament bundle assembly|cell morphogenesis	cytoplasm|microtubule	actin filament binding			pancreas(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATGCGCTCGTCCAGGTTGCGC	0.711													6	34	---	---	---	---	PASS
SHROOM1	134549	broad.mit.edu	37	5	132158629	132158629	+	Silent	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132158629C>A	uc003kxx.2	-	10	3223	c.2418G>T	c.(2416-2418)CTG>CTT	p.L806L	SHROOM1_uc003kxy.1_Silent_p.L801L	NM_133456	NP_597713	Q2M3G4	SHRM1_HUMAN	shroom family member 1	806	ASD2.				actin filament bundle assembly|cell morphogenesis	cytoplasm|microtubule	actin filament binding			pancreas(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGCGCTCGTCCAGGTTGCGCT	0.706													6	34	---	---	---	---	PASS
FAM114A2	10827	broad.mit.edu	37	5	153390869	153390869	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153390869A>T	uc003lvb.2	-	9	1513	c.925T>A	c.(925-927)TTT>ATT	p.F309I	FAM114A2_uc003lvc.2_Missense_Mutation_p.F309I|FAM114A2_uc003lvd.2_Missense_Mutation_p.F309I|FAM114A2_uc003lve.2_Missense_Mutation_p.F125I|FAM114A2_uc011dda.1_Missense_Mutation_p.F239I	NM_018691	NP_061161	Q9NRY5	F1142_HUMAN	hypothetical protein LOC10827	309							purine nucleotide binding				0						TCCTTGGTAAAATCTTCATCC	0.433													65	269	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160114825	160114825	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160114825A>G	uc003lym.1	-	5	1104	c.257T>C	c.(256-258)CTC>CCC	p.L86P	ATP10B_uc003lyp.2_Missense_Mutation_p.L86P|ATP10B_uc011deg.1_Missense_Mutation_p.L130P|ATP10B_uc003lyo.2_5'Flank	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	86	Helical; (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGCTCAAAGAGATTCCGGGG	0.343													7	494	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	32231923	32231923	+	3'UTR	SNP	T	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32231923T>A	uc003obd.1	+	2										Homo sapiens cDNA FLJ40408 fis, clone TESTI2037673.																		tactttaagttctaggatata	0.134													5	7	---	---	---	---	PASS
KIF6	221458	broad.mit.edu	37	6	39512380	39512380	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39512380T>C	uc003oot.2	-	12	1472	c.1377A>G	c.(1375-1377)GAA>GAG	p.E459E	KIF6_uc010jxa.1_Silent_p.E250E|KIF6_uc011dua.1_Silent_p.E459E|KIF6_uc010jxb.1_Silent_p.E459E	NM_145027	NP_659464	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	459	Potential.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3						TTCTATATTCTTCTTCTTTTA	0.348													8	779	---	---	---	---	PASS
IMPG1	3617	broad.mit.edu	37	6	76715211	76715211	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76715211T>C	uc003pik.1	-	10	1058	c.928A>G	c.(928-930)AGA>GGA	p.R310G		NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1	310	SEA 1.				visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GCACTGTGTCTCTTAAAGATG	0.463													6	317	---	---	---	---	PASS
IRAK1BP1	134728	broad.mit.edu	37	6	79607645	79607645	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79607645T>C	uc003pim.2	+	3	586	c.481T>C	c.(481-483)TAT>CAT	p.Y161H	IRAK1BP1_uc010kbg.1_RNA|IRAK1BP1_uc003pin.2_Missense_Mutation_p.Y74H	NM_001010844	NP_001010844	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1	161					I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus					0		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		ACCCCAGTTCTATCATACTCC	0.348													6	511	---	---	---	---	PASS
IFNGR1	3459	broad.mit.edu	37	6	137519168	137519168	+	Nonstop_Mutation	SNP	T	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137519168T>A	uc003qho.2	-	7	1573	c.1470A>T	c.(1468-1470)TGA>TGT	p.*490C	IFNGR1_uc011edm.1_Nonstop_Mutation_p.*462C	NM_000416	NP_000407	P15260	INGR1_HUMAN	interferon gamma receptor 1 precursor	490					regulation of interferon-gamma-mediated signaling pathway|response to virus	integral to plasma membrane	interferon-gamma receptor activity			upper_aerodigestive_tract(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	TTAGCTGATCTCATGAAAATT	0.353													62	121	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	153603767	153603767	+	IGR	SNP	A	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603767A>T								RGS17 (151378 upstream) : OPRM1 (727869 downstream)																							GACCACCAGCATTACCGCGGC	0.572													15	41	---	---	---	---	PASS
NT5C3	51251	broad.mit.edu	37	7	33054375	33054375	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33054375T>G	uc003tdk.2	-	9	1055	c.978A>C	c.(976-978)GAA>GAC	p.E326D	AVL9_uc011kai.1_Intron|NT5C3_uc003tdi.2_Missense_Mutation_p.E287D|NT5C3_uc003tdj.2_Missense_Mutation_p.E287D	NM_001002010	NP_001002010	Q9H0P0	5NT3_HUMAN	5'-nucleotidase, cytosolic III isoform 1	326					nucleotide metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol|endoplasmic reticulum	2'-phosphotransferase activity|5'-nucleotidase activity|magnesium ion binding|nucleotide binding			ovary(1)	1			GBM - Glioblastoma multiforme(11;0.0894)			AGTTGGCTACTTCTAATGATT	0.348													113	419	---	---	---	---	PASS
VSTM2A	222008	broad.mit.edu	37	7	54610378	54610378	+	5'UTR	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54610378T>C	uc010kzf.2	+	1					VSTM2A_uc010kze.2_5'UTR|VSTM2A_uc003tqc.3_5'UTR	NM_182546	NP_872352	Q8TAG5	VTM2A_HUMAN	V-set and transmembrane domain containing 2							extracellular region					0			STAD - Stomach adenocarcinoma(5;0.0525)			CTTTCAGGGCTTTTCGGCTGT	0.522													8	535	---	---	---	---	PASS
PEX1	5189	broad.mit.edu	37	7	92118722	92118722	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92118722T>C	uc003uly.2	-	23	3748	c.3652A>G	c.(3652-3654)AAC>GAC	p.N1218D	PEX1_uc011khr.1_Missense_Mutation_p.N1010D|PEX1_uc010ley.2_Missense_Mutation_p.N1161D|PEX1_uc011khs.1_Missense_Mutation_p.N896D	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1	1218					microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			CCTGGTTGGTTCATGGATTCG	0.368													7	449	---	---	---	---	PASS
TMEM229A	730130	broad.mit.edu	37	7	123672679	123672679	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123672679A>T	uc011kob.1	-	1	845	c.379T>A	c.(379-381)TCG>ACG	p.S127T	uc011koc.1_Intron	NM_001136002	NP_001129474	B2RXF0	T229A_HUMAN	transmembrane protein 229A	127	Helical; (Potential).					host cell nucleus|integral to membrane	sequence-specific DNA binding transcription factor activity				0						ACGTGGGCCGAGGGGTAGAGG	0.697													16	86	---	---	---	---	PASS
XKR6	286046	broad.mit.edu	37	8	10782233	10782233	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10782233C>T	uc003wtk.1	-	2	899	c.872G>A	c.(871-873)CGC>CAC	p.R291H		NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related	291						integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		CTCCAGGAGGCGCAGCATGTT	0.567													32	65	---	---	---	---	PASS
BNIP3L	665	broad.mit.edu	37	8	26238903	26238903	+	5'Flank	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26238903A>G	uc003xex.1	+						uc003xew.2_RNA|BNIP3L_uc010luh.1_5'Flank|BNIP3L_uc010lui.1_5'Flank	NM_004331	NP_004322	O60238	BNI3L_HUMAN	BCL2/adenovirus E1B 19kD-interacting protein						apoptosis|defense response to virus|induction of apoptosis|interspecies interaction between organisms|mitochondrial protein catabolic process|negative regulation of survival gene product expression	endoplasmic reticulum|integral to membrane|mitochondrial outer membrane|nuclear envelope	lamin binding|protein heterodimerization activity|protein homodimerization activity				0		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0019)|Epithelial(17;1.59e-12)|all cancers(2;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(2;2.57e-08)|Colorectal(74;0.135)		GCAATTTGAAAATCTCCACAT	0.428													6	339	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55542355	55542355	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55542355C>A	uc003xsd.1	+	4	6061	c.5913C>A	c.(5911-5913)AAC>AAA	p.N1971K	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1971					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			GGGAAGAGAACAATAAAGCAA	0.299													35	130	---	---	---	---	PASS
VPS13B	157680	broad.mit.edu	37	8	100711812	100711812	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100711812G>T	uc003yiv.2	+	36	6292	c.6181G>T	c.(6181-6183)GAT>TAT	p.D2061Y	VPS13B_uc003yiw.2_Missense_Mutation_p.D2036Y	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	2061					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CACCAAACTGGATCAGATAAA	0.348													30	138	---	---	---	---	PASS
RGS22	26166	broad.mit.edu	37	8	101075791	101075791	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101075791A>G	uc003yjb.1	-	8	1400	c.1205T>C	c.(1204-1206)ATT>ACT	p.I402T	RGS22_uc003yja.1_Missense_Mutation_p.I221T|RGS22_uc003yjc.1_Missense_Mutation_p.I390T|RGS22_uc011lgz.1_RNA|RGS22_uc010mbo.1_RNA	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	402					negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			CCTATGAGAAATACACCAGTC	0.388													7	625	---	---	---	---	PASS
DSCC1	79075	broad.mit.edu	37	8	120865431	120865431	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120865431G>T	uc003yov.2	-	2	342	c.207C>A	c.(205-207)GAC>GAA	p.D69E		NM_024094	NP_076999	Q9BVC3	DCC1_HUMAN	defective in sister chromatid cohesion 1	69					DNA replication|maintenance of mitotic sister chromatid cohesion|post-translational protein acetylation|regulation of DNA replication	chromatin|chromosome, centromeric region|nucleoplasm	DNA binding|protein binding			pancreas(1)	1	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CAGCTTGCTCGTCTTTATCAC	0.388													87	271	---	---	---	---	PASS
KIAA1432	57589	broad.mit.edu	37	9	5765320	5765320	+	Intron	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5765320C>A	uc003zji.2	+						KIAA1432_uc003zjh.2_Intron|KIAA1432_uc003zjl.3_Intron|KIAA1432_uc003zjj.1_Intron|ERMP1_uc011lme.1_RNA	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a							integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		GGTGTGGCTACATTCTTTGAG	0.333													8	62	---	---	---	---	PASS
TOPORS	10210	broad.mit.edu	37	9	32542019	32542019	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32542019T>C	uc003zrb.2	-	3	2671	c.2504A>G	c.(2503-2505)AAC>AGC	p.N835S	TOPORS_uc003zrc.2_Missense_Mutation_p.N768S	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	835	Interaction with TOP1.				DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		ATTTTTGTAGTTTCCATCCAA	0.413													8	557	---	---	---	---	PASS
KIAA1045	23349	broad.mit.edu	37	9	34971509	34971509	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34971509A>G	uc003zvq.2	+	2	392	c.214A>G	c.(214-216)AGT>GGT	p.S72G	KIAA1045_uc003zvr.2_Missense_Mutation_p.S72G	NM_015297	NP_056112	Q9UPV7	K1045_HUMAN	hypothetical protein LOC23349	72							calcium ion binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00575)			CCAGGAAGAGAGTAGTGCCGG	0.642													4	42	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66499795	66499795	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66499795G>A	uc004aee.1	+	1	605	c.605G>A	c.(604-606)CGC>CAC	p.R202H	LOC442421_uc004aed.1_RNA					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0						TGCAAGTCGCGCAAGGAGCAG	0.592													3	7	---	---	---	---	PASS
C10orf18	54906	broad.mit.edu	37	10	5789390	5789390	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5789390G>T	uc001iij.2	+	15	4631	c.4006G>T	c.(4006-4008)GAA>TAA	p.E1336*	C10orf18_uc001iik.2_Nonsense_Mutation_p.E180*	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	1336										ovary(1)|central_nervous_system(1)	2						AGAAAGCAGAGAAGTGAGTTC	0.423													28	113	---	---	---	---	PASS
MCM10	55388	broad.mit.edu	37	10	13237118	13237118	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13237118G>A	uc001ima.2	+	14	1927	c.1826G>A	c.(1825-1827)CGG>CAG	p.R609Q	MCM10_uc001imb.2_Missense_Mutation_p.R608Q|MCM10_uc001imc.2_Missense_Mutation_p.R608Q	NM_182751	NP_877428	Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	609					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						CAGCCTCCACGGACAGGATCC	0.532													6	142	---	---	---	---	PASS
KIF5B	3799	broad.mit.edu	37	10	32311891	32311891	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32311891T>C	uc001iwe.3	-	16	2269	c.1799A>G	c.(1798-1800)GAA>GGA	p.E600G		NM_004521	NP_004512	P33176	KINH_HUMAN	kinesin family member 5B	600					stress granule disassembly|vesicle transport along microtubule	kinesin complex|microtubule|perinuclear region of cytoplasm|vesicle	ATP binding|microtubule binding|microtubule motor activity		KIF5B/ALK(4)	lung(4)|ovary(1)	5		Prostate(175;0.0137)				GGTTTTTACTTCTGACTTCAT	0.373													8	617	---	---	---	---	PASS
PGBD3	267004	broad.mit.edu	37	10	50723725	50723725	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50723725C>G	uc001jht.2	-	2	1691	c.1436G>C	c.(1435-1437)GGA>GCA	p.G479A	ERCC6_uc001jhs.3_Intron|PGBD3_uc009xoe.2_Missense_Mutation_p.G947A|PGBD3_uc001jhu.2_Missense_Mutation_p.G947A	NM_170753	NP_736609	Q8N328	PGBD3_HUMAN	hypothetical protein LOC267004	479										pancreas(1)|breast(1)|skin(1)	3						CCATTTCTTTCCACGGATTGA	0.398													6	121	---	---	---	---	PASS
PBLD	64081	broad.mit.edu	37	10	70045109	70045109	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70045109C>A	uc001jns.1	-	9	953	c.750G>T	c.(748-750)ATG>ATT	p.M250I	PBLD_uc001jnr.1_Missense_Mutation_p.M217I|PBLD_uc001jnt.1_Missense_Mutation_p.M250I|PBLD_uc001jnu.1_Missense_Mutation_p.M250I	NM_022129	NP_071412	P30039	PBLD_HUMAN	MAWD binding protein isoform a	250					biosynthetic process		isomerase activity			skin(2)|ovary(1)	3						TCCTACCATGCATTTCTTTCT	0.413													8	221	---	---	---	---	PASS
ANXA7	310	broad.mit.edu	37	10	75148078	75148078	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75148078T>C	uc001jtz.2	-	7	669	c.596A>G	c.(595-597)AAG>AGG	p.K199R	ANXA7_uc001jua.2_Missense_Mutation_p.K177R|ANXA7_uc001jub.2_Missense_Mutation_p.K137R|ANXA7_uc010qki.1_Missense_Mutation_p.K87R|ANXA7_uc009xre.2_Missense_Mutation_p.K106R|ANXA7_uc009xrf.1_Missense_Mutation_p.K119R	NM_004034	NP_004025	P20073	ANXA7_HUMAN	annexin VII isoform 2	199	Annexin 1.						calcium ion binding|calcium-dependent phospholipid binding|calcium-dependent protein binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)					ACCAAAACCCTTCATTGCCTT	0.358													7	435	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89725043	89725043	+	Splice_Site	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89725043G>A	uc001kfb.2	+	10	2058	c.1027_splice	c.e10-1	p.V343_splice		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog						activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.?(4)|p.R55fs*1(4)|p.Y27fs*1(2)|p.N212fs*1(2)|p.G165_*404del(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TCTTTCTCTAGGTGAAGCTGT	0.333		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			10	198	---	---	---	---	PASS
TNKS2	80351	broad.mit.edu	37	10	93617230	93617230	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93617230A>G	uc001khp.2	+	24	3334	c.3037A>G	c.(3037-3039)AGA>GGA	p.R1013G		NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related	1013	PARP catalytic.				positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)				CACTCACCGGAGAAAAGAAGT	0.358													8	480	---	---	---	---	PASS
RAB11FIP2	22841	broad.mit.edu	37	10	119798744	119798744	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119798744C>T	uc001ldj.1	-	3	1444	c.1004G>A	c.(1003-1005)AGC>AAC	p.S335N	RAB11FIP2_uc009xyz.1_Missense_Mutation_p.S335N	NM_014904	NP_055719	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2	335					protein transport	plasma membrane|recycling endosome membrane	protein homodimerization activity				0		Colorectal(252;0.235)		all cancers(201;0.0238)		TAAATTCATGCTGCTGTCCCA	0.348													7	473	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093448	1093448	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093448C>A	uc001lsx.1	+	31	12380	c.12353C>A	c.(12352-12354)ACC>AAC	p.T4118N		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4118						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gtgaccccaaccccgacaccc	0.000													7	315	---	---	---	---	PASS
CCDC73	493860	broad.mit.edu	37	11	32635626	32635626	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32635626T>G	uc001mtv.2	-	16	2282	c.2238A>C	c.(2236-2238)AAA>AAC	p.K746N		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	746										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)					TACACATAGTTTTTCCCCCAG	0.333													70	248	---	---	---	---	PASS
OR4C6	219432	broad.mit.edu	37	11	55432900	55432900	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55432900G>T	uc001nht.3	+	3	523	c.258G>T	c.(256-258)AAG>AAT	p.K86N	OR4C6_uc010rik.1_Missense_Mutation_p.K86N	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	86	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						CCCTCTCCAAGAGCACTACCA	0.488													98	303	---	---	---	---	PASS
OR4C6	219432	broad.mit.edu	37	11	55433498	55433498	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55433498A>G	uc001nht.3	+	3	1121	c.856A>G	c.(856-858)ACA>GCA	p.T286A	OR4C6_uc010rik.1_Missense_Mutation_p.T286A	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	286	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						CTTGATCTATACACTGAGGAA	0.438													5	189	---	---	---	---	PASS
MS4A14	84689	broad.mit.edu	37	11	60164083	60164083	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60164083C>T	uc001npj.2	+	1	597	c.32C>T	c.(31-33)ACT>ATT	p.T11I	MS4A14_uc001npi.2_Intron|MS4A14_uc001npn.2_5'UTR|MS4A14_uc001npk.2_Missense_Mutation_p.T11I|MS4A14_uc001npl.2_5'UTR|MS4A14_uc001npm.2_5'UTR	NM_032597	NP_115986	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member	11						integral to membrane	receptor activity			breast(1)	1						AGAAGGGCAACTCACGTCATC	0.458													5	231	---	---	---	---	PASS
SLC22A6	9356	broad.mit.edu	37	11	62751512	62751512	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62751512A>G	uc001nwk.2	-	2	684	c.377T>C	c.(376-378)CTT>CCT	p.L126P	SLC22A6_uc001nwl.2_Missense_Mutation_p.L126P|SLC22A6_uc001nwj.2_Missense_Mutation_p.L126P|SLC22A6_uc001nwm.2_Missense_Mutation_p.L126P	NM_004790	NP_004781	Q4U2R8	S22A6_HUMAN	solute carrier family 22 member 6 isoform a	126	Extracellular (Potential).				alpha-ketoglutarate transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|protein binding				0						AGAGCACACAAGGTCCCACTG	0.612													4	58	---	---	---	---	PASS
PYGM	5837	broad.mit.edu	37	11	64527310	64527310	+	Missense_Mutation	SNP	C	T	T	rs145881639	byFrequency	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64527310C>T	uc001oax.3	-	1	878	c.61G>A	c.(61-63)GGC>AGC	p.G21S	PYGM_uc001oay.3_Missense_Mutation_p.G21S	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1	21					glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)	TTCTCCACGCCGGCCAGGCCA	0.572													53	142	---	---	---	---	PASS
LRP5	4041	broad.mit.edu	37	11	68216349	68216349	+	Silent	SNP	C	T	T	rs112415702		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68216349C>T	uc001ont.2	+	23	4734	c.4659C>T	c.(4657-4659)AGC>AGT	p.S1553S	LRP5_uc009ysg.2_Silent_p.S963S	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	1553	Pro-rich.|Cytoplasmic (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7						GCGACTACAGCGCCAGCCGCT	0.632													11	27	---	---	---	---	PASS
PRB3	5544	broad.mit.edu	37	12	11420779	11420779	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11420779G>A	uc001qzs.2	-	3	442	c.404C>T	c.(403-405)CCG>CTG	p.P135L	PRB4_uc001qzf.1_Intron	NM_006249	NP_006240	Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	135	4.|10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.					extracellular region	Gram-negative bacterial cell surface binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CGGACGAGGCGGGGGACCTTG	0.642													11	39	---	---	---	---	PASS
DUSP16	80824	broad.mit.edu	37	12	12653528	12653528	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12653528T>C	uc001rao.1	-	4	1088	c.456A>G	c.(454-456)TTA>TTG	p.L152L	DUSP16_uc001ran.1_Intron	NM_030640	NP_085143	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	152					inactivation of MAPK activity|MAPK export from nucleus|MAPK phosphatase export from nucleus, leptomycin B sensitive	cytoplasmic membrane-bounded vesicle|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)		TGGCAACAGGTAAGCAAGGCT	0.473													6	314	---	---	---	---	PASS
GPR19	2842	broad.mit.edu	37	12	12815351	12815351	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12815351T>C	uc001rar.3	-	2	225	c.32A>G	c.(31-33)AAG>AGG	p.K11R	GPR19_uc001raq.2_Missense_Mutation_p.K11R	NM_006143	NP_006134	Q15760	GPR19_HUMAN	G protein-coupled receptor 19	11	Extracellular (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.048)		CAAATGTGGCTTGCTGTTATC	0.428													6	214	---	---	---	---	PASS
TMTC1	83857	broad.mit.edu	37	12	29670370	29670370	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29670370C>T	uc001rjb.2	-	14	2309	c.1835G>A	c.(1834-1836)CGC>CAC	p.R612H	TMTC1_uc001riz.2_Missense_Mutation_p.R369H|TMTC1_uc001rja.2_Missense_Mutation_p.R456H|TMTC1_uc001riy.2_Missense_Mutation_p.R65H	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	720						integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					CAGTGCCAAGCGGAGCTCCCT	0.517													5	200	---	---	---	---	PASS
DENND5B	160518	broad.mit.edu	37	12	31540556	31540556	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31540556A>T	uc001rki.1	-	21	3992	c.3806T>A	c.(3805-3807)ATC>AAC	p.I1269N	DENND5B_uc001rkh.1_Missense_Mutation_p.I1304N|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	1269						integral to membrane				ovary(1)|central_nervous_system(1)	2						CACTCCTTTGATGAGTGATCC	0.502													48	207	---	---	---	---	PASS
ZCRB1	85437	broad.mit.edu	37	12	42706926	42706926	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42706926T>C	uc001rmz.2	-	8	806	c.597A>G	c.(595-597)AGA>AGG	p.R199R	PPHLN1_uc001rmy.2_Intron	NM_033114	NP_149105	Q8TBF4	ZCRB1_HUMAN	zinc finger CCHC-type and RNA binding motif 1	199					mRNA processing	nucleoplasm|U12-type spliceosomal complex	nucleotide binding|RNA binding|zinc ion binding			skin(1)	1	all_cancers(12;0.000348)|Breast(8;0.221)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0689)		TCCTTGGGCGTCTTGAATCAT	0.353													8	742	---	---	---	---	PASS
PRICKLE1	144165	broad.mit.edu	37	12	42864091	42864091	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42864091C>G	uc010skv.1	-	3	490	c.203G>C	c.(202-204)CGG>CCG	p.R68P	PRICKLE1_uc001rnl.2_Missense_Mutation_p.R68P|PRICKLE1_uc010skw.1_Missense_Mutation_p.R68P|PRICKLE1_uc001rnm.2_Missense_Mutation_p.R68P|PRICKLE1_uc009zka.2_Missense_Mutation_p.R64P	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	68	PET.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		CTGTTTAATCCGATGCTTCTC	0.398													86	287	---	---	---	---	PASS
ATP2B1	490	broad.mit.edu	37	12	90004273	90004273	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90004273T>C	uc001tbh.2	-	13	2441	c.2260A>G	c.(2260-2262)AGG>GGG	p.R754G	ATP2B1_uc001tbg.2_Missense_Mutation_p.R754G|ATP2B1_uc001tbf.2_Missense_Mutation_p.R424G	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b	754	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						TTGTCTATCCTCTCTTGCTCA	0.308													7	417	---	---	---	---	PASS
EEA1	8411	broad.mit.edu	37	12	93196300	93196300	+	Silent	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93196300A>G	uc001tck.2	-	19	2815	c.2550T>C	c.(2548-2550)GCT>GCC	p.A850A		NM_003566	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1, 162kD	850	Potential.				early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3						CTGTCATTAAAGCTTCTTTCT	0.303													8	740	---	---	---	---	PASS
SSH1	54434	broad.mit.edu	37	12	109182632	109182632	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109182632T>C	uc001tnm.2	-	15	2369	c.2282A>G	c.(2281-2283)CAC>CGC	p.H761R	SSH1_uc001tnl.2_Missense_Mutation_p.H449R	NM_018984	NP_061857	Q8WYL5	SSH1_HUMAN	slingshot 1 isoform 1	761					actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4						CTTATCACAGTGAGAATTCTT	0.512													16	304	---	---	---	---	PASS
PPP1CC	5501	broad.mit.edu	37	12	111158737	111158737	+	3'UTR	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111158737C>T	uc001tru.2	-	7						NM_002710	NP_002701	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma						cell division|glycogen metabolic process|mitotic prometaphase|triglyceride catabolic process	cleavage furrow|condensed chromosome kinetochore|cytosol|midbody|MLL5-L complex|nuclear speck|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|protein binding|protein kinase binding|protein serine/threonine phosphatase activity			lung(2)|central_nervous_system(1)	3						CAGCAAATGCCATTCACTAAA	0.343													4	111	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117728169	117728169	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117728169G>T	uc001twm.1	-	4	1601	c.915C>A	c.(913-915)TTC>TTA	p.F305L		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	305					multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	TGACCTTGAGGAAGCGTGGAC	0.557													18	85	---	---	---	---	PASS
ATP8A2	51761	broad.mit.edu	37	13	26125480	26125480	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26125480C>A	uc001uqk.2	+	11	1038	c.896C>A	c.(895-897)TCA>TAA	p.S299*	ATP8A2_uc010tdi.1_Nonsense_Mutation_p.S259*|ATP8A2_uc010tdj.1_RNA|ATP8A2_uc001uql.1_Nonsense_Mutation_p.S259*	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,	259	Cytoplasmic (Potential).				ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		GTGTAGAATTCAACCAAAGCG	0.463													27	316	---	---	---	---	PASS
C13orf33	84935	broad.mit.edu	37	13	31495869	31495869	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31495869T>C	uc001uth.3	+	4	1014	c.673T>C	c.(673-675)TCA>CCA	p.S225P	uc001utg.1_Intron	NM_032849	NP_116238	Q5VYS4	CM033_HUMAN	hypothetical protein LOC84935	225											0		Lung SC(185;0.0281)		all cancers(112;0.00914)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.0559)|GBM - Glioblastoma multiforme(144;0.244)		TCTGAATTTGTCAAGTACAAG	0.358													6	328	---	---	---	---	PASS
MED4	29079	broad.mit.edu	37	13	48651403	48651403	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48651403T>C	uc001vby.1	-	7	711	c.685A>G	c.(685-687)ATG>GTG	p.M229V	MED4_uc010tge.1_Missense_Mutation_p.M229V|MED4_uc010tgf.1_Missense_Mutation_p.M183V	NM_014166	NP_054885	Q9NPJ6	MED4_HUMAN	mediator complex subunit 4	229					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		all_cancers(8;2.93e-25)|all_epithelial(8;4.38e-13)|all_lung(13;7.37e-06)|all_hematologic(8;8.61e-05)|Breast(56;0.000141)|Lung NSC(96;0.000518)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.00559)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;5.18e-07)		AACATATTCATCGACATGTCA	0.373													69	198	---	---	---	---	PASS
PRMT5	10419	broad.mit.edu	37	14	23397792	23397792	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23397792G>A	uc001whm.1	-	2	234	c.143C>T	c.(142-144)CCG>CTG	p.P48L	PRMT5_uc001whl.1_Missense_Mutation_p.P31L|PRMT5_uc010akd.1_RNA|PRMT5_uc010tnf.1_Intron|PRMT5_uc010tng.1_Missense_Mutation_p.P31L|PRMT5_uc010tnh.1_Missense_Mutation_p.P48L|PRMT5_uc001whn.1_Missense_Mutation_p.P31L	NM_006109	NP_006100	O14744	ANM5_HUMAN	protein arginine methyltransferase 5 isoform a	48					cell proliferation|histone H4-R3 methylation|ncRNA metabolic process|regulation of mitosis|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	histone-arginine N-methyltransferase activity|protein binding|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding			ovary(1)	1	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		CTTGAAACGCGGATGGAAGAC	0.537													5	139	---	---	---	---	PASS
NYNRIN	57523	broad.mit.edu	37	14	24885224	24885224	+	Silent	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24885224C>T	uc001wpf.3	+	9	4587	c.4269C>T	c.(4267-4269)TCC>TCT	p.S1423S		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	1423	Helical; (Potential).				DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3						GCCTCTCATCCCTTCCGTTTA	0.617													13	184	---	---	---	---	PASS
ARHGAP5	394	broad.mit.edu	37	14	32560363	32560363	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32560363T>G	uc001wrl.2	+	2	727	c.488T>G	c.(487-489)ATT>AGT	p.I163S	ARHGAP5_uc001wrm.2_Missense_Mutation_p.I163S|ARHGAP5_uc001wrn.2_Missense_Mutation_p.I163S|ARHGAP5_uc001wro.2_Intron|ARHGAP5_uc001wrp.2_Intron	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b	163					cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(4)|central_nervous_system(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		TTATTATGCATTGATGTAAGT	0.333													23	51	---	---	---	---	PASS
MDGA2	161357	broad.mit.edu	37	14	47613333	47613333	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47613333A>T	uc001wwj.3	-	4	729	c.533T>A	c.(532-534)TTG>TAG	p.L178*	MDGA2_uc001wwi.3_5'UTR|MDGA2_uc010ani.2_5'UTR	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	178	Ig-like 2.				spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						TCCTTGCAGCAAGACCTCCTG	0.433													62	206	---	---	---	---	PASS
MAPK1IP1L	93487	broad.mit.edu	37	14	55531522	55531522	+	3'UTR	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55531522A>G	uc001xbq.1	+	4						NM_144578	NP_653179	Q8NDC0	MISSL_HUMAN	MAPK-interacting and spindle-stabilizing												0						CATCATATGTATACAATCAGA	0.338													7	9	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106236827	106236827	+	RNA	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106236827G>T	uc010tyt.1	-	3613		c.57521C>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_RNA|uc001ysi.1_RNA					Parts of antibodies, mostly variable regions.												0						CCTGGGCACCGTGGGCACGGG	0.637													6	336	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107087397	107087397	+	RNA	SNP	A	T	T	rs150534597	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107087397A>T	uc010tyt.1	-	108		c.5030T>A								Parts of antibodies, mostly variable regions.												0						GACCCAGTGCATAGCAGAGCT	0.537													3	37	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	28929443	28929443	+	RNA	SNP	C	T	T	rs692165	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28929443C>T	uc010azc.2	+	14		c.2148C>T								Homo sapiens I.M.A.G.E. clone 321824, mRNA sequence.																		TTTTGGGCTCCCTGGGTGGTC	0.532													4	45	---	---	---	---	PASS
FSIP1	161835	broad.mit.edu	37	15	39910135	39910135	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39910135T>C	uc001zki.2	-	11	1718	c.1500A>G	c.(1498-1500)GAA>GAG	p.E500E		NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	500										ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TATTCTCTGCTTCAGTGACAA	0.383													6	290	---	---	---	---	PASS
IQGAP1	8826	broad.mit.edu	37	15	91037977	91037977	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91037977A>G	uc002bpl.1	+	36	4762	c.4661A>G	c.(4660-4662)AAG>AGG	p.K1554R	IQGAP1_uc010uqg.1_Missense_Mutation_p.K175R	NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1554	C2.				energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			ATGAAAGGAAAGAAAAGCAAA	0.358													7	443	---	---	---	---	PASS
GSPT1	2935	broad.mit.edu	37	16	11980744	11980744	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11980744T>C	uc002dbr.2	-	6	615	c.588A>G	c.(586-588)AAA>AAG	p.K196K	GSPT1_uc002dbu.2_Silent_p.K333K|GSPT1_uc002dbt.2_Silent_p.K334K|GSPT1_uc010bux.2_Silent_p.K196K	NM_001130007	NP_001123479	P15170	ERF3A_HUMAN	G1 to S phase transition 1 isoform 3	196					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						TCTGTCCTCCTTTTTCAAATC	0.403													9	721	---	---	---	---	PASS
SLC5A11	115584	broad.mit.edu	37	16	24918068	24918068	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24918068T>C	uc002dmu.2	+	11	1329	c.1097T>C	c.(1096-1098)CTG>CCG	p.L366P	SLC5A11_uc002dms.2_Missense_Mutation_p.L302P|SLC5A11_uc010vcd.1_Missense_Mutation_p.L331P|SLC5A11_uc002dmt.2_Silent_p.A233A|SLC5A11_uc010vce.1_Missense_Mutation_p.L296P|SLC5A11_uc010bxt.2_Missense_Mutation_p.L302P|SLC5A11_uc002dmv.2_5'Flank	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	366	Extracellular (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		AAACTCGTGCTGGAACTCCTG	0.557											OREG0023688	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	22	74	---	---	---	---	PASS
FHOD1	29109	broad.mit.edu	37	16	67264547	67264547	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67264547G>T	uc002esl.2	-	18	2927	c.2815C>A	c.(2815-2817)CGT>AGT	p.R939S	FHOD1_uc002esk.2_5'UTR|FHOD1_uc010ced.2_Missense_Mutation_p.R746S	NM_013241	NP_037373	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	939	FH2.				actin cytoskeleton organization	cytoplasm|cytoskeleton|nucleus	actin binding			breast(2)|ovary(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		ATGGCAACACGGCGGGCACAC	0.652													15	35	---	---	---	---	PASS
NLRP1	22861	broad.mit.edu	37	17	5462474	5462474	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5462474C>T	uc002gci.2	-	4	2097	c.1542G>A	c.(1540-1542)TGG>TGA	p.W514*	NLRP1_uc002gcg.1_Nonsense_Mutation_p.W514*|NLRP1_uc002gck.2_Nonsense_Mutation_p.W514*|NLRP1_uc002gcj.2_Nonsense_Mutation_p.W514*|NLRP1_uc002gcl.2_Nonsense_Mutation_p.W514*|NLRP1_uc002gch.3_Nonsense_Mutation_p.W514*|NLRP1_uc010clh.2_Nonsense_Mutation_p.W514*	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	514	NACHT.				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)				GACACAGGGCCCAGAGCTCTT	0.488													21	82	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577580	7577580	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577580T>C	uc002gim.2	-	7	895	c.701A>G	c.(700-702)TAC>TGC	p.Y234C	TP53_uc002gig.1_Missense_Mutation_p.Y234C|TP53_uc002gih.2_Missense_Mutation_p.Y234C|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.Y102C|TP53_uc010cng.1_Missense_Mutation_p.Y102C|TP53_uc002gii.1_Missense_Mutation_p.Y102C|TP53_uc010cnh.1_Missense_Mutation_p.Y234C|TP53_uc010cni.1_Missense_Mutation_p.Y234C|TP53_uc002gij.2_Missense_Mutation_p.Y234C|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.Y141C|TP53_uc002gio.2_Missense_Mutation_p.Y102C	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	234	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		Y -> F (in a sporadic cancer; somatic mutation).|Y -> K (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|Y -> N (in sporadic cancers; somatic mutation).|Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> Q (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.Y234C(70)|p.Y234H(13)|p.Y234N(11)|p.0?(7)|p.Y234S(6)|p.Y234*(4)|p.Y234D(3)|p.Y234del(3)|p.Y234fs*2(1)|p.V225fs*23(1)|p.Y234fs*6(1)|p.Y234fs*5(1)|p.Y234fs*4(1)|p.Y234R(1)|p.Y234Y(1)|p.H233_C242del10(1)|p.D228fs*12(1)|p.Y234F(1)|p.I232_Y236delIHYNY(1)|p.Y141S(1)|p.T230_Y234delTTIHY(1)|p.H233fs*6(1)|p.Y234_N235insX(1)|p.I232fs*5(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CATGTAGTTGTAGTGGATGGT	0.572		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			8	125	---	---	---	---	PASS
ALOX12B	242	broad.mit.edu	37	17	7983835	7983835	+	Intron	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7983835G>A	uc002gjy.1	-						uc010cnq.1_RNA	NM_001139	NP_001130	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type						epidermis development|leukotriene biosynthetic process		arachidonate 12-lipoxygenase activity|iron ion binding|lipoxygenase activity				0						TCATGTCTCAGGTTTTCTGGG	0.557										Multiple Myeloma(8;0.094)	OREG0024153	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	15	---	---	---	---	PASS
SHMT1	6470	broad.mit.edu	37	17	18250958	18250958	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18250958T>A	uc002gta.2	-	5	561	c.371A>T	c.(370-372)AAC>ATC	p.N124I	SHMT1_uc002gtb.2_Missense_Mutation_p.N124I|SHMT1_uc010cqb.2_Missense_Mutation_p.N124I|SHMT1_uc010vxt.1_5'UTR|SHMT1_uc002gtd.1_Missense_Mutation_p.N124I|SHMT1_uc010vxu.1_Missense_Mutation_p.N124I	NM_004169	NP_004160	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	124					carnitine biosynthetic process|folic acid metabolic process|L-serine catabolic process|one-carbon metabolic process|purine base biosynthetic process	cytosol|nucleus	glycine hydroxymethyltransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					Glycine(DB00145)|Mimosine(DB01055)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	CACAGCAAAGTTTGCAGGGGA	0.567													32	72	---	---	---	---	PASS
IKZF3	22806	broad.mit.edu	37	17	37922527	37922527	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37922527G>A	uc002hsu.2	-	8	1108	c.1046C>T	c.(1045-1047)GCT>GTT	p.A349V	IKZF3_uc002htd.2_Missense_Mutation_p.A315V|IKZF3_uc010cwd.2_Missense_Mutation_p.A206V|IKZF3_uc002hsv.2_Missense_Mutation_p.A276V|IKZF3_uc010cwe.2_Missense_Mutation_p.A215V|IKZF3_uc010cwf.2_Missense_Mutation_p.A167V|IKZF3_uc010cwg.2_Missense_Mutation_p.A128V|IKZF3_uc002hsw.2_Missense_Mutation_p.A310V|IKZF3_uc002hsx.2_Missense_Mutation_p.A293V|IKZF3_uc002hsy.2_Missense_Mutation_p.A310V|IKZF3_uc002hsz.2_Missense_Mutation_p.A254V|IKZF3_uc002hta.2_Missense_Mutation_p.A271V|IKZF3_uc002htb.2_RNA|IKZF3_uc010cwh.2_Missense_Mutation_p.A262V|IKZF3_uc002htc.2_Missense_Mutation_p.A102V|IKZF3_uc010wel.1_Missense_Mutation_p.A102V	NM_012481	NP_036613	Q9UKT9	IKZF3_HUMAN	aiolos isoform 1	349					B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TGACATCTCAGCCCGGGTGAG	0.582													9	213	---	---	---	---	PASS
OR4D2	124538	broad.mit.edu	37	17	56247641	56247641	+	Missense_Mutation	SNP	G	A	A	rs149114670		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56247641G>A	uc010wnp.1	+	1	625	c.625G>A	c.(625-627)GTC>ATC	p.V209I		NM_001004707	NP_001004707	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D,	209	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.V209I(1)		ovary(1)|breast(1)	2						GCTGGATGTCGTCTGGTTCTT	0.527													49	143	---	---	---	---	PASS
USP32	84669	broad.mit.edu	37	17	58285530	58285530	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58285530T>C	uc002iyo.1	-	24	3101	c.2815A>G	c.(2815-2817)AGA>GGA	p.R939G	USP32_uc002iyn.1_Missense_Mutation_p.R609G	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32	939					protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			ATATTCAGTCTTAGTCCATAC	0.348													6	363	---	---	---	---	PASS
TCF4	6925	broad.mit.edu	37	18	52937099	52937099	+	Silent	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52937099G>A	uc002lfz.2	-	11	1497	c.885C>T	c.(883-885)TCC>TCT	p.S295S	TCF4_uc002lfw.3_Silent_p.S135S|TCF4_uc010xdu.1_Silent_p.S165S|TCF4_uc010xdv.1_Silent_p.S165S|TCF4_uc002lfx.2_Silent_p.S224S|TCF4_uc010xdw.1_Silent_p.S165S|TCF4_uc002lfy.2_Silent_p.S253S|TCF4_uc010xdx.1_Silent_p.S271S|TCF4_uc010dph.1_Silent_p.S295S|TCF4_uc010xdy.1_Silent_p.S271S|TCF4_uc002lga.2_Silent_p.S397S|TCF4_uc002lgb.1_Silent_p.S135S|TCF4_uc010dpi.2_Silent_p.S301S|TCF4_uc002lgc.3_Silent_p.S216S|TCF4_uc002lfv.2_Silent_p.S79S	NM_003199	NP_003190	P15884	ITF2_HUMAN	transcription factor 4 isoform b	295					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)		GAGGCGTACAGGAAGAGGTGC	0.458													76	264	---	---	---	---	PASS
ATP8B1	5205	broad.mit.edu	37	18	55319389	55319389	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55319389A>G	uc002lgw.2	-	25	3277	c.3277T>C	c.(3277-3279)TCT>CCT	p.S1093P	uc002lgu.1_Intron|uc002lgv.1_Intron	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1	1093	Cytoplasmic (Potential).				ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)				GTCCAATAAGAAGTATCCAAG	0.353									Byler_disease				5	180	---	---	---	---	PASS
TNFSF14	8740	broad.mit.edu	37	19	6665221	6665221	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6665221C>A	uc002mfk.1	-	5	821	c.439G>T	c.(439-441)GTG>TTG	p.V147L	TNFSF14_uc002mfj.1_Missense_Mutation_p.V111L	NM_003807	NP_003798	O43557	TNF14_HUMAN	tumor necrosis factor ligand superfamily, member	147	Extracellular (Potential).				cellular response to mechanical stimulus|immune response|induction of apoptosis|release of cytoplasmic sequestered NF-kappaB|T cell homeostasis|T cell proliferation	cytoplasm|extracellular space|integral to membrane|plasma membrane	caspase inhibitor activity|cytokine activity|tumor necrosis factor receptor binding			skin(1)	1						CCCAGCTGCACCTTGGAGTAG	0.647													3	18	---	---	---	---	PASS
FCER2	2208	broad.mit.edu	37	19	7762449	7762449	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7762449T>C	uc002mhn.2	-	5	401	c.217A>G	c.(217-219)AGC>GGC	p.S73G	FCER2_uc010xjs.1_5'UTR|FCER2_uc010xjt.1_5'UTR|FCER2_uc002mhm.2_Missense_Mutation_p.S73G|FCER2_uc010dvo.2_Missense_Mutation_p.S73G	NM_002002	NP_001993	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor	73	Extracellular (Potential).|				positive regulation of killing of cells of other organism|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of nitric-oxide synthase activity	extracellular region|integral to plasma membrane	IgE binding|integrin binding|receptor activity|sugar binding				0						CCGTGGTGGCTTTCCAAGTTC	0.577													5	139	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9085732	9085732	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9085732G>A	uc002mkp.2	-	1	6287	c.6083C>T	c.(6082-6084)TCT>TTT	p.S2028F		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	2028	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGAATATGGAGAGGATGTGCT	0.488													32	143	---	---	---	---	PASS
OR1I1	126370	broad.mit.edu	37	19	15198934	15198934	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15198934A>G	uc010xoe.1	+	1	1058	c.1058A>G	c.(1057-1059)GAC>GGC	p.D353G		NM_001004713	NP_001004713	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I,	353	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3						gggaacagagacatggaataa	0.050													4	45	---	---	---	---	PASS
AKAP8	10270	broad.mit.edu	37	19	15465831	15465831	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15465831T>C	uc002nav.2	-	14	2035	c.1974A>G	c.(1972-1974)GCA>GCG	p.A658A	AKAP8_uc010dzy.2_Silent_p.A207A	NM_005858	NP_005849	O43823	AKAP8_HUMAN	A-kinase anchor protein 8	658					signal transduction	nuclear matrix				ovary(1)|breast(1)	2						TTTCTGCCTCTGCTGCCATTG	0.587													8	27	---	---	---	---	PASS
PIK3R2	5296	broad.mit.edu	37	19	18278085	18278085	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18278085C>A	uc002nia.1	+	13	2217	c.1705C>A	c.(1705-1707)CAG>AAG	p.Q569K	PIK3R2_uc002nib.1_RNA|PIK3R2_uc010ebi.1_RNA	NM_005027	NP_005018	O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2	569					fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|negative regulation of anti-apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	GTPase activator activity|phosphatidylinositol 3-kinase regulator activity|protein binding			lung(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)	6						GGACCTCATGCAGCTGCGCAA	0.622													12	40	---	---	---	---	PASS
RPL18	6141	broad.mit.edu	37	19	49121088	49121088	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49121088T>G	uc002pjq.1	-	2	83	c.50A>C	c.(49-51)GAG>GCG	p.E17A	RPL18_uc002pjp.1_5'UTR|RPL18_uc010xzs.1_Missense_Mutation_p.E17A|SPHK2_uc002pjr.2_5'Flank|SPHK2_uc010xzt.1_5'Flank|SPHK2_uc002pjs.2_5'Flank|SPHK2_uc002pjt.2_5'Flank	NM_000979	NP_000970	Q07020	RL18_HUMAN	ribosomal protein L18	17					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.89e-05)|all cancers(93;0.00011)|GBM - Glioblastoma multiforme(486;0.0061)|Epithelial(262;0.0154)		GCTCTTGGGCTCCTTGCGCCG	0.572													24	100	---	---	---	---	PASS
ZNF17	7565	broad.mit.edu	37	19	57922632	57922632	+	5'UTR	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57922632C>T	uc002qoo.1	+	1					ZNF547_uc002qpm.3_Intron|ZNF17_uc002qop.1_5'UTR	NM_006959	NP_008890	P17021	ZNF17_HUMAN	zinc finger protein 17						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		GAAAAGGTTTCCCCGTTGTAC	0.577													4	4	---	---	---	---	PASS
ACSS1	84532	broad.mit.edu	37	20	24989936	24989936	+	Silent	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24989936G>A	uc002wub.2	-	13	2738	c.1860C>T	c.(1858-1860)ATC>ATT	p.I620I	ACSS1_uc002wuc.2_Silent_p.I618I|ACSS1_uc010gdc.2_Silent_p.I415I|ACSS1_uc002wud.1_RNA|ACSS1_uc002wua.2_Silent_p.I537I	NM_032501	NP_115890	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	620					acetyl-CoA biosynthetic process|ethanol oxidation|xenobiotic metabolic process	mitochondrial matrix	acetate-CoA ligase activity|AMP binding|ATP binding|protein binding			ovary(1)|skin(1)	2					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CATATTTGGCGATCTTGGTGG	0.507													5	270	---	---	---	---	PASS
KCNJ6	3763	broad.mit.edu	37	21	38997567	38997567	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38997567A>G	uc011aej.1	-	4	1219	c.1166T>C	c.(1165-1167)CTC>CCC	p.L389P	KCNJ6_uc002ywo.2_Missense_Mutation_p.L389P	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6	389	Cytoplasmic (By similarity).				synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	ATGTTGGTTGAGTTTGCTGGA	0.502													7	517	---	---	---	---	PASS
COMT	1312	broad.mit.edu	37	22	19956115	19956115	+	Silent	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19956115A>G	uc002zqu.2	+	6	921	c.672A>G	c.(670-672)CCA>CCG	p.P224P	COMT_uc002zqv.2_Silent_p.P224P|COMT_uc002zqw.2_Silent_p.P224P|COMT_uc011ahd.1_Silent_p.P224P|COMT_uc002zqx.2_Silent_p.P224P	NM_000754	NP_000745	P21964	COMT_HUMAN	catechol-O-methyltransferase isoform MB-COMT	224					neurotransmitter biosynthetic process|neurotransmitter catabolic process|xenobiotic metabolic process	cytosol|integral to membrane|intracellular membrane-bounded organelle|microsome|plasma membrane|soluble fraction	catechol O-methyltransferase activity|magnesium ion binding|protein binding			ovary(1)	1	Colorectal(54;0.0993)				Carbidopa(DB00190)|Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Folic Acid(DB00158)|L-Valine(DB00161)|Levodopa(DB01235)|Methyldopa(DB00968)|Modafinil(DB00745)|Morphine(DB00295)|S-Adenosylmethionine(DB00118)|Tolcapone(DB00323)	TGATCTGCCCAGGTGCGCCAG	0.622													24	58	---	---	---	---	PASS
DDX17	10521	broad.mit.edu	37	22	38884154	38884154	+	Intron	SNP	G	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38884154G>A	uc003avy.3	-						DDX17_uc003avw.3_5'UTR|DDX17_uc010gxp.2_5'UTR|DDX17_uc003avx.3_Intron	NM_001098504	NP_001091974	Q92841	DDX17_HUMAN	DEAD box polypeptide 17 isoform 3						RNA processing	nucleus	ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity			skin(3)|upper_aerodigestive_tract(1)	4	Melanoma(58;0.0286)					TGTGTAGGTTGATGTGGCAGG	0.453													25	96	---	---	---	---	PASS
CHADL	150356	broad.mit.edu	37	22	41632577	41632577	+	Silent	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41632577C>T	uc003azq.3	-	4	2024	c.1974G>A	c.(1972-1974)CTG>CTA	p.L658L	CHADL_uc010gyj.2_Silent_p.L658L	NM_138481	NP_612490	Q6NUI6	CHADL_HUMAN	chondroadherin-like precursor	658	LRR 19.					proteinaceous extracellular matrix					0						GCAGGGCAGGCAGGGCCCGAA	0.652													11	35	---	---	---	---	PASS
SEPT3	55964	broad.mit.edu	37	22	42388698	42388698	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42388698A>G	uc003bbr.3	+	8	934	c.796A>G	c.(796-798)AGT>GGT	p.S266G	WBP2NL_uc011ape.1_Intron|SEPT3_uc003bbs.3_Missense_Mutation_p.S266G|SEPT3_uc010gyr.2_Missense_Mutation_p.S202G|SEPT3_uc011apj.1_Missense_Mutation_p.S202G|SEPT3_uc010gys.2_Missense_Mutation_p.S46G	NM_145733	NP_663786	Q9UH03	SEPT3_HUMAN	septin 3 isoform A	266					cell cycle|cytokinesis	cell junction|septin complex	GTP binding				0						TGTGGTGGGAAGTGACAAGGA	0.522													7	331	---	---	---	---	PASS
IL3RA	3563	broad.mit.edu	37	X	1464288	1464288	+	Silent	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1464288C>T	uc004cps.2	+	3	493	c.144C>T	c.(142-144)ACC>ACT	p.T48T	IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor	48	Extracellular (Potential).					integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	GAAATGTGACCGATATCGAGT	0.358													6	565	---	---	---	---	PASS
FAM9A	171482	broad.mit.edu	37	X	8763259	8763259	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8763259C>T	uc004csg.2	-	7	802	c.691G>A	c.(691-693)GAG>AAG	p.E231K		NM_174951	NP_777611	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	231	Glu-rich.					nucleolus					0		Hepatocellular(5;0.219)				tctttctcctcctcctcctcc	0.015													14	36	---	---	---	---	PASS
PIGA	5277	broad.mit.edu	37	X	15349690	15349690	+	Silent	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15349690T>C	uc004cwr.2	-	2	463	c.363A>G	c.(361-363)AGA>AGG	p.R121R	PIGA_uc004cwq.2_Intron|PIGA_uc010nev.2_Intron|PIGA_uc004cws.2_Intron|PIGA_uc011miq.1_Intron|PIGA_uc010new.1_Intron	NM_002641	NP_002632	P37287	PIGA_HUMAN	phosphatidylinositol	121	Cytoplasmic (Potential).				C-terminal protein lipidation|positive regulation of metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity|protein binding				0	Hepatocellular(33;0.183)					TTATCGTGACTCTCTCCCGAA	0.463													5	162	---	---	---	---	PASS
BMX	660	broad.mit.edu	37	X	15540571	15540571	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15540571C>A	uc004cww.2	+	7	801	c.613C>A	c.(613-615)CAG>AAG	p.Q205K	BMX_uc004cwx.3_Missense_Mutation_p.Q205K|BMX_uc004cwy.3_Missense_Mutation_p.Q205K	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	205					cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)					CTATGGCTCCCAGCCACCATC	0.443													63	90	---	---	---	---	PASS
POLA1	5422	broad.mit.edu	37	X	24859940	24859940	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24859940A>G	uc004dbl.2	+	33	3913	c.3890A>G	c.(3889-3891)GAT>GGT	p.D1297G		NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1	1297	Potential.				cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	AATGTCTTTGATGGTTCGGTT	0.403													7	478	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	32716108	32716108	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32716108A>G	uc004dda.1	-	9	1083	c.839T>C	c.(838-840)GTC>GCC	p.V280A	DMD_uc004dcz.2_Missense_Mutation_p.V157A|DMD_uc004dcy.1_Missense_Mutation_p.V276A|DMD_uc004ddb.1_Missense_Mutation_p.V272A|DMD_uc010ngo.1_Intron|DMD_uc004ddf.2_Missense_Mutation_p.V272A|DMD_uc010ngp.1_Intron|DMD_uc010ngq.1_Intron|DMD_uc010ngr.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	280					muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TGCTAGACTGACCGTGATCTG	0.488													5	111	---	---	---	---	PASS
ARR3	407	broad.mit.edu	37	X	69496308	69496308	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69496308T>C	uc004dyb.2	+	7	439	c.371T>C	c.(370-372)GTG>GCG	p.V124A	ARR3_uc004dya.2_Missense_Mutation_p.V124A	NM_004312	NP_004303	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	124					signal transduction|visual perception	cytoplasm|soluble fraction				large_intestine(2)|ovary(2)	4						CCCTGTTCTGTGACACTGCAG	0.468													6	270	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15262	15262	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15262T>C	uc004coy.2	+	1	502	c.427T>C	c.(427-429)TCC>CCC	p.S143P	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		TCAGTAGACAGTCCCACCCTC	0.468											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	17	27	---	---	---	---	PASS
PRDM16	63976	broad.mit.edu	37	1	3278899	3278900	+	Intron	INS	-	C	C	rs140529930	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3278899_3278900insC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		TGCATGGGACACCCAGGCGTCC	0.545			T	EVI1	MDS|AML								4	3	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7327128	7327129	+	Intron	DEL	AG	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7327128_7327129delAG	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		tatgtcccttagaccctctggc	0.243													4	2	---	---	---	---	
UBR4	23352	broad.mit.edu	37	1	19484596	19484597	+	Intron	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19484596_19484597delCA	uc001bbi.2	-						UBR4_uc001bbl.1_5'Flank|UBR4_uc001bbm.1_Intron	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTCAGTCATTCAAAAGCAGTGA	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	29873754	29873754	+	IGR	DEL	T	-	-	rs66605834		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29873754delT								PTPRU (220439 upstream) : None (None downstream)																							TGCCTACGTCTTGTGCTGATA	0.383													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	30229422	30229423	+	IGR	DEL	GT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30229422_30229423delGT								PTPRU (576107 upstream) : MATN1 (954703 downstream)																							AATCTGCACAGTGACATACACA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	37918289	37918290	+	IGR	INS	-	T	T	rs150908692	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37918289_37918290insT								GRIK3 (418445 upstream) : ZC3H12A (21829 downstream)																							TGCTGCCAGGCTCAGAAGCTAC	0.594													5	7	---	---	---	---	
TRIT1	54802	broad.mit.edu	37	1	40307167	40307167	+	3'UTR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40307167delA	uc010oiz.1	-	11					TRIT1_uc001cec.3_RNA|TRIT1_uc001ced.3_3'UTR|TRIT1_uc001cee.3_RNA|TRIT1_uc001cef.3_RNA|TRIT1_uc001ceg.3_3'UTR|TRIT1_uc001ceh.3_3'UTR|TRIT1_uc009vvv.2_3'UTR|TRIT1_uc001cei.3_3'UTR|TRIT1_uc001ceq.2_3'UTR|TRIT1_uc001cek.2_3'UTR|TRIT1_uc009vvx.2_RNA|TRIT1_uc001cel.2_RNA|TRIT1_uc001cem.2_3'UTR|TRIT1_uc001cen.2_3'UTR|TRIT1_uc001ceo.2_3'UTR|TRIT1_uc001cep.2_3'UTR	NM_017646	NP_060116	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1 precursor						tRNA processing	mitochondrion	ATP binding|metal ion binding|tRNA dimethylallyltransferase activity			ovary(1)	1	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AGGTTCAAAGAAAAAAAAAAT	0.378													6	5	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49676189	49676189	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49676189delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.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)		TATTTTTAATAAACTGCCTCA	0.348													4	2	---	---	---	---	
ZCCHC11	23318	broad.mit.edu	37	1	52959078	52959078	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52959078delT	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Intron|ZCCHC11_uc001cuc.2_Intron	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						TAATATGGCATTTTTTTTTTT	0.149													4	3	---	---	---	---	
SCP2	6342	broad.mit.edu	37	1	53469679	53469680	+	Intron	DEL	AA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53469679_53469680delAA	uc001cur.1	+						SCP2_uc001cus.1_Intron|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron	NM_002979	NP_002970	P22307	NLTP_HUMAN	sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1						ggccatcattaagtaaactaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	54964018	54964018	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54964018delT								SSBP3 (91926 upstream) : ACOT11 (43912 downstream)																							TCCCTATTCCTTCTCCTGCTC	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55800186	55800186	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55800186delG								USP24 (119424 upstream) : None (None downstream)																							CAAGGGATCTGGGGATCCAGT	0.547													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	57472801	57472801	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57472801delT	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						ATCCATCAGGTAATATGTTAT	0.308													4	2	---	---	---	---	
WLS	79971	broad.mit.edu	37	1	68621133	68621135	+	Intron	DEL	CAA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68621133_68621135delCAA	uc001def.1	-						uc001deb.1_Intron|uc001dec.1_Intron|WLS_uc001dee.2_Intron|WLS_uc001deg.1_Intron|WLS_uc009wbf.1_Intron	NM_024911	NP_079187	Q5T9L3	WLS_HUMAN	G protein-coupled receptor 177 isoform 1						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0						AAACAAACATCAACAACAACAAC	0.404													4	2	---	---	---	---	
LRRC40	55631	broad.mit.edu	37	1	70653252	70653252	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70653252delA	uc001der.1	-							NM_017768	NP_060238	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40											ovary(1)	1						tcacacctgtaatcccagcac	0.134													4	2	---	---	---	---	
ELTD1	64123	broad.mit.edu	37	1	79445871	79445872	+	Intron	DEL	AC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79445871_79445872delAC	uc001diq.3	-							NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain						neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)|skin(1)	2				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		acagacacatacacacacacac	0.307													4	2	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82417394	82417394	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82417394delT	uc001dit.3	+						LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Intron|LPHN2_uc001div.2_Intron|LPHN2_uc009wcd.2_Intron|LPHN2_uc001diw.2_Intron	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		CTGGCTGAAATTTTTGAGAAA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98424053	98424053	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98424053delA								DPYD (37438 upstream) : MIR137 (87573 downstream)																							aatcacttacagggctgatca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	102651933	102651934	+	IGR	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102651933_102651934insT								OLFM3 (189143 upstream) : COL11A1 (690090 downstream)																							CAATTTTCCAATTTTTTTTCCC	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	110619024	110619024	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110619024delG								ALX3 (5702 upstream) : UBL4B (36038 downstream)																							TTGAGTGGATGGGGCAGAGAC	0.507													4	2	---	---	---	---	
CD58	965	broad.mit.edu	37	1	117086723	117086723	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117086723delC	uc001egm.2	-						CD58_uc001egn.2_Intron|CD58_uc010owy.1_Intron|CD58_uc001ego.1_Intron|CD58_uc001egp.3_Intron	NM_001779	NP_001770	P19256	LFA3_HUMAN	CD58 molecule isoform 1						blood coagulation|cell-cell adhesion|leukocyte migration	anchored to membrane|integral to plasma membrane	protein binding				0	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)		ATACTGTTCTCCCCACCTTGG	0.428													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145017964	145017965	+	5'UTR	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145017964_145017965insT	uc001elm.3	-	3					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emh.2_Intron|uc001emj.2_RNA	NM_001002810	NP_001002810	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)		TAGAATTCTTCTTTTTTTTATG	0.322			T	PDGFRB	MPD								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148864013	148864013	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148864013delC								NBPF16 (105702 upstream) : LOC645166 (64273 downstream)																							gatttataatcccaccccagc	0.000													6	7	---	---	---	---	
SF3B4	10262	broad.mit.edu	37	1	149899306	149899306	+	Intron	DEL	A	-	-	rs75973795		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149899306delA	uc001etj.1	-						SF3B4_uc001eti.1_5'Flank|SF3B4_uc001etk.1_Intron|SF3B4_uc009wll.1_Intron	NM_005850	NP_005841	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4							nucleoplasm|U12-type spliceosomal complex	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GGACAGGAGCAAAAAAAAAAG	0.443													10	7	---	---	---	---	
NUP210L	91181	broad.mit.edu	37	1	154072214	154072214	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154072214delA	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)			atacctcagtaaaaaaGAAGA	0.189													4	2	---	---	---	---	
C1orf182	128229	broad.mit.edu	37	1	156309299	156309299	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156309299delA	uc001foo.2	+						CCT3_uc001fol.1_5'Flank|CCT3_uc001fom.1_5'Flank|CCT3_uc001fon.1_5'Flank|CCT3_uc010phj.1_5'Flank|CCT3_uc010phk.1_5'Flank|CCT3_uc010phl.1_5'Flank|C1orf182_uc009wry.2_Intron|C1orf182_uc001fop.3_Intron	NM_144627	NP_653228	Q96A04	CA182_HUMAN	SSTK-interacting protein												0	Hepatocellular(266;0.158)					TTTTGTCCAGAAAAAAAAGGA	0.408													4	2	---	---	---	---	
KIRREL	55243	broad.mit.edu	37	1	158014786	158014787	+	Intron	DEL	CT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158014786_158014787delCT	uc001frn.3	+						KIRREL_uc010pib.1_Intron	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor							integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)					aaagaacttactcagaaggtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	160690500	160690500	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160690500delT								CD48 (8915 upstream) : SLAMF7 (18577 downstream)																							ggaatatggattttttttgcc	0.000													5	3	---	---	---	---	
UHMK1	127933	broad.mit.edu	37	1	162481974	162481974	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162481974delT	uc001gcc.1	+						UHMK1_uc001gcb.1_Intron|UHMK1_uc009wuu.1_Intron	NM_175866	NP_787062	Q8TAS1	UHMK1_HUMAN	kinase interacting stathmin						cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			CACCGATATCTTTTTTTTTTA	0.308													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166004194	166004197	+	IGR	DEL	TGTG	-	-	rs143962223		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166004194_166004197delTGTG								UCK2 (126857 upstream) : FAM78B (25219 downstream)																							TGTTTTGgcatgtgtgtacgctga	0.015													3	4	---	---	---	---	
NME7	29922	broad.mit.edu	37	1	169335785	169335785	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169335785delA	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|BLZF1_uc001gfw.2_5'Flank|BLZF1_uc001gfx.1_5'Flank|BLZF1_uc001gfy.2_5'Flank|NME7_uc001gfv.1_Intron	NM_013330	NP_037462	Q9Y5B8	NDK7_HUMAN	nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)					CACAGGAAAGAAAAAAACAAC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177538936	177538936	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177538936delT								FAM5B (287379 upstream) : SEC16B (358553 downstream)																							aaggcaagtattatgtcatat	0.010													4	2	---	---	---	---	
XPR1	9213	broad.mit.edu	37	1	180790143	180790143	+	Intron	DEL	T	-	-	rs148697141		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180790143delT	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0						tattcctcccttttttttttt	0.000													4	2	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	186143398	186143398	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186143398delA	uc001grq.1	+						HMCN1_uc001grs.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AGAGAAGGAGAAAAAAAGAAA	0.313													4	2	---	---	---	---	
TNNT2	7139	broad.mit.edu	37	1	201336197	201336197	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201336197delT	uc001gwf.2	-						TNNT2_uc001gwg.2_Intron|TNNT2_uc001gwh.2_Intron|TNNT2_uc001gwi.2_Intron|TNNT2_uc009wzr.2_Intron|TNNT2_uc001gwj.1_5'Flank|TNNT2_uc009wzs.1_5'Flank|TNNT2_uc001gwk.1_Intron|TNNT2_uc009wzt.1_Intron|TNNT2_uc001gwl.1_Intron	NM_000364	NP_000355	P45379	TNNT2_HUMAN	troponin T type 2, cardiac isoform 1						ATP catabolic process|muscle filament sliding|negative regulation of ATPase activity|positive regulation of ATPase activity|regulation of heart contraction|response to calcium ion|response to calcium ion|ventricular cardiac muscle tissue morphogenesis	cytosol|troponin complex	actin binding|tropomyosin binding|troponin C binding|troponin I binding				0						ACACTCCCCCTCCCATAGAGT	0.567													4	2	---	---	---	---	
PTPN7	5778	broad.mit.edu	37	1	202121510	202121511	+	Intron	DEL	AA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202121510_202121511delAA	uc001gxm.1	-						PTPN7_uc001gxl.1_Intron|PTPN7_uc001gxn.1_Intron|PTPN7_uc010ppv.1_Intron|PTPN7_uc010ppw.1_Intron|PTPN7_uc010ppx.1_Intron|PTPN7_uc010ppy.1_Intron|PTPN7_uc001gxo.1_Intron	NM_002832	NP_002823	P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type							cytosol|internal side of plasma membrane	protein binding|protein tyrosine phosphatase activity			skin(1)	1						TGAAGGAGGTAAAAAGAACAGA	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	208626824	208626825	+	IGR	INS	-	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208626824_208626825insC								PLXNA2 (209159 upstream) : LOC642587 (975343 downstream)																							ggttccctgtgccccagtcaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214450577	214450580	+	IGR	DEL	CTGT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214450577_214450580delCTGT								PROX1 (240817 upstream) : SMYD2 (3985 downstream)																							gcctcctctcctgtctgtgtcaaa	0.000													9	4	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236707828	236707829	+	Intron	INS	-	G	G	rs144740089	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236707828_236707829insG	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			CTGATTTTAAAGGGTTTTTTTT	0.411													4	6	---	---	---	---	
C1orf150	148823	broad.mit.edu	37	1	247712776	247712776	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247712776delT	uc001idf.2	+						C1orf150_uc009xgw.2_Intron|C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron	NM_145278	NP_660321	Q5JQS6	CA150_HUMAN	hypothetical protein LOC148823												0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0241)			cagaaaaacattttttttttt	0.080													4	2	---	---	---	---	
OR2T27	403239	broad.mit.edu	37	1	248814266	248814268	+	5'Flank	DEL	AAC	-	-	rs3033476		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248814266_248814268delAAC	uc010pzo.1	-							NM_001001824	NP_001001824	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTAGTCATGAACAAACCAAGGT	0.374													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5703442	5703443	+	IGR	DEL	GT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5703442_5703443delGT								None (None upstream) : SOX11 (129356 downstream)																							GCATGCAGTGgtgtgtgtgtgg	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	9955341	9955341	+	IGR	DEL	C	-	-	rs77051390		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9955341delC								YWHAQ (184235 upstream) : TAF1B (28230 downstream)																							TTCAGCTCTGCCCCCACCCTA	0.522													7	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	21184938	21184939	+	IGR	INS	-	G	G	rs138795477	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21184938_21184939insG								C2orf43 (162111 upstream) : APOB (39363 downstream)																							TGCCCCATGGCGGGGGGGTTGC	0.520													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	24692934	24692934	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24692934delT								ITSN2 (109537 upstream) : NCOA1 (94245 downstream)																							ACTGTGTACCTTTTTGATGCC	0.393													4	2	---	---	---	---	
CAD	790	broad.mit.edu	37	2	27457841	27457841	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27457841delA	uc002rji.2	+						CAD_uc010eyw.2_Intron	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate						'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)	tgctgcttccaaaaggggtga	0.104													4	2	---	---	---	---	
VIT	5212	broad.mit.edu	37	2	37008587	37008588	+	Intron	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37008587_37008588insT	uc002rpl.2	+						VIT_uc002rpm.2_Intron|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Intron	NM_053276	NP_444506	Q6UXI7	VITRN_HUMAN	vitrin							proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)				gagtggatgaatttttagttcc	0.109													4	2	---	---	---	---	
TIA1	7072	broad.mit.edu	37	2	70463511	70463514	+	Intron	DEL	AGTA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70463511_70463514delAGTA	uc002sgj.3	-						TIA1_uc002sgk.3_Intron|TIA1_uc002sgl.3_Intron|TIA1_uc002sgm.3_Intron|TIA1_uc010yqt.1_Intron	NM_022173	NP_071505	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding						apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0						ttgtatttttagtagagacggggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	71051517	71051517	+	IGR	DEL	C	-	-	rs67506291	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71051517delC								CLEC4F (3785 upstream) : CD207 (5831 downstream)																							atgatcttttcaaaaAaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91685682	91685682	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91685682delA								None (None upstream) : LOC654342 (119510 downstream)																							TGCAAGGGGGAAAAAGGATTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91729144	91729144	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91729144delG								None (None upstream) : LOC654342 (76048 downstream)																							agaaagacttgttttTTTTTT	0.119													4	2	---	---	---	---	
LIPT1	51601	broad.mit.edu	37	2	99778225	99778227	+	Intron	DEL	AAA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99778225_99778227delAAA	uc002szm.3	+						MRPL30_uc002szl.1_Intron|LIPT1_uc002szn.3_Intron|LIPT1_uc002szo.3_Intron|LIPT1_uc002szp.3_Intron|LIPT1_uc002szq.3_Intron|MRPL30_uc002szr.2_Intron	NM_145198	NP_660199	Q9Y234	LIPT_HUMAN	lipoyltransferase 1 precursor						lipid metabolic process|protein lipoylation	mitochondrion	acyltransferase activity				0					Lipoic Acid(DB00166)	AAATTATTTGAAATTTGTCTTCA	0.236													4	2	---	---	---	---	
MRPS9	64965	broad.mit.edu	37	2	105709772	105709773	+	Intron	INS	-	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105709772_105709773insG	uc002tcn.3	+							NM_182640	NP_872578	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9 precursor						DNA damage response, detection of DNA damage|translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0						CTAAAATGGAATTGAAGAACAA	0.292													4	2	---	---	---	---	
SLC20A1	6574	broad.mit.edu	37	2	113418431	113418432	+	Intron	INS	-	TACTA	TACTA	rs60682605		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113418431_113418432insTACTA	uc002tib.2	+							NM_005415	NP_005406	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate						phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to plasma membrane	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity			ovary(2)	2						TTATTTGTCTTGGGAGCTAAGA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	120196456	120196456	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120196456delG								TMEM37 (362 upstream) : SCTR (965 downstream)																							CCACACTGGCGGCATCTTAGC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126106742	126106742	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126106742delT								CNTNAP5 (433881 upstream) : None (None downstream)																							cactcccaacttttttttgtt	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131566429	131566430	+	IGR	DEL	CT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131566429_131566430delCT								FAM123C (40722 upstream) : ARHGEF4 (106356 downstream)																							tacacaaatgctcataacagta	0.000													4	2	---	---	---	---	
MCM6	4175	broad.mit.edu	37	2	136617182	136617183	+	Intron	DEL	TT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136617182_136617183delTT	uc002tuw.2	-							NM_005915	NP_005906	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6						cell cycle checkpoint|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	MCM complex	ATP binding|identical protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.166)	Atorvastatin(DB01076)	TCGGCttttctttttttttttt	0.188													6	3	---	---	---	---	
PKP4	8502	broad.mit.edu	37	2	159532384	159532384	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159532384delG	uc002tzv.2	+						PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Intron|PKP4_uc002uaa.2_Intron|uc002uab.1_Intron|PKP4_uc002uac.2_Intron|PKP4_uc002uad.2_Intron|PKP4_uc002uae.1_Intron	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a						cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						GTCAAGGTTTGGGGGGCTGTT	0.368										HNSCC(62;0.18)			4	2	---	---	---	---	
LRP2	4036	broad.mit.edu	37	2	170128122	170128135	+	Intron	DEL	CACACACACACACA	-	-	rs146955000		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170128122_170128135delCACACACACACACA	uc002ues.2	-						LRP2_uc010zdf.1_Intron	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	GCAAAacatgcacacacacacacacacacacaca	0.196													7	8	---	---	---	---	
UBR3	130507	broad.mit.edu	37	2	170933587	170933588	+	Intron	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170933587_170933588insT	uc010zdi.1	+						UBR3_uc002ufr.3_Intron|UBR3_uc010fqa.2_Intron|UBR3_uc002uft.3_Intron|UBR3_uc010zdj.1_Intron|UBR3_uc002ufu.3_Intron	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0						TTAAGACCGAATTTTTTTTTCC	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	171742504	171742505	+	IGR	DEL	TT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171742504_171742505delTT								GAD1 (24847 upstream) : GORASP2 (42477 downstream)																							AGCAGCTTCCTTTTTTACTTAA	0.446													4	2	---	---	---	---	
PLEKHA3	65977	broad.mit.edu	37	2	179362668	179362668	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179362668delT	uc002umn.2	+							NM_019091	NP_061964	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A							cytoplasm|membrane				ovary(1)|kidney(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AATCTTCATGtttttttttta	0.194													3	3	---	---	---	---	
DNAH7	56171	broad.mit.edu	37	2	196892425	196892425	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196892425delA	uc002utj.3	-							NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TAAGGCATGTAAAGCTATACA	0.289													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	200900984	200900984	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200900984delG								C2orf47 (72139 upstream) : SPATS2L (269620 downstream)																							CCCTTGCTCTGGACTGCCCTG	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217533678	217533678	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217533678delA								IGFBP2 (4522 upstream) : IGFBP5 (3151 downstream)																							aaaacaaaacaaaaAAACATG	0.249													4	2	---	---	---	---	
DIS3L2	129563	broad.mit.edu	37	2	233128583	233128583	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233128583delA	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)		GAAGGCTTGGAAAAAAAGTAT	0.388													6	3	---	---	---	---	
IQCA1	79781	broad.mit.edu	37	2	237395124	237395124	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237395124delA	uc002vvz.1	-						IQCA1_uc002vwb.2_Intron|IQCA1_uc002vwa.1_Intron|IQCA1_uc010zni.1_Intron	NM_024726	NP_079002	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1								ATP binding			ovary(1)	1						CCAGCACCAGAAAAAAAAAAA	0.318													4	3	---	---	---	---	
KIF1A	547	broad.mit.edu	37	2	241743443	241743443	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241743443delG	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles						anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		ccagcactttggaaggccgag	0.085													4	2	---	---	---	---	
RARB	5915	broad.mit.edu	37	3	25626107	25626107	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25626107delA	uc011awl.1	+						RARB_uc003cdi.1_Intron|RARB_uc003cdh.2_Intron	NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	gtgtgcctggaagggagtgag	0.000													4	2	---	---	---	---	
TRAK1	22906	broad.mit.edu	37	3	42251012	42251012	+	Intron	DEL	A	-	-	rs71994031		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42251012delA	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron|TRAK1_uc011azj.1_Intron|TRAK1_uc003cla.2_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						ATTTTACTTTAAAAAAAAAAT	0.403													4	2	---	---	---	---	
SEMA3B	7869	broad.mit.edu	37	3	50305232	50305232	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50305232delG	uc003cyu.2	+						SEMA3B_uc010hlh.1_Intron|SEMA3B_uc003cyt.2_Intron|SEMA3B_uc003cyv.2_5'Flank|SEMA3B_uc003cyw.2_5'Flank|SEMA3B_uc010hli.2_5'Flank|SEMA3B_uc003cyx.2_5'Flank	NM_004636	NP_004627	Q13214	SEM3B_HUMAN	semaphorin 3B isoform 1 precursor						axon guidance|cell-cell signaling	endoplasmic reticulum|extracellular region|membrane	receptor activity			lung(2)|central_nervous_system(2)|kidney(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GGAGGGAGGTGGGGGTCCTGG	0.637													4	2	---	---	---	---	
GRM2	2912	broad.mit.edu	37	3	51749554	51749555	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51749554_51749555delTT	uc010hlv.2	+	4	2004_2005	c.1765_1766delTT	c.(1765-1767)TTTfs	p.F589fs	GRM2_uc003dbo.3_5'UTR|GRM2_uc010hlu.2_RNA	NM_000839	NP_000830	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2 isoform a	589	Helical; Name=1; (Potential).				synaptic transmission	integral to plasma membrane				lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)	GCTGGGTGTCTTTGTGCGGCAC	0.619													22	14	---	---	---	---	
NEK4	6787	broad.mit.edu	37	3	52768704	52768705	+	Intron	DEL	AG	-	-	rs59075830		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52768704_52768705delAG	uc003dfq.3	-						NEK4_uc011bej.1_Intron	NM_003157	NP_003148	P51957	NEK4_HUMAN	NIMA-related kinase 4						cell division|mitosis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		aaaaaaaaaaagaaCAGTTATA	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	59238440	59238440	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59238440delT								C3orf67 (202682 upstream) : FHIT (496598 downstream)																							ataagttgccttttttttcta	0.249													4	2	---	---	---	---	
ATXN7	6314	broad.mit.edu	37	3	63910215	63910215	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63910215delG	uc003dlw.3	+						ATXN7_uc003dlv.2_Intron|ATXN7_uc010hnv.2_Intron	NM_000333	NP_000324	O15265	ATX7_HUMAN	ataxin 7 isoform a						cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		tcttcagtgaggcagtaagga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72697246	72697247	+	IGR	DEL	AG	-	-	rs4054969		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72697246_72697247delAG								RYBP (201472 upstream) : SHQ1 (101183 downstream)																							agcggttgacaggggctgatca	0.054													3	4	---	---	---	---	
KIAA1524	57650	broad.mit.edu	37	3	108300737	108300737	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108300737delT	uc003dxb.3	-						KIAA1524_uc003dxc.1_Intron|KIAA1524_uc010hpw.1_Intron	NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen							cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						TGCTTTACAATTTTTTTTTCC	0.269													4	3	---	---	---	---	
SLC9A10	285335	broad.mit.edu	37	3	111949993	111949996	+	Intron	DEL	CTTT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111949993_111949996delCTTT	uc003dyu.2	-						SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5						ctttttctccctttctttctttct	0.127													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117683887	117683888	+	IGR	DEL	TG	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117683887_117683888delTG								None (None upstream) : IGSF11 (935593 downstream)																							ATCAGGTGACtgtgtgtgtgtg	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117967911	117967911	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117967911delA								None (None upstream) : IGSF11 (651570 downstream)																							gccaaaccacaaaaaaaaacc	0.080													4	2	---	---	---	---	
SLC15A2	6565	broad.mit.edu	37	3	121630123	121630124	+	Intron	DEL	TG	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121630123_121630124delTG	uc003eep.2	+						SLC15A2_uc011bjn.1_Intron	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a						protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)	AGGGTTTCTCTGTGTGTGTGTG	0.436													4	2	---	---	---	---	
KIAA1257	57501	broad.mit.edu	37	3	128706154	128706154	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128706154delT	uc003elj.3	-						KIAA1257_uc003elg.1_Intron|KIAA1257_uc003eli.3_Intron	NM_020741	NP_065792	Q9ULG3	K1257_HUMAN	hypothetical protein LOC57501												0						ttgttttttgttttttttttt	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	134125189	134125189	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134125189delG								AMOTL2 (30930 upstream) : ANAPC13 (71358 downstream)																							GTATAAATTCGGAGGATCAGA	0.542													4	2	---	---	---	---	
EPHB1	2047	broad.mit.edu	37	3	134895371	134895372	+	Intron	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134895371_134895372delCA	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						TATATGTGTGCACACACACACA	0.490													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	137061658	137061658	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137061658delC								IL20RB (331738 upstream) : SOX14 (421921 downstream)																							AAGGCTGATGCCCCTGCCTAG	0.488													4	2	---	---	---	---	
ATR	545	broad.mit.edu	37	3	142277366	142277369	+	Intron	DEL	AAAT	-	-	rs72319579		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142277366_142277369delAAAT	uc003eux.3	-							NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						tccgtctcaaaaataaataaataa	0.069								Other_conserved_DNA_damage_response_genes					3	6	---	---	---	---	
C3orf58	205428	broad.mit.edu	37	3	143697058	143697058	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143697058delT	uc003evo.2	+						C3orf58_uc011bnl.1_Intron	NM_173552	NP_775823	Q8NDZ4	CC058_HUMAN	hypothetical protein LOC205428 isoform a							COPI vesicle coat|extracellular region				ovary(1)	1						CAGAATGCTATTTTTTTCTTT	0.333													4	2	---	---	---	---	
HPS3	84343	broad.mit.edu	37	3	148860978	148860979	+	Intron	DEL	AA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148860978_148860979delAA	uc003ewu.1	+						HPS3_uc003ewt.1_Intron|HPS3_uc011bnq.1_Intron	NM_032383	NP_115759	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein							cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			atatgaccttaactctaagccc	0.079									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
HPS3	84343	broad.mit.edu	37	3	148886037	148886037	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148886037delT	uc003ewu.1	+						CP_uc011bnr.1_Intron|HPS3_uc011bnq.1_Intron|HPS3_uc003ewv.1_Intron	NM_032383	NP_115759	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3 protein							cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AGCATCAGTGTTTTAAAATGT	0.284									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	154620040	154620040	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154620040delA								GPR149 (472536 upstream) : MME (121873 downstream)																							ACAGAGCCAGAAAAAAACACC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159807262	159807264	+	Intron	DEL	TAA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159807262_159807264delTAA	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		TTGCTGGCCTTAATCTCTGGTCA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168105164	168105165	+	IGR	DEL	AC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168105164_168105165delAC								GOLIM4 (291747 upstream) : MIR551B (164477 downstream)																							agtgttaaagacacacacacac	0.094													4	3	---	---	---	---	
TRA2B	6434	broad.mit.edu	37	3	185635830	185635831	+	Intron	DEL	TT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185635830_185635831delTT	uc003fpv.2	-						TRA2B_uc003fpt.2_Intron|TRA2B_uc003fpu.2_Intron|TRA2B_uc010hym.2_Intron|TRA2B_uc003fpw.2_Intron	NM_004593	NP_004584	P62995	TRA2B_HUMAN	splicing factor, arginine/serine-rich 10						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)	2						TTATTTACTGTTTCAATTAGAA	0.312													4	2	---	---	---	---	
DGKG	1608	broad.mit.edu	37	3	186049007	186049007	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186049007delC	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	caactcaaagcaagactgaca	0.000													4	2	---	---	---	---	
SDHAP2	727956	broad.mit.edu	37	3	195410327	195410327	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195410327delT	uc003fuw.2	+						SDHAP2_uc003fuv.2_Intron					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						GGAGGTAGTCTCCCAGCGCTT	0.289													3	4	---	---	---	---	
TNK2	10188	broad.mit.edu	37	3	195590410	195590410	+	3'UTR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195590410delG	uc003fvu.1	-	15					TNK2_uc003fvq.1_3'UTR|TNK2_uc003fvr.1_3'UTR|TNK2_uc003fvs.1_3'UTR|TNK2_uc003fvt.1_3'UTR	NM_005781	NP_005772	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 1						positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction	adherens junction|cytoplasmic vesicle membrane|endosome|nucleus	ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1)	10	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	TTCCAGCCCTGGGGCCTTGGG	0.627											OREG0016001	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	4	554558	554559	+	IGR	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:554558_554559delCA								PIGG (21239 upstream) : PDE6B (64804 downstream)																							TCATAACCTTCAGCAGGTGACA	0.342													4	2	---	---	---	---	
KIAA1530	57654	broad.mit.edu	37	4	1373699	1373700	+	Intron	INS	-	TTT	TTT	rs140840696	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1373699_1373700insTTT	uc003gde.3	+						KIAA1530_uc010ibv.2_Intron	NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654												0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)			TGACCGTGTTCTCCCTGGGTGC	0.644													4	3	---	---	---	---	
MXD4	10608	broad.mit.edu	37	4	2263440	2263440	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2263440delG	uc003geu.1	-						MXD4_uc003gev.1_Intron	NM_006454	NP_006445	Q14582	MAD4_HUMAN	MAD4						negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|transcription corepressor activity				0						ggtcgggagcgggggGCGGTA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3585546	3585547	+	Intron	DEL	AT	-	-	rs140342020		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3585546_3585547delAT	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		ctgtgtgccgatacctaattgt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	11956474	11956475	+	IGR	INS	-	A	A	rs149187146	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11956474_11956475insA								HS3ST1 (525937 upstream) : None (None downstream)																							gcaaaGAAGAGAAAAAAAACAA	0.188													9	5	---	---	---	---	
GBA3	57733	broad.mit.edu	37	4	22772910	22772910	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22772910delT	uc003gqp.3	+						GBA3_uc010iep.2_Intron|GBA3_uc011bxo.1_Intron	NM_020973	NP_066024	Q9H227	GBA3_HUMAN	cytosolic beta-glucosidase isoform a						glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity				0						TTTGGAGTAGTTTTTTTTCTT	0.259													4	2	---	---	---	---	
PDS5A	23244	broad.mit.edu	37	4	39878937	39878938	+	Intron	INS	-	ATCAGACATT	ATCAGACATT	rs145057027	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39878937_39878938insATCAGACATT	uc003guv.3	-						PDS5A_uc010ifo.2_Intron	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						agttatggctaATCAGAAATAC	0.272													4	2	---	---	---	---	
GABRB1	2560	broad.mit.edu	37	4	47107498	47107498	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47107498delT	uc003gxh.2	+						GABRB1_uc011bze.1_Intron	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	tggatgaggcttcctcagtga	0.139													4	3	---	---	---	---	
PTPN13	5783	broad.mit.edu	37	4	87674711	87674711	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87674711delT	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		tagggaccagTTTTTAATCTT	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	94719311	94719311	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94719311delA								GRID2 (25663 upstream) : ATOH1 (30767 downstream)																							tctcaagaagaaaaaaaataa	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	98257574	98257574	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98257574delA								None (None upstream) : C4orf37 (222460 downstream)																							AAGCCAGCCCAAAGAAAGAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	115515626	115515626	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115515626delT								ARSJ (614748 upstream) : UGT8 (3985 downstream)																							ctcccttgggttttcaggtaa	0.000													4	2	---	---	---	---	
ANKRD50	57182	broad.mit.edu	37	4	125629505	125629506	+	Intron	DEL	TT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125629505_125629506delTT	uc003ifg.3	-						ANKRD50_uc011cgo.1_Intron|ANKRD50_uc010inw.2_Intron	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50											central_nervous_system(1)	1						GATACAACAGTTTTAACGCTGA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	166705057	166705057	+	IGR	DEL	T	-	-	rs11324036		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166705057delT								CPE (285576 upstream) : TLL1 (89353 downstream)																							ACTCTCTCACTTTTTTTTTTT	0.408													4	4	---	---	---	---	
DDX60	55601	broad.mit.edu	37	4	169235473	169235474	+	Intron	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169235473_169235474delCA	uc003irp.2	-							NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		ATTGAacactcacacacacaca	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	171312657	171312657	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171312657delT								AADAT (301285 upstream) : None (None downstream)																							TTAACTTTCCTTCCACTTTGT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	171387289	171387289	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171387289delT								AADAT (375917 upstream) : None (None downstream)																							tttcacctccttaggtctgtt	0.000													3	3	---	---	---	---	
ZFP42	132625	broad.mit.edu	37	4	188925071	188925071	+	3'UTR	DEL	T	-	-	rs79051567		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188925071delT	uc003izg.1	+	3					ZFP42_uc003izh.1_3'UTR|ZFP42_uc003izi.1_3'UTR	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42						female gonad development|male gonad development|meiosis	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		ACATGGTGCATTTTTTTTTCT	0.308													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2720673	2720673	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2720673delC								IRX4 (837793 upstream) : IRX2 (25608 downstream)																							CATTCTCCCTCCCACCCACAC	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	14509859	14509859	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14509859delG								TRIO (409 upstream) : FAM105A (72032 downstream)																							GCACTGGTGTGGGGAGTCCTT	0.507													4	2	---	---	---	---	
OXCT1	5019	broad.mit.edu	37	5	41844904	41844904	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41844904delC	uc003jmn.2	-							NM_000436	NP_000427	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1 precursor						cellular lipid metabolic process|ketone body catabolic process	mitochondrial matrix	3-oxoacid CoA-transferase activity|protein homodimerization activity			ovary(2)|large_intestine(1)	3					Succinic acid(DB00139)	gttggctctaccatgaacata	0.000													4	2	---	---	---	---	
HMGCS1	3157	broad.mit.edu	37	5	43297941	43297941	+	Intron	DEL	A	-	-	rs75413713		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43297941delA	uc003jnr.3	-						HMGCS1_uc003jnp.3_5'Flank|HMGCS1_uc003jnq.3_Intron	NM_001098272	NP_001091742	Q01581	HMCS1_HUMAN	hydroxymethylglutaryl-CoA synthase 1						cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	hydroxymethylglutaryl-CoA synthase activity				0						actcggtctcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	61138540	61138540	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61138540delG								FLJ37543 (136178 upstream) : KIF2A (463449 downstream)																							ATGCAGAAATGGGGACAGCTG	0.502													4	2	---	---	---	---	
RGNEF	64283	broad.mit.edu	37	5	73210972	73210972	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73210972delG	uc011csq.1	+						RGNEF_uc010izf.2_Intron|RGNEF_uc011csr.1_Intron|RGNEF_uc003kcz.3_Intron|RGNEF_uc003kda.3_Intron	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor						cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)		TGTTTTTATTGGTTTTTTTTT	0.338													4	2	---	---	---	---	
COL4A3BP	10087	broad.mit.edu	37	5	74674982	74674983	+	Intron	DEL	AG	-	-	rs11746794		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74674982_74674983delAG	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron	NM_005713	NP_005704	Q9Y5P4	C43BP_HUMAN	alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		acttcagcttaggaaacagagc	0.074													4	2	---	---	---	---	
RGMB	285704	broad.mit.edu	37	5	98115932	98115934	+	Intron	DEL	GTT	-	-	rs2250807	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98115932_98115934delGTT	uc003knc.2	+						RGMB_uc003knb.2_3'UTR	NM_001012761	NP_001012779	Q6NW40	RGMB_HUMAN	RGM domain family, member B						axon guidance|BMP signaling pathway|cell adhesion|positive regulation of transcription, DNA-dependent	anchored to plasma membrane|ER-Golgi intermediate compartment|membrane raft	identical protein binding				0		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		TTGATAAAGGGTTAAATAAAAAT	0.261													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	118088234	118088234	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118088234delA								None (None upstream) : DTWD2 (84337 downstream)																							ATTTCATAATAAAAAAAAAAT	0.328													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124475196	124475197	+	IGR	INS	-	T	T	rs143738859	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124475196_124475197insT								ZNF608 (390696 upstream) : None (None downstream)																							ttggcaggaaattttttttgtg	0.000													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129634809	129634809	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129634809delT								CHSY3 (112483 upstream) : HINT1 (860066 downstream)																							caagaaaagctttgaagaaca	0.000													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148334267	148334268	+	RNA	DEL	CT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148334267_148334268delCT	uc003lpp.1	-	18		c.4125_4126delAG				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)			TCCTCATTACCTCTCTCTCTCT	0.480													4	2	---	---	---	---	
GRIA1	2890	broad.mit.edu	37	5	152870806	152870806	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152870806delA	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_5'Flank|GRIA1_uc011dcy.1_5'Flank|GRIA1_uc011dcz.1_5'Flank|GRIA1_uc010jia.1_Intron	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GCTTTGGAGGAAAAAAAAAAT	0.433													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154617829	154617829	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154617829delA								KIF4B (220144 upstream) : SGCD (517234 downstream)																							GGAATGCAGTAAAAAAAAAAC	0.403													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165692364	165692364	+	IGR	DEL	A	-	-	rs67197968		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165692364delA								None (None upstream) : None (None downstream)																							gaattaagggaaaaaaagact	0.070													6	4	---	---	---	---	
BTNL9	153579	broad.mit.edu	37	5	180473350	180473351	+	Intron	INS	-	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180473350_180473351insC	uc003mmt.2	+						BTNL9_uc011dhi.1_Intron	NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor							integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACCTCCTGCACACTTCCCAGC	0.569													3	3	---	---	---	---	
MYLK4	340156	broad.mit.edu	37	6	2678805	2678806	+	Intron	DEL	AT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2678805_2678806delAT	uc003mty.3	-						MYLK4_uc003mtx.3_Intron	NM_001012418	NP_001012418	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4								ATP binding|protein serine/threonine kinase activity			breast(3)|ovary(1)	4	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				AACTGCAGCAATAACAGAATAT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	21386970	21386973	+	IGR	DEL	GAGA	-	-	rs71731827		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21386970_21386973delGAGA								CDKAL1 (154338 upstream) : SOX4 (206999 downstream)																							GAGGGGATTGGAGAGAGAAAGTAG	0.520													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28083623	28083623	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28083623delA	uc010jqw.1	-											SubName: Full=cDNA FLJ45995 fis, clone SKNMC2003639;																		GATGAGTGTGAAAAAGTCTTT	0.373													4	2	---	---	---	---	
RNF39	80352	broad.mit.edu	37	6	30040345	30040345	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30040345delT	uc003npe.2	-						RNF39_uc003npd.2_Intron	NM_025236	NP_079512	Q9H2S5	RNF39_HUMAN	ring finger protein 39 isoform 1							cytoplasm	zinc ion binding				0						CAGGGATCTGTTGTTTGAATG	0.393													4	2	---	---	---	---	
CYP39A1	51302	broad.mit.edu	37	6	46522788	46522789	+	Intron	DEL	AC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46522788_46522789delAC	uc003oyf.1	-						CYP39A1_uc011dwa.1_Intron|CYP39A1_uc010jzd.1_Intron	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,						bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1						gcagacacagacacacacacac	0.233													4	2	---	---	---	---	
GPR116	221395	broad.mit.edu	37	6	46863793	46863793	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46863793delT	uc003oyo.3	-						GPR116_uc003oyp.3_Intron|GPR116_uc003oyq.3_Intron|GPR116_uc003oyr.2_Intron	NM_001098518	NP_001091988	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)			cctctgcttctttcctatctt	0.035													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57413897	57413898	+	Intron	INS	-	TT	TT	rs139691483		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57413897_57413898insTT	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)		AAGGTGGACTCTTTTTTGCCAA	0.366													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57565434	57565436	+	IGR	DEL	TGT	-	-	rs148602557		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57565434_57565436delTGT								PRIM2 (52059 upstream) : GUSBL2 (680723 downstream)																							CTTAAGAAGATGTTTTTttttct	0.167													4	2	---	---	---	---	
TMEM30A	55754	broad.mit.edu	37	6	75985674	75985675	+	Intron	INS	-	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75985674_75985675insG	uc003phw.2	-						TMEM30A_uc003phx.2_Intron	NM_018247	NP_060717	Q9NV96	CC50A_HUMAN	transmembrane protein 30A isoform 1							integral to membrane					0						aatagacctgtgggaaggggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85995862	85995863	+	IGR	INS	-	AGCGGACAC	AGCGGACAC			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85995862_85995863insAGCGGACAC								TBX18 (521963 upstream) : NT5E (163439 downstream)																							agcggtggtggagcggacacag	0.233													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	91352814	91352814	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91352814delG								MAP3K7 (55907 upstream) : None (None downstream)																							CCCGGCTTTTGGTGTCATTCC	0.348													4	2	---	---	---	---	
TRDN	10345	broad.mit.edu	37	6	123856390	123856390	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123856390delG	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron|TRDN_uc010keo.1_Intron	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)		CTGAGTCACTGGTAGCTTTGC	0.388													4	2	---	---	---	---	
LAMA2	3908	broad.mit.edu	37	6	129613067	129613067	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129613067delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		ACCTTAAACATTTTTTTTTGG	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148003172	148003173	+	IGR	DEL	TC	-	-	rs112821788		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148003172_148003173delTC								SAMD5 (112015 upstream) : SASH1 (660556 downstream)																							aatcctggaatctctcattctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166478178	166478179	+	IGR	DEL	GT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166478178_166478179delGT								LOC441177 (75075 upstream) : T (92907 downstream)																							TTCATAATGGGTGTGAACAATG	0.535													4	2	---	---	---	---	
SDK1	221935	broad.mit.edu	37	7	3941835	3941836	+	Intron	DEL	TG	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3941835_3941836delTG	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)		cgcgtgtgcatgtgtgtgtgtg	0.000													4	3	---	---	---	---	
TMEM106B	54664	broad.mit.edu	37	7	12258399	12258400	+	Intron	DEL	AC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12258399_12258400delAC	uc011jxk.1	+						TMEM106B_uc003ssh.2_Intron	NM_018374	NP_060844	Q9NUM4	T106B_HUMAN	transmembrane protein 106B							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		AGCAGTACAAACACACACACAC	0.361													4	2	---	---	---	---	
BBS9	27241	broad.mit.edu	37	7	33544889	33544890	+	Intron	INS	-	T	T	rs141283591	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33544889_33544890insT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc003tdr.1_Intron|BBS9_uc003tds.1_Intron|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)			TACTGTGGGCATTTTTTTTTAA	0.366									Bardet-Biedl_syndrome				4	7	---	---	---	---	
AMPH	273	broad.mit.edu	37	7	38577438	38577438	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38577438delA	uc003tgu.2	-						AMPH_uc003tgv.2_Intron	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						atctggagccaaaaaaaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41090256	41090256	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41090256delT								C7orf10 (189899 upstream) : INHBA (638347 downstream)																							aaacttcctatttccccaaat	0.000													4	2	---	---	---	---	
LOC285954	285954	broad.mit.edu	37	7	41797976	41797976	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41797976delT	uc003tht.3	+							NR_027118				Homo sapiens cDNA FLJ38947 fis, clone NT2NE2017792.												0						taaacactgattttttttttc	0.000													9	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	52865984	52865984	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52865984delA								None (None upstream) : POM121L12 (237365 downstream)																							GATGAAGCAGAAAAGGAAAAA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61976261	61976261	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61976261delT								None (None upstream) : LOC643955 (775411 downstream)																							aatttgcaagtggagatttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	73065111	73065114	+	IGR	DEL	GTGT	-	-	rs71517402		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73065111_73065114delGTGT								MLXIPL (26241 upstream) : VPS37D (17060 downstream)																							cagagtcagcgtgtgtgtgtgtgt	0.216													4	2	---	---	---	---	
GTF2I	2969	broad.mit.edu	37	7	74160447	74160447	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74160447delA	uc003uau.2	+						GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|GTF2I_uc003uba.2_5'Flank	NM_032999	NP_127492	P78347	GTF2I_HUMAN	general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0						TTTTTTTTTTAAAAAAAACAA	0.338													3	3	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76626961	76626962	+	Intron	INS	-	TG	TG	rs140820337		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76626961_76626962insTG	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						ggaggtggggatgtggggtgtg	0.000													9	5	---	---	---	---	
PCLO	27445	broad.mit.edu	37	7	82721710	82721711	+	Intron	INS	-	A	A	rs149017834	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82721710_82721711insA	uc003uhx.2	-						PCLO_uc003uhv.2_Intron	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1						cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						CCATGGACCCGGCACAAATATA	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	97337852	97337852	+	IGR	DEL	A	-	-	rs140745260		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97337852delA								ACN9 (526779 upstream) : TAC1 (23419 downstream)																							gacctcactcaaaaaaaaaaa	0.085													4	2	---	---	---	---	
EMID2	136227	broad.mit.edu	37	7	101189230	101189230	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101189230delT	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)					tcagcaggtgtttagtgagca	0.358													4	2	---	---	---	---	
EMID2	136227	broad.mit.edu	37	7	101198725	101198725	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101198725delG	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)					CAGGACATGTGGGGGAAGCTg	0.284													4	2	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101898041	101898042	+	Intron	DEL	GT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101898041_101898042delGT	uc003uyt.2	+						CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron|uc003uyy.2_5'Flank	NM_001913	NP_001904	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform b						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						TGGCGAGGTGGTGACCTGAGGC	0.550													4	2	---	---	---	---	
COG5	10466	broad.mit.edu	37	7	107056320	107056323	+	Intron	DEL	TGTG	-	-	rs62482539		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107056320_107056323delTGTG	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4						tatgtatgtatgtgtgTGTATATA	0.039													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111625241	111625241	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111625241delC	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron|DOCK4_uc003vgb.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)				CTCCAGGGCACCCACGGTACA	0.453													4	2	---	---	---	---	
KCP	375616	broad.mit.edu	37	7	128515056	128515056	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128515056delG	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						GTGTGACCCCGAAAGAGGGAG	0.517													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	132018277	132018279	+	Intron	DEL	CTG	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132018277_132018279delCTG	uc003vra.3	-							NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						CCCCTGACTCCTGCTGCTGCTGA	0.611													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140965457	140965457	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140965457delG								MRPS33 (250676 upstream) : AGK (285621 downstream)																							GCAGTTAGGTGGGGCACGTCT	0.303													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153985865	153985865	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153985865delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			atatgctggtaaaaaaaaaca	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155882438	155882438	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155882438delC								SHH (277471 upstream) : C7orf4 (450747 downstream)																							gctccagtgacaaaaattata	0.000													4	2	---	---	---	---	
ARHGEF10	9639	broad.mit.edu	37	8	1882338	1882338	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1882338delA	uc003wpr.2	+						ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc010lre.2_Intron	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		ctgtccctacaaaaaaattag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2226648	2226649	+	IGR	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2226648_2226649insT								MYOM2 (133269 upstream) : CSMD1 (566227 downstream)																							ctttgactgtcatgtctgtgtt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12721912	12721913	+	IGR	INS	-	A	A	rs145778340	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12721912_12721913insA								LOC340357 (53002 upstream) : C8orf79 (81238 downstream)																							AGAAGTTTGCCATCTCTATCTC	0.401													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21017961	21017962	+	IGR	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21017961_21017962delCA								LZTS1 (905158 upstream) : GFRA2 (531568 downstream)																							GCACACCATTCACACACACTAT	0.257													4	2	---	---	---	---	
DOCK5	80005	broad.mit.edu	37	8	25222435	25222435	+	Intron	DEL	A	-	-	rs3215160		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25222435delA	uc003xeg.2	+						DOCK5_uc010luf.1_Intron|DOCK5_uc003xeh.1_Intron|DOCK5_uc003xei.2_Intron|DOCK5_uc003xej.2_Intron	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TAACATATGTAAAAAAAAAAT	0.318													7	4	---	---	---	---	
CCDC25	55246	broad.mit.edu	37	8	27592873	27592874	+	3'UTR	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27592873_27592874insT	uc003xgc.2	-	9					CCDC25_uc003xgd.2_3'UTR|CCDC25_uc011lan.1_RNA|CCDC25_uc011lao.1_RNA|CCDC25_uc003xge.2_RNA	NM_018246	NP_060716	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25												0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		TTAGTTCCTTCTAAAATCATAA	0.436													4	2	---	---	---	---	
DUSP26	78986	broad.mit.edu	37	8	33451770	33451770	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33451770delG	uc003xjp.2	-						DUSP26_uc003xjq.2_Intron	NM_024025	NP_076930	Q9BV47	DUS26_HUMAN	dual specificity phosphatase 26							Golgi apparatus|nucleus	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0				KIRC - Kidney renal clear cell carcinoma(67;0.0918)|Kidney(114;0.111)		tgttttgcctggagaagagaa	0.085													4	2	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40511737	40511737	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40511737delC	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			agactccctgccatgctgctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	59701840	59701840	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59701840delG								NSMAF (129436 upstream) : TOX (16137 downstream)																							ggctggaacagccctgcagag	0.000													2	4	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	69032010	69032010	+	Intron	DEL	T	-	-	rs113191686		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69032010delT	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						CTTTTTAGTATTTTTTTTTGT	0.279													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	76708251	76708252	+	IGR	DEL	TC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76708251_76708252delTC								HNF4G (229192 upstream) : LOC100192378 (814863 downstream)																							tttctttctatctCTctctctc	0.035													9	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	88800612	88800612	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88800612delT								CNBD1 (405657 upstream) : DCAF4L2 (82361 downstream)																							GCTTGTCATATTTTTTTTTGT	0.358													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96312338	96312338	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96312338delT								C8orf37 (30901 upstream) : GDF6 (842222 downstream)																							tgggggggggtgctcttgtgc	0.000													4	2	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100865043	100865043	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100865043delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			tcatgagggattttttgagct	0.000													4	2	---	---	---	---	
FER1L6	654463	broad.mit.edu	37	8	125061612	125061612	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125061612delT	uc003yqw.2	+						uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			ATACAGGTCCTTTTAGGATCA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135244660	135244660	+	IGR	DEL	A	-	-	rs112859771		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135244660delA								ST3GAL1 (660477 upstream) : ZFAT (245373 downstream)																							aggcaaaaagaaaaaaaaaag	0.000													5	4	---	---	---	---	
SLC24A2	25769	broad.mit.edu	37	9	19741085	19741088	+	Intron	DEL	CACC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19741085_19741088delCACC	uc003zoa.1	-						SLC24A2_uc003zob.1_Intron	NM_020344	NP_065077	Q9UI40	NCKX2_HUMAN	solute carrier family 24						visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		AATGCTGTCTCACCCTTCCTGGGC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	23609299	23609300	+	Intron	DEL	AC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23609299_23609300delAC	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																		TTTTTTAAAAACACACACACAC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	33571222	33571222	+	IGR	DEL	T	-	-	rs143529725		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33571222delT								SUGT1P1 (60175 upstream) : ANXA2P2 (53001 downstream)																							attattattattttttttttt	0.249													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67301383	67301384	+	IGR	INS	-	G	G	rs144184994		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67301383_67301384insG								AQP7P1 (11891 upstream) : FAM27B (491546 downstream)																							GGAGCATGTTTGGGCATCAGTG	0.569													3	7	---	---	---	---	
APBA1	320	broad.mit.edu	37	9	72072716	72072716	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72072716delC	uc004ahh.2	-							NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,						axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1						TTTTTTGCATCCAGCAATCTG	0.413													4	2	---	---	---	---	
OSTF1	26578	broad.mit.edu	37	9	77742812	77742813	+	Intron	INS	-	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77742812_77742813insA	uc004ajv.3	+						OSTF1_uc004ajw.3_Intron|OSTF1_uc004ajx.3_Intron	NM_012383	NP_036515	Q92882	OSTF1_HUMAN	osteoclast stimulating factor 1						ossification|signal transduction	cytoplasm	identical protein binding			skin(1)	1						taatttaagtgaaaaaaaaagc	0.134													4	2	---	---	---	---	
DAPK1	1612	broad.mit.edu	37	9	90317794	90317794	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90317794delA	uc004apc.2	+						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						ctaaaaaaagaaaaaaaaACG	0.224									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	95662111	95662111	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95662111delT								ANKRD19 (11138 upstream) : FGD3 (47490 downstream)																							TTATTTTAAGTTTAGATAATA	0.254													4	2	---	---	---	---	
PTGR1	22949	broad.mit.edu	37	9	114354959	114354959	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114354959delT	uc004bfh.2	-						PTGR1_uc011lwr.1_Intron|PTGR1_uc004bfi.3_Intron|PTGR1_uc004bfj.3_Intron|PTGR1_uc010mue.2_Intron	NM_012212	NP_036344	Q14914	PTGR1_HUMAN	prostaglandin reductase 1 isoform 1						leukotriene metabolic process	cytoplasm	15-oxoprostaglandin 13-oxidase activity|2-alkenal reductase activity|alcohol dehydrogenase (NAD) activity|zinc ion binding				0						GGACAAATACTTTTTTTTTTT	0.209													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115122654	115122655	+	IGR	DEL	AT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115122654_115122655delAT								ROD1 (26710 upstream) : HSDL2 (19696 downstream)																							tttttgtagaatcagggtgtca	0.010													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115122663	115122664	+	IGR	INS	-	TG	TG			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115122663_115122664insTG								ROD1 (26719 upstream) : HSDL2 (19687 downstream)																							aatcagggtgtcactgttgccc	0.035													4	3	---	---	---	---	
PAPPA	5069	broad.mit.edu	37	9	118992075	118992075	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118992075delG	uc004bjn.2	+						PAPPA_uc011lxp.1_Intron|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9						aaatccagctgaggaatgatg	0.025													4	2	---	---	---	---	
C5	727	broad.mit.edu	37	9	123742155	123742156	+	Intron	DEL	TT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123742155_123742156delTT	uc004bkv.2	-							NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)	agaacctgtcttaaaaaaaaga	0.059													4	2	---	---	---	---	
OLFML2A	169611	broad.mit.edu	37	9	127571880	127571881	+	Intron	DEL	TT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127571880_127571881delTT	uc004bov.2	+						OLFML2A_uc004bow.2_Intron	NM_182487	NP_872293	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A precursor												0						cctctgagccttttttttttta	0.139													4	2	---	---	---	---	
SCAI	286205	broad.mit.edu	37	9	127731224	127731224	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127731224delA	uc004bpe.2	-						SCAI_uc004bpd.2_Intron|SCAI_uc010mwu.2_Intron	NM_001144877	NP_001138349	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion isoform 2						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5						tattttttggaaaaaaaaaaa	0.080													6	3	---	---	---	---	
UCK1	83549	broad.mit.edu	37	9	134400283	134400283	+	3'UTR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134400283delC	uc004cay.2	-	7					UCK1_uc010mzk.2_3'UTR|UCK1_uc004cba.2_3'UTR|UCK1_uc004caz.2_RNA	NM_031432	NP_113620	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1 isoform a						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		ATCTGAGTTTCCACTCCTGAG	0.577													4	2	---	---	---	---	
ADAMTS13	11093	broad.mit.edu	37	9	136301484	136301492	+	Intron	DEL	CAGTGTGGT	-	-	rs36219903		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136301484_136301492delCAGTGTGGT	uc004cdv.3	+						ADAMTS13_uc004cdp.3_Intron|ADAMTS13_uc004cdt.1_Intron|ADAMTS13_uc004cdu.1_Intron|ADAMTS13_uc004cdw.3_Intron|ADAMTS13_uc004cdx.3_Intron|ADAMTS13_uc004cdy.1_Intron|ADAMTS13_uc004cdz.3_Intron|ADAMTS13_uc004cds.1_Intron|ADAMTS13_uc004cdr.1_Intron	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1						cell-matrix adhesion|glycoprotein metabolic process|integrin-mediated signaling pathway|peptide catabolic process|platelet activation|protein processing|proteolysis	cell surface|proteinaceous extracellular matrix	calcium ion binding|integrin binding|metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|kidney(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		TTCGTGGAGGCAGTGTGGTCAGTGTGGCT	0.579													4	2	---	---	---	---	
COL5A1	1289	broad.mit.edu	37	9	137667737	137667737	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137667737delG	uc004cfe.2	+							NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TGGCCGCCCTGGGGCATGGAG	0.557													4	2	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	637038	637039	+	Intron	INS	-	AG	AG	rs141263403	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:637038_637039insAG	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)		TCACAGATAACAGTCAGGTTTC	0.257													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	5539909	5539910	+	IGR	INS	-	ACACACAG	ACACACAG			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5539909_5539910insACACACAG								NET1 (39485 upstream) : CALML5 (748 downstream)																							tacacagacacacacagacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10041381	10041381	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10041381delA								None (None upstream) : SFTA1P (785021 downstream)																							TGACTTCCTTAAAAAAAATGG	0.398													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11176652	11176652	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11176652delG	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						ctgagtgaatgaaCACACGCT	0.264													4	2	---	---	---	---	
SEC61A2	55176	broad.mit.edu	37	10	12199340	12199340	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12199340delT	uc001ile.2	+						SEC61A2_uc010qbq.1_Intron|SEC61A2_uc001ilf.3_Intron|SEC61A2_uc001ilh.3_Intron|SEC61A2_uc001ilg.3_Intron	NM_018144	NP_060614	Q9H9S3	S61A2_HUMAN	Sec61 alpha form 2 isoform a							endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1		Renal(717;0.228)				ttttcttttctttttttttcc	0.174													1	5	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12587996	12587996	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12587996delG	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		TGTTTGTACTGGGGACAGTGG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	16448583	16448584	+	IGR	DEL	CC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16448583_16448584delCC								FAM188A (546064 upstream) : PTER (30383 downstream)																							GGATTCACCTCCGAATGTGCTA	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35193718	35193718	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35193718delG								PARD3 (89795 upstream) : CUL2 (105090 downstream)																							aaaaaaaaaagaaagaaaCTA	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45067523	45067524	+	IGR	INS	-	GA	GA	rs140916439	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45067523_45067524insGA								CXCL12 (186981 upstream) : TMEM72 (339240 downstream)																							cagacacacacgagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	48169615	48169615	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48169615delG								FAM21B (220199 upstream) : ZNF488 (185474 downstream)																							aaaaaaaaaaGATTTTTTTAG	0.199													7	4	---	---	---	---	
WDFY4	57705	broad.mit.edu	37	10	49999190	49999191	+	Intron	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49999190_49999191insT	uc001jha.3	+							NM_020945	NP_065996	Q6ZS81	WDFY4_HUMAN	WDFY family member 4							integral to membrane	binding				0						CTGATTGTGGCTTCTGGCCCTT	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	58672029	58672029	+	IGR	DEL	G	-	-	rs35848596		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58672029delG								ZWINT (550995 upstream) : None (None downstream)																							GGAGGGTAAAGGCTGATAAAT	0.418													4	3	---	---	---	---	
H2AFY2	55506	broad.mit.edu	37	10	71830756	71830757	+	Intron	DEL	TG	-	-	rs72093984		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71830756_71830757delTG	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						tgcatgtgcatgtgtgtgtgtg	0.134													4	2	---	---	---	---	
DNAJC9	23234	broad.mit.edu	37	10	75002916	75002916	+	3'UTR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75002916delC	uc001jtr.2	-	5					DNAJC9_uc010qkg.1_3'UTR	NM_015190	NP_056005	Q8WXX5	DNJC9_HUMAN	DnaJ homolog, subfamily C, member 9						protein folding		heat shock protein binding|unfolded protein binding				0	Prostate(51;0.0119)					CTGCCTCCCTCCACCCTCCCA	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	79713755	79713755	+	IGR	DEL	T	-	-	rs80158467		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79713755delT								LOC100128292 (24173 upstream) : POLR3A (22151 downstream)																							tttttctttctttttttttta	0.179													8	4	---	---	---	---	
GHITM	27069	broad.mit.edu	37	10	85903461	85903462	+	Intron	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85903461_85903462delCA	uc001kcs.1	+						GHITM_uc010qma.1_Intron|GHITM_uc010qmb.1_Intron	NM_014394	NP_055209	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0						TAATAGGTATCACAGAAGTAGC	0.361													4	2	---	---	---	---	
BMPR1A	657	broad.mit.edu	37	10	88614691	88614691	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88614691delT	uc001kdy.2	+							NM_004329	NP_004320	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA						BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	8						Tttctttttcttttttttttt	0.189			Mis|N|F			gastrointestinal polyps			Hereditary_Mixed_Polyposis_syndrome_type_2|Juvenile_Polyposis				6	3	---	---	---	---	
RNLS	55328	broad.mit.edu	37	10	90263574	90263575	+	Intron	DEL	TT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90263574_90263575delTT	uc001kfe.2	-						RNLS_uc010qms.1_Intron|RNLS_uc001kfd.2_Intron|RNLS_uc009xtj.2_Intron	NM_001031709	NP_001026879	Q5VYX0	RNLS_HUMAN	renalase isoform 1							extracellular region	oxidoreductase activity			ovary(1)	1						tcacttctagtttataaaatat	0.000													4	2	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97146495	97146496	+	Intron	INS	-	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97146495_97146496insA	uc001kkp.2	-						SORBS1_uc001kkk.2_5'Flank|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TATGTACTTTGAAAAGGAGAGG	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	112136300	112136300	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112136300delC								SMNDC1 (71593 upstream) : DUSP5 (121325 downstream)																							ATCAGTCATTCCCACACTGGC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	115199959	115199960	+	IGR	DEL	AA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115199959_115199960delAA								TCF7L2 (272525 upstream) : HABP2 (112818 downstream)																							ACCAATAGCTAAAAATCTGCCT	0.257													4	2	---	---	---	---	
C10orf82	143379	broad.mit.edu	37	10	118424916	118424916	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118424916delA	uc001lcr.2	-						C10orf82_uc001lcs.1_3'UTR	NM_144661	NP_653262	Q8WW14	CJ082_HUMAN	hypothetical protein LOC143379												0				all cancers(201;0.0143)		actccgtctcaaaaaaaaaaa	0.129													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	123707061	123707061	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123707061delC								ATE1 (18844 upstream) : NSMCE4A (9548 downstream)																							tgcccactcacccagcctcct	0.025													4	2	---	---	---	---	
FAM53B	9679	broad.mit.edu	37	10	126361373	126361373	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126361373delA	uc001lhv.1	-						FAM53B_uc001lhu.1_Intron|FAM53B_uc001lhw.2_Intron	NM_014661	NP_055476	Q14153	FA53B_HUMAN	hypothetical protein LOC9679											ovary(1)|pancreas(1)	2		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		ctgggctagcaaatcacagat	0.134													4	2	---	---	---	---	
ADAM12	8038	broad.mit.edu	37	10	128021095	128021096	+	Intron	INS	-	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128021095_128021096insA	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		TATTTCAAAGTAAAAAAAAATT	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133871002	133871002	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133871002delC								BNIP3 (75567 upstream) : JAKMIP3 (47311 downstream)																							GGGATGCTCACAGGACACACG	0.632													4	3	---	---	---	---	
LOC650368	650368	broad.mit.edu	37	11	3425129	3425129	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3425129delT	uc010qxs.1	+						LOC650368_uc001lxx.2_Intron|LOC650368_uc001lxy.2_Intron	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						TCCAAGCATCTTTTTTTTGTT	0.214													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	4536290	4536291	+	IGR	INS	-	GGATAT	GGATAT	rs141170428	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4536290_4536291insGGATAT								OR52K1 (25215 upstream) : OR52M1 (30130 downstream)																							GTTGGCCAAAAggatatggata	0.396													4	2	---	---	---	---	
FAR1	84188	broad.mit.edu	37	11	13733839	13733839	+	Intron	DEL	A	-	-	rs72447632		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13733839delA	uc001mld.2	+						FAR1_uc009ygp.2_Intron	NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2						CTTAAAAATGAAAAAAAAAAA	0.289													1	5	---	---	---	---	
ABTB2	25841	broad.mit.edu	37	11	34349170	34349171	+	Intron	INS	-	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34349170_34349171insC	uc001mvl.1	-							NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing								DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				ACATACTCCTTCCTTGGGGGTA	0.406													4	2	---	---	---	---	
PAMR1	25891	broad.mit.edu	37	11	35457302	35457302	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35457302delA	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						AAGCCAAAGGAAAAAAAAAGC	0.383													4	2	---	---	---	---	
TTC17	55761	broad.mit.edu	37	11	43469865	43469865	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43469865delT	uc001mxi.2	+						TTC17_uc010rfj.1_Intron|TTC17_uc001mxl.2_5'Flank	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17								binding			ovary(5)	5						TGTGCCCCCCTTCCCGGTGCC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69213662	69213662	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69213662delG								MYEOV (57213 upstream) : CCND1 (242211 downstream)																							GGTCCACATCGGGGGGGCTCA	0.667													4	2	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70894691	70894691	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70894691delG	uc001oqc.2	-							NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			taccctgactgcagctgctgt	0.000													4	2	---	---	---	---	
PDE2A	5138	broad.mit.edu	37	11	72372467	72372467	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72372467delT	uc010rrc.1	-						PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_Intron|PDE2A_uc001osq.2_Intron	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	TTTGGGGGGGTTTTTTGGCCC	0.453													4	2	---	---	---	---	
RELT	84957	broad.mit.edu	37	11	73088315	73088316	+	Intron	DEL	GT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73088315_73088316delGT	uc001otv.2	+						RELT_uc001otw.2_Intron	NM_152222	NP_689408	Q969Z4	TR19L_HUMAN	RELT tumor necrosis factor receptor precursor							cytoplasm|integral to membrane|plasma membrane	binding|receptor activity			upper_aerodigestive_tract(1)	1						AGTGGTGTCAgtgtgtgtgtgt	0.530													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	89970459	89970459	+	IGR	DEL	A	-	-	rs35485430		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89970459delA								CHORDC1 (13927 upstream) : MIR1261 (631830 downstream)																							CAACACACACAAAAAAAATGG	0.323													4	2	---	---	---	---	
MED17	9440	broad.mit.edu	37	11	93540568	93540569	+	Intron	INS	-	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93540568_93540569insC	uc001pem.3	+							NM_004268	NP_004259	Q9NVC6	MED17_HUMAN	mediator complex subunit 17						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				aacaggctttgagactttgtct	0.069													6	4	---	---	---	---	
SLN	6588	broad.mit.edu	37	11	107582644	107582645	+	Intron	DEL	AC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107582644_107582645delAC	uc001pjp.2	-							NM_003063	NP_003054	O00631	SARCO_HUMAN	sarcolipin						calcium ion transport|regulation of calcium ion transport	integral to membrane|sarcoplasmic reticulum membrane	enzyme regulator activity				0		Melanoma(852;1.46e-05)|all_epithelial(67;1.72e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;2.71e-05)|Epithelial(105;0.000112)|all cancers(92;0.00219)		TGCAGCTTGTACACACACACAC	0.436													4	2	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108548785	108548785	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108548785delT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		CATTTGATTATTTTTTTTTCT	0.353			T	NUP98	AML*								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	108843168	108843169	+	IGR	INS	-	TG	TG	rs148425444	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108843168_108843169insTG								DDX10 (31522 upstream) : C11orf87 (449706 downstream)																							GAATTTGAGTCtgtgtgtgtgt	0.356													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	110914852	110914852	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110914852delT								ARHGAP20 (330940 upstream) : C11orf53 (211855 downstream)																							AAATCTTTCCTTTTTTTTCCT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112652883	112652883	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112652883delA								PTS (512206 upstream) : NCAM1 (179112 downstream)																							tgaaacagacaaaaaaaaata	0.000													6	3	---	---	---	---	
DRD2	1813	broad.mit.edu	37	11	113308341	113308341	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113308341delG	uc001poa.3	-						DRD2_uc001pob.3_Intron|DRD2_uc009yyr.1_Intron	NM_000795	NP_000786	P14416	DRD2_HUMAN	dopamine receptor D2 isoform long						activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning	integral to plasma membrane	dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding			pancreas(1)|skin(1)	2		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624)	ACTCTGACAAGGGAGCTCCGA	0.552													4	2	---	---	---	---	
CADM1	23705	broad.mit.edu	37	11	115119354	115119354	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115119354delA	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001ppl.2_Intron	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1						adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		CTGGTAGGTGAAAACCTGAGA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116594566	116594566	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116594566delC								None (None upstream) : BUD13 (24322 downstream)																							CCTCTCCTCTCCTGCCCACCC	0.602													4	2	---	---	---	---	
PAFAH1B2	5049	broad.mit.edu	37	11	117032228	117032229	+	Intron	INS	-	T	T	rs35812569		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117032228_117032229insT	uc001pqe.1	+						PAFAH1B2_uc009yzk.1_Intron|PAFAH1B2_uc009yzl.1_Intron|PAFAH1B2_uc009yzm.2_Intron|PAFAH1B2_uc009yzn.2_Intron|PAFAH1B2_uc009yzj.1_Intron	NM_002572	NP_002563	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase,						lipid catabolic process	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)		TGAAGGAAGAGttttttttttt	0.134			T	IGH@	MLCLS								3	3	---	---	---	---	
C11orf63	79864	broad.mit.edu	37	11	122828409	122828409	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122828409delA	uc001pym.2	+							NM_024806	NP_079082	Q6NUN7	CK063_HUMAN	hypothetical protein LOC79864 isoform 1											ovary(3)	3		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		CTTGTAACTTAAAAAAAAAAC	0.209													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	123101401	123101401	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123101401delC								ASAM (35394 upstream) : GRAMD1B (295127 downstream)																							AGAAAGAGGGCCCCCAAGTGT	0.502													4	2	---	---	---	---	
OR10G9	219870	broad.mit.edu	37	11	123893481	123893506	+	5'Flank	DEL	AGAGAGAGAGAGAGAGAGAGAGAGAG	-	-	rs72075895		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123893481_123893506delAGAGAGAGAGAGAGAGAGAGAGAGAG	uc010sad.1	+							NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TGTATGTGACagagagagagagagagagagagagagagagagagag	0.217													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131512672	131512672	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131512672delT	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						TCACCCACTATTTTTTTCATT	0.393													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132564795	132564796	+	Intron	INS	-	AGAAG	AGAAG	rs112000659		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132564795_132564796insAGAAG	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		TGGCAAGACTTAGAAACTATAG	0.391													2	4	---	---	---	---	
WNK1	65125	broad.mit.edu	37	12	996697	996697	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:996697delT	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TTGATACTAATTTTTTTTTTA	0.318													3	3	---	---	---	---	
TSPAN9	10867	broad.mit.edu	37	12	3373935	3373935	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3373935delA	uc001qlp.2	+							NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			taggaagtttattttcatgaa	0.139													4	2	---	---	---	---	
TSPAN9	10867	broad.mit.edu	37	12	3373940	3373941	+	Intron	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3373940_3373941delCA	uc001qlp.2	+							NM_006675	NP_006666	O75954	TSN9_HUMAN	tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			agtttattttcatgaacctcat	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16225910	16225910	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16225910delT								DERA (35596 upstream) : MGST1 (274166 downstream)																							AAAAAATAGCTTTTTTTTGAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	24772287	24772319	+	IGR	DEL	GAGGTTTAGCAAGCAGTTGTGAAAGTGAGTCTG	-	-	rs11830251	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24772287_24772319delGAGGTTTAGCAAGCAGTTGTGAAAGTGAGTCTG								SOX5 (56907 upstream) : BCAT1 (191962 downstream)																							GAATAAAGGAGAGGTTTAGCAAGCAGTTGTGAAAGTGAGTCTGGAGCCTGGGG	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54753715	54753715	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54753715delT								COPZ1 (8082 upstream) : GPR84 (2516 downstream)																							GTCTCCTGAGTTTTTTTTTTT	0.488													6	5	---	---	---	---	
PTPRQ	374462	broad.mit.edu	37	12	80922384	80922384	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80922384delA	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0						GCCCTTTGCTAAATCTCACTC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	104779967	104779971	+	IGR	DEL	AAAGA	-	-	rs71895701		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104779967_104779971delAAAGA								TXNRD1 (35909 upstream) : CHST11 (70778 downstream)																							aaacagaaagaaagaaaagaaaaga	0.166													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	107696806	107696806	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107696806delT								CRY1 (209208 upstream) : BTBD11 (15391 downstream)																							CTCCTGGGACTCCAGAAAAGC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108414380	108414380	+	IGR	DEL	A	-	-	rs10547015		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108414380delA								ASCL4 (243960 upstream) : WSCD2 (109131 downstream)																							GCATTTAAAGAAAAAAAAAAC	0.308													4	2	---	---	---	---	
TCTN1	79600	broad.mit.edu	37	12	111054565	111054565	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111054565delG	uc009zvs.2	+						TCTN1_uc010syb.1_Intron|TCTN1_uc009zvr.1_Intron|TCTN1_uc001trl.2_Intron|TCTN1_uc001trm.2_Intron|TCTN1_uc010syc.1_Intron|TCTN1_uc001tro.2_Intron|TCTN1_uc001trp.3_Intron|TCTN1_uc001trn.3_Intron|TCTN1_uc001tri.2_Intron|TCTN1_uc001trj.1_Intron|TCTN1_uc001trk.3_Intron	NM_001082537	NP_001076006	Q2MV58	TECT1_HUMAN	tectonic family member 1 isoform 2						multicellular organismal development	extracellular region					0						CACGCAACTTGTAGATATCGG	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	111242547	111242547	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111242547delC								PPP1CC (61790 upstream) : CCDC63 (42264 downstream)																							ccatggtggaccccaaggtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115135960	115135963	+	IGR	DEL	GCGT	-	-	rs141609032		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115135960_115135963delGCGT								TBX3 (13991 upstream) : None (None downstream)																							GCGCGCGCGCGCgtgtgtgtgagt	0.412													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	117153492	117153493	+	IGR	DEL	AG	-	-	rs33961643		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117153492_117153493delAG								MAP1LC3B2 (139067 upstream) : C12orf49 (103 downstream)																							GGCAAGAGAcagggggaagagg	0.272													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	119701416	119701416	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119701416delA								HSPB8 (68866 upstream) : LOC144742 (20214 downstream)																							GAGAGGGAACAAAAAAAACCC	0.428													6	3	---	---	---	---	
CABP1	9478	broad.mit.edu	37	12	121088237	121088237	+	Intron	DEL	A	-	-	rs11322476		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121088237delA	uc001tyu.2	+						CABP1_uc001tyv.2_5'Flank|CABP1_uc001tyw.2_5'Flank	NM_001033677	NP_001028849	Q9NZU7	CABP1_HUMAN	calcium binding protein 1 isoform 3							cell cortex|cell junction|Golgi apparatus|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|calcium-dependent protein binding|enzyme inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CAATCCACCCAAAAAAAAAAA	0.512													4	3	---	---	---	---	
GTF2H3	2967	broad.mit.edu	37	12	124130360	124130360	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124130360delA	uc001ufo.1	+						GTF2H3_uc010tau.1_Intron	NM_001516	NP_001507	Q13889	TF2H3_HUMAN	general transcription factor IIH, polypeptide 3,						mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	core TFIIH complex|holo TFIIH complex	damaged DNA binding|metal ion binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|translation factor activity, nucleic acid binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.1e-05)|Epithelial(86;0.000388)|all cancers(50;0.00362)		TTATTTAGGCAAAAAGGGAAA	0.299								NER					4	2	---	---	---	---	
ATP6V0A2	23545	broad.mit.edu	37	12	124232621	124232621	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124232621delT	uc001ufr.2	+							NM_012463	NP_036595	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		GCCATATTCCTTTTTTATTTT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130569805	130569806	+	IGR	DEL	TC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130569805_130569806delTC								LOC100190940 (42918 upstream) : FZD10 (77226 downstream)																							AATTCCCCGTTCTGCAGAAAGA	0.589													4	2	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133365502	133365503	+	Intron	INS	-	AC	AC			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133365502_133365503insAC	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		ccccgacccagacagaccccgc	0.312													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22778118	22778118	+	Intron	DEL	A	-	-	rs34486609		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22778118delA	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																		GAGAAGAGTCAGGGGGTGAGC	0.473													5	3	---	---	---	---	
PARP4	143	broad.mit.edu	37	13	25075498	25075498	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25075498delC	uc001upl.2	-						PARP4_uc010tdc.1_Intron	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4						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)		GCTTTCCCCTCCCCCTAGTTA	0.378													4	2	---	---	---	---	
CDX2	1045	broad.mit.edu	37	13	28542693	28542693	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28542693delC	uc001urv.2	-	1	625	c.451delG	c.(451-453)GCTfs	p.A151fs		NM_001265	NP_001256	Q99626	CDX2_HUMAN	caudal type homeobox 2	151					organ morphogenesis|transcription from RNA polymerase II promoter		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)	1	all_cancers(110;0.191)|all_hematologic(3;0.0447)|Acute lymphoblastic leukemia(6;0.155)	Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199)		TCGGCGGCAGCGGTGGCGGCG	0.642			T	ETV6	AML								5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	38940982	38940982	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38940982delT								UFM1 (3840 upstream) : FREM2 (320191 downstream)																							TAGATTGCTATTTAATATTTC	0.308													4	2	---	---	---	---	
LRCH1	23143	broad.mit.edu	37	13	47279738	47279739	+	Intron	INS	-	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47279738_47279739insC	uc001vbj.2	+						LRCH1_uc010acp.2_3'UTR|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		ATACATAGGGAATCTGCCTGTG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51270169	51270169	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51270169delC								DLEU1 (167499 upstream) : DLEU7 (16590 downstream)																							caaatatggtcccccaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	58644810	58644810	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58644810delA								PCDH17 (341745 upstream) : None (None downstream)																							tacactgaagaaaaaaaaagc	0.035													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66651431	66651432	+	IGR	DEL	GT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66651431_66651432delGT								None (None upstream) : PCDH9 (225535 downstream)																							cacacacctggtgaaccctagc	0.000													4	2	---	---	---	---	
GPC5	2262	broad.mit.edu	37	13	92797458	92797459	+	Intron	INS	-	A	A	rs77994325	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92797458_92797459insA	uc010tif.1	+							NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				AGTTTTCTGTGAAAAAAAACTA	0.282													4	2	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	93962630	93962630	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93962630delT	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GGGTTTTGACTTTTTTGTTGA	0.468													4	2	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110821845	110821846	+	Intron	DEL	AC	-	-	rs67599645		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110821845_110821846delAC	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TGggagtgtaacacacacacac	0.223													4	3	---	---	---	---	
CARKD	55739	broad.mit.edu	37	13	111291261	111291261	+	3'UTR	DEL	T	-	-	rs113610388		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111291261delT	uc001vrb.2	+	10					CARKD_uc010tjj.1_3'UTR|CARKD_uc001vqz.2_RNA|CARKD_uc001vra.2_RNA|CARKD_uc010tjk.1_3'UTR|CARKD_uc010tjl.1_3'UTR|CARKD_uc001vrc.2_3'UTR			Q8IW45	CARKD_HUMAN	RecName: Full=Carbohydrate kinase domain-containing protein; Flags: Precursor;											skin(1)	1						CCTTCGTTCCTCCTCTGCTTC	0.577													3	3	---	---	---	---	
FAM70B	348013	broad.mit.edu	37	13	114463764	114463765	+	Intron	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114463764_114463765insT	uc001vuh.2	+						FAM70B_uc010tkh.1_Intron	NM_182614	NP_872420	Q8WV15	FA70B_HUMAN	family with sequence similarity 70, member B							integral to membrane					0	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.123)|all_epithelial(44;0.133)	all cancers(43;0.181)			TTTGGGGTATCGGGGGTGGGTT	0.505													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	25827413	25827413	+	IGR	DEL	T	-	-	rs71121825		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25827413delT								STXBP6 (308242 upstream) : None (None downstream)																							TCTCTCTCTCTTTTTTTTTTT	0.448													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	27365761	27365761	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27365761delA								NOVA1 (298801 upstream) : None (None downstream)																							AGAGAAATGGAGGGGGCTAGT	0.423													4	2	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50300781	50300781	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50300781delT	uc001wxc.2	-						SDCCAG1_uc010anj.1_Intron|SDCCAG1_uc010tqi.1_Intron|SDCCAG1_uc001wxe.2_Intron|SDCCAG1_uc001wxd.1_5'Flank|SDCCAG1_uc010anq.1_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)		TCTCATTCAATTTTTTTTTTT	0.229													6	3	---	---	---	---	
DDHD1	80821	broad.mit.edu	37	14	53525495	53525495	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53525495delC	uc001xai.2	-						DDHD1_uc001xaj.2_Intron|DDHD1_uc001xah.2_Intron|DDHD1_uc001xag.2_Intron|DDHD1_uc001xak.1_Intron	NM_001160148	NP_001153620	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1 isoform c						lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(2)	2	Breast(41;0.037)					ATGGGCTCTGCCAACCATTAA	0.274													4	2	---	---	---	---	
KTN1	3895	broad.mit.edu	37	14	56110361	56110361	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56110361delT	uc001xcb.2	+						KTN1_uc001xce.2_Intron|KTN1_uc001xcc.2_Intron|KTN1_uc001xcd.2_Intron|KTN1_uc010trb.1_Intron|KTN1_uc001xcf.1_Intron|KTN1_uc010aoq.2_5'Flank	NM_182926	NP_891556	Q86UP2	KTN1_HUMAN	kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7						CTGGCGACTCTTATTTAAACA	0.299			T	RET	papillary thryoid								4	2	---	---	---	---	
GPR135	64582	broad.mit.edu	37	14	59917644	59917644	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59917644delG	uc001xed.2	-							NM_022571		Q8IZ08	GP135_HUMAN	G protein-coupled receptor 135							integral to membrane|plasma membrane	G-protein coupled receptor activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.134)		gtatagagctgggttgcacat	0.109													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	70325847	70325847	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70325847delT								SLC10A1 (61841 upstream) : SMOC1 (20296 downstream)																							CATGTAAAGCTTTGAACATGA	0.294													4	2	---	---	---	---	
CCDC88C	440193	broad.mit.edu	37	14	91787783	91787783	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91787783delG	uc010aty.2	-							NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				CAGGTCAGCTGGGGACCCTTC	0.657													4	2	---	---	---	---	
CCDC88C	440193	broad.mit.edu	37	14	91845972	91845972	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91845972delG	uc010aty.2	-						CCDC88C_uc010twk.1_Intron|CCDC88C_uc001xzl.3_3'UTR	NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				TCCTGGGGTAGGAACTCCGGC	0.592													4	2	---	---	---	---	
PPP4R4	57718	broad.mit.edu	37	14	94709035	94709035	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94709035delA	uc001ycs.1	+							NM_058237	NP_478144	Q6NUP7	PP4R4_HUMAN	HEAT-like repeat-containing protein isoform 1							cytoplasm|protein serine/threonine phosphatase complex	protein binding			skin(3)|upper_aerodigestive_tract(1)	4						TGCGGATTTTAAAGTAAAATC	0.284													4	2	---	---	---	---	
CCDC85C	317762	broad.mit.edu	37	14	100040629	100040629	+	Intron	DEL	T	-	-	rs35444198		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100040629delT	uc010avr.2	-							NM_001144995	NP_001138467	A6NKD9	CC85C_HUMAN	coiled-coil domain containing 85C												0						GCTCCAGGGATTTTTTTTTGT	0.532													6	3	---	---	---	---	
RCOR1	23186	broad.mit.edu	37	14	103180416	103180417	+	Intron	DEL	TG	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103180416_103180417delTG	uc001ymb.2	+							NM_015156	NP_055971	Q9UKL0	RCOR1_HUMAN	REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1						TAAATACAGATGTGTGTGTGGC	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22448191	22448191	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22448191delC								OR4N3P (33806 upstream) : MIR1268 (65038 downstream)																							aaaaaaaaaaCACCAAAAAAC	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	27920328	27920329	+	IGR	DEL	AG	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27920328_27920329delAG								GABRG3 (142194 upstream) : OCA2 (79696 downstream)																							CACACTTCCTAGGCACATGCGC	0.510													4	2	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33941160	33941160	+	Intron	DEL	A	-	-	rs112518422		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33941160delA	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)		ACTTTTCCAGAAAAAAAAGGG	0.502													4	2	---	---	---	---	
SPRED1	161742	broad.mit.edu	37	15	38545202	38545202	+	5'UTR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38545202delG	uc001zka.3	+	1						NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain						inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		ACCCCCCTGCGGGGGTGGCCG	0.642									Legius_syndrome				4	2	---	---	---	---	
CHAC1	79094	broad.mit.edu	37	15	41246774	41246774	+	Intron	DEL	T	-	-	rs72422019		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41246774delT	uc001znh.2	+						CHAC1_uc010uct.1_Intron	NM_024111	NP_077016	Q9BUX1	CHAC1_HUMAN	ChaC, cation transport regulator-like 1 isoform						apoptosis in response to endoplasmic reticulum stress|response to unfolded protein	cytosol	protein binding				0		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.66e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.163)		TTGTCAACTGTTTTTTTTTTt	0.090													6	4	---	---	---	---	
DMXL2	23312	broad.mit.edu	37	15	51755890	51755890	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51755890delA	uc002abf.2	-						DMXL2_uc002abd.2_Intron|DMXL2_uc010ufy.1_Intron|DMXL2_uc010bfa.2_Intron	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2							cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)		TAGTTCTCCTAAAAATCATTT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	64189349	64189350	+	IGR	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64189349_64189350delCA								MIR422A (26131 upstream) : DAPK2 (9886 downstream)																							cactcagatgcacacacacaca	0.347											OREG0031369	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	4	3	---	---	---	---	
LRRC49	54839	broad.mit.edu	37	15	71300477	71300478	+	Intron	INS	-	TT	TT			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71300477_71300478insTT	uc002asw.2	+						LRRC49_uc002asu.2_Intron|LRRC49_uc002asx.2_Intron|LRRC49_uc010ukf.1_Intron|LRRC49_uc002asy.2_Intron|LRRC49_uc002asz.2_Intron	NM_017691	NP_060161	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49							cytoplasm|microtubule				ovary(1)	1						CATGGATAGAAATAATTTGGGT	0.282													3	3	---	---	---	---	
ALPK3	57538	broad.mit.edu	37	15	85385725	85385726	+	Intron	INS	-	AC	AC	rs144886158	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85385725_85385726insAC	uc002ble.2	+							NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3						heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CAGGGGTAGGGACAGAGGACAG	0.515													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88929648	88929648	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88929648delC								NTRK3 (129987 upstream) : MRPL46 (73060 downstream)																							TCCCCCAGGTCCCCAGACTCC	0.507													4	2	---	---	---	---	
IGF1R	3480	broad.mit.edu	37	15	99270956	99270956	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99270956delG	uc002bul.2	+						IGF1R_uc010urq.1_Intron|IGF1R_uc010bon.2_Intron	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	CTTTCCTCTCGGCCTGCTTGT	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	102036087	102036088	+	IGR	INS	-	CT	CT	rs145834939	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102036087_102036088insCT								PCSK6 (5900 upstream) : TM2D3 (137092 downstream)																							GGTGACTCTGACTTTCCCCACC	0.436													1	11	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7614801	7614801	+	Intron	DEL	T	-	-	rs149893452		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7614801delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		ATTCATCCTATTTTTTTCCCA	0.378													2	4	---	---	---	---	
ATF7IP2	80063	broad.mit.edu	37	16	10576311	10576311	+	3'UTR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10576311delA	uc002czu.2	+	12					ATF7IP2_uc002czv.2_3'UTR|ATF7IP2_uc010uyo.1_RNA|ATF7IP2_uc010uyp.1_3'UTR|ATF7IP2_uc002czw.2_3'UTR|ATF7IP2_uc010uyq.1_RNA	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						GATAAGTTCTAAAACATACGC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11715422	11715423	+	IGR	INS	-	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11715422_11715423insC								LITAF (34100 upstream) : SNN (46878 downstream)																							ACTggtattaacccccctcaga	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	12679757	12679758	+	IGR	DEL	AC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12679757_12679758delAC								SNX29 (11612 upstream) : CPPED1 (73899 downstream)																							aaaaaccccaacacacttctcc	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32819313	32819317	+	IGR	DEL	TTTCA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32819313_32819317delTTTCA								TP53TG3B (130435 upstream) : SLC6A10P (69480 downstream)																							catttcatcttttcatttcatttca	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55134278	55134279	+	IGR	INS	-	G	G	rs149480481	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55134278_55134279insG								IRX5 (165885 upstream) : IRX6 (224192 downstream)																							ggggcctttgttatgtggttct	0.104													7	5	---	---	---	---	
CIAPIN1	57019	broad.mit.edu	37	16	57464912	57464912	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57464912delT	uc002ell.1	-						CIAPIN1_uc002elk.1_Intron|CIAPIN1_uc002elm.1_Intron|CIAPIN1_uc002eln.1_Intron|CIAPIN1_uc010cda.1_Intron|CIAPIN1_uc002elo.1_Intron	NM_020313	NP_064709	Q6FI81	CPIN1_HUMAN	cytokine induced apoptosis inhibitor 1						anti-apoptosis|apoptosis	cytoplasm|nucleolus					0						gcctggctaattttttttttt	0.085													4	2	---	---	---	---	
CCDC113	29070	broad.mit.edu	37	16	58296667	58296668	+	Intron	INS	-	TAGA	TAGA	rs28479863	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58296667_58296668insTAGA	uc002ene.2	+						CCDC113_uc010vid.1_Intron	NM_014157	NP_054876	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113 isoform 1							protein complex					0						tagatgataggtagatagatag	0.292													4	3	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	70909014	70909015	+	Intron	DEL	TC	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70909014_70909015delTC	uc002ezr.2	-							NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				gaacattcagtcagatcagccc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	80194624	80194624	+	IGR	DEL	T	-	-	rs113533150		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80194624delT								MAF (560002 upstream) : DYNLRB2 (380230 downstream)																							GTGCCATCTATTTTTTTTTTC	0.423													3	3	---	---	---	---	
CMIP	80790	broad.mit.edu	37	16	81695746	81695747	+	Intron	INS	-	AGCT	AGCT	rs137959128	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81695746_81695747insAGCT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron|CMIP_uc002fgr.1_Intron	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0						AGAGAACGGCCAGCTGCTCCTC	0.535													3	3	---	---	---	---	
TRIM16	10626	broad.mit.edu	37	17	15516423	15516424	+	Intron	DEL	GA	-	-	rs10599550		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15516423_15516424delGA	uc002gor.1	-						CDRT1_uc002gov.3_Intron			O95361	TRI16_HUMAN	SubName: Full=Putative uncharacterized protein; Flags: Fragment;						histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		CTCTGCTGGGGAAAAAAAAAAA	0.460													4	3	---	---	---	---	
PRPSAP2	5636	broad.mit.edu	37	17	18812312	18812312	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18812312delA	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron	NM_002767	NP_002758	O60256	KPRB_HUMAN	phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1						TTCAACATTCaaaaaaaaaga	0.144													4	2	---	---	---	---	
FAM83G	644815	broad.mit.edu	37	17	18895279	18895280	+	Intron	INS	-	G	G			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18895279_18895280insG	uc002guw.2	-						SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815											ovary(1)|central_nervous_system(1)	2						TGGCCATGCCTGGGGGGCAGAG	0.658													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	26524755	26524755	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26524755delT								NLK (1353 upstream) : PYY2 (28834 downstream)																							AGAATTTTTGTTTTTTTTTGT	0.254													5	3	---	---	---	---	
GOSR1	9527	broad.mit.edu	37	17	28820011	28820011	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28820011delT	uc002hfe.2	+						GOSR1_uc002hfd.2_Intron|GOSR1_uc002hff.2_Intron	NM_004871	NP_004862	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1 isoform 1						intra-Golgi vesicle-mediated transport|protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|SNARE complex	SNAP receptor activity				0						ATGGTTGTTAttttttttttt	0.154													6	3	---	---	---	---	
RHBDL3	162494	broad.mit.edu	37	17	30618367	30618367	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30618367delA	uc002hhe.1	+						RHBDL3_uc010csw.1_Intron|RHBDL3_uc010csx.1_Intron|RHBDL3_uc010csy.1_Intron|RHBDL3_uc002hhf.1_Intron	NM_138328	NP_612201	P58872	RHBL3_HUMAN	rhomboid protease 3						proteolysis	integral to membrane	calcium ion binding|serine-type endopeptidase activity			ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)				agaaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SLC4A1	6521	broad.mit.edu	37	17	42335974	42335974	+	Frame_Shift_Del	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42335974delG	uc002igf.3	-	10	1043	c.894delC	c.(892-894)GCCfs	p.A298fs	SLC4A1_uc002igg.3_Frame_Shift_Del_p.A298fs	NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	298	Cytoplasmic.				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GAGCCATGTAGGCATCTATGC	0.657													30	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43094267	43094267	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43094267delG								C1QL1 (48623 upstream) : DCAKD (6439 downstream)																							AGGTCTTCCTGGCTTGACAAA	0.458													4	2	---	---	---	---	
MYST2	11143	broad.mit.edu	37	17	47874429	47874429	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47874429delT	uc002ipm.2	+						MYST2_uc002ipl.1_Intron|MYST2_uc010wma.1_Intron|MYST2_uc010wmb.1_Intron|MYST2_uc010wmc.1_Intron|MYST2_uc010wmd.1_Intron|MYST2_uc010wme.1_Intron	NM_007067	NP_008998	O95251	MYST2_HUMAN	MYST histone acetyltransferase 2						DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3						ttcttatgtcttttttttttt	0.209													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	54738794	54738794	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54738794delA								NOG (65843 upstream) : C17orf67 (130481 downstream)																							GGTGGACAGTAAAACAACACA	0.602													4	2	---	---	---	---	
MED13	9969	broad.mit.edu	37	17	60049798	60049798	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60049798delA	uc002izo.2	-							NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						TTTTGCCTTTAAAAAAAAAAT	0.164													4	2	---	---	---	---	
WIPI1	55062	broad.mit.edu	37	17	66453573	66453581	+	5'UTR	DEL	GCCCGGGAA	-	-	rs71142184		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66453573_66453581delGCCCGGGAA	uc010dey.2	-	1					WIPI1_uc002jhd.3_RNA|WIPI1_uc010wqo.1_5'UTR|WIPI1_uc002jhe.3_RNA	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting						macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0						CGGGGGCTCGGCCCGGGAAGCCGCAGCTC	0.651													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69610404	69610405	+	IGR	DEL	GT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69610404_69610405delGT								None (None upstream) : SOX9 (506756 downstream)																							tgtgggggtggtgtgtgtgtgg	0.292													4	2	---	---	---	---	
KIF19	124602	broad.mit.edu	37	17	72336059	72336059	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72336059delG	uc002jkm.3	+						KIF19_uc002jkj.2_Intron|KIF19_uc002jkk.2_Intron|KIF19_uc002jkl.2_Intron	NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						GTGGAGTTGTGGGTCTCGACT	0.577													4	2	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78736649	78736650	+	Intron	INS	-	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78736649_78736650insA	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						ttcttctctctaaaaaaaaacg	0.000													4	2	---	---	---	---	
CLUL1	27098	broad.mit.edu	37	18	645263	645263	+	Intron	DEL	A	-	-	rs112345887		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:645263delA	uc002kkp.2	+						CLUL1_uc010wys.1_Intron|CLUL1_uc002kkq.2_Intron	NM_014410	NP_055225	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal) precursor						cell death	extracellular region				ovary(2)	2						tttgcaaattaaaaaaaaacc	0.000													4	2	---	---	---	---	
ENOSF1	55556	broad.mit.edu	37	18	688168	688168	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:688168delA	uc002kku.3	-						ENOSF1_uc002kkt.3_Intron|ENOSF1_uc010dke.2_Intron|ENOSF1_uc010dkf.2_Intron|ENOSF1_uc002kkv.3_Intron|ENOSF1_uc002kkw.3_Intron|ENOSF1_uc002kkx.3_Intron	NM_017512	NP_059982	Q7L5Y1	ENOF1_HUMAN	enolase superfamily 1 isoform rTS beta						cellular amino acid catabolic process	mitochondrion	isomerase activity|metal ion binding			ovary(1)	1						acttcatctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11250767	11250768	+	IGR	INS	-	T	T	rs79002794		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11250767_11250768insT								FAM38B (548788 upstream) : GNAL (438368 downstream)																							TGACTTTATGATTTTTTTTTTG	0.337													5	3	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13292205	13292206	+	Intron	INS	-	T	T			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13292205_13292206insT	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		CATTCACTGGCTTGGGTGCTTC	0.584													4	2	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13478828	13478829	+	Intron	DEL	AA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13478828_13478829delAA	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		cacagtactgaagggcaagagc	0.000													4	2	---	---	---	---	
RNMT	8731	broad.mit.edu	37	18	13737859	13737859	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13737859delT	uc002ksk.1	+						RNMT_uc002ksl.1_Intron|RNMT_uc002ksm.1_Intron|RNMT_uc010dlk.2_Intron|RNMT_uc010xae.1_Intron	NM_003799	NP_003790	O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase						mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	mRNA (guanine-N7-)-methyltransferase activity|RNA binding				0						gggcagttccttttttttttc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38507535	38507536	+	IGR	INS	-	A	A	rs138970969	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38507535_38507536insA								None (None upstream) : KC6 (552702 downstream)																							CTCTAATGGggaaaaaatgcac	0.149													5	3	---	---	---	---	
SETBP1	26040	broad.mit.edu	37	18	42428038	42428041	+	Intron	DEL	GTGT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42428038_42428041delGTGT	uc010dni.2	+						SETBP1_uc002lay.2_Intron	NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		CTCTCTGAAGgtgtgtgtgtgtgt	0.137									Schinzel-Giedion_syndrome				3	3	---	---	---	---	
ZCCHC2	54877	broad.mit.edu	37	18	60243084	60243084	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60243084delT	uc002lip.3	+						ZCCHC2_uc002lio.2_Intron|ZCCHC2_uc002liq.2_Intron	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2						cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding			lung(1)|prostate(1)	2						CTTGCAGCACTTTTTTTTTTT	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75806411	75806413	+	IGR	DEL	CTT	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75806411_75806413delCTT								GALR1 (824317 upstream) : SALL3 (933862 downstream)																							TCACCACCAGCTTCTTCTACCAT	0.443													4	4	---	---	---	---	
KCNG2	26251	broad.mit.edu	37	18	77639483	77639483	+	Intron	DEL	C	-	-	rs79539077		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77639483delC	uc010xfl.1	+							NM_012283	NP_036415	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G,						energy reserve metabolic process|regulation of heart contraction|regulation of insulin secretion	voltage-gated potassium channel complex	delayed rectifier potassium channel activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		gaaacaagaacaagacgccat	0.214													3	3	---	---	---	---	
LPPR3	79948	broad.mit.edu	37	19	814017	814017	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:814017delG	uc002lpx.1	-						LPPR3_uc010dru.1_Intron|LPPR3_uc002lpw.1_Intron|LPPR3_uc002lpy.1_Intron	NM_024888	NP_079164	Q6T4P5	LPPR3_HUMAN	plasticity-related protein 2							integral to membrane	phosphatidate phosphatase activity				0						CTTGTCCAGTGGGACCGGTTC	0.662													4	2	---	---	---	---	
SLC25A41	284427	broad.mit.edu	37	19	6432330	6432330	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6432330delT	uc010dus.2	-						SLC25A41_uc010dut.2_Intron	NM_173637	NP_775908	Q8N5S1	S2541_HUMAN	solute carrier family 25, member 41						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0						CAAGTCTGCAttttttttttt	0.313													6	3	---	---	---	---	
ADAMTS10	81794	broad.mit.edu	37	19	8672542	8672542	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8672542delT	uc002mkj.1	-						ADAMTS10_uc002mkk.1_Intron	NM_030957	NP_112219	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			pancreas(2)|skin(2)	4						GGGAGCCAGGTTTTTGCCAAG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	14431176	14431177	+	IGR	INS	-	AGA	AGA	rs140564352	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14431176_14431177insAGA								LPHN1 (114179 upstream) : CD97 (61036 downstream)																							gttgtggggagagaagaggatt	0.233													2	5	---	---	---	---	
MYO9B	4650	broad.mit.edu	37	19	17224697	17224697	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17224697delT	uc010eak.2	+						MYO9B_uc002nfi.2_Intron|MYO9B_uc002nfj.1_Intron	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1						actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1						ATAGGGTCAGTTTTAGACCTC	0.468													4	2	---	---	---	---	
KIRREL2	84063	broad.mit.edu	37	19	36355897	36355898	+	Intron	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36355897_36355898delCA	uc002ocb.3	+						KIRREL2_uc002obz.3_Intron|KIRREL2_uc002oca.3_Intron|KIRREL2_uc002occ.3_Intron|KIRREL2_uc002ocd.3_Intron	NM_199180	NP_954649	Q6UWL6	KIRR2_HUMAN	kin of IRRE-like 2 isoform c						cell adhesion	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)|skin(1)	3	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTCTCCTCATCACGGTCAAGCC	0.406													4	2	---	---	---	---	
LRFN3	79414	broad.mit.edu	37	19	36429581	36429581	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36429581delG	uc002oco.2	+							NM_024509	NP_078785	Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III						cell adhesion	axon|cell junction|dendrite|integral to membrane|postsynaptic membrane|presynaptic membrane					0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TGACCACCTTGCTGGCTTTGG	0.582													4	2	---	---	---	---	
SAE1	10055	broad.mit.edu	37	19	47658718	47658718	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47658718delT	uc002pgc.2	+						SAE1_uc002pgd.2_Intron|SAE1_uc010ekx.2_Intron|SAE1_uc010ekw.2_Intron|SAE1_uc010xyk.1_Intron|SAE1_uc002pge.2_Intron	NM_016402	NP_057486	Q9UBE0	SAE1_HUMAN	SubName: Full=SUMO-1 activating enzyme subunit 1, isoform CRA_b; SubName: Full=cDNA, FLJ96708, Homo sapiens SUMO-1 activating enzyme subunit 1 (SAE1), mRNA;						protein sumoylation|protein ubiquitination	nucleus	ATP-dependent protein binding|enzyme activator activity|ligase activity|protein C-terminus binding|protein heterodimerization activity|ubiquitin activating enzyme activity			ovary(1)	1		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		TGTCCCAAACttttttttttg	0.045													5	3	---	---	---	---	
EHD2	30846	broad.mit.edu	37	19	48243008	48243008	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48243008delT	uc002phj.3	+						EHD2_uc010xyu.1_Intron|EHD2_uc010xyv.1_Intron	NM_014601	NP_055416	Q9NZN4	EHD2_HUMAN	EH-domain containing 2						blood coagulation|endocytic recycling	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding			ovary(1)|skin(1)	2		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		GCCTGCTGAGTTTTTTTTTTT	0.244													4	2	---	---	---	---	
IZUMO1	284359	broad.mit.edu	37	19	49247998	49247999	+	Intron	INS	-	C	C	rs150963534	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49247998_49247999insC	uc002pkj.2	-						IZUMO1_uc010eme.2_Intron|IZUMO1_uc010emf.2_Intron	NM_182575	NP_872381	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1 precursor						fusion of sperm to egg plasma membrane	integral to membrane				ovary(1)	1		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		aggctggagtgtgtggtgtaat	0.188													6	4	---	---	---	---	
IL4I1	259307	broad.mit.edu	37	19	50399704	50399704	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50399704delT	uc002pqt.1	-						IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqw.1_Intron|IL4I1_uc002pqu.1_Intron	NM_152899	NP_690863	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1 isoform 1 precursor							lysosome	L-amino-acid oxidase activity			lung(1)|ovary(1)|prostate(1)	3		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)		cctttctttctttttttttta	0.244													4	2	---	---	---	---	
VRK3	51231	broad.mit.edu	37	19	50492608	50492608	+	Intron	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50492608delG	uc002prg.2	-						VRK3_uc002prh.1_Intron|VRK3_uc002pri.1_Intron|VRK3_uc010ens.2_Intron|VRK3_uc010ybl.1_Intron|VRK3_uc010ybm.1_Intron|VRK3_uc002prj.1_Intron|VRK3_uc002prk.1_Intron|VRK3_uc010ent.1_Intron|VRK3_uc002prl.2_Intron	NM_016440	NP_057524	Q8IV63	VRK3_HUMAN	vaccinia related kinase 3 isoform 1							nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)		agcccctcctggatgactcct	0.000													4	2	---	---	---	---	
TARM1	441864	broad.mit.edu	37	19	54573524	54573524	+	Intron	DEL	T	-	-	rs7250959	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54573524delT	uc010yei.1	-							NM_001135686	NP_001129158	B6A8C7	TARM1_HUMAN	OSCAR-like transcript-2							integral to membrane					0						GGttttttggttttttttttt	0.234													5	3	---	---	---	---	
C19orf51	352909	broad.mit.edu	37	19	55673785	55673785	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55673785delC	uc002qji.1	-						C19orf51_uc002qjh.1_5'Flank|C19orf51_uc002qjj.1_Intron|C19orf51_uc002qjk.1_Intron|C19orf51_uc002qjl.1_Intron			Q8N9W5	CS051_HUMAN	RecName: Full=UPF0470 protein C19orf51;												0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CCCCACGCATCCCAAAAACTA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	56701005	56701005	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56701005delA								GALP (3861 upstream) : ZSCAN5B (54 downstream)																							AACAGACACTAAAATAAATCT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57074090	57074091	+	Intron	INS	-	C	C	rs147757985	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57074090_57074091insC	uc002qnk.1	-											Homo sapiens cDNA FLJ33357 fis, clone BRACE2005189.																		CGTCCCCACctcccagtgattc	0.059													4	4	---	---	---	---	
ZNF274	10782	broad.mit.edu	37	19	58723422	58723422	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58723422delA	uc002qrq.1	+						ZNF274_uc002qrr.1_Intron|ZNF274_uc002qrs.1_Intron|ZNF274_uc010eum.1_Intron	NM_133502	NP_598009	Q96GC6	ZN274_HUMAN	zinc finger protein 274 isoform c						viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		TATTTGGGAGAAAAAAAAAAT	0.443													14	8	---	---	---	---	
EBF4	57593	broad.mit.edu	37	20	2736011	2736011	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2736011delT	uc002wgt.3	+						EBF4_uc002wgs.3_Intron	NM_001110514	NP_001103984	Q9BQW3	COE4_HUMAN	early B-cell factor 4						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding				0						CCACTGTTTGTTTTTTTTGAA	0.493													4	2	---	---	---	---	
PCSK2	5126	broad.mit.edu	37	20	17378809	17378809	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17378809delA	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TATAACAGGGAGGCTATGGAT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22538127	22538128	+	IGR	DEL	TG	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22538127_22538128delTG								LOC284788 (136846 upstream) : C20orf56 (3066 downstream)																							ACCGGAAGGCtgtgtgtgtgtg	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22939832	22939832	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22939832delC	uc002wsp.2	+											full-length cDNA clone CS0DI028YD21 of Placenta Cot 25-normalized of Homo sapiens (human).																		GAGATAACCTCCCCCAACCCC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	24746039	24746040	+	IGR	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24746039_24746040delCA								TMEM90B (98872 upstream) : CST7 (183826 downstream)																							ATTTGTCTGTCACAAGTTCTTC	0.465													4	2	---	---	---	---	
NFS1	9054	broad.mit.edu	37	20	34284029	34284029	+	Intron	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34284029delA	uc002xdw.1	-						NFS1_uc002xdt.1_Intron|NFS1_uc002xdu.1_Intron|NFS1_uc002xdv.1_Intron|NFS1_uc010zvk.1_Intron|NFS1_uc010zvl.1_Intron|NFS1_uc002xdx.2_Intron	NM_021100	NP_066923	Q9Y697	NFS1_HUMAN	NFS1 nitrogen fixation 1 precursor						cysteine metabolic process|iron incorporation into metallo-sulfur cluster|Mo-molybdopterin cofactor biosynthetic process|protein complex assembly|water-soluble vitamin metabolic process	cytosol|mitochondrial matrix|nucleus	cysteine desulfurase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)	ACTGCCAGACAAAAAAAAAAC	0.328													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44771310	44771310	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44771310delC								CD40 (12926 upstream) : CDH22 (31066 downstream)																							tccctctcttcttgctttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	45158075	45158076	+	IGR	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45158075_45158076delCA								ZNF334 (15881 upstream) : C20orf123 (11509 downstream)																							CCCAGCCCTTCACAGCTAAGTT	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48869492	48869492	+	IGR	DEL	G	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48869492delG								CEBPB (60280 upstream) : PTPN1 (257399 downstream)																							agtggccaaaggtgacactgt	0.090													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60458390	60458390	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60458390delT	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GTCGGTCTCCTCCCCTAGAGC	0.303													4	2	---	---	---	---	
EEF1A2	1917	broad.mit.edu	37	20	62122732	62122733	+	Intron	INS	-	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62122732_62122733insC	uc002yfd.1	-						EEF1A2_uc002yfe.1_Intron|EEF1A2_uc010gkg.1_Intron	NM_001958	NP_001949	Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha							nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			GGGGGTCTTGTCCCCCCCCAGG	0.599													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10718027	10718028	+	IGR	INS	-	A	A	rs145389672		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10718027_10718028insA								None (None upstream) : TPTE (188715 downstream)																							ttgcagatcctaaaaaaagtgt	0.000													10	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11065298	11065299	+	Intron	INS	-	AGC	AGC	rs146184689		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11065298_11065299insAGC	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ataacaaataGAGCAGCATTTC	0.168													6	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088831	11088831	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088831delT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TATGTCTGTATTTTTTTTCTA	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26734357	26734358	+	IGR	INS	-	C	C			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26734357_26734358insC								None (None upstream) : NCRNA00158 (23776 downstream)																							CCACTTCCGGGCCCCCCAGCCG	0.584													4	2	---	---	---	---	
NCRNA00158	54072	broad.mit.edu	37	21	26798751	26798751	+	Intron	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26798751delT	uc002ylk.2	-						NCRNA00158_uc010glg.2_Intron	NR_024027				Homo sapiens C21orf42 protein mRNA, complete cds, alternatively spliced.												0						TGGAGACACATTTTTTTTTGG	0.358													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37025503	37025506	+	Intron	DEL	CTGA	-	-	rs141906989		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37025503_37025506delCTGA	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						gttggggtctctgactaataAGCC	0.083			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
UBASH3A	53347	broad.mit.edu	37	21	43826184	43826185	+	Intron	INS	-	TT	TT	rs117834816	by1000genomes	TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43826184_43826185insTT	uc002zbe.2	+						UBASH3A_uc002zbf.2_Intron|UBASH3A_uc010gpc.2_Intron|UBASH3A_uc010gpd.2_Intron|UBASH3A_uc010gpe.2_Intron	NM_018961	NP_061834	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing,							cytosol|nucleus				ovary(3)	3						GGGCTGAAGCGGGTAGCCAGGG	0.658													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44593867	44593868	+	IGR	INS	-	CC	CC	rs75526846		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44593867_44593868insCC								CRYAA (954 upstream) : SIK1 (240530 downstream)																							ctccacacacaacacactccac	0.347													6	3	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45843708	45843710	+	Intron	DEL	GAG	-	-	rs143108860		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45843708_45843710delGAG	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron|uc011afe.1_Intron|TRPM2_uc011aff.1_5'Flank	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						GGAGGGCTCTGAGGAGTGATGGT	0.650													6	4	---	---	---	---	
ZNRF3	84133	broad.mit.edu	37	22	29322200	29322201	+	Intron	DEL	CA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29322200_29322201delCA	uc003aeg.2	+							NM_032173	NP_115549	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1						ACATTCTGTTCAGAGACTGCAG	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35854107	35854107	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35854107delC								MCM5 (33613 upstream) : RASD2 (83245 downstream)																							tgggacaaagccaggacattg	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37148314	37148314	+	IGR	DEL	T	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37148314delT								CACNG2 (49411 upstream) : IFT27 (5941 downstream)																							taatagtttctttttttttta	0.075													4	2	---	---	---	---	
KDELR3	11015	broad.mit.edu	37	22	38877080	38877083	+	Intron	DEL	ATTA	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38877080_38877083delATTA	uc003avv.2	+						KDELR3_uc003avu.2_Intron	NM_006855	NP_006846	O43731	ERD23_HUMAN	KDEL receptor 3 isoform a						protein retention in ER lumen|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane	ER retention sequence binding|receptor activity			ovary(2)	2	Melanoma(58;0.0286)					TGattaaaatattataatttttat	0.304													16	7	---	---	---	---	
CELSR1	9620	broad.mit.edu	37	22	46792368	46792368	+	Intron	DEL	A	-	-	rs77439378		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46792368delA	uc003bhw.1	-						CELSR1_uc011arc.1_Intron	NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		ATGCCAAATTAAAAAAAAATA	0.239													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47634445	47634447	+	IGR	DEL	CTC	-	-	rs147275137		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47634445_47634447delCTC								TBC1D22A (64723 upstream) : None (None downstream)																							GTCCCTAGTTCTCCTTCCTCAGA	0.631													4	6	---	---	---	---	
DMD	1756	broad.mit.edu	37	X	32404213	32404213	+	Intron	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32404213delC	uc004dda.1	-						DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AATGAGAATTCCACATCGAAa	0.219													4	2	---	---	---	---	
FUNDC1	139341	broad.mit.edu	37	X	44401934	44401935	+	Intron	INS	-	A	A			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44401934_44401935insA	uc004dgc.2	-							NM_173794	NP_776155	Q8IVP5	FUND1_HUMAN	FUN14 domain containing 1												0						GGGGCTGCCTTAAAAAAAAAAT	0.589													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	47657593	47657593	+	IGR	DEL	C	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47657593delC								LOC100133957 (137817 upstream) : ZNF81 (38708 downstream)																							gatgttctgtcccactggact	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	63401617	63401617	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63401617delA								MIR1468 (395650 upstream) : FAM123B (3381 downstream)																							GGAAGAACCTAACATCTCAGG	0.358													4	2	---	---	---	---	
TEX11	56159	broad.mit.edu	37	X	69944894	69944894	+	Intron	DEL	T	-	-	rs72283702		TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69944894delT	uc004dyl.2	-						TEX11_uc004dyk.2_5'Flank|TEX11_uc004dym.2_Intron	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	testis expressed sequence 11 isoform 1								protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)					TTTATTCAGCTTTTTTTAAAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9861348	9861348	+	IGR	DEL	A	-	-			TCGA-B0-4810-01A-01D-1501-10	TCGA-B0-4810-11A-02D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9861348delA								TTTY22 (210494 upstream) : None (None downstream)																							aggaaataacaagtgtttgag	0.000													4	2	---	---	---	---	
