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
EIF4G3	8672	broad.mit.edu	37	1	21226401	21226401	+	Silent	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21226401T>C	uc001bec.2	-	11	1876	c.1620A>G	c.(1618-1620)GTA>GTG	p.V540V	EIF4G3_uc010odi.1_Silent_p.V144V|EIF4G3_uc010odj.1_Silent_p.V539V|EIF4G3_uc009vpz.2_Silent_p.V260V|EIF4G3_uc001bed.2_Silent_p.V540V|EIF4G3_uc001bef.2_Silent_p.V539V|EIF4G3_uc001bee.2_Silent_p.V546V	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4	540					interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		CAGATTCAAGTACTTTGTCAA	0.358													85	351	---	---	---	---	PASS
TINAGL1	64129	broad.mit.edu	37	1	32044806	32044806	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32044806A>G	uc001bta.2	+	3	438	c.312A>G	c.(310-312)GGA>GGG	p.G104G	TINAGL1_uc001bsz.2_Intron|TINAGL1_uc010ogi.1_Silent_p.G104G|TINAGL1_uc010ogj.1_Silent_p.G104G|TINAGL1_uc010ogk.1_Silent_p.G104G	NM_022164	NP_071447	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1	104					endosome transport|immune response|proteolysis	extracellular region	cysteine-type endopeptidase activity|extracellular matrix structural constituent|polysaccharide binding|scavenger receptor activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		TTCCAACAGGATGTATGCATG	0.498													7	617	---	---	---	---	PASS
SPOCD1	90853	broad.mit.edu	37	1	32267264	32267264	+	Splice_Site	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32267264C>T	uc001bts.1	-	3	1483	c.1425_splice	c.e3+1	p.Y475_splice	SPOCD1_uc001btt.2_5'Flank|SPOCD1_uc001btu.2_Splice_Site_p.Y475_splice|SPOCD1_uc001btv.2_Splice_Site	NM_144569	NP_653170	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1						transcription, DNA-dependent					ovary(5)|breast(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		TAAAAACCTACGTAGCACACA	0.502													6	246	---	---	---	---	PASS
C8B	732	broad.mit.edu	37	1	57415368	57415368	+	Missense_Mutation	SNP	G	A	A	rs150146785	byFrequency	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57415368G>A	uc001cyp.2	-	6	791	c.724C>T	c.(724-726)CGC>TGC	p.R242C	C8B_uc010oon.1_Missense_Mutation_p.R180C|C8B_uc010ooo.1_Missense_Mutation_p.R190C	NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	242	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex		p.R242G(1)		central_nervous_system(2)|large_intestine(1)|ovary(1)	4						GTGACATTGCGTTCAAAATCT	0.338													90	306	---	---	---	---	PASS
SLC44A3	126969	broad.mit.edu	37	1	95286513	95286513	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95286513A>G	uc001dqv.3	+	2	143	c.36A>G	c.(34-36)GCA>GCG	p.A12A	uc001dqu.2_5'Flank|SLC44A3_uc001dqx.3_Silent_p.A12A|SLC44A3_uc010otq.1_Intron|SLC44A3_uc010otr.1_Intron|SLC44A3_uc001dqw.3_Intron|SLC44A3_uc010ots.1_Intron	NM_001114106	NP_001107578	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3 isoform 1	12						integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	AGGTTTCTGCAGAAGGAGCCC	0.473													65	273	---	---	---	---	PASS
KCNC4	3749	broad.mit.edu	37	1	110775414	110775414	+	3'UTR	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110775414G>A	uc001dzh.2	+	4					KCNC4_uc001dzg.2_Intron|KCNC4_uc001dzi.2_Intron	NM_004978	NP_004969	Q03721	KCNC4_HUMAN	Shaw-related voltage-gated potassium channel						synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		TCCTTCTAACGTCTCATTCTT	0.557													3	46	---	---	---	---	PASS
CEPT1	10390	broad.mit.edu	37	1	111726876	111726876	+	Silent	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111726876C>T	uc001eah.1	+	9	1403	c.1195C>T	c.(1195-1197)CTG>TTG	p.L399L	CEPT1_uc001eai.1_Silent_p.L399L|CEPT1_uc001eaj.1_Silent_p.L399L|CEPT1_uc009wfz.1_Silent_p.L133L	NM_001007794	NP_001007795	Q9Y6K0	CEPT1_HUMAN	choline/ethanolaminephosphotransferase	399						endoplasmic reticulum membrane|integral to membrane|nuclear membrane	diacylglycerol cholinephosphotransferase activity|ethanolaminephosphotransferase activity|metal ion binding				0		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	TGCGTCTCACCTGCACATACA	0.393													5	524	---	---	---	---	PASS
WDR3	10885	broad.mit.edu	37	1	118492436	118492436	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118492436A>G	uc010oxe.1	+	14	1653	c.1587A>G	c.(1585-1587)AAA>AAG	p.K529K	WDR3_uc001ehi.2_Intron	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3	529	WD 9.					nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		AGTTAGTGAAAGATGAAAATA	0.348													8	683	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144863482	144863482	+	Intron	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144863482T>C	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron|PDE4DIP_uc001ema.2_3'UTR	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ATGGCAGAGCTACTCAGCCAC	0.527			T	PDGFRB	MPD								4	103	---	---	---	---	PASS
TDRD10	126668	broad.mit.edu	37	1	154492793	154492793	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154492793A>G	uc009wow.2	+	5	993	c.155A>G	c.(154-156)TAC>TGC	p.Y52C	TDRD10_uc001ffd.2_Missense_Mutation_p.Y52C|TDRD10_uc001ffe.2_5'Flank	NM_001098475	NP_001091945	Q5VZ19	TDR10_HUMAN	tudor domain containing 10 isoform a	52	RRM.						nucleotide binding|RNA binding			ovary(1)	1	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			GAAATTCTGTACCTTCTAAAG	0.433													7	512	---	---	---	---	PASS
ATP1A2	477	broad.mit.edu	37	1	160098716	160098716	+	Intron	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160098716A>G	uc001fvc.2	+						ATP1A2_uc001fvb.2_Intron|ATP1A2_uc010piz.1_3'UTR|ATP1A2_uc001fvd.2_Intron|ATP1A2_uc009wtg.1_Intron	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein						ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			TGAGTGGTTGAGATAAAGGCT	0.587													4	53	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201029869	201029869	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201029869C>T	uc001gvv.2	-	26	3558	c.3331G>A	c.(3331-3333)GTG>ATG	p.V1111M		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1111	Cytoplasmic (Potential).|IV.				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	ATGTACCACACCTGGTACTGG	0.527													65	277	---	---	---	---	PASS
C1orf227	149643	broad.mit.edu	37	1	213009428	213009428	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213009428G>T	uc001hjq.2	-	2	172	c.64C>A	c.(64-66)CTG>ATG	p.L22M		NM_001024601	NP_001019772	Q537H7	CA227_HUMAN	hypothetical protein LOC149643	22											0						ATCTCCTCCAGGAGATGTTGT	0.403													5	462	---	---	---	---	PASS
C2orf43	60526	broad.mit.edu	37	2	20901394	20901394	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20901394C>A	uc002rec.2	-	6	755	c.722G>T	c.(721-723)GGG>GTG	p.G241V	C2orf43_uc002rea.1_Missense_Mutation_p.G241V|C2orf43_uc002reb.1_RNA|C2orf43_uc010yka.1_Missense_Mutation_p.G121W|C2orf43_uc010ykb.1_Missense_Mutation_p.G111V|C2orf43_uc010ykc.1_Missense_Mutation_p.G193V|C2orf43_uc010ykd.1_Missense_Mutation_p.G163W|C2orf43_uc010yke.1_Missense_Mutation_p.G199V|C2orf43_uc010ykf.1_Missense_Mutation_p.G111V	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526	241											0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCTTGGCCCCCAAGGTAGGC	0.323													6	557	---	---	---	---	PASS
HEATR5B	54497	broad.mit.edu	37	2	37297446	37297446	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37297446A>G	uc002rpp.1	-	7	950	c.854T>C	c.(853-855)TTC>TCC	p.F285S		NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	285							binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)				GCTCTTTAAGAAACCTGACCC	0.423													6	295	---	---	---	---	PASS
PIGF	5281	broad.mit.edu	37	2	46808416	46808416	+	3'UTR	SNP	A	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46808416A>T	uc002rvd.2	-	6					RHOQ_uc002rva.2_3'UTR|uc002rvb.2_5'Flank|PIGF_uc002rvc.2_3'UTR	NM_002643	NP_002634	Q07326	PIGF_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	ethanolaminephosphotransferase activity				0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			CAGCATCTGAAGCCACAATCT	0.323													5	36	---	---	---	---	PASS
SPRED2	200734	broad.mit.edu	37	2	65541212	65541212	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65541212C>T	uc002sdr.3	-	6	1215	c.680G>A	c.(679-681)GGG>GAG	p.G227E	SPRED2_uc010fcw.2_Missense_Mutation_p.G224E	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	sprouty-related protein with EVH-1 domain 2	227	KBD.				inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3						ATCCTCGTACCCCGTCATCCA	0.672													7	17	---	---	---	---	PASS
FBXO41	150726	broad.mit.edu	37	2	73496700	73496700	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73496700C>T	uc002sjb.1	-	2	242	c.242G>A	c.(241-243)CGG>CAG	p.R81Q		NM_001080410	NP_001073879	Q8TF61	FBX41_HUMAN	F-box protein 41	20						intracellular	protein binding|zinc ion binding			breast(2)|pancreas(1)	3						CGACAGGCTCCGGAAGCGCTT	0.493													4	1	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109397736	109397736	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109397736C>T	uc002tem.3	+	26	8737	c.8611C>T	c.(8611-8613)CAA>TAA	p.Q2871*		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	2871					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						TAAAAATTTCCAATGGGCAAA	0.373													4	272	---	---	---	---	PASS
DPP10	57628	broad.mit.edu	37	2	116525924	116525924	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116525924C>T	uc002tla.1	+	13	1622	c.1165C>T	c.(1165-1167)CCT>TCT	p.P389S	DPP10_uc002tlb.1_Missense_Mutation_p.P339S|DPP10_uc002tlc.1_Missense_Mutation_p.P385S|DPP10_uc002tle.2_Missense_Mutation_p.P393S|DPP10_uc002tlf.1_Missense_Mutation_p.P382S	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	389	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						TATGACAGTGCCTGTTAAGCA	0.433													6	675	---	---	---	---	PASS
MAP3K2	10746	broad.mit.edu	37	2	128066323	128066323	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128066323C>A	uc002toj.1	-	15	1537	c.1472G>T	c.(1471-1473)CGA>CTA	p.R491L		NM_006609	NP_006600	Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase	491	Protein kinase.				activation of JUN kinase activity|cellular response to mechanical stimulus	nucleus	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein kinase binding			lung(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)		TGTTGAATCTCGCAGGATATT	0.428													33	127	---	---	---	---	PASS
THSD7B	80731	broad.mit.edu	37	2	138434238	138434238	+	3'UTR	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138434238C>T	uc002tva.1	+	27						NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		TTGTAGCTCTCAGACTTCTCA	0.373													4	167	---	---	---	---	PASS
SCN7A	6332	broad.mit.edu	37	2	167328884	167328884	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167328884G>A	uc002udu.1	-	5	642	c.515C>T	c.(514-516)TCA>TTA	p.S172L	SCN7A_uc010fpm.1_RNA	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	172					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1						GAAGGAAAATGATCCTGCCCA	0.343													66	233	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179439168	179439168	+	Nonsense_Mutation	SNP	A	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179439168A>C	uc010zfg.1	-	275	64211	c.63987T>G	c.(63985-63987)TAT>TAG	p.Y21329*	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Nonsense_Mutation_p.Y15024*|TTN_uc010zfi.1_Nonsense_Mutation_p.Y14957*|TTN_uc010zfj.1_Nonsense_Mutation_p.Y14832*	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22256							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)			CCCGGAACTCATAAGCAATAC	0.438													29	119	---	---	---	---	PASS
GPR1	2825	broad.mit.edu	37	2	207041288	207041288	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207041288A>G	uc002vbl.3	-	3	1070	c.684T>C	c.(682-684)TGT>TGC	p.C228C	GPR1_uc010fue.2_Silent_p.C228C|GPR1_uc010fuf.2_Silent_p.C228C	NM_005279	NP_005270	P46091	GPR1_HUMAN	G protein-coupled receptor 1	228	Helical; Name=5; (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TGAAGATGAGACACAAGTAGC	0.443													5	144	---	---	---	---	PASS
UNC80	285175	broad.mit.edu	37	2	210795713	210795713	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210795713C>T	uc010zjc.1	+	37	5811	c.5731C>T	c.(5731-5733)CGC>TGC	p.R1911C	UNC80_uc002vdk.2_Missense_Mutation_p.R1072C	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1	1911						integral to membrane					0						GTACATGCTGCGCAAACTTCT	0.348													6	357	---	---	---	---	PASS
PTMA	5757	broad.mit.edu	37	2	232577853	232577853	+	3'UTR	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232577853T>C	uc002vsc.3	+	5					PTMA_uc002vsb.3_3'UTR|PTMA_uc010zmf.1_RNA|MIR1244_hsa-mir-1244-1|MI0006379_5'Flank	NM_001099285	NP_001092755	P06454	PTMA_HUMAN	prothymosin, alpha isoform 1						transcription, DNA-dependent	nucleus					0		Renal(207;0.0112)|all_hematologic(139;0.0315)|Acute lymphoblastic leukemia(138;0.0921)|all_lung(227;0.142)		Epithelial(121;1.75e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00221)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		TTTTATATTTTTGTACATATT	0.348													11	192	---	---	---	---	PASS
ATG16L1	55054	broad.mit.edu	37	2	234191377	234191377	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234191377C>T	uc002vty.2	+	12	1438	c.1181C>T	c.(1180-1182)ACT>ATT	p.T394I	ATG16L1_uc002vtx.1_Missense_Mutation_p.T231I|ATG16L1_uc002vua.2_Missense_Mutation_p.T375I|ATG16L1_uc002vub.2_Missense_Mutation_p.T252I|ATG16L1_uc002vtz.2_Missense_Mutation_p.T215I|ATG16L1_uc002vud.3_Missense_Mutation_p.T310I	NM_030803	NP_110430	Q676U5	A16L1_HUMAN	APG16 autophagy 16-like isoform 1	394	WD 2.				autophagic vacuole assembly|protein homooligomerization|protein transport	autophagic vacuole|pre-autophagosomal structure membrane	protein binding				0		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CGAATCTGGACTGTGGATGAT	0.408													5	382	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238233406	238233406	+	3'UTR	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238233406G>A	uc002vwl.2	-	44					COL6A3_uc002vwo.2_3'UTR|COL6A3_uc010znj.1_3'UTR|COL6A3_uc002vwj.2_3'UTR	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TATGATGTTGGCCACCCACGC	0.547													20	65	---	---	---	---	PASS
KAT2B	8850	broad.mit.edu	37	3	20113834	20113834	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20113834T>C	uc003cbq.2	+	2	759	c.313T>C	c.(313-315)TCT>CCT	p.S105P		NM_003884	NP_003875	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	105					cell cycle arrest|cellular response to insulin stimulus|chromatin remodeling|histone H3 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|negative regulation of cell proliferation|transcription initiation from RNA polymerase I promoter	Ada2/Gcn5/Ada3 transcription activator complex|chromatin remodeling complex|PCAF complex	cyclin-dependent protein kinase inhibitor activity|histone acetyltransferase activity|histone deacetylase binding|protein kinase binding|transcription coactivator activity|transcription factor binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						GGCCGAGGAGTCTTGTAAATG	0.428													6	351	---	---	---	---	PASS
UBP1	7342	broad.mit.edu	37	3	33454286	33454286	+	Silent	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33454286G>A	uc003cfq.3	-	4	906	c.376C>T	c.(376-378)CTA>TTA	p.L126L	UBP1_uc003cfr.3_Silent_p.L126L|UBP1_uc010hga.2_Silent_p.L126L	NM_014517	NP_055332	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a) isoform a	126					negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			kidney(2)	2						GTGTATTGTAGCCGTCTGTCA	0.438													5	587	---	---	---	---	PASS
RPL14	9045	broad.mit.edu	37	3	40498846	40498846	+	5'UTR	SNP	G	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40498846G>T	uc003ckg.2	+	1					RPL14_uc003ckh.2_5'UTR|RPL14_uc003cki.2_5'Flank	NM_003973	NP_003964	P50914	RL14_HUMAN	ribosomal protein L14						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GCCTAACGCCGCCAACATGGT	0.642													7	29	---	---	---	---	PASS
RHOA	387	broad.mit.edu	37	3	49397568	49397568	+	3'UTR	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49397568C>T	uc003cwu.2	-	5					RHOA_uc010hku.2_3'UTR|GPX1_uc011bcl.1_5'Flank|GPX1_uc011bcm.1_5'Flank	NM_001664	NP_001655	P61586	RHOA_HUMAN	ras homolog gene family, member A precursor						axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis	cytoskeleton|cytosol|plasma membrane	GTP binding|GTPase activity|myosin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	Atorvastatin(DB01076)|Simvastatin(DB00641)	TGAAAAAGGCCAGTAATCATA	0.353													6	755	---	---	---	---	PASS
CACNA1D	776	broad.mit.edu	37	3	53757596	53757596	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53757596A>C	uc003dgv.3	+	13	1965	c.1802A>C	c.(1801-1803)GAG>GCG	p.E601A	CACNA1D_uc003dgu.3_Missense_Mutation_p.E621A|CACNA1D_uc003dgy.3_Missense_Mutation_p.E601A|CACNA1D_uc003dgw.3_Missense_Mutation_p.E268A	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	601	Helical; Name=S3 of repeat II; (Potential).|II.				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)	GGAATCACTGAGACGATCTTG	0.473													25	420	---	---	---	---	PASS
CADPS	8618	broad.mit.edu	37	3	62522164	62522164	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62522164G>A	uc003dll.2	-	12	2419	c.2059C>T	c.(2059-2061)CGC>TGC	p.R687C	CADPS_uc003dlk.1_Missense_Mutation_p.R191C|CADPS_uc003dlm.2_Missense_Mutation_p.R687C|CADPS_uc003dln.2_Intron	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	687					exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		AAAGTAAGGCGTTGTACCATC	0.373													10	506	---	---	---	---	PASS
FOXP1	27086	broad.mit.edu	37	3	71008395	71008395	+	3'UTR	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71008395T>C	uc003dol.2	-	17					FOXP1_uc003dom.2_3'UTR|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_3'UTR|FOXP1_uc003dop.2_3'UTR|FOXP1_uc003doq.1_Intron|FOXP1_uc003doi.2_3'UTR|FOXP1_uc003doj.2_3'UTR|FOXP1_uc003dok.2_3'UTR	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		CCCGCCCCGATAGTCACTCCA	0.443			T	PAX5	ALL								9	324	---	---	---	---	PASS
LOC220729	220729	broad.mit.edu	37	3	197348646	197348646	+	RNA	SNP	T	C	C	rs138265355	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197348646T>C	uc011bug.1	-	4		c.445A>G			LOC220729_uc003fxw.2_RNA|LOC220729_uc003fxy.2_RNA|LOC220729_uc010iao.1_Intron					Homo sapiens cDNA FLJ60865 complete cds, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1).												0						TGGGCCTGCCTGCCCTTTCCA	0.532													6	118	---	---	---	---	PASS
PDE6B	5158	broad.mit.edu	37	4	649741	649741	+	Silent	SNP	C	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:649741C>G	uc003gap.2	+	7	1058	c.1005C>G	c.(1003-1005)GCC>GCG	p.A335A	PDE6B_uc003gao.3_Silent_p.A335A|PDE6B_uc011buy.1_Silent_p.A56A|uc003gaq.1_5'Flank	NM_000283	NP_000274	P35913	PDE6B_HUMAN	phosphodiesterase 6B isoform 1	335	GAF 2.				cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0						CACCCTCAGCCGATCACTGGG	0.647													8	46	---	---	---	---	PASS
PGM2	55276	broad.mit.edu	37	4	37839173	37839173	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37839173A>G	uc011byb.1	+	4	452	c.379A>G	c.(379-381)ACA>GCA	p.T127A	PGM2_uc011bya.1_5'UTR|PGM2_uc011byc.1_Intron	NM_018290	NP_060760	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	127					glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity|phosphopentomutase activity			ovary(1)	1						TGCTGCAACCACATTTATCAG	0.443													85	327	---	---	---	---	PASS
CENPC1	1060	broad.mit.edu	37	4	68358686	68358686	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68358686G>C	uc003hdd.1	-	15	2503	c.2320C>G	c.(2320-2322)CCA>GCA	p.P774A	CENPC1_uc010ihj.1_RNA|CENPC1_uc010ihk.1_RNA|CENPC1_uc010ihl.2_5'UTR	NM_001812	NP_001803	Q03188	CENPC_HUMAN	centromere protein C 1	774					mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2						ATTGTGTCTGGAGATAGTACT	0.299													117	437	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123150305	123150305	+	Silent	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123150305T>C	uc003ieh.2	+	23	2997	c.2952T>C	c.(2950-2952)ACT>ACC	p.T984T	KIAA1109_uc003iei.1_Silent_p.T737T|KIAA1109_uc010ins.1_Silent_p.T327T	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	984					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						CTTGTCCAACTTCAGATGATT	0.323													143	635	---	---	---	---	PASS
KIAA1109	84162	broad.mit.edu	37	4	123150307	123150307	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123150307C>A	uc003ieh.2	+	23	2999	c.2954C>A	c.(2953-2955)TCA>TAA	p.S985*	KIAA1109_uc003iei.1_Nonsense_Mutation_p.S738*|KIAA1109_uc010ins.1_Nonsense_Mutation_p.S328*	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	985					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						TGTCCAACTTCAGATGATTTG	0.323													139	638	---	---	---	---	PASS
SLC25A31	83447	broad.mit.edu	37	4	128694815	128694815	+	3'UTR	SNP	G	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128694815G>T	uc003ifl.2	+	6						NM_031291	NP_112581	Q9H0C2	ADT4_HUMAN	solute carrier family 25 (mitochondrial carrier;						transmembrane transport	cilium|flagellum|integral to membrane|mitochondrial inner membrane	binding|transporter activity				0						TTTTGATAGTGTTATTGTCTG	0.294													29	92	---	---	---	---	PASS
FNIP2	57600	broad.mit.edu	37	4	159789573	159789573	+	Silent	SNP	G	C	C	rs143166945	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159789573G>C	uc003iqe.3	+	13	1968	c.1785G>C	c.(1783-1785)CCG>CCC	p.P595P		NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	595	Interaction with PRKAA1.				DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		ACCCCTGGCCGACAGGGTTTC	0.562													14	92	---	---	---	---	PASS
FSTL5	56884	broad.mit.edu	37	4	163032520	163032520	+	Missense_Mutation	SNP	A	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163032520A>T	uc003iqh.2	-	2	465	c.29T>A	c.(28-30)GTT>GAT	p.V10D	FSTL5_uc003iqi.2_Missense_Mutation_p.V10D|FSTL5_uc010iqv.2_Missense_Mutation_p.V10D	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	10						extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		GAATCCGAGAACCAAGACAAC	0.368													5	318	---	---	---	---	PASS
SNX25	83891	broad.mit.edu	37	4	186244946	186244946	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186244946G>A	uc003ixh.2	+	9	1438	c.1249G>A	c.(1249-1251)GAT>AAT	p.D417N	SNX25_uc010ish.2_Missense_Mutation_p.D188N|SNX25_uc003ixi.2_5'UTR	NM_031953	NP_114159	Q9H3E2	SNX25_HUMAN	sorting nexin 25	417					cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		TTCCAACAAGGATGAGATGGT	0.348													17	64	---	---	---	---	PASS
SLC12A7	10723	broad.mit.edu	37	5	1065466	1065466	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1065466G>A	uc003jbu.2	-	18	2435	c.2369C>T	c.(2368-2370)ACG>ATG	p.T790M		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	790					potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CATGAGCACCGTGTTGTGCTT	0.627													5	20	---	---	---	---	PASS
SDHAP3	728609	broad.mit.edu	37	5	1572275	1572275	+	Intron	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1572275A>G	uc011cmd.1	-						SDHAP3_uc011cme.1_RNA					Homo sapiens cDNA FLJ58919 complete cds, moderately similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC1.3.5.1).												0						GGACACATGCATGAGCTATTA	0.507													7	43	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35712917	35712917	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35712917C>T	uc003jjo.2	+	20	2954	c.2843C>T	c.(2842-2844)GCC>GTC	p.A948V	SPEF2_uc003jjp.1_Missense_Mutation_p.A434V	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	948					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGTTTAGAAGCCCCGCATGGT	0.363													5	440	---	---	---	---	PASS
DDX4	54514	broad.mit.edu	37	5	55086409	55086409	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55086409G>A	uc003jqg.3	+	16	1252	c.1178G>A	c.(1177-1179)TGT>TAT	p.C393Y	DDX4_uc010ivz.2_Missense_Mutation_p.C373Y|DDX4_uc003jqh.3_Missense_Mutation_p.C359Y|DDX4_uc003jqj.2_Missense_Mutation_p.C244Y	NM_001136034	NP_001129506	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform	393	Helicase ATP-binding.				multicellular organismal development|sperm motility	perinuclear region of cytoplasm|pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				AATAGGACTTGTGTAAGAGCT	0.318													69	355	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469495	75469495	+	Intron	SNP	G	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469495G>T	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)		GCCTTCCCAGGCACTGGAGTT	0.388													7	503	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75581040	75581040	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75581040G>A	uc003kei.1	+	5	1101	c.967G>A	c.(967-969)GTC>ATC	p.V323I		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	323	Helical; (Potential).				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)		GCGTGTGTTTGTCATCGTCTG	0.542													5	368	---	---	---	---	PASS
MCC	4163	broad.mit.edu	37	5	112363104	112363104	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112363104C>T	uc003kqj.3	-	17	2915	c.2385G>A	c.(2383-2385)ATG>ATA	p.M795I	MCC_uc003kqk.3_RNA|MCC_uc003kql.3_Missense_Mutation_p.M985I	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2	795					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CCACCATGGCCATCATCTGCG	0.478													6	537	---	---	---	---	PASS
ADAMTS19	171019	broad.mit.edu	37	5	128957927	128957927	+	Silent	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128957927G>A	uc003kvb.1	+	10	1638	c.1638G>A	c.(1636-1638)CCG>CCA	p.P546P	ADAMTS19_uc010jdh.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	546	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AAACAAATCCGCAGAGTGTCA	0.423													15	428	---	---	---	---	PASS
FAM13B	51306	broad.mit.edu	37	5	137278882	137278882	+	Silent	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137278882C>T	uc003lbz.2	-	20	2832	c.2298G>A	c.(2296-2298)AGG>AGA	p.R766R	FAM13B_uc003lcb.2_Silent_p.R642R|FAM13B_uc003lca.2_Silent_p.R738R	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1	766					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						ACATCTGACCCCTTCGCTTGG	0.338													108	541	---	---	---	---	PASS
KIF20A	10112	broad.mit.edu	37	5	137519224	137519224	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137519224A>G	uc003lcj.2	+	9	1589	c.1093A>G	c.(1093-1095)AAC>GAC	p.N365D	KIF20A_uc011cyo.1_Missense_Mutation_p.N347D	NM_005733	NP_005724	O95235	KI20A_HUMAN	kinesin family member 20A	365	Kinesin-motor.				cytokinesis|M phase of mitotic cell cycle|microtubule-based movement|protein transport|vesicle-mediated transport	Golgi apparatus|microtubule|nucleoplasm	ATP binding|microtubule motor activity|protein binding|transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GGGTCGTAAGAACCAGAGCTT	0.498													38	144	---	---	---	---	PASS
PCDHAC2	56134	broad.mit.edu	37	5	140389517	140389517	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140389517C>G	uc003lii.2	+	4	3259	c.3019C>G	c.(3019-3021)CAG>GAG	p.Q1007E	PCDHA1_uc003lha.2_Missense_Mutation_p.Q686E|PCDHA1_uc003lhb.2_Missense_Mutation_p.Q950E|PCDHA2_uc003lhd.2_Missense_Mutation_p.Q948E|PCDHA3_uc003lhf.2_Missense_Mutation_p.Q950E|PCDHA4_uc003lhi.2_Missense_Mutation_p.Q947E|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Missense_Mutation_p.Q936E|PCDHA6_uc003lhn.2_Missense_Mutation_p.Q686E|PCDHA6_uc003lho.2_Missense_Mutation_p.Q950E|PCDHA7_uc003lhq.2_Missense_Mutation_p.Q937E|PCDHA8_uc003lhs.2_Missense_Mutation_p.Q950E|PCDHA9_uc003lhu.2_Missense_Mutation_p.Q950E|PCDHA10_uc003lhw.2_Missense_Mutation_p.Q685E|PCDHA10_uc003lhx.2_Missense_Mutation_p.Q948E|PCDHA11_uc003lia.2_Missense_Mutation_p.Q949E|PCDHA12_uc003lic.2_Missense_Mutation_p.Q941E|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Missense_Mutation_p.Q950E|PCDHAC1_uc003lih.2_Missense_Mutation_p.Q963E	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1	1007	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAACAGTGACCAGTGAGGTCC	0.363													13	211	---	---	---	---	PASS
PCDHB8	56128	broad.mit.edu	37	5	140559035	140559035	+	Missense_Mutation	SNP	G	A	A	rs149925643		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140559035G>A	uc011dai.1	+	1	1606	c.1420G>A	c.(1420-1422)GTC>ATC	p.V474I	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	474	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CATCGGCAGCGTCAGCGCCAC	0.662													3	31	---	---	---	---	PASS
HMMR	3161	broad.mit.edu	37	5	162900387	162900387	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162900387G>A	uc003lzf.2	+	9	907	c.725G>A	c.(724-726)TGT>TAT	p.C242Y	HMMR_uc003lzh.2_Missense_Mutation_p.C243Y|HMMR_uc003lzg.2_Missense_Mutation_p.C227Y|HMMR_uc011dem.1_Missense_Mutation_p.C156Y	NM_012484	NP_036616	O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor isoform b	242						cell surface|cytoplasm	hyaluronic acid binding				0	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)		TAATGCAGTTGTGCTTCAGAT	0.299													23	439	---	---	---	---	PASS
BTNL3	10917	broad.mit.edu	37	5	180432814	180432814	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180432814C>T	uc003mmr.2	+	8	1471	c.1343C>T	c.(1342-1344)GCG>GTG	p.A448V	BTNL3_uc010jlp.2_Missense_Mutation_p.A233V	NM_197975	NP_932079	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3 precursor	448	B30.2/SPRY.|Cytoplasmic (Potential).				lipid metabolic process	integral to membrane					0	all_cancers(89;3.37e-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;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			ATCCAGCATGCGATGTATGAC	0.493													49	216	---	---	---	---	PASS
GCM2	9247	broad.mit.edu	37	6	10876186	10876186	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10876186C>T	uc003mzn.3	-	4	592	c.520G>A	c.(520-522)GCC>ACC	p.A174T	SYCP2L_uc011dim.1_Intron	NM_004752	NP_004743	O75603	GCM2_HUMAN	glial cells missing homolog 2	174	GCM.				cellular calcium ion homeostasis|cellular phosphate ion homeostasis|parathyroid gland development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				CTCTTGATGGCGCTTCTTCTA	0.463													5	638	---	---	---	---	PASS
DAXX	1616	broad.mit.edu	37	6	33287883	33287883	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33287883T>A	uc003oec.2	-	5	1574	c.1370A>T	c.(1369-1371)GAG>GTG	p.E457V	ZBTB22_uc003oeb.2_5'Flank|ZBTB22_uc010juu.2_5'Flank|DAXX_uc011drd.1_Missense_Mutation_p.E382V|DAXX_uc011dre.1_Missense_Mutation_p.E469V|DAXX_uc003oed.2_Missense_Mutation_p.E457V	NM_001350	NP_001341	Q9UER7	DAXX_HUMAN	death-domain associated protein isoform a	457	Asp/Glu-rich (acidic).|Potential.|Necessary for interaction with USP7.				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding			pancreas(18)|ovary(2)|skin(2)|prostate(1)	23						ATCTGTGGcctcctcctcttc	0.244			Mis|F|N		Pancreatic neuroendocrine tumors								38	178	---	---	---	---	PASS
ENPP1	5167	broad.mit.edu	37	6	132204835	132204835	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132204835A>G	uc011ecf.1	+	22	2252	c.2232A>G	c.(2230-2232)CAA>CAG	p.Q744Q		NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	744	Nuclease.|Extracellular (Potential).				3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	TCTTTGTAGAACTAAATAAAA	0.294													7	237	---	---	---	---	PASS
AHR	196	broad.mit.edu	37	7	17367439	17367439	+	Silent	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17367439T>C	uc011jxz.1	+	4	1030	c.417T>C	c.(415-417)TCT>TCC	p.S139S	AHR_uc003stt.3_RNA	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor	139	PAS 1.				apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)					TTTATGCTTCTTCTACTATAC	0.254													8	434	---	---	---	---	PASS
POLR2J4	84820	broad.mit.edu	37	7	44026251	44026251	+	Missense_Mutation	SNP	T	G	G	rs75823018		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44026251T>G	uc010kxw.2	-	6	665	c.544A>C	c.(544-546)AAA>CAA	p.K182Q	POLR2J4_uc003tjc.2_RNA|POLR2J4_uc003tjd.2_Intron					SubName: Full=cDNA FLJ58900, weakly similar to Uroplakin-3B;												0						ACGGGTCCTTTGTCATTCATC	0.602													5	75	---	---	---	---	PASS
NSUN5	55695	broad.mit.edu	37	7	72717575	72717575	+	3'UTR	SNP	A	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72717575A>T	uc003txw.2	-	9					FKBP6_uc003twz.2_Intron|NSUN5_uc003txv.2_Intron|NSUN5_uc003txx.2_3'UTR|NSUN5_uc011kev.1_Intron	NM_018044	NP_060514	Q96P11	NSUN5_HUMAN	NOL1/NOP2/Sun domain family, member 5 isoform 2								methyltransferase activity				0		Lung NSC(55;0.163)				TGCGCCTCCCAAGCACGCCCC	0.602													39	140	---	---	---	---	PASS
CLDN12	9069	broad.mit.edu	37	7	90042424	90042424	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90042424C>G	uc003ukp.2	+	5	1070	c.434C>G	c.(433-435)ACT>AGT	p.T145S	CLDN12_uc003ukq.2_Missense_Mutation_p.T145S|CLDN12_uc010leq.2_Missense_Mutation_p.T145S|CLDN12_uc003ukr.2_Missense_Mutation_p.T145S|CLDN12_uc003uks.2_Missense_Mutation_p.T145S	NM_012129	NP_036261	P56749	CLD12_HUMAN	claudin 12	145	Helical; (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity				0						CTGGCAGGTACTGTGAGCCTC	0.488													55	188	---	---	---	---	PASS
CYP3A4	1576	broad.mit.edu	37	7	99364831	99364831	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99364831A>G	uc003urv.1	-	8	825	c.721T>C	c.(721-723)TTT>CTT	p.F241L	CYP3A4_uc003urw.1_Missense_Mutation_p.F240L|CYP3A4_uc011kiz.1_Missense_Mutation_p.F200L|CYP3A4_uc011kja.1_Missense_Mutation_p.F192L|CYP3A4_uc011kjb.1_Missense_Mutation_p.F91L	NM_017460	NP_059488	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A,	241					alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process	cell surface|endoplasmic reticulum membrane|integral to membrane|microsome	albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity			central_nervous_system(3)|ovary(1)	4	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)	TCTCTTGGAAACACACAGATA	0.318													7	613	---	---	---	---	PASS
PUS7	54517	broad.mit.edu	37	7	105111238	105111238	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105111238G>A	uc003vcx.2	-	11	1514	c.1295C>T	c.(1294-1296)ACT>ATT	p.T432I	PUS7_uc010lji.2_Missense_Mutation_p.T438I|PUS7_uc003vcy.2_Missense_Mutation_p.T432I|PUS7_uc003vcz.1_Missense_Mutation_p.T432I	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog	432	TRUD.				pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						GAGGGCAGCAGTTGGGTCTTT	0.453													97	378	---	---	---	---	PASS
NUP205	23165	broad.mit.edu	37	7	135282917	135282917	+	Nonsense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135282917C>T	uc003vsw.2	+	15	2267	c.2236C>T	c.(2236-2238)CGA>TGA	p.R746*		NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	746					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						TGTGTTTCTACGATTCCGTAC	0.433													4	278	---	---	---	---	PASS
BRAF	673	broad.mit.edu	37	7	140494178	140494178	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140494178A>G	uc003vwc.3	-	8	1131	c.1070T>C	c.(1069-1071)TTT>TCT	p.F357S		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	357					activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGTTGCCCAAATTGATTTCG	0.428		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				11	725	---	---	---	---	PASS
WDR60	55112	broad.mit.edu	37	7	158698696	158698696	+	Silent	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158698696T>C	uc003woe.3	+	11	1532	c.1374T>C	c.(1372-1374)CCT>CCC	p.P458P	WDR60_uc010lqv.2_RNA|WDR60_uc010lqw.2_Silent_p.P90P	NM_018051	NP_060521	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	458										ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		ACAGTTCCCCTTCCAGAGCCT	0.408													6	334	---	---	---	---	PASS
PSD3	23362	broad.mit.edu	37	8	18662289	18662289	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18662289G>A	uc003wza.2	-	5	1857	c.1754C>T	c.(1753-1755)GCC>GTC	p.A585V	PSD3_uc003wyy.2_Missense_Mutation_p.A51V|PSD3_uc003wyz.2_5'UTR	NM_015310	NP_056125	Q9NYI0	PSD3_HUMAN	ADP-ribosylation factor guanine nucleotide	585	SEC7.				regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		CAACCTTTTGGCTGCTTCCAC	0.458													117	438	---	---	---	---	PASS
ADAMDEC1	27299	broad.mit.edu	37	8	24242084	24242084	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24242084T>C	uc003xdz.2	+	1	287	c.67T>C	c.(67-69)TGG>CGG	p.W23R	ADAMDEC1_uc010lub.2_5'UTR|ADAMDEC1_uc011lab.1_5'UTR	NM_014479	NP_055294	O15204	ADEC1_HUMAN	ADAM-like, decysin 1 isoform 1	23					integrin-mediated signaling pathway|negative regulation of cell adhesion|proteolysis	extracellular region|integral to membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)	2		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		GCCTGTACTTTGGCTCATTGT	0.433													59	241	---	---	---	---	PASS
XKR4	114786	broad.mit.edu	37	8	56436104	56436104	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56436104G>T	uc003xsf.2	+	3	1303	c.1271G>T	c.(1270-1272)TGT>TTT	p.C424F		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	424						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			ACAGAATTCTGTATCACCAAA	0.483													67	241	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110445335	110445335	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110445335G>A	uc003yne.2	+	28	3334	c.3230G>A	c.(3229-3231)GGG>GAG	p.G1077E		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	1077	Extracellular (Potential).|IPT/TIG 4.				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TCATTTTTAGGGTCCTATGAA	0.318										HNSCC(38;0.096)			57	539	---	---	---	---	PASS
ZNF250	58500	broad.mit.edu	37	8	146115429	146115429	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146115429C>T	uc003zeq.3	-	3	190	c.73G>A	c.(73-75)GAG>AAG	p.E25K	COMMD5_uc010mgf.2_5'UTR|ZNF250_uc003zer.3_Missense_Mutation_p.E20K|ZNF250_uc010mgg.2_Missense_Mutation_p.E20K|ZNF250_uc003zes.2_3'UTR	NM_021061	NP_066405	P15622	ZN250_HUMAN	zinc finger protein 250 isoform a	25	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)		GCCACATCCTCGAAGGTCAGC	0.542													4	96	---	---	---	---	PASS
TEK	7010	broad.mit.edu	37	9	27202840	27202840	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27202840C>G	uc003zqi.3	+	13	2374	c.1932C>G	c.(1930-1932)AAC>AAG	p.N644K	TEK_uc011lno.1_Missense_Mutation_p.N601K|TEK_uc011lnp.1_Missense_Mutation_p.N497K|TEK_uc003zqj.1_Missense_Mutation_p.N578K	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	644	Extracellular (Potential).|Fibronectin type-III 3.				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)		AACCAGAAAACATCAAGATTT	0.343													45	373	---	---	---	---	PASS
UBQLN1	29979	broad.mit.edu	37	9	86284234	86284234	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86284234A>G	uc004amv.2	-	7	1688	c.1114T>C	c.(1114-1116)TTC>CTC	p.F372L	UBQLN1_uc004amw.2_Missense_Mutation_p.F372L	NM_013438	NP_038466	Q9UMX0	UBQL1_HUMAN	ubiquilin 1 isoform 1	372					apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0						GGTGTGTTGAACATACTAGCT	0.328													6	406	---	---	---	---	PASS
CEP110	11064	broad.mit.edu	37	9	123929881	123929881	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123929881A>G	uc004bkx.1	+	35	5801	c.5770A>G	c.(5770-5772)ACA>GCA	p.T1924A	CEP110_uc004blb.1_Missense_Mutation_p.T593A|CEP110_uc010mvp.1_5'UTR	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa	1924	Potential.				cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						AGAAGAGGAGACAAAACAACA	0.403													5	138	---	---	---	---	PASS
RABGAP1	23637	broad.mit.edu	37	9	125719332	125719332	+	5'UTR	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125719332T>C	uc011lzh.1	+	2					RABGAP1_uc004bnl.3_RNA|RABGAP1_uc004bnm.1_5'UTR	NM_012197	NP_036329	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1						cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5						AGACTCATTCTTGAGTTATGG	0.333													6	298	---	---	---	---	PASS
ABL1	25	broad.mit.edu	37	9	133589643	133589643	+	Translation_Start_Site	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133589643C>T	uc004bzv.2	+	1	376	c.-63C>T	c.(-65--61)TACGC>TATGC			NM_007313	NP_009297	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase						actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)	TTTCCCTCTACGCTCGCTGAC	0.453			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								6	67	---	---	---	---	PASS
MEIG1	644890	broad.mit.edu	37	10	15008547	15008547	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15008547T>C	uc009xjk.1	+	2	228	c.80T>C	c.(79-81)TTT>TCT	p.F27S		NM_001080836	NP_001074305	Q5JSS6	MEIG1_HUMAN	meiosis expressed gene 1 homolog	27											0						CTGTACAGATTTCAACAAGCA	0.363													5	236	---	---	---	---	PASS
SLC39A12	221074	broad.mit.edu	37	10	18284634	18284634	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18284634C>G	uc001ipo.2	+	10	1856	c.1583C>G	c.(1582-1584)ACA>AGA	p.T528R	SLC39A12_uc001ipn.2_Missense_Mutation_p.T491R|SLC39A12_uc001ipp.2_Missense_Mutation_p.T527R|SLC39A12_uc010qck.1_Missense_Mutation_p.T394R	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	528	Extracellular (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2						GGCAGTATGACAGCCTCCAAC	0.328													6	159	---	---	---	---	PASS
YME1L1	10730	broad.mit.edu	37	10	27420850	27420850	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27420850C>G	uc001iti.2	-	9	1149	c.967G>C	c.(967-969)GGG>CGG	p.G323R	YME1L1_uc001itj.2_Missense_Mutation_p.G266R|YME1L1_uc010qdl.1_Missense_Mutation_p.G233R|YME1L1_uc009xkv.2_RNA	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1	323					protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						GAATCAAGCCCTGTTGTTGTC	0.313													37	295	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37422855	37422855	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37422855T>G	uc001iza.1	+	5	560	c.461T>G	c.(460-462)ATG>AGG	p.M154R		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	210	ANK 5.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						ACAGCCCTCATGCTTGCTGTA	0.373													39	262	---	---	---	---	PASS
BMS1	9790	broad.mit.edu	37	10	43288427	43288427	+	Silent	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43288427T>C	uc001jaj.2	+	8	1282	c.924T>C	c.(922-924)AGT>AGC	p.S308S		NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein	308					ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3						TTGCCGTGAGTGACATCAGTT	0.473													10	95	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	55582089	55582089	+	Silent	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55582089G>A	uc001jju.1	-	33	5792	c.5397C>T	c.(5395-5397)TCC>TCT	p.S1799S	PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Silent_p.S1796S|PCDH15_uc010qhw.1_Silent_p.S1759S|PCDH15_uc010qhx.1_Silent_p.S1730S|PCDH15_uc010qhy.1_Silent_p.S1806S|PCDH15_uc010qhz.1_Silent_p.S1801S|PCDH15_uc010qia.1_Silent_p.S1779S|PCDH15_uc010qib.1_Silent_p.S1776S	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1799	Cytoplasmic (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ACGTTGAAACGGAAAGTGGAA	0.100										HNSCC(58;0.16)			5	188	---	---	---	---	PASS
PSAP	5660	broad.mit.edu	37	10	73579284	73579284	+	Missense_Mutation	SNP	G	T	T	rs121918109		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73579284G>T	uc001jsm.2	-	11	1392	c.1288C>A	c.(1288-1290)CAG>AAG	p.Q430K	PSAP_uc001jsl.2_Missense_Mutation_p.Q154K	NM_002778	NP_002769	P07602	SAP_HUMAN	prosaposin isoform a preproprotein	430	Saposin B-type 4.				glycosphingolipid metabolic process|lipid transport|platelet activation|platelet degranulation	extracellular space|Golgi apparatus|integral to membrane|lysosomal lumen	enzyme activator activity|lipid binding			ovary(1)	1						AGGATCTCCTGCTTGGTGCTG	0.572													10	154	---	---	---	---	PASS
LDB3	11155	broad.mit.edu	37	10	88476170	88476170	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88476170T>C	uc001kdv.2	+	9	1341	c.1318T>C	c.(1318-1320)TCC>CCC	p.S440P	LDB3_uc010qml.1_Missense_Mutation_p.S377P|LDB3_uc010qmm.1_Missense_Mutation_p.S445P|LDB3_uc001kdu.2_Missense_Mutation_p.S330P|LDB3_uc009xsz.2_Missense_Mutation_p.S69P|LDB3_uc009xta.1_5'Flank	NM_007078	NP_009009	O75112	LDB3_HUMAN	LIM domain binding 3 isoform 1	440						cytoskeleton|perinuclear region of cytoplasm|pseudopodium	zinc ion binding			ovary(1)	1						ctacaccccctcccctgcccc	0.234													9	67	---	---	---	---	PASS
IFIT3	3437	broad.mit.edu	37	10	91092356	91092356	+	Intron	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91092356C>T	uc001kgf.2	+						LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|uc001kgd.2_Intron|IFIT3_uc001kgg.2_5'UTR	NM_001549	NP_001540	O14879	IFIT3_HUMAN	interferon-induced protein with						type I interferon-mediated signaling pathway		protein binding			central_nervous_system(1)	1						CCCAGCTTTTCAGAACTGCAG	0.428													63	198	---	---	---	---	PASS
PIPSL	266971	broad.mit.edu	37	10	95719635	95719635	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95719635A>G	uc009xuj.2	-	1	2038	c.1519T>C	c.(1519-1521)TTA>CTA	p.L507L		NR_002319				RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha;          Short=PtdIns(4)P-5-kinase alpha;          Short=PIP5KIalpha;          EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha;												0						CGGGTGGGTAAGAAGTCTCCA	0.502													5	123	---	---	---	---	PASS
DNTT	1791	broad.mit.edu	37	10	98097902	98097902	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98097902T>C	uc001kmf.2	+	11	1621	c.1451T>C	c.(1450-1452)TTC>TCC	p.F484S	DNTT_uc001kmg.2_Missense_Mutation_p.F483S	NM_004088	NP_004079	P04053	TDT_HUMAN	terminal deoxynucleotidyltransferase isoform 1	484	Mediates interaction with DNTTIP2.				DNA modification	nucleus	DNA binding|DNA nucleotidylexotransferase activity|DNA-directed DNA polymerase activity|metal ion binding			ovary(1)	1		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)		CAGAGGATATTCCTCAAAGCA	0.353													7	672	---	---	---	---	PASS
TLL2	7093	broad.mit.edu	37	10	98156994	98156994	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98156994A>G	uc001kml.1	-	11	1559	c.1333T>C	c.(1333-1335)TTC>CTC	p.F445L	TLL2_uc009xvf.1_Missense_Mutation_p.F423L	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	445	CUB 1.				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		CTGCTGCGGAACTCCACCCAG	0.577													4	59	---	---	---	---	PASS
SLK	9748	broad.mit.edu	37	10	105750469	105750469	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105750469A>G	uc001kxo.1	+	2	221	c.187A>G	c.(187-189)AAA>GAA	p.K63E	SLK_uc001kxp.1_Missense_Mutation_p.K63E	NM_014720	NP_055535	Q9H2G2	SLK_HUMAN	serine/threonine kinase 2	63	Protein kinase.	ATP (By similarity).		K->R: Loss of activity.	apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity			ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AGCTGCTGCAAAAGTGATTGA	0.328													69	281	---	---	---	---	PASS
IGF2	3481	broad.mit.edu	37	11	2161456	2161456	+	5'Flank	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2161456C>T	uc009yde.2	-						IGF2_uc001lvg.2_5'Flank|IGF2_uc009ydf.2_Missense_Mutation_p.R24H|IGF2_uc001lvh.2_Intron|INS-IGF2_uc001lvi.2_Intron|INS-IGF2_uc001lvj.1_5'Flank|IGF2AS_uc001lvk.1_5'Flank|IGF2AS_uc010qxi.1_5'Flank|IGF2AS_uc001lvl.1_5'Flank	NM_001007139	NP_001007140	P01344	IGF2_HUMAN	insulin-like growth factor 2 isoform 1						glucose metabolic process|ossification|phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling|positive regulation of activated T cell proliferation|positive regulation of cell division|positive regulation of glycogen (starch) synthase activity|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|skeletal system development	extracellular space	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|protein serine/threonine kinase activator activity|receptor activator activity			central_nervous_system(1)	1		all_epithelial(84;5.04e-06)|Breast(177;0.000777)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.0179)|COAD - Colon adenocarcinoma(6;0.029)	BRCA - Breast invasive adenocarcinoma(625;1.09e-05)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		GTCCTCAGTGCGTTGGACTTG	0.547													3	45	---	---	---	---	PASS
OR6A2	8590	broad.mit.edu	37	11	6816240	6816240	+	Missense_Mutation	SNP	G	A	A	rs2741745		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6816240G>A	uc001mes.1	-	1	900	c.700C>T	c.(700-702)CCT>TCT	p.P234S		NM_003696	NP_003687	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A,	234	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GCAGCCGAAGGAATGTGCATC	0.493													25	70	---	---	---	---	PASS
SLC1A2	6506	broad.mit.edu	37	11	35282252	35282252	+	3'UTR	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35282252T>C	uc001mwd.2	-	11					SLC1A2_uc001mwe.2_3'UTR	NM_004171	NP_004162	P43004	EAA2_HUMAN	excitatory amino acid transporter 2						D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)	TAAAGCATTATTTGGCAAAGA	0.398													12	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	43283988	43283988	+	RNA	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43283988T>C	uc001mxe.1	-	2		c.948A>G								Homo sapiens cDNA FLJ44864 fis, clone BRALZ2013621, moderately similar to Heterogeneous nuclear ribonucleoprotein K.																		CATGTATCTATTGCAGAGTCC	0.483													4	40	---	---	---	---	PASS
FAM86C	55199	broad.mit.edu	37	11	71507232	71507232	+	Intron	SNP	C	G	G	rs113587125	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71507232C>G	uc001oqv.3	+						FAM86C_uc009ysr.2_Intron|FAM86C_uc001oqw.3_Intron|FAM86C_uc009yss.2_Intron|FAM86C_uc010rqq.1_RNA|uc001oqx.1_Intron	NM_018172	NP_060642	Q9NVL1	FA86C_HUMAN	hypothetical protein LOC55199 isoform 1												0						CACGCCCACCCGGGCCTGCAT	0.612													5	56	---	---	---	---	PASS
FAM86C	55199	broad.mit.edu	37	11	71507261	71507261	+	Intron	SNP	A	G	G	rs111708284	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71507261A>G	uc001oqv.3	+						FAM86C_uc009ysr.2_Intron|FAM86C_uc001oqw.3_Intron|FAM86C_uc009yss.2_Intron|FAM86C_uc010rqq.1_RNA|uc001oqx.1_Intron	NM_018172	NP_060642	Q9NVL1	FA86C_HUMAN	hypothetical protein LOC55199 isoform 1												0						AGCTGTCCCTACAGGACTCCA	0.627													6	49	---	---	---	---	PASS
CCDC90B	60492	broad.mit.edu	37	11	82985713	82985713	+	Missense_Mutation	SNP	C	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82985713C>G	uc001pae.2	-	4	757	c.395G>C	c.(394-396)AGT>ACT	p.S132T	CCDC90B_uc001pac.2_Missense_Mutation_p.S31T|CCDC90B_uc001pad.2_Missense_Mutation_p.S31T|CCDC90B_uc001paf.2_Missense_Mutation_p.S123T	NM_021825	NP_068597	Q9GZT6	CC90B_HUMAN	coiled-coil domain containing 90B precursor	132	Potential.					integral to membrane|mitochondrion|mitochondrion					0		Acute lymphoblastic leukemia(157;0.103)				TGCAAATTCACTTTTCTCTAG	0.303													30	576	---	---	---	---	PASS
BCL9L	283149	broad.mit.edu	37	11	118774132	118774132	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118774132C>A	uc001pug.2	-	4	1527	c.562G>T	c.(562-564)GCC>TCC	p.A188S	BCL9L_uc009zal.2_Missense_Mutation_p.A183S	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	188					negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		AGCTGTGGGGCCGCCATGGCT	0.647													8	18	---	---	---	---	PASS
IGSF9B	22997	broad.mit.edu	37	11	133794770	133794770	+	Silent	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133794770G>A	uc001qgx.3	-	15	2295	c.2064C>T	c.(2062-2064)GCC>GCT	p.A688A	IGSF9B_uc001qgy.1_Silent_p.A530A	NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	688	Fibronectin type-III 2.|Extracellular (Potential).					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCTGCATGACGGCCAGAACCC	0.577													3	62	---	---	---	---	PASS
PRB1	5542	broad.mit.edu	37	12	11506399	11506399	+	Missense_Mutation	SNP	T	C	C	rs111543911		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11506399T>C	uc001qzw.1	-	4	675	c.638A>G	c.(637-639)CAA>CGA	p.Q213R	PRB1_uc001qzu.1_Intron|PRB1_uc001qzv.1_Intron	NM_005039	NP_005030	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1 isoform 1	274	11.|15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in clone CP-4).|Missing (in clone CP-5).	Q -> R (in Ref. 5; CAA30395).		extracellular region					0			OV - Ovarian serous cystadenocarcinoma(49;0.185)			TGGAGGAGATTGGGAACTTCG	0.612													3	12	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32134405	32134405	+	Silent	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32134405T>C	uc001rks.2	+	4	930	c.516T>C	c.(514-516)AAT>AAC	p.N172N		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	172										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			TCCCTTCTAATTCTACACGAC	0.413													49	156	---	---	---	---	PASS
OR9K2	441639	broad.mit.edu	37	12	55523606	55523606	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55523606A>G	uc010spe.1	+	1	54	c.54A>G	c.(52-54)CAA>CAG	p.Q18Q		NM_001005243	NP_001005243	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K,	18	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|pancreas(1)	2						GTGCCTCTCAACAGGTTTCTA	0.413													50	555	---	---	---	---	PASS
DNAJC14	85406	broad.mit.edu	37	12	56216895	56216895	+	Silent	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56216895T>C	uc001shx.1	-	4	1797	c.1593A>G	c.(1591-1593)GCA>GCG	p.A531A	DNAJC14_uc001shu.1_Silent_p.A531A|DNAJC14_uc009zob.1_Silent_p.A531A	NM_032364	NP_115740	Q6Y2X3	DJC14_HUMAN	dopamine receptor interacting protein	531					protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4						TAGTATTCATTGCCTCCTTGA	0.438													40	160	---	---	---	---	PASS
NUPL1	9818	broad.mit.edu	37	13	25914398	25914398	+	3'UTR	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25914398C>T	uc001uqi.2	+	16					NUPL1_uc001uqj.2_3'UTR	NM_014089	NP_054808	Q9BVL2	NUPL1_HUMAN	nucleoporin like 1 isoform a						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore					0		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.0092)|Epithelial(112;0.0477)|OV - Ovarian serous cystadenocarcinoma(117;0.165)|GBM - Glioblastoma multiforme(144;0.244)		TTTCCCTACTCTGGAATTTGA	0.323													3	25	---	---	---	---	PASS
ATP8A2	51761	broad.mit.edu	37	13	26145884	26145884	+	Intron	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26145884T>C	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron|ATP8A2_uc001uql.1_3'UTR	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,						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)		GAAGATTGTGTGTGTGAAATG	0.378													7	74	---	---	---	---	PASS
BRCA2	675	broad.mit.edu	37	13	32900684	32900684	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32900684G>C	uc001uub.1	+	7	792	c.565G>C	c.(565-567)GAT>CAT	p.D189H	BRCA2_uc001uua.1_Missense_Mutation_p.D66H	NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	189					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AGCTGAGGTGGATCCTGATAT	0.383			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			84	323	---	---	---	---	PASS
KIAA0564	23078	broad.mit.edu	37	13	42461433	42461433	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42461433A>G	uc001uyj.2	-	6	786	c.716T>C	c.(715-717)ATT>ACT	p.I239T	KIAA0564_uc001uyk.2_Missense_Mutation_p.I239T	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	239						extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		GCCCAAGGCAATCACTCGGAA	0.408													37	180	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	101760063	101760063	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101760063T>G	uc001vox.1	-	21	2631	c.2442A>C	c.(2440-2442)CAA>CAC	p.Q814H		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	814	Cytoplasmic (Potential).|Potential.					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TCATCTCTGCTTGCTCCTTTT	0.403													16	762	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22932049	22932049	+	Intron	SNP	G	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22932049G>C	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_Intron|uc001wdv.3_Intron|uc001wdx.3_Missense_Mutation_p.E31Q|uc010ajs.1_Missense_Mutation_p.E31Q|uc001wdz.3_Missense_Mutation_p.E31Q|uc010tms.1_Missense_Mutation_p.E31Q|uc010ajt.2_Missense_Mutation_p.E56Q|uc010aju.1_Missense_Mutation_p.E56Q|uc001wea.3_Missense_Mutation_p.E56Q					SubName: Full=Alpha-chain C region; Flags: Fragment;																		GAAGATAACAGAGTTTGATCC	0.383													22	106	---	---	---	---	PASS
GNG2	54331	broad.mit.edu	37	14	52417395	52417395	+	5'UTR	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52417395C>T	uc001wzi.2	+	3					GNG2_uc001wzh.2_RNA|GNG2_uc010aoc.1_RNA|GNG2_uc001wzj.2_RNA|GNG2_uc001wzk.2_5'UTR|GNG2_uc010aob.1_RNA	NM_053064	NP_444292	P59768	GBG2_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|platelet activation|synaptic transmission	heterotrimeric G-protein complex	protein binding|signal transducer activity				0	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)	TCCAGCACTCCGATGGCCAGC	0.448													6	103	---	---	---	---	PASS
CGRRF1	10668	broad.mit.edu	37	14	54997352	54997352	+	Intron	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54997352C>T	uc001xay.2	+						CGRRF1_uc010tra.1_Intron|CGRRF1_uc001xaz.2_RNA	NM_006568	NP_006559	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1						cell cycle arrest|negative regulation of cell proliferation|response to stress		zinc ion binding			ovary(1)	1						AGACTTCTTACGGATAAAGTG	0.358													3	32	---	---	---	---	PASS
KIAA0586	9786	broad.mit.edu	37	14	58954685	58954685	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58954685T>G	uc001xdv.3	+	22	3430	c.3157T>G	c.(3157-3159)TTT>GTT	p.F1053V	KIAA0586_uc010trr.1_Missense_Mutation_p.F1170V|KIAA0586_uc001xdt.3_Missense_Mutation_p.F1085V|KIAA0586_uc001xdu.3_Missense_Mutation_p.F1114V|KIAA0586_uc010trs.1_Missense_Mutation_p.F1044V|KIAA0586_uc010trt.1_Missense_Mutation_p.F989V|KIAA0586_uc010tru.1_Missense_Mutation_p.F989V	NM_014749	NP_055564	E9PGW8	E9PGW8_HUMAN	talpid3 protein	1053										ovary(1)	1						GGCGGCAGTTTTTACCCCAAC	0.443													14	158	---	---	---	---	PASS
PROX2	283571	broad.mit.edu	37	14	75329252	75329252	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75329252A>C	uc001xqr.1	-	1	1286	c.1286T>G	c.(1285-1287)CTG>CGG	p.L429R	PROX2_uc001xqq.1_Intron	NM_001080408	NP_001073877	Q3B8N5	PROX2_HUMAN	prospero homeobox 2	429					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)		AGAGAAAGGCAGTGCCTCCAT	0.373													10	63	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106877562	106877562	+	Intron	SNP	A	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106877562A>C	uc010tyt.1	-						uc010tyu.1_Silent_p.A130A					Parts of antibodies, mostly variable regions.												0						CCGCCCCCTCAGCCTCCCTGC	0.652													4	7	---	---	---	---	PASS
OR4M2	390538	broad.mit.edu	37	15	22368793	22368793	+	Missense_Mutation	SNP	A	G	G	rs143458729		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22368793A>G	uc010tzu.1	+	1	218	c.218A>G	c.(217-219)TAC>TGC	p.Y73C	LOC727924_uc001yua.2_Intron|LOC727924_uc001yub.1_Intron|OR4N4_uc001yuc.1_Intron	NM_001004719	NP_001004719	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M,	73	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		GATATTTGGTACTCTTCCATT	0.413													8	786	---	---	---	---	PASS
NIPA2	81614	broad.mit.edu	37	15	23006147	23006147	+	3'UTR	SNP	T	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23006147T>A	uc001yux.2	-	8					NIPA2_uc001yuy.2_3'UTR|NIPA2_uc001yuz.2_3'UTR|NIPA2_uc001yva.2_3'UTR|NIPA2_uc001yvb.2_3'UTR|NIPA2_uc010ayb.2_3'UTR	NM_030922	NP_112184	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome							early endosome|integral to membrane|plasma membrane				haematopoietic_and_lymphoid_tissue(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		AGGACAATGTTTTTTCAGACA	0.274													5	27	---	---	---	---	PASS
ATP8B4	79895	broad.mit.edu	37	15	50271933	50271933	+	Missense_Mutation	SNP	T	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50271933T>G	uc001zxu.2	-	12	1057	c.915A>C	c.(913-915)CAA>CAC	p.Q305H	ATP8B4_uc010ber.2_Missense_Mutation_p.Q178H|ATP8B4_uc010ufd.1_Missense_Mutation_p.Q178H|ATP8B4_uc010ufe.1_RNA	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4	305	Extracellular (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			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		AAGTTCTGAATTGGTCCCCAG	0.368													6	385	---	---	---	---	PASS
MYO5A	4644	broad.mit.edu	37	15	52645836	52645836	+	Missense_Mutation	SNP	A	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52645836A>C	uc002aby.2	-	27	3831	c.3587T>G	c.(3586-3588)ATT>AGT	p.I1196S	MYO5A_uc002abx.3_Missense_Mutation_p.I1196S|MYO5A_uc010ugd.1_5'Flank|MYO5A_uc002aca.1_5'Flank|MYO5A_uc002acb.1_5'Flank|MYO5A_uc002acc.1_5'Flank	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1	1196	Potential.				actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		TGCACCTCTAATTTGTGGTCT	0.358													105	387	---	---	---	---	PASS
KIAA1370	56204	broad.mit.edu	37	15	52902171	52902171	+	Missense_Mutation	SNP	G	T	T	rs75977811		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52902171G>T	uc002acg.3	-	6	1093	c.940C>A	c.(940-942)CAA>AAA	p.Q314K	KIAA1370_uc002ach.3_RNA|KIAA1370_uc010bfg.1_Missense_Mutation_p.Q226K|KIAA1370_uc010ugf.1_Missense_Mutation_p.Q321K	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204	314											0				all cancers(107;0.0803)		ATATTGGCTTGAGATGTCCCA	0.373													10	162	---	---	---	---	PASS
MNS1	55329	broad.mit.edu	37	15	56735643	56735643	+	Nonsense_Mutation	SNP	A	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56735643A>C	uc002adr.2	-	7	1161	c.996T>G	c.(994-996)TAT>TAG	p.Y332*	MNS1_uc010bfo.2_Nonsense_Mutation_p.Y200*|TEX9_uc002adp.2_Intron|TEX9_uc010ugl.1_Intron	NM_018365	NP_060835	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	332	Potential.|Glu-rich.				meiosis					ovary(1)	1				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		GCTTGCTCTTATATATTTCAG	0.279													147	637	---	---	---	---	PASS
MYO1E	4643	broad.mit.edu	37	15	59515376	59515376	+	Silent	SNP	C	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59515376C>G	uc002aga.2	-	9	1164	c.792G>C	c.(790-792)GTG>GTC	p.V264V		NM_004998	NP_004989	Q12965	MYO1E_HUMAN	myosin IE	264	Myosin head-like.				actin filament-based movement	myosin complex	actin binding|ATP binding|ATPase activity, coupled|calmodulin binding|microfilament motor activity			central_nervous_system(3)	3				all cancers(107;0.207)		AGATCCCAATCACATTCATGG	0.493													5	77	---	---	---	---	PASS
ANKRD34C	390616	broad.mit.edu	37	15	79585881	79585881	+	Silent	SNP	C	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79585881C>A	uc002bet.2	+	2	724	c.255C>A	c.(253-255)GGC>GGA	p.G85G		NM_001146341	NP_001139813			ankyrin repeat domain 34C												0						ATAAGTCTGGCAAGACTGCCC	0.517													13	69	---	---	---	---	PASS
PDE8A	5151	broad.mit.edu	37	15	85632630	85632630	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85632630G>A	uc002blh.2	+	7	886	c.697G>A	c.(697-699)GAA>AAA	p.E233K	PDE8A_uc002bli.2_Missense_Mutation_p.E233K|PDE8A_uc010bnc.2_5'UTR|PDE8A_uc010bnd.2_Intron|PDE8A_uc002blj.2_Intron|PDE8A_uc002blk.2_Intron	NM_002605	NP_002596	O60658	PDE8A_HUMAN	phosphodiesterase 8A isoform 1	233	PAS.				cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)			AATTACAAGCGAAGACCGTTT	0.313													33	704	---	---	---	---	PASS
RHBDF1	64285	broad.mit.edu	37	16	114923	114923	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:114923T>C	uc002cfl.3	-	5	239	c.91A>G	c.(91-93)ACG>GCG	p.T31A	RHBDF1_uc010uty.1_Missense_Mutation_p.T31A|RHBDF1_uc010utz.1_Missense_Mutation_p.T31A|RHBDF1_uc010bqo.1_RNA	NM_022450	NP_071895	Q96CC6	RHDF1_HUMAN	rhomboid family 1	31	Cytoplasmic (Potential).				cell migration|cell proliferation|negative regulation of protein secretion|protein transport|proteolysis|regulation of epidermal growth factor receptor signaling pathway|regulation of proteasomal protein catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity			ovary(1)|pancreas(1)	2		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				TCTTCTGCCGTCAGGGGCACC	0.657													4	74	---	---	---	---	PASS
USP7	7874	broad.mit.edu	37	16	8987742	8987742	+	3'UTR	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8987742A>G	uc002czl.2	-	31					USP7_uc002czj.2_RNA|USP7_uc010uyj.1_3'UTR|USP7_uc002czk.2_3'UTR	NM_003470	NP_003461	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7						interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3						AATTAACACCAGCAGCGAATC	0.448													17	68	---	---	---	---	PASS
RRN3	54700	broad.mit.edu	37	16	15155580	15155580	+	3'UTR	SNP	C	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15155580C>A	uc002dde.2	-	18					PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_3'UTR|RRN3_uc010uzq.1_3'UTR	NM_018427	NP_060897	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor						regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1						AATGTCACATCTCAGTCACAA	0.537													21	82	---	---	---	---	PASS
IQCK	124152	broad.mit.edu	37	16	19746758	19746758	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19746758G>A	uc002dgr.2	+	5	1159	c.460G>A	c.(460-462)GAA>AAA	p.E154K	IQCK_uc002dgs.2_RNA|IQCK_uc010vat.1_Missense_Mutation_p.E154K|IQCK_uc010bwc.2_Intron|IQCK_uc010vau.1_Missense_Mutation_p.E66K	NM_153208	NP_694940	Q8N0W5	IQCK_HUMAN	IQ motif containing K	154										skin(1)	1						AGCGAAGAAAGAAAAATGTTT	0.363													5	601	---	---	---	---	PASS
FUS	2521	broad.mit.edu	37	16	31193930	31193930	+	Silent	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31193930G>A	uc002ebf.2	+	3	218	c.135G>A	c.(133-135)ACG>ACA	p.T45T	FUS_uc002ebe.1_Silent_p.T45T|FUS_uc002ebh.2_Silent_p.T45T|FUS_uc002ebg.2_5'UTR|FUS_uc002ebi.2_Silent_p.T45T|FUS_uc002ebj.2_5'UTR|FUS_uc010vfi.1_Silent_p.T45T	NM_004960	NP_004951	P35637	FUS_HUMAN	fusion (involved in t(12;16) in malignant	45	Gln/Gly/Ser/Tyr-rich.				cell death|nuclear mRNA splicing, via spliceosome	nucleoplasm	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		FUS/DDIT3(623)|FUS/ERG(163)|FUS/CREB3L2(158)|FUS/CREB3L1(6)|FUS/ATF1(4)|FUS/FEV(2)	soft_tissue(791)|haematopoietic_and_lymphoid_tissue(153)|bone(12)|breast(2)	958		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		GCCAGTCCACGGACACTTCAG	0.547			T	DDIT3|ERG|FEV|ATF1|CREB3L2|CREB3L1	liposarcoma|AML|Ewing sarcoma|angiomatoid fibrous histiocytoma|fibromyxoid sarcoma								38	195	---	---	---	---	PASS
FUS	2521	broad.mit.edu	37	16	31193931	31193931	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31193931G>C	uc002ebf.2	+	3	219	c.136G>C	c.(136-138)GAC>CAC	p.D46H	FUS_uc002ebe.1_Missense_Mutation_p.D46H|FUS_uc002ebh.2_Missense_Mutation_p.D46H|FUS_uc002ebg.2_5'UTR|FUS_uc002ebi.2_Missense_Mutation_p.D46H|FUS_uc002ebj.2_5'UTR|FUS_uc010vfi.1_Missense_Mutation_p.D46H	NM_004960	NP_004951	P35637	FUS_HUMAN	fusion (involved in t(12;16) in malignant	46	Gln/Gly/Ser/Tyr-rich.				cell death|nuclear mRNA splicing, via spliceosome	nucleoplasm	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		FUS/DDIT3(623)|FUS/ERG(163)|FUS/CREB3L2(158)|FUS/CREB3L1(6)|FUS/ATF1(4)|FUS/FEV(2)	soft_tissue(791)|haematopoietic_and_lymphoid_tissue(153)|bone(12)|breast(2)	958		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		CCAGTCCACGGACACTTCAGG	0.547			T	DDIT3|ERG|FEV|ATF1|CREB3L2|CREB3L1	liposarcoma|AML|Ewing sarcoma|angiomatoid fibrous histiocytoma|fibromyxoid sarcoma								37	195	---	---	---	---	PASS
PHKB	5257	broad.mit.edu	37	16	47697613	47697613	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47697613A>G	uc002eev.3	+	24	2356	c.2304A>G	c.(2302-2304)AGA>AGG	p.R768R	PHKB_uc002eeu.3_Silent_p.R761R|PHKB_uc002eew.3_5'Flank	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a	768	Calmodulin-binding (Potential).				glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				ACATTGAGAGAGTCTATAGAA	0.318													10	800	---	---	---	---	PASS
KATNB1	10300	broad.mit.edu	37	16	57785950	57785950	+	Silent	SNP	C	T	T	rs141576914		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57785950C>T	uc002eml.1	+	8	989	c.615C>T	c.(613-615)GCC>GCT	p.A205A		NM_005886	NP_005877	Q9BVA0	KTNB1_HUMAN	katanin p80 subunit B 1	205	Interaction with centrosomes.|WD 5.|Interaction with dynein (By similarity).				cell division|mitosis|negative regulation of microtubule depolymerization|positive regulation of microtubule depolymerization|protein targeting	katanin complex|microtubule|spindle pole	microtubule binding|protein heterodimerization activity				0		all_neural(199;0.223)				ACCTCCTGGCCTCCGGCAGCT	0.602													10	27	---	---	---	---	PASS
PKD1L3	342372	broad.mit.edu	37	16	72012155	72012155	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72012155T>C	uc010vmm.1	-	10	1526	c.1526A>G	c.(1525-1527)GAG>GGG	p.E509G		NM_181536	NP_853514			polycystin 1-like 3 precursor												0						AGTTCCTACCTCAATGTCCTC	0.373													8	444	---	---	---	---	PASS
SPNS3	201305	broad.mit.edu	37	17	4389784	4389784	+	Silent	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4389784C>T	uc002fxt.2	+	11	1400	c.1356C>T	c.(1354-1356)TGC>TGT	p.C452C	SPNS3_uc002fxu.2_Silent_p.C325C|SPNS3_uc002fxv.2_Silent_p.C103C|uc002fxw.1_5'Flank	NM_182538	NP_872344	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3	452	Helical; (Potential).				lipid transport|transmembrane transport	integral to membrane				large_intestine(1)	1						GCTTCCTGTGCTGCGCCTTTG	0.652													6	28	---	---	---	---	PASS
TOM1L2	146691	broad.mit.edu	37	17	17810845	17810845	+	Missense_Mutation	SNP	T	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17810845T>A	uc002grz.3	-	2	210	c.53A>T	c.(52-54)GAA>GTA	p.E18V	TOM1L2_uc002gry.3_Missense_Mutation_p.E18V|TOM1L2_uc010vwy.1_Missense_Mutation_p.E18V|TOM1L2_uc010cpr.2_Missense_Mutation_p.E18V|TOM1L2_uc010vwz.1_Missense_Mutation_p.E18V|TOM1L2_uc010vxa.1_Missense_Mutation_p.E18V|TOM1L2_uc010vxb.1_Missense_Mutation_p.E18V	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3	18					intracellular protein transport	intracellular					0	all_neural(463;0.228)					TGTTGCCTTTTCTGTGAAATC	0.483													29	116	---	---	---	---	PASS
HOXB4	3214	broad.mit.edu	37	17	46654168	46654168	+	Silent	SNP	G	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46654168G>C	uc002inp.2	-	2	734	c.672C>G	c.(670-672)CCC>CCG	p.P224P	HOXB3_uc010wlm.1_Intron|HOXB3_uc010dbf.2_Intron|HOXB3_uc010dbg.2_Intron|HOXB3_uc002ino.2_5'Flank|HOXB3_uc010wlk.1_5'Flank|HOXB3_uc010wll.1_Intron	NM_024015	NP_076920	P17483	HXB4_HUMAN	homeobox B4	224						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						TCTTGGTGTTGGGCAACTTGT	0.677													5	26	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60140520	60140520	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60140520C>T	uc002izo.2	-	2	286	c.209G>A	c.(208-210)CGG>CAG	p.R70Q		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	70					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						TTGATCTCGCCGCCAAACACC	0.468													70	300	---	---	---	---	PASS
MFSD11	79157	broad.mit.edu	37	17	74740469	74740469	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74740469T>C	uc002jta.2	+	8	1535	c.562T>C	c.(562-564)TTT>CTT	p.F188L	MFSD11_uc002jtb.2_Missense_Mutation_p.F188L|MFSD11_uc010dha.2_Missense_Mutation_p.F136L|MFSD11_uc002jtc.2_Missense_Mutation_p.F188L|MFSD11_uc002jtd.3_Missense_Mutation_p.F188L|MFSD11_uc010dhb.2_Missense_Mutation_p.F136L|MFSD11_uc002jte.2_Missense_Mutation_p.F188L	NM_024311	NP_077287	O43934	MFS11_HUMAN	major facilitator superfamily domain containing	188	Helical; (Potential).					integral to membrane				ovary(1)	1						AGTTCTATTCTTTCTCATTCG	0.413													8	501	---	---	---	---	PASS
ANKRD30B	374860	broad.mit.edu	37	18	14831396	14831396	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14831396C>T	uc010dlo.2	+	28	2612	c.2432C>T	c.(2431-2433)CCG>CTG	p.P811L		NM_001145029	NP_001138501	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	896										ovary(1)|skin(1)	2						TTTGGCAAACCGACTACTGAA	0.313													4	209	---	---	---	---	PASS
ESCO1	114799	broad.mit.edu	37	18	19153558	19153558	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19153558C>T	uc002kth.1	-	4	2181	c.1247G>A	c.(1246-1248)GGC>GAC	p.G416D	ESCO1_uc002kti.1_RNA	NM_052911	NP_443143	Q5FWF5	ESCO1_HUMAN	establishment of cohesion 1 homolog 1	416					cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding				0						TCGTAATAAGCCTAATTTAGG	0.373													4	162	---	---	---	---	PASS
MIB1	57534	broad.mit.edu	37	18	19429293	19429293	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19429293T>C	uc002ktq.2	+	17	2530	c.2530T>C	c.(2530-2532)TCT>CCT	p.S844P	MIB1_uc002ktp.2_Missense_Mutation_p.S483P	NM_020774	NP_065825	Q86YT6	MIB1_HUMAN	mindbomb homolog 1	844	RING-type 1.				Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)			TTCTTTATGTTCTCCACGTGT	0.348													6	340	---	---	---	---	PASS
SS18	6760	broad.mit.edu	37	18	23614967	23614967	+	Splice_Site	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23614967A>G	uc002kvm.2	-	9	1174	c.1096_splice	c.e9+1	p.G366_splice	SS18_uc002kvn.2_Splice_Site_p.G335_splice|SS18_uc010xbf.1_Splice_Site_p.G284_splice|SS18_uc010xbg.1_Splice_Site_p.G283_splice|SS18_uc010xbh.1_Splice_Site_p.G283_splice|SS18_uc010xbi.1_Splice_Site_p.G343_splice	NM_001007559	NP_001007560	Q15532	SSXT_HUMAN	synovial sarcoma translocation, chromosome 18						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	ligand-dependent nuclear receptor transcription coactivator activity|protein binding		SS18/SSX1(1169)|SS18/SSX2(702)|SS18/SSX4(12)	soft_tissue(1883)|ovary(1)	1884	all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124)					ACAAAGCTTTACCGTAGCCCT	0.418			T	SSX1| SSX2	synovial sarcoma								5	349	---	---	---	---	PASS
RTTN	25914	broad.mit.edu	37	18	67724983	67724983	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67724983C>T	uc002lkp.2	-	37	5094	c.5026G>A	c.(5026-5028)GCT>ACT	p.A1676T	RTTN_uc002lko.2_RNA|RTTN_uc010xfb.1_Missense_Mutation_p.A764T|RTTN_uc010dqp.2_5'UTR	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	1676							binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)				CTTACCTGAGCCTGAGTGTGT	0.448													5	271	---	---	---	---	PASS
CYB5A	1528	broad.mit.edu	37	18	71930704	71930704	+	Silent	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71930704A>G	uc002lli.2	-	2	249	c.138T>C	c.(136-138)GGT>GGC	p.G46G	CYB5A_uc002llh.2_Silent_p.G46G	NM_148923	NP_683725	P00167	CYB5_HUMAN	cytochrome b-5 isoform 1	46	Cytochrome b5 heme-binding.				electron transport chain|water-soluble vitamin metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane	aldo-keto reductase (NADP) activity|cytochrome-c oxidase activity|enzyme binding|heme binding				0		Esophageal squamous(42;0.0749)|Prostate(75;0.157)|Melanoma(33;0.211)			Methoxyflurane(DB01028)	CTTCTTCCCCACCAGGATGCT	0.413													37	92	---	---	---	---	PASS
THEG	51298	broad.mit.edu	37	19	371296	371296	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:371296C>A	uc002lol.2	-	6	701	c.662G>T	c.(661-663)CGG>CTG	p.R221L	THEG_uc002lom.2_Missense_Mutation_p.R197L	NM_016585	NP_057669	Q9P2T0	THEG_HUMAN	Theg homolog isoform 1	221					cell differentiation|chaperone-mediated protein complex assembly|multicellular organismal development|spermatogenesis	nucleus	protein binding			ovary(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGGAGGACCGAGGAATGGG	0.542													3	60	---	---	---	---	PASS
PRR22	163154	broad.mit.edu	37	19	5784427	5784427	+	5'UTR	SNP	G	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5784427G>T	uc002mdb.1	-	1					PRR22_uc010xiv.1_Missense_Mutation_p.P52T	NM_153359	NP_699190	Q8IZ63	PRR22_HUMAN	proline rich 22 isoform 2												0						TCTGGGTCTGGGGGATGATAC	0.637													23	101	---	---	---	---	PASS
SYDE1	85360	broad.mit.edu	37	19	15223181	15223181	+	Missense_Mutation	SNP	C	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15223181C>A	uc002nah.1	+	7	1634	c.1603C>A	c.(1603-1605)CAC>AAC	p.H535N	SYDE1_uc002nai.1_Missense_Mutation_p.H468N|SYDE1_uc002naj.1_Missense_Mutation_p.H192N	NM_033025	NP_149014	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1	535	Rho-GAP.				activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|pancreas(1)	2						TCTCCTGGACCACCTGCGCCT	0.627													14	47	---	---	---	---	PASS
ZNF714	148206	broad.mit.edu	37	19	21300510	21300510	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21300510A>G	uc002npo.3	+	6	1403	c.1043A>G	c.(1042-1044)AAA>AGA	p.K348R	ZNF714_uc002npl.2_Missense_Mutation_p.K193R|ZNF714_uc010ecp.1_Missense_Mutation_p.K299R|ZNF714_uc002npn.2_RNA	NM_182515	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	348	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GAATGTGGCAAAGCCTTTAAT	0.388													11	41	---	---	---	---	PASS
ZNF180	7733	broad.mit.edu	37	19	45004270	45004270	+	Missense_Mutation	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45004270G>A	uc002ozf.3	-	1	305	c.23C>T	c.(22-24)ACG>ATG	p.T8M	ZNF180_uc002ozh.3_Intron|ZNF180_uc002ozi.3_Intron|ZNF180_uc002ozg.3_Silent_p.Y5Y|ZNF180_uc010ejm.2_Missense_Mutation_p.T8M	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	8					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)				AGCTTCCCGCGTAGACCCTGC	0.672											OREG0025537	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	21	---	---	---	---	PASS
PPFIA3	8541	broad.mit.edu	37	19	49641602	49641602	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49641602C>T	uc002pmr.2	+	16	2326	c.1994C>T	c.(1993-1995)GCC>GTC	p.A665V	PPFIA3_uc010yai.1_Intron|PPFIA3_uc010yaj.1_Intron|PPFIA3_uc002pms.2_Missense_Mutation_p.A533V	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3	665						cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		TCTACCCTTGCCAGCCCCTCC	0.677													6	27	---	---	---	---	PASS
PIH1D1	55011	broad.mit.edu	37	19	49950324	49950324	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49950324T>C	uc002pns.2	-	7	928	c.644A>G	c.(643-645)GAA>GGA	p.E215G	uc002pnr.1_5'Flank	NM_017916	NP_060386	Q9NWS0	PIHD1_HUMAN	NOP17	215					box C/D snoRNP assembly	pre-snoRNP complex					0		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		GTCGGGGGCTTCCAGCCACAG	0.597													5	98	---	---	---	---	PASS
MACROD2	140733	broad.mit.edu	37	20	15967710	15967710	+	Splice_Site	SNP	G	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15967710G>C	uc002wou.2	+	15	1325	c.1061_splice	c.e15-1	p.E354_splice	MACROD2_uc002wot.2_Splice_Site_p.E354_splice|MACROD2_uc002woz.2_Splice_Site_p.E119_splice|MACROD2_uc002wpb.2_Splice_Site_p.E119_splice|MACROD2_uc002wpd.2_Splice_Site_p.E5_splice	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				ATTCTATTTAGAACTTTCATC	0.388													106	495	---	---	---	---	PASS
KIAA0406	9675	broad.mit.edu	37	20	36641291	36641291	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36641291G>T	uc002xhl.2	-	3	1137	c.928C>A	c.(928-930)CTG>ATG	p.L310M	KIAA0406_uc002xhm.2_Missense_Mutation_p.L310M	NM_014657	NP_055472	O43156	TTI1_HUMAN	hypothetical protein LOC9675	310							binding				0		Myeloproliferative disorder(115;0.00874)				AGTTCTACCAGTTCCAGTCTC	0.433													70	195	---	---	---	---	PASS
LBP	3929	broad.mit.edu	37	20	36978015	36978015	+	Silent	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36978015C>T	uc002xic.1	+	2	224	c.189C>T	c.(187-189)ACC>ACT	p.T63T		NM_004139	NP_004130	P18428	LBP_HUMAN	lipopolysaccharide-binding protein precursor	63					acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)				CTGACTTCACCGGGGACTTGA	0.617													9	35	---	---	---	---	PASS
TIAM1	7074	broad.mit.edu	37	21	32638797	32638797	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32638797G>C	uc002yow.1	-	5	964	c.492C>G	c.(490-492)AGC>AGG	p.S164R	TIAM1_uc011adk.1_Missense_Mutation_p.S164R|TIAM1_uc011adl.1_Missense_Mutation_p.S164R|TIAM1_uc002yox.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	164					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						TCTTCTTAAAGCTCGCCGTCT	0.507													9	129	---	---	---	---	PASS
SFRS15	57466	broad.mit.edu	37	21	33060639	33060639	+	Missense_Mutation	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33060639A>G	uc002ypd.2	-	16	2450	c.2024T>C	c.(2023-2025)ATA>ACA	p.I675T	SFRS15_uc002ype.2_Missense_Mutation_p.I675T|SFRS15_uc010glu.2_Missense_Mutation_p.I660T|SFRS15_uc002ypf.1_Missense_Mutation_p.I349T	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	675						nucleus	nucleotide binding|RNA binding				0						TGGCACTGTTATAGGTGCAGG	0.443													6	705	---	---	---	---	PASS
IL10RB	3588	broad.mit.edu	37	21	34652157	34652157	+	Silent	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34652157T>C	uc002yrk.1	+	4	531	c.432T>C	c.(430-432)ACT>ACC	p.T144T	IL10RB_uc002yrh.1_Silent_p.T214T|IL10RB_uc002yri.1_Silent_p.T97T|IL10RB_uc002yrl.1_Silent_p.T146T	NM_000628	NP_000619	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta precursor	144	Fibronectin type-III.|Extracellular (Potential).				immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0						AAACTTGGACTATGAAGAATG	0.378													6	748	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18844615	18844615	+	RNA	SNP	A	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18844615A>G	uc002zoe.2	+	4		c.1869A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		CCTCCTTGAGAAATATGGATG	0.552													4	9	---	---	---	---	PASS
UPB1	51733	broad.mit.edu	37	22	24898325	24898325	+	Intron	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24898325G>A	uc003aaf.2	+						UPB1_uc003aae.2_Intron|UPB1_uc011ajt.1_Intron	NM_016327	NP_057411	Q9UBR1	BUP1_HUMAN	beta-ureidopropionase						pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	cytosol	beta-ureidopropionase activity|metal ion binding			ovary(2)	2	Colorectal(2;0.0339)					ACATCACCAGGAACCCCGGCC	0.408													21	75	---	---	---	---	PASS
DEPDC5	9681	broad.mit.edu	37	22	32161021	32161021	+	Missense_Mutation	SNP	T	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32161021T>C	uc003als.2	+	5	396	c.254T>C	c.(253-255)GTC>GCC	p.V85A	DEPDC5_uc011als.1_Missense_Mutation_p.V85A|DEPDC5_uc011alu.1_Missense_Mutation_p.V85A|DEPDC5_uc011alv.1_RNA|DEPDC5_uc003alt.2_Missense_Mutation_p.V85A|DEPDC5_uc003alr.1_Missense_Mutation_p.V85A|DEPDC5_uc011alt.1_Missense_Mutation_p.V85A	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	85					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						TATCAGGATGTCTATGTTAAT	0.378													8	612	---	---	---	---	PASS
EFCAB6	64800	broad.mit.edu	37	22	44004465	44004465	+	Missense_Mutation	SNP	C	A	A	rs55698170	byFrequency	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44004465C>A	uc003bdy.1	-	22	2793	c.2578G>T	c.(2578-2580)GAT>TAT	p.D860Y	EFCAB6_uc003bdz.1_Missense_Mutation_p.D708Y|EFCAB6_uc010gzi.1_Missense_Mutation_p.D708Y|EFCAB6_uc010gzj.1_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	860	EF-hand 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				CCCTCATTATCGGTTTCTAGA	0.413													38	198	---	---	---	---	PASS
CD99	4267	broad.mit.edu	37	X	2638466	2638466	+	Splice_Site	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2638466G>A	uc004cqm.2	+	5	436	c.262_splice	c.e5+1	p.G88_splice	CD99_uc010nda.2_Splice_Site_p.G72_splice|CD99_uc004cqn.2_Splice_Site|CD99_uc004cqo.2_Splice_Site_p.G88_splice	NM_002414	NP_002405	P14209	CD99_HUMAN	CD99 antigen isoform a precursor						cell adhesion	cytoplasm|integral to plasma membrane				skin(1)	1						AGTTCCTCCGGTAAGAGTCTC	0.473													13	600	---	---	---	---	PASS
PTCHD1	139411	broad.mit.edu	37	X	23398406	23398406	+	Intron	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23398406G>A	uc004dal.3	+						PTCHD1_uc010nfu.1_Silent_p.L350L	NM_173495	NP_775766	Q96NR3	PTHD1_HUMAN	patched domain containing 1						cognition|smoothened signaling pathway	integral to membrane|plasma membrane	hedgehog receptor activity			ovary(4)|kidney(1)|skin(1)	6						TCCGCCTGCTGGTGGTGTTGA	0.433													3	27	---	---	---	---	PASS
PHF8	23133	broad.mit.edu	37	X	54044120	54044120	+	Missense_Mutation	SNP	G	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54044120G>T	uc004dsu.2	-	5	609	c.536C>A	c.(535-537)ACT>AAT	p.T179N	PHF8_uc004dst.2_Missense_Mutation_p.T143N|PHF8_uc004dsv.2_Missense_Mutation_p.T9N|PHF8_uc004dsw.2_Missense_Mutation_p.T143N|PHF8_uc004dsy.2_Missense_Mutation_p.T143N	NM_015107	NP_055922	Q9UPP1	PHF8_HUMAN	PHD finger protein 8	179					brain development|G1/S transition of mitotic cell cycle|negative regulation of chromatin silencing at rDNA|positive regulation of transcription from RNA polymerase I promoter|transcription, DNA-dependent	nucleolus	chromatin binding|histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(3)	3						ATCCCTCACAGTGAATGATGG	0.483													38	52	---	---	---	---	PASS
STAG2	10735	broad.mit.edu	37	X	123181245	123181245	+	Missense_Mutation	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123181245C>T	uc004etz.3	+	8	1048	c.709C>T	c.(709-711)CTT>TTT	p.L237F	STAG2_uc004eua.2_Missense_Mutation_p.L237F|STAG2_uc004eub.2_Missense_Mutation_p.L237F|STAG2_uc004euc.2_Missense_Mutation_p.L237F|STAG2_uc004eud.2_Missense_Mutation_p.L237F|STAG2_uc004eue.2_Missense_Mutation_p.L237F	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	237					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						GGCACTAAATCTTAGCATTAA	0.328													4	193	---	---	---	---	PASS
IGSF1	3547	broad.mit.edu	37	X	130410026	130410026	+	Silent	SNP	C	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130410026C>T	uc004ewd.2	-	15	3043	c.2805G>A	c.(2803-2805)GAG>GAA	p.E935E	IGSF1_uc004ewe.3_Silent_p.E929E|IGSF1_uc004ewf.2_Silent_p.E915E	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	935	Extracellular (Potential).|Ig-like C2-type 9.				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5						TCCCAGAGTCCTCTGCTCCAA	0.512													11	23	---	---	---	---	PASS
SPANXN1	494118	broad.mit.edu	37	X	144329148	144329148	+	Missense_Mutation	SNP	G	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144329148G>C	uc004fcb.2	+	1	42	c.42G>C	c.(40-42)AAG>AAC	p.K14N		NM_001009614	NP_001009614	Q5VSR9	SPXN1_HUMAN	SPANX-N1 protein	14											0	Acute lymphoblastic leukemia(192;6.56e-05)					AGAAGAGGAAGAGCCCCTGTG	0.313													8	655	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2011	2011	+	5'Flank	SNP	G	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2011G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		ACCGAGCCTGGTGATAGCTGG	0.423													45	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	700532	700532	+	RNA	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:700532delT	uc001abo.2	-	7		c.1022delA								Homo sapiens cDNA clone IMAGE:4129277, partial cds.																		aaaaaaaaaaTTCCTTTGGGA	0.214													9	4	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16942104	16942104	+	5'Flank	DEL	G	-	-	rs57642153		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16942104delG	uc009vos.1	-						NBPF1_uc001aza.3_5'Flank|NBPF1_uc001azb.1_5'Flank|NBPF1_uc001azc.1_5'Flank	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		ttgtctcaaagagagagagag	0.149													4	3	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16942106	16942106	+	5'Flank	DEL	G	-	-	rs66498732		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16942106delG	uc009vos.1	-						NBPF1_uc001aza.3_5'Flank|NBPF1_uc001azb.1_5'Flank|NBPF1_uc001azc.1_5'Flank	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		gtctcaaagagagagagagag	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19922722	19922723	+	IGR	DEL	TG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19922722_19922723delTG								CAPZB (110730 upstream) : C1orf151 (744 downstream)																							tgtatgtgtatgtgtgtgtgtg	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20770736	20770737	+	IGR	DEL	AC	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20770736_20770737delAC								VWA5B1 (89349 upstream) : CAMK2N1 (38148 downstream)																							acacacacaaacacacacacac	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	36795306	36795306	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36795306delA								C1orf113 (4822 upstream) : STK40 (9919 downstream)																							gaacacaatgaaaaaaaaaat	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	39272863	39272863	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39272863delG								POU3F1 (760413 upstream) : RRAGC (32152 downstream)																							tggggtcagagggcagattac	0.045													4	2	---	---	---	---	
MUTYH	4595	broad.mit.edu	37	1	45804224	45804224	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45804224delT	uc001cnm.2	-						MUTYH_uc001cnf.2_Intron|MUTYH_uc009vxo.2_5'UTR|MUTYH_uc001cng.2_Intron|MUTYH_uc001cnj.2_Intron|MUTYH_uc001cni.2_Intron|MUTYH_uc001cnh.2_Intron|MUTYH_uc001cno.2_Intron|MUTYH_uc001cnk.2_Intron|MUTYH_uc010oll.1_Intron|MUTYH_uc001cnl.2_Intron|MUTYH_uc009vxp.2_Intron|MUTYH_uc001cnn.2_Intron|TOE1_uc009vxq.2_5'Flank|TOE1_uc001cnq.3_5'Flank|TOE1_uc010olm.1_5'Flank|TOE1_uc010oln.1_5'Flank|TOE1_uc001cnr.3_5'Flank	NM_012222	NP_036354	Q9UIF7	MUTYH_HUMAN	mutY homolog isoform 1						depurination|mismatch repair	nucleoplasm	4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding				0	Acute lymphoblastic leukemia(166;0.155)					cagtgtgtacttcctgaattt	0.000			Mis			colorectal		BER_DNA_glycosylases	MUTYH-associated_polyposis				4	2	---	---	---	---	
STIL	6491	broad.mit.edu	37	1	47756527	47756527	+	Intron	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47756527delC	uc001crc.1	-						TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Intron|STIL_uc010omo.1_Intron|STIL_uc001crd.1_Intron|STIL_uc001cre.1_Intron|STIL_uc001crg.1_Intron	NM_003035	NP_003026	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 2						cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				caacagccctccactcacctc	0.030													4	2	---	---	---	---	
ORC1L	4998	broad.mit.edu	37	1	52842404	52842404	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52842404delG	uc001ctt.2	-						ORC1L_uc010oni.1_Intron|ORC1L_uc001ctu.2_Intron|ORC1L_uc009vzd.2_Intron	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1						cell cycle checkpoint|DNA-dependent DNA replication initiation|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	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0						GGGGAACTCTGGGGGGTAAGG	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56807589	56807589	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56807589delA								None (None upstream) : PPAP2B (152844 downstream)																							gtggaatgttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
JAK1	3716	broad.mit.edu	37	1	65366026	65366026	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65366026delA	uc001dbu.1	-						JAK1_uc009wam.1_Intron	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		AGGTAAAGGGAACAGATGAGC	0.383			Mis		ALL								4	2	---	---	---	---	
DNAJC6	9829	broad.mit.edu	37	1	65744541	65744541	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65744541delA	uc001dcd.1	+						DNAJC6_uc001dcc.1_Intron|DNAJC6_uc010opc.1_Intron	NM_014787	NP_055602	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6						cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol	heat shock protein binding|protein tyrosine phosphatase activity|SH3 domain binding			large_intestine(1)|lung(1)|ovary(1)	3						aTTGATCAGGAAAGGGGTGGG	0.284													4	2	---	---	---	---	
LRRC8B	23507	broad.mit.edu	37	1	90060838	90060838	+	3'UTR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90060838delT	uc001dni.2	+	8					LRRC8B_uc001dnh.2_3'UTR|LRRC8B_uc001dnj.2_3'UTR	NM_001134476	NP_001127948	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member							integral to membrane				ovary(2)	2		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		GTTATTTTCATTTTTTAAAGT	0.313													4	2	---	---	---	---	
ZNF644	84146	broad.mit.edu	37	1	91402769	91402769	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91402769delT	uc001dnw.2	-						ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron	NM_201269	NP_958357	Q9H582	ZN644_HUMAN	zinc finger protein 644 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TTGTTTGTTGTTTTTATTGTG	0.383													4	2	---	---	---	---	
FNBP1L	54874	broad.mit.edu	37	1	93998820	93998820	+	Intron	DEL	A	-	-	rs35424674		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93998820delA	uc001dpw.2	+						FNBP1L_uc001dpv.2_Intron|FNBP1L_uc010otk.1_Intron	NM_001024948	NP_001020119	Q5T0N5	FBP1L_HUMAN	formin binding protein 1-like isoform 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	lipid binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00902)|Melanoma(281;0.155)		all cancers(265;0.00666)|GBM - Glioblastoma multiforme(16;0.0378)|Epithelial(280;0.111)		ATTCTTTCTTAAAAAAAAAAA	0.303													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	95920466	95920466	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95920466delT								RWDD3 (207693 upstream) : None (None downstream)																							tacatctccattgtgcttcta	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	98736549	98736549	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98736549delA								MIR137 (224822 upstream) : SNX7 (390687 downstream)																							agggcaatggaaaaggcattg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	116760637	116760637	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116760637delA								C1orf161 (82776 upstream) : ATP1A1 (154367 downstream)																							CCGATTTTCTAAAAACACTTT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120316908	120316908	+	IGR	DEL	A	-	-	rs3834765		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120316908delA								HMGCS2 (5390 upstream) : REG4 (19734 downstream)																							TTAAACAGTTAAAAAAAAAAA	0.368													10	7	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120592822	120592823	+	Intron	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120592822_120592823insA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAAGATTTAGAAAAAACACAC	0.337			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143543620	143543621	+	IGR	INS	-	A	A	rs67235135		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143543620_143543621insA								None (None upstream) : LOC100286793 (104018 downstream)																							aatgatcaattaaaaaaaaaaa	0.109													5	4	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145310834	145310834	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145310834delA	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_5'Flank|NBPF10_uc010oyl.1_5'Flank|NBPF10_uc001emq.1_Intron|NBPF10_uc010oyj.1_5'Flank	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TTTATTGGGGAAAAAATTGCT	0.368													6	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145604790	145604791	+	Intron	INS	-	T	T	rs36107432	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145604790_145604791insT	uc001emp.3	+						POLR3C_uc001eog.2_Intron|POLR3C_uc001eoh.2_Intron|POLR3C_uc001eoi.2_Intron|POLR3C_uc009wix.2_Intron	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ctcctaactgggtttttttttt	0.139													4	2	---	---	---	---	
ASH1L	55870	broad.mit.edu	37	1	155427301	155427301	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155427301delT	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CCCACTTGCCTACTTAAGTAA	0.294													4	2	---	---	---	---	
MNDA	4332	broad.mit.edu	37	1	158818700	158818701	+	Intron	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158818700_158818701insA	uc001fsz.1	+							NM_002432	NP_002423	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen						B cell receptor signaling pathway|cellular defense response|negative regulation of B cell proliferation|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(2)|skin(2)	4	all_hematologic(112;0.0378)					tcgaaacttttAAAAAAAAATG	0.178													4	2	---	---	---	---	
UHMK1	127933	broad.mit.edu	37	1	162487664	162487664	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162487664delA	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)			gactctgtctaaaaaaaaaaa	0.129													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163579736	163579736	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163579736delG								NUF2 (254183 upstream) : PBX1 (949066 downstream)																							AAAAAGTGCTGAAGAGTATTG	0.423													4	2	---	---	---	---	
SEC16B	89866	broad.mit.edu	37	1	177911291	177911301	+	Intron	DEL	AATACCAAGAG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177911291_177911301delAATACCAAGAG	uc001gli.1	-						SEC16B_uc001glk.1_Intron|SEC16B_uc009wwy.1_Intron|SEC16B_uc001glh.1_Intron|SEC16B_uc009wwz.1_Intron|SEC16B_uc001glj.1_Intron	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN	leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4						CTGGCATCCAAATACCAAGAGGCTTGTGCCA	0.474													18	12	---	---	---	---	
C1orf49	84066	broad.mit.edu	37	1	178492736	178492738	+	Intron	DEL	TGT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178492736_178492738delTGT	uc001glv.1	+									Q5T0J7	CA049_HUMAN	Homo sapiens cDNA FLJ35950 fis, clone TESTI2012090.							microtubule cytoskeleton					0						ATATGGACCGTGTAGAAATAAGT	0.335													4	2	---	---	---	---	
NCF2	4688	broad.mit.edu	37	1	183524978	183524979	+	3'UTR	INS	-	GAA	GAA	rs145548581	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183524978_183524979insGAA	uc001gqj.3	-	15					NCF2_uc010pod.1_3'UTR|NCF2_uc010poe.1_3'UTR|NCF2_uc001gqk.3_3'UTR	NM_000433	NP_000424	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2						cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding			ovary(3)	3						atcagtacctggaagactctct	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	188040128	188040129	+	IGR	INS	-	T	T	rs149794004	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188040128_188040129insT								None (None upstream) : None (None downstream)																							ttgctgggaagtaaaatgctat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	196826686	196826687	+	IGR	INS	-	TATA	TATA			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196826686_196826687insTATA								CFHR1 (25370 upstream) : CFHR4 (30525 downstream)																							ATATGATTATTTATTACAGTAA	0.243													10	7	---	---	---	---	
CFHR4	10877	broad.mit.edu	37	1	196871341	196871341	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196871341delA	uc001gto.2	+						CFHR4_uc009wyy.2_Intron|CFHR4_uc001gtp.2_Intron	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor							extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3						AGGGTACATTAAATAGGTCTG	0.403													4	2	---	---	---	---	
TIMM17A	10440	broad.mit.edu	37	1	201926928	201926929	+	Intron	INS	-	T	T	rs11480520		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201926928_201926929insT	uc001gxc.2	+							NM_006335	NP_006326	Q99595	TI17A_HUMAN	translocase of inner mitochondrial membrane 17						protein targeting to mitochondrion	integral to membrane|mitochondrial inner membrane presequence translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity				0						ACACTCGGTGATTTTTTTTTTT	0.252													6	3	---	---	---	---	
LGR6	59352	broad.mit.edu	37	1	202173587	202173588	+	Intron	INS	-	CC	CC	rs143610412	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202173587_202173588insCC	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron	NM_001017403	NP_001017403	Q9HBX8	LGR6_HUMAN	leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10						acacacacacacctccacacac	0.000													2	5	---	---	---	---	
HHAT	55733	broad.mit.edu	37	1	210622418	210622419	+	Intron	INS	-	T	T	rs149257647	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210622418_210622419insT	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron|HHAT_uc010psu.1_Intron|HHAT_uc001hia.3_Intron	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		caacaaaaatcatttagatgca	0.000													2	5	---	---	---	---	
PPP2R5A	5525	broad.mit.edu	37	1	212465827	212465828	+	Intron	INS	-	AGTC	AGTC	rs142585178	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212465827_212465828insAGTC	uc001hjb.2	+							NM_006243	NP_006234	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B						negative regulation of establishment of protein localization in plasma membrane|negative regulation of lipid kinase activity|positive regulation of protein dephosphorylation|signal transduction	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex	kinase binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		GGTTGTCTTATAGTCACTCCTT	0.307													1	5	---	---	---	---	
ESRRG	2104	broad.mit.edu	37	1	216737932	216737933	+	Intron	INS	-	T	T	rs151309051	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216737932_216737933insT	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	AGAATGTAGTCTTTTTTTTTCT	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223656196	223656196	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223656196delT								C1orf65 (87384 upstream) : CAPN8 (58776 downstream)																							CTGAATCCTCTTTTGGGGTGG	0.323													4	2	---	---	---	---	
CDC42BPA	8476	broad.mit.edu	37	1	227484511	227484511	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227484511delA	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B						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)				aaagcacaagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
NUP133	55746	broad.mit.edu	37	1	229602743	229602744	+	Intron	INS	-	TTTA	TTTA	rs145850949	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229602743_229602744insTTTA	uc001htn.2	-							NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TTACTGAGATTTTTAAGCGATG	0.317													4	5	---	---	---	---	
TARBP1	6894	broad.mit.edu	37	1	234580441	234580441	+	Intron	DEL	A	-	-	rs5781785		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234580441delA	uc001hwd.2	-							NM_005646	NP_005637	Q13395	TARB1_HUMAN	TAR RNA binding protein 1						regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			ctctttccttaaaaaaaaaac	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	235514962	235514962	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235514962delT								GGPS1 (7120 upstream) : TBCE (15766 downstream)																							TTGTTATGCCTTACAGACCAA	0.398													4	2	---	---	---	---	
LYST	1130	broad.mit.edu	37	1	235912735	235912736	+	Intron	DEL	AG	-	-	rs73126564	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235912735_235912736delAG	uc001hxj.2	-						LYST_uc009xga.1_Intron	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GAGAGACTTCAGAGAGAGAGAG	0.436									Chediak-Higashi_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	236487939	236487939	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236487939delA								ERO1LB (42600 upstream) : EDARADD (69741 downstream)																							cttaagcaacaaaaggtcaaa	0.000													4	2	---	---	---	---	
FMN2	56776	broad.mit.edu	37	1	240354446	240354446	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240354446delA	uc010pyd.1	+						FMN2_uc010pye.1_Intron	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GCCGAGTTGGAAAGCATCCTC	0.438													4	2	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245861178	245861178	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245861178delA	uc001ibf.1	+							NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			gtcgtctctcaaaaaaaaaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5171761	5171761	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5171761delT								None (None upstream) : SOX11 (661038 downstream)																							agtcttctcatttttttgata	0.030													4	2	---	---	---	---	
LPIN1	23175	broad.mit.edu	37	2	11950512	11950512	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11950512delA	uc010yjn.1	+						LPIN1_uc010yjm.1_Intron|LPIN1_uc002rbt.2_Intron|LPIN1_uc010yjo.1_Intron	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1						fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		agtaggagcgagaggggaggc	0.000													0	7	---	---	---	---	
SMC6	79677	broad.mit.edu	37	2	17852698	17852699	+	Intron	INS	-	CA	CA	rs149724208	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17852698_17852699insCA	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					aacctcatctccacacacacac	0.064													4	2	---	---	---	---	
C2orf28	51374	broad.mit.edu	37	2	27440014	27440014	+	3'UTR	DEL	T	-	-	rs78234645		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27440014delT	uc002rjf.2	+	7					C2orf28_uc002rjg.2_3'UTR|C2orf28_uc002rjh.2_RNA|CAD_uc002rji.2_5'Flank|CAD_uc010eyw.2_5'Flank	NM_080592	NP_542159	Q6UW56	APR3_HUMAN	apoptosis related protein 3 isoform b							integral to membrane|plasma membrane				skin(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAATAAACACTTTTTTCTTTT	0.453													3	3	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28404901	28404901	+	Intron	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28404901delC	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					gatcaaggatcagtatcccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37984142	37984142	+	IGR	DEL	T	-	-	rs112508808		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37984142delT								CDC42EP3 (84816 upstream) : FAM82A1 (168320 downstream)																							TATTACATTCTTTTCCCCATT	0.408													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48298810	48298810	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48298810delA								FBXO11 (165996 upstream) : FOXN2 (242985 downstream)																							GTAAGGTTAGAAAAAAGGGAG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57247649	57247650	+	IGR	DEL	AC	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57247649_57247650delAC								CCDC85A (634341 upstream) : VRK2 (887136 downstream)																							acacacatatacacacacacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58014882	58014883	+	IGR	DEL	TG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58014882_58014883delTG								None (None upstream) : VRK2 (119903 downstream)																							TAACACAGACTGGAAGGATATT	0.292													4	2	---	---	---	---	
BCL11A	53335	broad.mit.edu	37	2	60695141	60695143	+	Intron	DEL	TGA	-	-	rs59285971	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60695141_60695143delTGA	uc002sae.1	-						BCL11A_uc002sab.2_Intron|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Intron|BCL11A_uc002sad.1_Intron|BCL11A_uc002saf.1_Intron	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1						negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			gtggtggtggtgatggtggtggt	0.000			T	IGH@	B-CLL								3	3	---	---	---	---	
EHBP1	23301	broad.mit.edu	37	2	63220869	63220870	+	Intron	DEL	TA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63220869_63220870delTA	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			ctatatatagtatatatatata	0.183									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71708825	71708826	+	Intron	INS	-	ATCC	ATCC	rs75288288	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71708825_71708826insATCC	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						GGTCTTcatctatccatccatc	0.248													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	79027785	79027785	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79027785delA								SNAR-H (845633 upstream) : REG3G (225041 downstream)																							tgagtgggagaaaaaaaagat	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91798819	91798820	+	IGR	INS	-	AA	AA	rs71204456		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91798819_91798820insAA								None (None upstream) : LOC654342 (6372 downstream)																							aaaaacaaaCCCCCCCCCCATA	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92176673	92176675	+	IGR	DEL	GAT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92176673_92176675delGAT								FKSG73 (46179 upstream) : None (None downstream)																							aatgagatgagatgataagatga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92194836	92194837	+	IGR	INS	-	T	T	rs145003390		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92194836_92194837insT								FKSG73 (64342 upstream) : None (None downstream)																							AGAGCAGGCTCTTGCCCACATC	0.495													5	3	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97818757	97818758	+	Intron	INS	-	G	G	rs147267624	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97818757_97818758insG	uc010yva.1	+						ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						TAACCATCAAATTTTAAAGGCA	0.351													1	5	---	---	---	---	
EIF5B	9669	broad.mit.edu	37	2	100000789	100000790	+	Intron	INS	-	A	A	rs138885335	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100000789_100000790insA	uc002tab.2	+							NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B						regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3						accaactgctcagagaaaaaga	0.000													2	5	---	---	---	---	
ST6GAL2	84620	broad.mit.edu	37	2	107449321	107449321	+	Intron	DEL	A	-	-	rs56781498	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107449321delA	uc002tdq.2	-						ST6GAL2_uc002tdr.2_Intron|ST6GAL2_uc002tds.3_Intron	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide						growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(4)|skin(1)	11						ACTTTTTTTTAAAAAAAAGCA	0.418													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114082256	114082258	+	IGR	DEL	GCA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114082256_114082258delGCA								PAX8 (45758 upstream) : CBWD2 (113010 downstream)																							ctccttttttgcatcctctttgg	0.241													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114162796	114162796	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114162796delG								PAX8 (126298 upstream) : CBWD2 (32472 downstream)																							GATAGGAGATGGAGACTCTCT	0.443													4	2	---	---	---	---	
TFCP2L1	29842	broad.mit.edu	37	2	121993151	121993151	+	Intron	DEL	T	-	-	rs34634906		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121993151delT	uc002tmx.2	-						TFCP2L1_uc010flr.2_Intron|TFCP2L1_uc010flq.2_5'Flank	NM_014553	NP_055368	Q9NZI6	TF2L1_HUMAN	LBP-9						female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			pancreas(2)|ovary(1)	3	Renal(3;0.01)					tctttctttcttttttttttt	0.229													4	2	---	---	---	---	
BIN1	274	broad.mit.edu	37	2	127811712	127811713	+	Intron	INS	-	CA	CA	rs138460912	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127811712_127811713insCA	uc002tns.1	-						BIN1_uc010yzf.1_Intron|BIN1_uc010yzg.1_Intron|BIN1_uc002tnu.1_Intron|BIN1_uc002toa.1_Intron|BIN1_uc002tnt.1_Intron|BIN1_uc002tnv.1_Intron|BIN1_uc002tnw.1_Intron|BIN1_uc002tnx.1_Intron|BIN1_uc002tny.1_Intron|BIN1_uc002tnz.1_Intron|BIN1_uc002tob.1_Intron|BIN1_uc002toc.1_Intron	NM_139343	NP_647593	O00499	BIN1_HUMAN	bridging integrator 1 isoform 1						cell proliferation|endocytosis|interspecies interaction between organisms|multicellular organismal development	actin cytoskeleton|nucleus				ovary(2)|central_nervous_system(2)|skin(2)|lung(1)	7	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		caccacgcatgcagagcaagcg	0.470													8	5	---	---	---	---	
LOC150776	150776	broad.mit.edu	37	2	132273427	132273431	+	5'Flank	DEL	GAGTC	-	-	rs147707520		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132273427_132273431delGAGTC	uc002tsz.3	+						LOC150776_uc010zaz.1_Intron|LOC150776_uc010fna.2_Intron|LOC150776_uc002tsy.3_Intron					Homo sapiens cDNA FLJ41352 fis, clone BRAWH2014645.												0						AGGGTGAGGGGAGTCCCTTTCTGTT	0.654													4	3	---	---	---	---	
LOC150776	150776	broad.mit.edu	37	2	132273797	132273798	+	5'Flank	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132273797_132273798insA	uc002tsz.3	+						LOC150776_uc010zaz.1_Intron|LOC150776_uc010fna.2_Intron|LOC150776_uc002tsy.3_Intron					Homo sapiens cDNA FLJ41352 fis, clone BRAWH2014645.												0						CACGGTGGAGCCAACCCTCACT	0.450													9	4	---	---	---	---	
GPR39	2863	broad.mit.edu	37	2	133224344	133224345	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133224344_133224345insT	uc002ttl.2	+							NM_001508	NP_001499	O43194	GPR39_HUMAN	G protein-coupled receptor 39							integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0						TTTCAGGGCTGTTTTTTTTATT	0.411													4	2	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133516237	133516238	+	Intron	DEL	CT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133516237_133516238delCT	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						CTTTCTTTCCCTCTCTCTCTCC	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134959655	134959658	+	IGR	DEL	TATC	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134959655_134959658delTATC								NCKAP5 (633624 upstream) : MGAT5 (52172 downstream)																							CAGTAACTCATATCTATCTATGAC	0.397													4	3	---	---	---	---	
R3HDM1	23518	broad.mit.edu	37	2	136388975	136388975	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136388975delA	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_5'Flank	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)		GTGTGTAAGCAAAAAAAAAAA	0.169													5	3	---	---	---	---	
LCT	3938	broad.mit.edu	37	2	136552616	136552617	+	Intron	DEL	CA	-	-	rs70973482		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136552616_136552617delCA	uc002tuu.1	-							NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)		cgcgcgcgcgcacacacacaca	0.297													4	2	---	---	---	---	
SPOPL	339745	broad.mit.edu	37	2	139275718	139275718	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139275718delA	uc002tvh.2	+							NM_001001664	NP_001001664	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like							nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)		TGATTTTGTTAAAAAAAAAAG	0.274													4	2	---	---	---	---	
ORC4L	5000	broad.mit.edu	37	2	148772683	148772683	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148772683delA	uc002twi.2	-						ORC4L_uc002twj.2_Intron|ORC4L_uc010zbo.1_Intron|ORC4L_uc010zbp.1_Intron|ORC4L_uc010fnr.2_Intron|ORC4L_uc010zbq.1_Intron|ORC4L_uc002twk.2_Intron|ORC4L_uc010zbr.1_Intron	NM_181741	NP_859525	O43929	ORC4_HUMAN	origin recognition complex subunit 4						cell cycle checkpoint|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	nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|nucleoside-triphosphatase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.0963)|COAD - Colon adenocarcinoma(177;0.203)		TGACTAGGAGAAAAAAAAAAA	0.214													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	150452941	150452941	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150452941delT								MMADHC (8611 upstream) : RND3 (871771 downstream)																							caatgaTTTCTTTTTAATTCT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	161728043	161728044	+	IGR	INS	-	TC	TC	rs151193705		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161728043_161728044insTC								RBMS1 (377725 upstream) : TANK (265422 downstream)																							cctcttttttttttTTTTTTTt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	167002355	167002356	+	Intron	DEL	AA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167002355_167002356delAA	uc002udp.2	+											Homo sapiens, clone IMAGE:3681561, mRNA.																		TTTATCTTCTAAACTCTTTGAT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173087734	173087734	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173087734delC								DLX2 (120256 upstream) : ITGA6 (204348 downstream)																							TGCAGTAAGACCTAGTTTGTC	0.353													4	2	---	---	---	---	
PDE11A	50940	broad.mit.edu	37	2	178679380	178679380	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178679380delA	uc002ulq.2	-						PDE11A_uc002ulp.2_Intron|PDE11A_uc002ulr.2_Intron|PDE11A_uc002uls.1_Intron|PDE11A_uc002ult.1_Intron|PDE11A_uc002ulu.1_Intron	NM_016953	NP_058649	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)			TCACAAGGCTAAGAGTTGGGC	0.388									Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				4	2	---	---	---	---	
OSBPL6	114880	broad.mit.edu	37	2	179102073	179102074	+	Intron	INS	-	TTTTG	TTTTG	rs139067920	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179102073_179102074insTTTTG	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TCAATTTGTTTTTTTGTTTTGT	0.366													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181120477	181120479	+	IGR	DEL	AAG	-	-	rs150457085		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181120477_181120479delAAG								CWC22 (248637 upstream) : UBE2E3 (724633 downstream)																							ACTCAGATATAAGAAGAACACAG	0.355													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	181559147	181559147	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181559147delT								CWC22 (687307 upstream) : UBE2E3 (285965 downstream)																							TGCGATAATCTTTTTTTTTTT	0.284													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	196214646	196214646	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196214646delA								None (None upstream) : SLC39A10 (306886 downstream)																							GGCTCTCTAGAAAAGGGCATA	0.279													4	2	---	---	---	---	
ALS2CR12	130540	broad.mit.edu	37	2	202153880	202153881	+	Intron	INS	-	C	C	rs142645837	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202153880_202153881insC	uc010ftg.2	-						ALS2CR12_uc002uya.3_Intron|ALS2CR12_uc010fth.2_Intron	NM_139163	NP_631902	Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)						regulation of GTPase activity		protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3						GGATTTAAAAACCACCCTCAGT	0.436													3	3	---	---	---	---	
ICA1L	130026	broad.mit.edu	37	2	203661856	203661867	+	Intron	DEL	TGTGTGTGTGTG	-	-	rs72418209	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203661856_203661867delTGTGTGTGTGTG	uc002uzh.1	-						ICA1L_uc002uzi.1_Intron	NM_138468	NP_612477	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like isoform 1												0						aaatCACATTtgtgtgtgtgtgtgtgtgtgtg	0.217													2	4	---	---	---	---	
NDUFS1	4719	broad.mit.edu	37	2	206989170	206989170	+	Intron	DEL	C	-	-	rs2045858	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206989170delC	uc002vbe.2	-						NDUFS1_uc010ziq.1_Intron|NDUFS1_uc010zir.1_Intron|NDUFS1_uc010zis.1_Intron|NDUFS1_uc010zit.1_Intron|NDUFS1_uc010ziu.1_Intron	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)	TTACTGGCCACATGCTTTCAA	0.348													4	2	---	---	---	---	
EPHA4	2043	broad.mit.edu	37	2	222300861	222300861	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222300861delA	uc002vmq.2	-						EPHA4_uc002vmr.2_Intron|EPHA4_uc010zlm.1_Intron|EPHA4_uc010zln.1_Intron	NM_004438	NP_004429	P54764	EPHA4_HUMAN	ephrin receptor EphA4 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(6)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	12		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		CTGCCCTCCCAAAAAAAAACA	0.358													4	2	---	---	---	---	
WDFY1	57590	broad.mit.edu	37	2	224770401	224770401	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224770401delA	uc002vnq.2	-							NM_020830	NP_065881	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1							cytosol|early endosome|nucleus	1-phosphatidylinositol binding|zinc ion binding			lung(1)	1		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)		GTGTGTTATCAAAAAAAAAAT	0.164													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	237541450	237541450	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237541450delG								CXCR7 (50458 upstream) : COPS8 (452634 downstream)																							atgcccgagtggggtttcaaa	0.000													4	2	---	---	---	---	
LRRFIP1	9208	broad.mit.edu	37	2	238575220	238575221	+	Intron	INS	-	TC	TC	rs143634464	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238575220_238575221insTC	uc002vxc.2	+							NM_001137550	NP_001131022	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		GGGGATTTTCATCTCTTCCTGG	0.520													3	4	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2654844	2654844	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2654844delG	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		GATAGCTTCCGTAGTTCTAAG	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	15694304	15694305	+	IGR	INS	-	TA	TA			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15694304_15694305insTA								BTD (6980 upstream) : ANKRD28 (14439 downstream)																							ATCTCTCCCACTATATATATAT	0.386													4	2	---	---	---	---	
STT3B	201595	broad.mit.edu	37	3	31658222	31658222	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31658222delA	uc011axe.1	+						STT3B_uc010hft.1_Intron|STT3B_uc003cer.1_Intron|STT3B_uc003cet.2_Intron	NM_178862	NP_849193	Q8TCJ2	STT3B_HUMAN	source of immunodominant MHC-associated						protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0						ATCATTTAGGAAAAAAAAAAA	0.328													4	2	---	---	---	---	
FBXL2	25827	broad.mit.edu	37	3	33427797	33427797	+	3'UTR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33427797delA	uc003cfp.2	+	15					FBXL2_uc011axo.1_3'UTR|FBXL2_uc011axp.1_3'UTR|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron	NM_012157	NP_036289	Q9UKC9	FBXL2_HUMAN	F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1						GCCTGATTGGAAAGTAGAAGC	0.433													4	2	---	---	---	---	
HIGD1A	25994	broad.mit.edu	37	3	42842324	42842324	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42842324delA	uc003cma.3	-						HIGD1A_uc010hid.2_Intron|HIGD1A_uc003cmb.3_Intron	NM_001099669	NP_001093139	Q9Y241	HIG1A_HUMAN	HIG1 domain family, member 1A isoform b						response to stress	integral to membrane|protein complex	protein binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.217)		CCGGTCCTTTAAAAAAAAAAA	0.398													7	4	---	---	---	---	
ALS2CL	259173	broad.mit.edu	37	3	46725897	46725898	+	Intron	INS	-	ACT	ACT	rs146103108	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46725897_46725898insACT	uc003cqa.1	-						ALS2CL_uc003cpz.1_5'Flank|ALS2CL_uc003cqb.1_Intron|ALS2CL_uc003cqc.1_Intron	NM_147129	NP_667340	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like isoform 1						endosome organization|regulation of Rho protein signal transduction		GTPase activator activity|identical protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)|central_nervous_system(2)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CCTCACAGACCACTACGCCATC	0.421													4	2	---	---	---	---	
MAP4	4134	broad.mit.edu	37	3	47956040	47956040	+	Intron	DEL	A	-	-	rs75344940		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47956040delA	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc011bbf.1_Intron|MAP4_uc003csf.3_Intron	NM_002375	NP_002366	P27816	MAP4_HUMAN	microtubule-associated protein 4 isoform 1						negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)		actctgtctcaaaaaaaaaaa	0.119													3	5	---	---	---	---	
RBM6	10180	broad.mit.edu	37	3	50114316	50114316	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50114316delA	uc003cyc.2	+						RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		gactccatctaaaaaaaaaaa	0.184													5	4	---	---	---	---	
CACNA1D	776	broad.mit.edu	37	3	53538310	53538311	+	Intron	INS	-	T	T	rs146694454	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53538310_53538311insT	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)	GGAAAGATGCAGTTGAGCGATA	0.431													4	3	---	---	---	---	
SYNPR	132204	broad.mit.edu	37	3	63514309	63514310	+	Intron	INS	-	T	T	rs147821217	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63514309_63514310insT	uc003dlq.2	+						SYNPR_uc003dlp.2_Intron|SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron|SYNPR_uc010hnt.2_Intron|SYNPR_uc011bfm.1_Intron	NM_144642	NP_653243	Q8TBG9	SYNPR_HUMAN	synaptoporin isoform 2							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		AAGAAGATGCATTTTTTTTTTA	0.332													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	66027999	66028000	+	IGR	INS	-	TTTG	TTTG	rs138396331	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66027999_66028000insTTTG								MAGI1 (3490 upstream) : SLC25A26 (91285 downstream)																							tttgtttggtttttgtttgttt	0.153													6	4	---	---	---	---	
LOC255025	255025	broad.mit.edu	37	3	94809126	94809126	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94809126delA	uc003drn.2	+											Homo sapiens hypothetical protein LOC255025, mRNA (cDNA clone IMAGE:5267157).												0						CCCCTCCGGCaaaaaaaaaaa	0.244													15	8	---	---	---	---	
ESYT3	83850	broad.mit.edu	37	3	138175990	138175991	+	Intron	INS	-	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138175990_138175991insC	uc003esk.2	+						ESYT3_uc010hug.2_Intron	NM_031913	NP_114119	A0FGR9	ESYT3_HUMAN	family with sequence similarity 62 (C2 domain							integral to membrane|plasma membrane					0						ATGTTTTTCAGCTGCCATAAGC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	138209370	138209370	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138209370delC								ESYT3 (12115 upstream) : CEP70 (3819 downstream)																							aggaatgctacattttctagg	0.000													4	2	---	---	---	---	
ATR	545	broad.mit.edu	37	3	142256301	142256301	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142256301delA	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						GACTATGTACAAAAAAATTTA	0.214								Other_conserved_DNA_damage_response_genes					3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149788781	149788781	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149788781delG								PFN2 (100040 upstream) : TSC22D2 (338007 downstream)																							acaatctagaggggggaacac	0.000													4	2	---	---	---	---	
C3orf55	152078	broad.mit.edu	37	3	157269977	157269977	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157269977delG	uc003fbp.3	+						C3orf55_uc011bos.1_Intron|C3orf55_uc003fbo.2_Intron|C3orf55_uc011bot.1_Intron|C3orf55_uc010hvv.2_Intron	NM_001130002	NP_001123474	A1A4F0	CC055_HUMAN	hypothetical protein LOC152078 isoform 1												0			Lung(72;0.0215)|LUSC - Lung squamous cell carcinoma(72;0.037)			ccatgagtcagggggagtttt	0.000													1	6	---	---	---	---	
FAM131A	131408	broad.mit.edu	37	3	184060105	184060105	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184060105delT	uc003fog.2	+						FAM131A_uc003fob.1_Intron|FAM131A_uc003foc.2_Intron|FAM131A_uc003foe.2_Intron	NM_144635	NP_653236	Q6UXB0	F131A_HUMAN	hypothetical protein LOC131408 precursor							extracellular region				breast(1)	1	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ttttatttaatttttttttga	0.229													7	4	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188480556	188480556	+	Intron	DEL	T	-	-	rs113530350		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188480556delT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		ATTCTAACCATTTTTTTTTTT	0.294			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189112142	189112142	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189112142delT								TPRG1 (70872 upstream) : TP63 (237074 downstream)																							GTCCTGGGCCTTCCCAGTAAC	0.333													4	2	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189407912	189407912	+	Intron	DEL	A	-	-	rs11360431		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189407912delA	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		tggccttgggaaaaatcgctt	0.164									Hay-Wells_syndrome	HNSCC(45;0.13)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193614283	193614283	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193614283delG								OPA1 (198684 upstream) : LOC100128023 (96601 downstream)																							CATGACTTGTGGGGAGACCCC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194047701	194047702	+	IGR	DEL	CA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194047701_194047702delCA								LOC100131551 (17108 upstream) : CPN2 (12793 downstream)																							caacacacaccacacacacaac	0.000													4	2	---	---	---	---	
TFRC	7037	broad.mit.edu	37	3	195802438	195802438	+	Intron	DEL	T	-	-	rs71949472		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195802438delT	uc003fvz.3	-						TFRC_uc003fwa.3_Intron|TFRC_uc010hzy.2_Intron|TFRC_uc011btr.1_Intron	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor						cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)		TTTTTGTAAAttttttttttt	0.234			T	BCL6	NHL								4	2	---	---	---	---	
FAM157A	728262	broad.mit.edu	37	3	197880887	197880887	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197880887delT	uc011bup.1	+							NM_001145248	NP_001138720	C9JC47	F157A_HUMAN	family with sequence similarity 157, member A												0						aaaacgtgggtttttttttgt	0.184													4	3	---	---	---	---	
GAK	2580	broad.mit.edu	37	4	904556	904557	+	Intron	INS	-	GA	GA	rs147700569	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:904556_904557insGA	uc003gbm.3	-						GAK_uc003gbn.3_Intron|GAK_uc010ibk.1_Intron|GAK_uc003gbo.2_Intron|GAK_uc003gbl.3_Intron	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase						cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)		CAGACGCAGGGGTCACTAGTGT	0.673													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	19984871	19984871	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19984871delC								None (None upstream) : SLIT2 (270364 downstream)																							TGTGGTAAATCCTAAGTACAC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	40722715	40722715	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40722715delC								RBM47 (90075 upstream) : NSUN7 (29199 downstream)																							tcacctccttccctttacagt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	45732620	45732620	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45732620delG								None (None upstream) : GABRG1 (305169 downstream)																							taaggatcttgggatagggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49246087	49246087	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49246087delC								CWH43 (181994 upstream) : None (None downstream)																							CAAAAACAAACAAAAAAAAAT	0.249													4	2	---	---	---	---	
PDGFRA	5156	broad.mit.edu	37	4	54279693	54279693	+	Intron	DEL	T	-	-	rs71662222		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54279693delT	uc003haa.2	+						FIP1L1_uc003gzx.3_Intron|FIP1L1_uc011bzt.1_Intron|FIP1L1_uc003gzy.2_Intron|FIP1L1_uc011bzu.1_Intron|FIP1L1_uc003gzz.2_Intron|FIP1L1_uc003hab.2_Intron|FIP1L1_uc003hac.2_Intron|FIP1L1_uc010ign.2_Intron	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	ttgcatctccttttttttcca	0.000			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63369783	63369784	+	IGR	DEL	TC	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63369783_63369784delTC								LPHN3 (431616 upstream) : None (None downstream)																							AACTAATTATTCAAAAACATTT	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	63369787	63369788	+	IGR	INS	-	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63369787_63369788insG								LPHN3 (431620 upstream) : None (None downstream)																							AATTATTCAAAAACATTTTTAA	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	88742455	88742455	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88742455delT								IBSP (8856 upstream) : MEPE (11685 downstream)																							GAATTTTTTCTTTTTTTTCCC	0.264													4	2	---	---	---	---	
PAPSS1	9061	broad.mit.edu	37	4	108603517	108603517	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108603517delA	uc003hyk.2	-						PAPSS1_uc011cfh.1_Intron	NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		acaaaaatgtaaaaaatgtga	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	119419012	119419012	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119419012delC								PRSS12 (145090 upstream) : CEP170L (18483 downstream)																							atcttggaatcaaaagcagag	0.040													4	2	---	---	---	---	
KIAA1109	84162	broad.mit.edu	37	4	123272649	123272649	+	Intron	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123272649delC	uc003ieh.2	+						KIAA1109_uc003iem.2_Intron	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						ctaaaaatgtcctctataatg	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	123703789	123703790	+	IGR	DEL	TG	-	-	rs35148743		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123703789_123703790delTG								BBS12 (37692 upstream) : FGF2 (44073 downstream)																							GAGTATGGTCTGTGGTTTGTGT	0.391													9	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	132664122	132664123	+	IGR	INS	-	TT	TT	rs76143910		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132664122_132664123insTT								None (None upstream) : None (None downstream)																							gtgtgtgtgtgtgtgtgtgtgt	0.064													4	2	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143066777	143066777	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143066777delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					GTAAGATAAGAAAAAAAAAAG	0.343													8	5	---	---	---	---	
ZNF827	152485	broad.mit.edu	37	4	146770908	146770908	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146770908delT	uc003ikn.2	-						ZNF827_uc003ikm.2_Intron|ZNF827_uc010iox.2_Intron	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)					GAGACTTCAGTTTTTTTTAGC	0.488													4	2	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148800705	148800706	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148800705_148800706insT	uc003ilf.2	+						ARHGAP10_uc003ilg.2_5'Flank	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		AAACCACTAGAttttttttttt	0.149													4	2	---	---	---	---	
PLRG1	5356	broad.mit.edu	37	4	155470615	155470615	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155470615delA	uc003iny.2	-						PLRG1_uc003inz.2_Intron|PLRG1_uc011cil.1_Intron	NM_002669	NP_002660	O43660	PLRG1_HUMAN	pleiotropic regulator 1 (PRL1 homolog,							catalytic step 2 spliceosome|nuclear speck	protein binding|signal transducer activity|transcription corepressor activity				0	all_hematologic(180;0.215)	Renal(120;0.0854)				aATGTCATGTAAAAAAAAGTT	0.040													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	156546824	156546824	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156546824delA								MAP9 (248702 upstream) : GUCY1A3 (41038 downstream)																							atagggggttaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	158790630	158790631	+	IGR	INS	-	G	G	rs139264711	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158790630_158790631insG								LOC340017 (293335 upstream) : FAM198B (255102 downstream)																							tgggaataaatgggttgctcaa	0.040													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	163612860	163612861	+	IGR	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163612860_163612861insT								FSTL5 (527674 upstream) : NAF1 (434999 downstream)																							CATTGTTTTAATTTTTTTTTTA	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	169957831	169957831	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169957831delA								CBR4 (26409 upstream) : SH3RF1 (57576 downstream)																							TCACTGGTTTAAAAAAAAAAA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	178961360	178961363	+	IGR	DEL	CTTA	-	-	rs145227417		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178961360_178961363delCTTA								LOC285501 (49457 upstream) : None (None downstream)																							AGTGAATTGCCTTACTTAACTAAT	0.240													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190547515	190547516	+	IGR	INS	-	A	A	rs111951194		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190547515_190547516insA								None (None upstream) : FRG1 (314458 downstream)																							TTCTACTTTTGAAAATCATTAA	0.347													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	3330539	3330539	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3330539delC								C5orf38 (575027 upstream) : IRX1 (265629 downstream)																							TTACCGCTGACCCTTCCCCAG	0.224													4	2	---	---	---	---	
CMBL	134147	broad.mit.edu	37	5	10291108	10291108	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10291108delA	uc003jes.2	-							NM_138809	NP_620164	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase							cytosol	hydrolase activity|protein binding			skin(1)	1						acaaaacaacaaaaaatagcg	0.129													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22812981	22812982	+	Intron	INS	-	G	G			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22812981_22812982insG	uc003jgk.2	-							NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						AATACAGCATAATGACCACTGG	0.436										HNSCC(59;0.17)			4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24425075	24425075	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24425075delA								PRDM9 (896371 upstream) : CDH10 (62135 downstream)																							aaacaaaaacaaaaaaAACAG	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29990264	29990264	+	IGR	DEL	C	-	-	rs34608143		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29990264delC								None (None upstream) : None (None downstream)																							AAAAACACTGCTTCCCTTGGA	0.333													4	2	---	---	---	---	
MTMR12	54545	broad.mit.edu	37	5	32233561	32233562	+	Intron	INS	-	AC	AC	rs71598927		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32233561_32233562insAC	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1						TTACTCTACTAacacacacaca	0.332													6	3	---	---	---	---	
RPL37	6167	broad.mit.edu	37	5	40835567	40835568	+	5'Flank	DEL	AC	-	-	rs138214351		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40835567_40835568delAC	uc003jme.1	-						SNORD72_uc003jmf.1_5'Flank	NM_000997	NP_000988	P61927	RL37_HUMAN	ribosomal protein L37						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	metal ion binding|protein binding|rRNA binding|structural constituent of ribosome				0		Breast(839;0.238)				CGTTTAGATTACAGTTTTGCTT	0.460													2	6	---	---	---	---	
SLC38A9	153129	broad.mit.edu	37	5	54945329	54945330	+	Intron	INS	-	A	A	rs142108347	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54945329_54945330insA	uc003jqf.2	-						SLC38A9_uc003jqd.2_Intron|SLC38A9_uc010ivx.2_Intron|SLC38A9_uc003jqe.2_Intron|SLC38A9_uc010ivy.2_Intron	NM_173514	NP_775785	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9						amino acid transport|sodium ion transport	integral to membrane					0		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				AGAAAAAAAACAAAACACTCTA	0.282													12	7	---	---	---	---	
MIER3	166968	broad.mit.edu	37	5	56226156	56226157	+	Intron	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56226156_56226157insA	uc003jrd.1	-						MIER3_uc003jqz.1_Intron|MIER3_uc003jra.1_Intron|MIER3_uc003jrb.1_Intron|MIER3_uc003jrc.1_Intron	NM_152622	NP_689835	Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		CTGTCTGGCTGAAAAAAAAAAA	0.262													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	86061948	86061948	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86061948delG								COX7C (145367 upstream) : RASA1 (502203 downstream)																							cacctagcctgGAAACCAACA	0.179													4	2	---	---	---	---	
MCTP1	79772	broad.mit.edu	37	5	94104243	94104243	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94104243delA	uc003kkx.2	-						MCTP1_uc003kkv.2_Intron|MCTP1_uc003kkw.2_Intron|MCTP1_uc003kku.2_Intron	NM_024717	NP_078993	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		caactcaactaaaaaaaccca	0.000													4	2	---	---	---	---	
FAM81B	153643	broad.mit.edu	37	5	94771998	94771998	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94771998delG	uc003kla.1	+						FAM81B_uc010jbe.1_Intron	NM_152548	NP_689761	Q96LP2	FA81B_HUMAN	hypothetical protein LOC153643											ovary(1)|skin(1)	2		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)		AATACTATCTGGAAATCTTGG	0.279													4	2	---	---	---	---	
TMEM232	642987	broad.mit.edu	37	5	109953890	109953890	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109953890delA	uc011cvh.1	-						TMEM232_uc003kow.1_Intron|TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;							integral to membrane					0						TGCATTTAATAAAAAAAAAAC	0.294													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	112016669	112016669	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112016669delC								FLJ11235 (259996 upstream) : APC (26549 downstream)																							CCCACAGCTTCACCTTTCCTT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	115094913	115094913	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115094913delA								TMED7-TICAM2 (133043 upstream) : CDO1 (45519 downstream)																							AACAATTAGGAAAAAAAATTA	0.289													4	2	---	---	---	---	
COMMD10	51397	broad.mit.edu	37	5	115481142	115481143	+	Intron	DEL	TG	-	-	rs149068119		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115481142_115481143delTG	uc003krt.1	+							NM_016144	NP_057228	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		agggtttgtctgtgtctatgaa	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	123737843	123737843	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123737843delT								CSNK1G3 (785381 upstream) : ZNF608 (234767 downstream)																							CAACAGGACCTTTTGTGGGCT	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124097750	124097750	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124097750delT								ZNF608 (13250 upstream) : None (None downstream)																							tttctttttcttttttttttt	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	126052102	126052103	+	IGR	DEL	TG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126052102_126052103delTG								C5orf48 (80128 upstream) : LMNB1 (60730 downstream)																							tgtgtgtgtctgtgtgtgtgtg	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133014254	133014255	+	IGR	DEL	GT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133014254_133014255delGT								FSTL4 (66031 upstream) : C5orf15 (276944 downstream)																							gtgtttgagcgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
KDM3B	51780	broad.mit.edu	37	5	137750647	137750648	+	Intron	INS	-	AAAT	AAAT	rs148266134	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137750647_137750648insAAAT	uc003lcy.1	+						KDM3B_uc010jew.1_Intron|KDM3B_uc011cys.1_Intron	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11						ccttgtctcaaaaataaataaa	0.139													11	10	---	---	---	---	
CTNNA1	1495	broad.mit.edu	37	5	138196645	138196646	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138196645_138196646insT	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TCCCACTGCCATTTTTTTCCTC	0.391													4	2	---	---	---	---	
KCTD16	57528	broad.mit.edu	37	5	143594178	143594178	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143594178delT	uc003lnm.1	+						KCTD16_uc003lnn.1_Intron	NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			tgcatgttcattttttgtgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	150070188	150070188	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150070188delA								MYOZ3 (11263 upstream) : RBM22 (165 downstream)																							GGCTGAGGTTAAAAAAAAATA	0.209													4	2	---	---	---	---	
CCDC69	26112	broad.mit.edu	37	5	150597550	150597550	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150597550delA	uc003ltq.2	-						CCDC69_uc010jhu.2_Intron	NM_015621	NP_056436	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69											ovary(2)	2		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACACTCAGTGAAAAAAAACTC	0.483													3	4	---	---	---	---	
WWC1	23286	broad.mit.edu	37	5	167801814	167801814	+	Intron	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167801814delC	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		agtccaggcgccctagacctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170953958	170953958	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170953958delG								FGF18 (69796 upstream) : FBXW11 (334598 downstream)																							caaccatccaggcaagagata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174097086	174097086	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174097086delG								HMP19 (560905 upstream) : MSX2 (54489 downstream)																							CTCCTTTAGTGGGGGCAGCTG	0.478													4	2	---	---	---	---	
EXOC2	55770	broad.mit.edu	37	6	511399	511399	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:511399delA	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		AATGGAAGGCAAAAAAAAAAT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3817128	3817129	+	IGR	DEL	CG	-	-	rs4499973	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3817128_3817129delCG								C6orf145 (64882 upstream) : FAM50B (32503 downstream)																							cacacacacacgtgtaatatgc	0.035													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	10471888	10471889	+	IGR	DEL	TC	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10471888_10471889delTC								C6orf218 (36833 upstream) : GCNT2 (20567 downstream)																							ttagaacaaatctctgtcttcc	0.000													0	6	---	---	---	---	
NEDD9	4739	broad.mit.edu	37	6	11369149	11369150	+	Intron	DEL	TG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11369149_11369150delTG	uc010joz.2	-						NEDD9_uc003mzw.3_Intron	NM_001142393	NP_001135865	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally						actin filament bundle assembly|cell adhesion|cell division|integrin-mediated signaling pathway|mitosis|regulation of growth	cell cortex|focal adhesion|Golgi apparatus|lamellipodium|nucleus	protein binding				0	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			ctttaggtgctgtgtgtgtgtt	0.119													4	2	---	---	---	---	
CDKAL1	54901	broad.mit.edu	37	6	21034204	21034206	+	Intron	DEL	AGC	-	-	rs35161624		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21034204_21034206delAGC	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244	Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			ATAGTGAGGAagcagcagcagca	0.384													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23903275	23903275	+	IGR	DEL	A	-	-	rs35270955		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23903275delA								None (None upstream) : NRSN1 (223139 downstream)																							aatagaggagataaacttcag	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32577874	32577874	+	IGR	DEL	G	-	-	rs66522632		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32577874delG								HLA-DRB1 (20312 upstream) : HLA-DQA1 (27309 downstream)																							AAGAATGGCTGACGATGTAGT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	33822282	33822283	+	IGR	INS	-	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33822282_33822283insC								MLN (50489 upstream) : MIR1275 (145466 downstream)																							CCATTCTCGGGCTGCCACAAGT	0.495													4	2	---	---	---	---	
C6orf106	64771	broad.mit.edu	37	6	34605641	34605642	+	Intron	INS	-	TGT	TGT	rs12201114		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34605641_34605642insTGT	uc003ojr.2	-						C6orf106_uc003ojs.2_Intron	NM_024294	NP_077270	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3						gctgctgctgctgttgttgttg	0.119													4	2	---	---	---	---	
PNPLA1	285848	broad.mit.edu	37	6	36227378	36227378	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36227378delA	uc010jwe.1	+						PNPLA1_uc003olw.1_Intron	NM_001145716	NP_001139188	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1						lipid catabolic process		hydrolase activity			large_intestine(1)|pancreas(1)|breast(1)|skin(1)	4						ttttcaggagaaaaaaaaaac	0.114													4	2	---	---	---	---	
CPNE5	57699	broad.mit.edu	37	6	36742533	36742534	+	Intron	INS	-	AG	AG	rs141427086	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36742533_36742534insAG	uc003omr.1	-						CPNE5_uc003oms.1_Intron	NM_020939	NP_065990	Q9HCH3	CPNE5_HUMAN	copine V											skin(1)	1						TGTGAAGAGGCAGACATTGCCG	0.609													4	9	---	---	---	---	
BTBD9	114781	broad.mit.edu	37	6	38436867	38436867	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38436867delA	uc003ooa.3	-						BTBD9_uc003ony.3_Intron|BTBD9_uc010jwv.2_Intron|BTBD9_uc010jww.2_Intron|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a						cell adhesion						0						AAGTTGCATTAAAAAAAAAAG	0.333													3	3	---	---	---	---	
TRERF1	55809	broad.mit.edu	37	6	42391465	42391465	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42391465delA	uc003osd.2	-						TRERF1_uc003osb.2_Intron|TRERF1_uc003osc.2_Intron|TRERF1_uc003ose.2_Intron|TRERF1_uc010jxu.1_Intron	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGGGTTATTTAAAAAAAAAAG	0.323													23	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	53593506	53593506	+	IGR	DEL	A	-	-	rs5876331		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53593506delA								KLHL31 (63000 upstream) : LRRC1 (66272 downstream)																							CTCATCCTTCAAAGGAAACTT	0.507													4	6	---	---	---	---	
ZNF451	26036	broad.mit.edu	37	6	56999205	56999205	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56999205delT	uc003pdm.1	+						ZNF451_uc003pdl.2_Intron|ZNF451_uc003pdn.1_Intron|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Intron	NM_001031623	NP_001026794	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			gttgtgagtcttatggtaacc	0.035													4	2	---	---	---	---	
GABRR1	2569	broad.mit.edu	37	6	89902142	89902143	+	Intron	DEL	CA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89902142_89902143delCA	uc003pna.2	-						GABRR1_uc011dzv.1_Intron	NM_002042	NP_002033	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 1						gamma-aminobutyric acid signaling pathway|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			pancreas(1)	1		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Picrotoxin(DB00466)	aaactgcaggcacacacacacc	0.208													4	2	---	---	---	---	
BET3L	100128327	broad.mit.edu	37	6	116864756	116864756	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116864756delG	uc011ebh.1	-						FAM26D_uc003pwz.2_Intron|FAM26D_uc003pxa.2_Intron|FAM26D_uc010ked.2_Intron	NM_001139444	NP_001132916	Q5T215	TPC3L_HUMAN	BET3 like						vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0						GATGTGAGGTGGGGGAGAGAG	0.328													4	2	---	---	---	---	
GPRC6A	222545	broad.mit.edu	37	6	117121544	117121545	+	Intron	DEL	CT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117121544_117121545delCT	uc003pxj.1	-						GPRC6A_uc003pxk.1_Intron|GPRC6A_uc003pxl.1_Intron	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, family C, group 6,						response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)|skin(2)	6		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CCCTCCCTCCctctctctctct	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	131105881	131105881	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131105881delA								TMEM200A (341673 upstream) : LOC285733 (42443 downstream)																							CCTCCTTAGGAAGTTTTCACA	0.418													4	2	---	---	---	---	
HBS1L	10767	broad.mit.edu	37	6	135357536	135357536	+	Intron	DEL	A	-	-	rs55825814		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135357536delA	uc003qez.2	-						HBS1L_uc011ecy.1_Intron|HBS1L_uc011ecz.1_Intron|HBS1L_uc011eda.1_Intron|HBS1L_uc003qfa.2_3'UTR	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	Hsp70 subfamily B suppressor 1-like protein						signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AGACATAGTTAAAAAAAAAAT	0.294													5	3	---	---	---	---	
IFNGR1	3459	broad.mit.edu	37	6	137521826	137521826	+	Intron	DEL	A	-	-	rs75396334		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137521826delA	uc003qho.2	-						IFNGR1_uc011edm.1_Intron	NM_000416	NP_000407	P15260	INGR1_HUMAN	interferon gamma receptor 1 precursor						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)	CCCTGAGAATAAAAAAAAAAA	0.209													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	142973401	142973401	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142973401delG								LOC153910 (14375 upstream) : HIVEP2 (99204 downstream)																							TCAGCCACTTGGGGAATGGTA	0.408													4	2	---	---	---	---	
AIG1	51390	broad.mit.edu	37	6	143544614	143544614	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143544614delT	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron	NM_016108	NP_057192	Q9NVV5	AIG1_HUMAN	androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)		AATGAATTAATTTTTTTTCAA	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145440755	145440755	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145440755delC								UTRN (266587 upstream) : EPM2A (505691 downstream)																							catcatccatcccagtcatcc	0.000													4	2	---	---	---	---	
SHPRH	257218	broad.mit.edu	37	6	146215051	146215051	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146215051delA	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a						DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TTCCTGTACTAAAAAAAAAAA	0.368													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	146773509	146773509	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146773509delC								GRM1 (14778 upstream) : RAB32 (91319 downstream)																							gctgaaggagccagggaacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148217753	148217753	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148217753delT								SAMD5 (326596 upstream) : SASH1 (445976 downstream)																							CAGATTGTAATTTTTAAAGTA	0.338													4	2	---	---	---	---	
MLLT4	4301	broad.mit.edu	37	6	168276400	168276400	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168276400delA	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		TACAGCTCTTAAAAAAAAaaa	0.184			T	MLL	AL								6	5	---	---	---	---	
KIF25	3834	broad.mit.edu	37	6	168430556	168430556	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168430556delA	uc003qwk.1	+						KIF25_uc003qwl.1_Intron	NM_030615	NP_085118	Q9UIL4	KIF25_HUMAN	kinesin family member 25 isoform 1						microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		AACACCTCATAAGGGTCCCCT	0.468													1	6	---	---	---	---	
ICA1	3382	broad.mit.edu	37	7	8192295	8192295	+	Intron	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8192295delC	uc003srm.2	-						ICA1_uc010ktr.2_Intron|ICA1_uc003srl.2_Intron|ICA1_uc003srn.3_Intron|ICA1_uc003srp.3_Intron|ICA1_uc010kts.2_Intron|ICA1_uc003srq.2_Intron|ICA1_uc003srr.2_Intron|ICA1_uc003sro.3_Intron	NM_022307	NP_071682	Q05084	ICA69_HUMAN	islet cell autoantigen 1						neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		accaccaccaccaccattatc	0.000													3	3	---	---	---	---	
ICA1	3382	broad.mit.edu	37	7	8192298	8192299	+	Intron	DEL	CC	-	-	rs147378008	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8192298_8192299delCC	uc003srm.2	-						ICA1_uc010ktr.2_Intron|ICA1_uc003srl.2_Intron|ICA1_uc003srn.3_Intron|ICA1_uc003srp.3_Intron|ICA1_uc010kts.2_Intron|ICA1_uc003srq.2_Intron|ICA1_uc003srr.2_Intron|ICA1_uc003sro.3_Intron	NM_022307	NP_071682	Q05084	ICA69_HUMAN	islet cell autoantigen 1						neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		accaccaccaccattatctcct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	22576823	22576824	+	IGR	INS	-	TCTTT	TCTTT	rs150939033	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22576823_22576824insTCTTT								MGC87042 (37025 upstream) : IL6 (188679 downstream)																							actgcattttctcttttctttt	0.005													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	25771145	25771147	+	IGR	DEL	TCT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25771145_25771147delTCT								NPVF (503040 upstream) : MIR148A (218392 downstream)																							CATCTCCTCCTCTACACTGTTTT	0.374													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	27229919	27229919	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27229919delG								HOXA11AS (1007 upstream) : HOXA13 (6580 downstream)																							TCATTATTTTGCCTCCTCCTG	0.468													4	2	---	---	---	---	
HIBADH	11112	broad.mit.edu	37	7	27669327	27669328	+	Intron	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27669327_27669328insA	uc003szf.2	-						HIBADH_uc003szg.2_Intron|HIBADH_uc003szh.2_Intron|HIBADH_uc003szi.2_Intron	NM_152740	NP_689953	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase precursor						branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)	TCAAAAGATCCAAAAAAAACCT	0.257													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53405864	53405864	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53405864delT								POM121L12 (301247 upstream) : HPVC1 (863053 downstream)																							tctgccttcctttttttttca	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57921217	57921217	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57921217delA								ZNF716 (387952 upstream) : None (None downstream)																							TTTTGATGATAAAATTTAAAA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68308235	68308235	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68308235delT								None (None upstream) : AUTS2 (755670 downstream)																							TCTTTTTTTATTTTTGGCAGT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	77642840	77642840	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77642840delC								PHTF2 (56022 upstream) : MAGI2 (3535 downstream)																							CTGCTTTCATCCCCGCCCTCC	0.468													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78248126	78248126	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78248126delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				atctggaatcaaaaaaagtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	86247868	86247868	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86247868delT								None (None upstream) : GRM3 (25362 downstream)																							cacatccttattttttgtggt	0.000													4	2	---	---	---	---	
ANKIB1	54467	broad.mit.edu	37	7	92020810	92020810	+	Intron	DEL	T	-	-	rs11311575		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92020810delT	uc003ulw.2	+						ANKIB1_uc010lew.1_Intron	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TTTTTGGTGATTTTTTTTTTC	0.279													6	3	---	---	---	---	
BAIAP2L1	55971	broad.mit.edu	37	7	97944937	97944938	+	Intron	INS	-	TAAT	TAAT	rs80039560		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97944937_97944938insTAAT	uc003upj.2	-							NM_018842	NP_061330	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			aaaaaaaaaaaaataataataa	0.361													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	99586062	99586067	+	Intron	DEL	CTTTTT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99586062_99586067delCTTTTT	uc003usi.2	+											RecName: Full=Putative zinc-alpha-2-glycoprotein-like 2; Flags: Precursor;																		TTTTTTCTTCCtttttcttttttttt	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	135545437	135545437	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135545437delC								FAM180A (111843 upstream) : LUZP6 (66068 downstream)																							TGATGTGTCACCCAGAATTCT	0.413													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	146681544	146681544	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146681544delT	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TTTCACTTTATTTTTTTTTCT	0.299										HNSCC(39;0.1)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	150521429	150521429	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150521429delC								TMEM176A (19221 upstream) : ABP1 (4640 downstream)																							GTGGTGCTATCCCCAGTGAGC	0.383													4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152104993	152104994	+	Intron	DEL	TC	-	-	rs146856728		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152104993_152104994delTC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		TTAAAATTTATCTTGTTAGAAT	0.262			N		medulloblastoma								5	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152111936	152111936	+	Intron	DEL	T	-	-	rs113511589		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152111936delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		ACtttctttcttttttttttt	0.050			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153058294	153058294	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153058294delT								ACTR3B (505831 upstream) : DPP6 (526125 downstream)																							TCATTTTTCCTTTTTTTTTTT	0.328													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155909590	155909591	+	IGR	INS	-	AG	AG	rs143980334	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155909590_155909591insAG								SHH (304623 upstream) : C7orf4 (423594 downstream)																							aacagagagaaagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	8142562	8142563	+	IGR	INS	-	T	T	rs139776077	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8142562_8142563insT								FLJ10661 (40176 upstream) : SGK223 (32696 downstream)																							ttccaggtccgttggctcgggc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9247518	9247518	+	IGR	DEL	T	-	-	rs10712880		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9247518delT								PPP1R3B (238434 upstream) : TNKS (165927 downstream)																							GCAAAGAGAATTTTTTTTTTT	0.443													3	3	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	14187368	14187369	+	Intron	INS	-	T	T	rs141254624	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14187368_14187369insT	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		tttgtatttgcttttttttCAT	0.243													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23028151	23028151	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23028151delG								TNFRSF10D (6611 upstream) : TNFRSF10A (20820 downstream)																							gcctcggggtggggggaacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	23491832	23491832	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23491832delT								SLC25A37 (61771 upstream) : NKX3-1 (44375 downstream)																							AAAATTTAGATTTTTTTGGTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	24906565	24906566	+	IGR	DEL	AA	-	-	rs10569667		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24906565_24906566delAA								NEFL (92434 upstream) : DOCK5 (135721 downstream)																							TGCGAGAAACAAAGTGATGTTT	0.446													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30094472	30094472	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30094472delA								DCTN6 (53413 upstream) : RBPMS (147472 downstream)																							ttatctccagaaaaatctaaa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	39925564	39925564	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39925564delT								IDO2 (51654 upstream) : C8orf4 (85425 downstream)																							ctctatgccctttctcttttg	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	50710226	50710226	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50710226delG								C8orf22 (721585 upstream) : SNTG1 (112123 downstream)																							acctgggaaagggtggagaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54111444	54111461	+	IGR	DEL	TGTGTGTGTGTGTGTGTG	-	-	rs10583066		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54111444_54111461delTGTGTGTGTGTGTGTGTG								NPBWR1 (257991 upstream) : OPRK1 (26815 downstream)																							Agtgtgtgtttgtgtgtgtgtgtgtgtgtgtgtgtgtg	0.252													3	5	---	---	---	---	
PLAG1	5324	broad.mit.edu	37	8	57107136	57107137	+	Intron	DEL	GT	-	-	rs36079543	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57107136_57107137delGT	uc003xsr.3	-						PLAG1_uc010lyi.2_Intron|PLAG1_uc010lyj.2_Intron	NM_002655	NP_002646	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1 isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding		CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3)	salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1)	129		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)			TCAGCACTGGgtgtgtgtgtgt	0.332			T	TCEA1|LIFR|CTNNB1|CHCHD7	salivary adenoma								7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	57975050	57975051	+	IGR	INS	-	A	A	rs35021183		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57975050_57975051insA								IMPAD1 (68623 upstream) : C8orf71 (217051 downstream)																							ACAATCCCCTTAAAAAAAAAAA	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58169037	58169038	+	IGR	INS	-	C	C	rs148837861	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58169037_58169038insC								IMPAD1 (262610 upstream) : C8orf71 (23064 downstream)																							TCAGCTCAGCACTGCTGGTCAT	0.455													4	2	---	---	---	---	
TOX	9760	broad.mit.edu	37	8	59976458	59976459	+	Intron	DEL	TG	-	-	rs35691859		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59976458_59976459delTG	uc003xtw.1	-							NM_014729	NP_055544	O94900	TOX_HUMAN	thymus high mobility group box protein TOX							nucleus	DNA binding			kidney(2)|lung(1)|skin(1)	4		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				AAATCAtgtatgtgtgtgtgtg	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60461565	60461565	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60461565delG								TOX (429798 upstream) : CA8 (639858 downstream)																							GTGAGAGTGAGAAGGAAATAC	0.299													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65060392	65060394	+	IGR	DEL	CAC	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65060392_65060394delCAC								YTHDF3 (935047 upstream) : MIR124-2 (231312 downstream)																							gccttcaagtcaccaccaccacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	68829281	68829281	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68829281delT								CPA6 (170661 upstream) : PREX2 (35067 downstream)																							CTCTCCCTGGTTTTTTATTCT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	80488125	80488125	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80488125delT								IL7 (770367 upstream) : STMN2 (35255 downstream)																							CAAAAAGAGCTTTTTTTTTCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	82437068	82437069	+	IGR	INS	-	TAT	TAT	rs149791527	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82437068_82437069insTAT								FABP4 (41595 upstream) : FABP12 (214 downstream)																							CTCTCTGAAAATATCCCAGCCT	0.371													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	89614252	89614252	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89614252delT								MMP16 (274535 upstream) : None (None downstream)																							CAATTTATGCTTTTTATTTCC	0.254													4	2	---	---	---	---	
PGCP	10404	broad.mit.edu	37	8	98067604	98067604	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98067604delT	uc003yhw.2	+							NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)					ATAGAGATGGTTTTGTGGCTA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98421669	98421669	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98421669delC								TSPYL5 (131493 upstream) : MTDH (234738 downstream)																							agcaccacAGCCTCAGAAAAC	0.229													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98864930	98864930	+	IGR	DEL	G	-	-	rs35775446		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98864930delG								LAPTM4B (101 upstream) : MATN2 (16381 downstream)																							GCTTTTTTTTGGGGGGGGGAG	0.403													6	3	---	---	---	---	
SAMD12	401474	broad.mit.edu	37	8	119404180	119404180	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119404180delA	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			AGTTCTGGTTAAAAAAAAAAA	0.184													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	132766150	132766152	+	IGR	DEL	CAT	-	-	rs145399072	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132766150_132766152delCAT								ADCY8 (713315 upstream) : EFR3A (150207 downstream)																							tcaccatcaccatcatcatcatc	0.399													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	134730711	134730711	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134730711delG								ST3GAL1 (146528 upstream) : ZFAT (759322 downstream)																							ACTGGTTTTTGGGTTTTTTTT	0.333													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139587564	139587565	+	IGR	INS	-	T	T	rs113755820		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139587564_139587565insT								FAM135B (78499 upstream) : COL22A1 (12914 downstream)																							CCTGACTTAACTTTTTTTTTTT	0.436													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141167143	141167143	+	Intron	DEL	T	-	-	rs67192772		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141167143delT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						AAAGCCTCCCTTTTCCATTCA	0.458													5	4	---	---	---	---	
ZC3H3	23144	broad.mit.edu	37	8	144554414	144554414	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144554414delG	uc003yyd.2	-							NM_015117	NP_055932	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3						mRNA polyadenylation|poly(A)+ mRNA export from nucleus|regulation of mRNA export from nucleus	nucleus	nucleic acid binding|zinc ion binding			skin(1)	1	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			CAGAAGGGCTGGGGGAACCAG	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	3127123	3127123	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3127123delC								KIAA0020 (282993 upstream) : RFX3 (97526 downstream)																							tacttttgcaccaacctaaTA	0.259													4	2	---	---	---	---	
KIAA2026	158358	broad.mit.edu	37	9	5974119	5974119	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5974119delA	uc003zjq.3	-							NM_001017969	NP_001017969	Q5HYC2	K2026_HUMAN	hypothetical protein LOC158358											ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		agacatacacaaaaaaaatct	0.000													4	2	---	---	---	---	
GLDC	2731	broad.mit.edu	37	9	6609559	6609560	+	Intron	DEL	TG	-	-	rs7030089		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6609559_6609560delTG	uc003zkc.2	-							NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	CACTCAGTCATGTGTGTGTGTT	0.550													4	2	---	---	---	---	
FREM1	158326	broad.mit.edu	37	9	14890108	14890108	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14890108delG	uc003zlm.2	-						FREM1_uc010mic.2_Intron	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor						cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)		ctgctgttcaggggagaaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	14978697	14978697	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14978697delT								FREM1 (67704 upstream) : LOC389705 (14628 downstream)																							ggttgtgcaatttttttttta	0.343													4	2	---	---	---	---	
CNTLN	54875	broad.mit.edu	37	9	17308889	17308890	+	Intron	INS	-	T	T	rs144083775	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17308889_17308890insT	uc003zmz.2	+						CNTLN_uc003zmy.2_Intron|CNTLN_uc010mio.2_Intron	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)		taaattagttattttttGTGTT	0.178													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22511122	22511122	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22511122delA								DMRTA1 (58650 upstream) : None (None downstream)																							TAGAATCTAGAAAAAAAAAGT	0.264													4	2	---	---	---	---	
MOBKL2B	79817	broad.mit.edu	37	9	27454967	27454967	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27454967delT	uc003zqn.2	-							NM_024761	NP_079037	Q86TA1	MOL2B_HUMAN	MOB1, Mps One Binder kinase activator-like 2B								metal ion binding|protein binding			ovary(1)|pleura(1)	2		all_neural(11;9.12e-11)		Lung(218;6.54e-05)|LUSC - Lung squamous cell carcinoma(38;0.000397)		gtccataaagttttttttttc	0.239													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	27944891	27944892	+	5'Flank	DEL	TC	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27944891_27944892delTC	uc003zqt.2	-											Homo sapiens mRNA; cDNA DKFZp686E1944 (from clone DKFZp686E1944).																		TCAGTGAAAGTCAAGGAAGAAC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	47188452	47188453	+	IGR	DEL	CA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:47188452_47188453delCA								KGFLP1 (440067 upstream) : None (None downstream)																							gcacataaaccacacacacaaa	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66481125	66481125	+	IGR	DEL	G	-	-	rs2220719	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66481125delG								FAM74A4 (986739 upstream) : LOC442421 (15345 downstream)																							ttaagggtttgttgtgtctct	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69059945	69059945	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69059945delG								MIR1299 (57624 upstream) : PGM5P2 (20300 downstream)																							TTGTAATTTTGGGGGGGTTCT	0.284													6	3	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668426	71668427	+	Intron	INS	-	GG	GG	rs58150402	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668426_71668427insGG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						gatggatggatagatagataga	0.059													3	3	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668427	71668428	+	Intron	INS	-	TG	TG	rs75408130	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668427_71668428insTG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						atggatggatagatagatagat	0.059													3	3	---	---	---	---	
TRPM6	140803	broad.mit.edu	37	9	77422624	77422624	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77422624delA	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,						response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						aaaagaaaagaaaaaaaaaga	0.299													4	2	---	---	---	---	
BARX1	56033	broad.mit.edu	37	9	96715495	96715495	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96715495delG	uc010mrh.2	-						BARX1_uc004aud.2_5'UTR	NM_021570	NP_067545	Q9HBU1	BARX1_HUMAN	BARX homeobox 1							nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						ATGAGGACCCGGGTGAGCTAC	0.687													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	105585656	105585656	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105585656delT								None (None upstream) : CYLC2 (171937 downstream)																							CTTTGTAATGTTTTTTAGTGT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107366673	107366673	+	IGR	DEL	A	-	-	rs75507694		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107366673delA								OR13C5 (4979 upstream) : OR13C2 (280 downstream)																							TCCAATGCAGAAAAAAAAACC	0.328													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	120002787	120002787	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120002787delA	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						ggagcagagtaagaaagggga	0.269													4	2	---	---	---	---	
FAM125B	89853	broad.mit.edu	37	9	129146379	129146379	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129146379delA	uc004bqh.1	+						FAM125B_uc004bqg.1_Intron|FAM125B_uc011lzy.1_Intron|FAM125B_uc010mxd.2_Intron|FAM125B_uc011lzz.1_Intron	NM_033446	NP_258257	Q9H7P6	F125B_HUMAN	hypothetical protein LOC89853 isoform 1						protein transport	late endosome membrane					0						AACTGCCATGAAAAAAAATTA	0.408													4	2	---	---	---	---	
GARNL3	84253	broad.mit.edu	37	9	130076035	130076035	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130076035delA	uc011mae.1	+						GARNL3_uc011mad.1_Intron	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						TGGCCTTTTGAAAAAAAAAAA	0.244													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	136461853	136461853	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136461853delG								FAM163B (16508 upstream) : DBH (39632 downstream)																							gctgctccgtgggggaccgtg	0.000													4	2	---	---	---	---	
RXRA	6256	broad.mit.edu	37	9	137236550	137236550	+	Intron	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137236550delC	uc004cfb.2	+						RXRA_uc004cfa.1_Intron	NM_002957	NP_002948	P19793	RXRA_HUMAN	retinoid X receptor, alpha						cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)	GCCACGGACGCCCCTTCATCC	0.642													4	2	---	---	---	---	
NACC2	138151	broad.mit.edu	37	9	138907998	138907999	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138907998_138907999insT	uc004cgw.2	-						NACC2_uc010nbh.2_Intron	NM_144653	NP_653254	Q96BF6	NACC2_HUMAN	BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0						GAAATTTAAGATTTTTTTTTTG	0.307													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2168240	2168240	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2168240delA								ADARB2 (388522 upstream) : PFKP (941512 downstream)																							tgggtggAATAGGGGATTGTG	0.045													4	2	---	---	---	---	
PFKFB3	5209	broad.mit.edu	37	10	6212562	6212562	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6212562delG	uc010qaw.1	+						PFKFB3_uc001ijd.2_Intron|PFKFB3_uc009xii.2_Intron	NM_001145443	NP_001138915	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3						AAAAATCCATGGGGTCATTGA	0.333													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11326377	11326378	+	Intron	DEL	TG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11326377_11326378delTG	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbk.1_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc010qbo.1_Intron|CELF2_uc010qbp.1_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						gatggatgactgtgtggtaggt	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11920610	11920610	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11920610delT	uc001iky.1	-											Homo sapiens cDNA FLJ32141 fis, clone PLACE5000067.																		aaccagatcctcctggtttca	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	16474188	16474188	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16474188delT								FAM188A (571669 upstream) : PTER (4779 downstream)																							TAGGTCCTGCTTTTTTTTCCT	0.323													3	4	---	---	---	---	
MSRB2	22921	broad.mit.edu	37	10	23409435	23409435	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23409435delT	uc001iro.2	+							NM_012228	NP_036360	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2 precursor						protein repair	mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0					L-Methionine(DB00134)	attatccccatttttagatga	0.085													4	2	---	---	---	---	
MYO3A	53904	broad.mit.edu	37	10	26407957	26407957	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26407957delT	uc001isn.2	+						MYO3A_uc009xko.1_Intron|MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						cctcaccctcttccagccctc	0.000													4	2	---	---	---	---	
KIF5B	3799	broad.mit.edu	37	10	32298588	32298588	+	3'UTR	DEL	A	-	-	rs71651785		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32298588delA	uc001iwe.3	-	26						NM_004521	NP_004512	P33176	KINH_HUMAN	kinesin family member 5B						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)				GAAAAAAGAGAAAAAAAAATT	0.333													4	2	---	---	---	---	
C10orf68	79741	broad.mit.edu	37	10	32913751	32913751	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32913751delG	uc001iwn.3	+						C10orf68_uc001iwl.1_Intron|C10orf68_uc001iwm.1_Intron	NM_024688	NP_078964	Q9H943	CJ068_HUMAN	chromosome 10 open reading frame 68											skin(2)|ovary(1)	3						agtctattttggtcatttgcc	0.090													4	2	---	---	---	---	
GPRIN2	9721	broad.mit.edu	37	10	46991245	46991245	+	5'Flank	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46991245delC	uc001jec.2	+							NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth												0						gagctgagagccccaggtttg	0.214													4	2	---	---	---	---	
FRMPD2	143162	broad.mit.edu	37	10	49419161	49419161	+	Intron	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49419161delC	uc001jgi.2	-						FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3						tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		CCGCAGTCCTCCCCACAAGAC	0.507													4	2	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	56076865	56076867	+	Intron	DEL	AAA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56076865_56076867delAAA	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				TCTTTGTGTTAAAAATGTATTCA	0.236										HNSCC(58;0.16)			9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	57639068	57639068	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57639068delT								PCDH15 (251366 upstream) : ZWINT (478131 downstream)																							ctCtttgaagttttttttttt	0.050													4	2	---	---	---	---	
HERC4	26091	broad.mit.edu	37	10	69701067	69701068	+	Intron	DEL	AA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69701067_69701068delAA	uc001jng.3	-						HERC4_uc009xpq.2_Intron|HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron	NM_022079	NP_071362	Q5GLZ8	HERC4_HUMAN	hect domain and RLD 4 isoform a						cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3						tctCAGACTTAAAAAAAATATA	0.168													4	2	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73303708	73303708	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73303708delA	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jrv.2_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						TGAGAAGGAGAAAAAAAAAAG	0.453													3	3	---	---	---	---	
CYP17A1	1586	broad.mit.edu	37	10	104590294	104590294	+	3'UTR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104590294delA	uc001kwg.2	-	8					C10orf26_uc009xxg.1_Intron	NM_000102	NP_000093	P05093	CP17A_HUMAN	cytochrome P450, family 17						androgen biosynthetic process|glucocorticoid biosynthetic process|sex differentiation|xenobiotic metabolic process	endoplasmic reticulum membrane	electron carrier activity|heme binding|oxygen binding|steroid 17-alpha-monooxygenase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	NADH(DB00157)|Progesterone(DB00396)	GACCTTATGGAAAAAAAAAAA	0.318													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107057281	107057281	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107057281delA								SORCS3 (32288 upstream) : None (None downstream)																							agagaattctaaaaacagaaa	0.000													4	2	---	---	---	---	
HABP2	3026	broad.mit.edu	37	10	115334697	115334698	+	Intron	DEL	TA	-	-	rs4244309	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115334697_115334698delTA	uc001lai.3	+						HABP2_uc010qrz.1_Intron|HABP2_uc010qry.1_Intron	NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein						cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)		tgtgtgtgtgtatgtgtgcata	0.342													4	2	---	---	---	---	
ATRNL1	26033	broad.mit.edu	37	10	117653475	117653476	+	Intron	INS	-	AA	AA			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117653475_117653476insAA	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		AAGAATGGACCAAAAAAAAAAA	0.381													4	2	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127586308	127586309	+	Intron	INS	-	T	T	rs33969384		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127586308_127586309insT	uc001ljh.3	+						DHX32_uc001ljg.1_5'Flank|FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				TGGATTCTACATTTTTTTAACC	0.342													6	5	---	---	---	---	
C10orf90	118611	broad.mit.edu	37	10	128331317	128331317	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128331317delT	uc010qum.1	-						C10orf90_uc009yao.2_Intron	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		gacctgtctcttgatctctat	0.000													4	2	---	---	---	---	
TMEM9B	56674	broad.mit.edu	37	11	8975054	8975054	+	Intron	DEL	A	-	-	rs3833779		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8975054delA	uc001mhe.1	-						TMEM9B_uc001mhf.1_Intron|TMEM9B_uc010rbt.1_Intron	NM_020644	NP_065695	Q9NQ34	TMM9B_HUMAN	TMEM9 domain family, member B precursor						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity				0				Epithelial(150;4.39e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0237)		ATTATTTAAGAAAAAAAGAGG	0.353													7	6	---	---	---	---	
CTR9	9646	broad.mit.edu	37	11	10780260	10780260	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10780260delT	uc001mja.2	+							NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1						histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		aatttctgcctttttttttct	0.000													4	4	---	---	---	---	
PDE3B	5140	broad.mit.edu	37	11	14854498	14854498	+	Intron	DEL	T	-	-	rs80137325		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14854498delT	uc001mln.2	+						PDE3B_uc010rcr.1_Intron	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B						cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0						TGAAAttttcttttttttttt	0.129													6	4	---	---	---	---	
SERGEF	26297	broad.mit.edu	37	11	17840682	17840682	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17840682delT	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron	NM_012139	NP_036271	Q9UGK8	SRGEF_HUMAN	deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1						tgaagactcctttttaatatc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28014071	28014071	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28014071delA								BDNF (270466 upstream) : KIF18A (28092 downstream)																							agccaaaaacaaagggaaaaa	0.000													4	2	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40584485	40584485	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40584485delT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)				actcctttccttttttttttt	0.000													7	4	---	---	---	---	
MS4A10	341116	broad.mit.edu	37	11	60553663	60553664	+	Intron	DEL	CA	-	-	rs559157		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60553663_60553664delCA	uc001npz.1	+							NM_206893	NP_996776	Q96PG2	M4A10_HUMAN	membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity			ovary(1)|skin(1)	2						cacacacacgcacacacacaca	0.347													4	4	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	69971958	69971959	+	Intron	DEL	AC	-	-	rs10792912		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69971958_69971959delAC	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						tcaaaaaaaaacaaaaaaagag	0.262													3	3	---	---	---	---	
NADSYN1	55191	broad.mit.edu	37	11	71211634	71211634	+	Intron	DEL	A	-	-	rs11354381		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71211634delA	uc001oqn.2	+						NADSYN1_uc001oqo.2_Intron|NADSYN1_uc001oqp.2_Intron	NM_018161	NP_060631	Q6IA69	NADE_HUMAN	NAD synthetase 1						NAD biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	aggaatgctgAACATTTGGGA	0.224													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79895991	79895991	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79895991delT								ODZ4 (744296 upstream) : None (None downstream)																							gctcttcaccttacattctgt	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	89546381	89546382	+	IGR	DEL	CT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89546381_89546382delCT								TRIM49 (4638 upstream) : TRIM53 (28844 downstream)																							CACCTATAGGCTAAGTGGATAC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	117815519	117815519	+	IGR	DEL	C	-	-	rs72153165		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117815519delC								TMPRSS13 (15404 upstream) : IL10RA (41587 downstream)																							GAAGCTCAGGCCAATAAGAGG	0.488													2	5	---	---	---	---	
FOXR1	283150	broad.mit.edu	37	11	118850570	118850570	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118850570delT	uc001pui.2	+						FOXR1_uc001puj.2_Intron|FOXR1_uc001puk.2_Intron	NM_181721	NP_859072	Q6PIV2	FOXR1_HUMAN	forkhead box R1						embryo development|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		ATGGCTTTAGTTTTTTTTTTC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	120862683	120862684	+	IGR	DEL	TG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120862683_120862684delTG								GRIK4 (5714 upstream) : TBCEL (32119 downstream)																							TTCCTGCCACtgtgtgtgtgtg	0.119													3	3	---	---	---	---	
EI24	9538	broad.mit.edu	37	11	125452094	125452095	+	Intron	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125452094_125452095insA	uc001qca.2	+						EI24_uc001qcb.2_Intron|EI24_uc010sbd.1_Intron|EI24_uc009zbl.2_Intron|EI24_uc001qcc.2_Intron|EI24_uc010sbe.1_Intron|EI24_uc010sbf.1_Intron	NM_004879	NP_004870	O14681	EI24_HUMAN	etoposide induced 2.4 isoform 1						apoptosis|autophagy|induction of apoptosis|negative regulation of cell growth	endoplasmic reticulum membrane|integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		gactccatctcaaaaaaaaaaa	0.149													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134649632	134649633	+	IGR	INS	-	G	G	rs148146723	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134649632_134649633insG								B3GAT1 (367820 upstream) : None (None downstream)																							GGGGAGTCAAATTTCCTGGACA	0.406													2	4	---	---	---	---	
ZNF384	171017	broad.mit.edu	37	12	6782014	6782014	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6782014delG	uc010sfh.1	-						ZNF384_uc001qpz.2_Intron|ZNF384_uc001qqa.2_Intron|ZNF384_uc001qqb.2_Intron|ZNF384_uc001qqc.2_Intron|ZNF384_uc001qqd.2_Intron|ZNF384_uc001qqe.2_Intron	NM_001135734	NP_001129206	Q8TF68	ZN384_HUMAN	nuclear matrix transcription factor 4 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/ZNF384(4)	haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1)	8						CAGACACCCTGCTTCCAAATA	0.458			T	EWSR1|TAF15 	ALL								4	2	---	---	---	---	
CLEC7A	64581	broad.mit.edu	37	12	10271430	10271430	+	Intron	DEL	A	-	-	rs11053598	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10271430delA	uc001qxg.2	-						CLEC7A_uc001qxe.3_Intron|CLEC7A_uc001qxf.2_Intron|CLEC7A_uc001qxh.2_Intron|CLEC7A_uc001qxi.2_Intron|CLEC7A_uc001qxj.2_Intron|CLEC7A_uc009zhg.1_Intron|CLEC7A_uc001qxk.1_Intron	NM_197947	NP_922938	Q9BXN2	CLC7A_HUMAN	dendritic cell-associated C-type lectin 1						carbohydrate mediated signaling|defense response to protozoan|inflammatory response|innate immune response|phagocytosis, recognition|T cell activation	cytoplasm|integral to membrane	metal ion binding|MHC protein binding|sugar binding			central_nervous_system(1)	1						TGCATAAACTAAAAAAAAAGT	0.259													4	2	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11417378	11417378	+	Intron	DEL	A	-	-	rs12305020	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11417378delA	uc001qzf.1	-							NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						tgtgtgttttaaaaaaaaatg	0.000										HNSCC(22;0.051)			4	2	---	---	---	---	
KIAA0528	9847	broad.mit.edu	37	12	22642785	22642785	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22642785delA	uc001rfq.2	-						KIAA0528_uc010sir.1_Intron|KIAA0528_uc010sis.1_Intron|KIAA0528_uc010sit.1_Intron|KIAA0528_uc010siu.1_Intron|KIAA0528_uc001rfr.2_Intron|KIAA0528_uc009ziy.1_Intron	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847								protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						ATGACAAAGCAAAAAAAAATG	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	45863281	45863281	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45863281delC								ANO6 (29094 upstream) : LOC400027 (256529 downstream)																							cctcttctttcccgcccatgg	0.000													4	2	---	---	---	---	
LARP4	113251	broad.mit.edu	37	12	50861115	50861115	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50861115delT	uc001rwp.1	+						LARP4_uc001rwo.1_Intron|LARP4_uc001rwq.1_Intron|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Intron|LARP4_uc009zlr.1_Intron|LARP4_uc001rwt.1_Intron	NM_052879	NP_443111	Q71RC2	LARP4_HUMAN	c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1						CATGTCTTTGTTTTTTTTTTT	0.159													4	4	---	---	---	---	
KRT85	3891	broad.mit.edu	37	12	52755631	52755631	+	Intron	DEL	G	-	-	rs3837477		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52755631delG	uc001sag.2	-							NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85						epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		AATGCATATAGAAGTGCATCA	0.383													2	4	---	---	---	---	
SMARCC2	6601	broad.mit.edu	37	12	56562166	56562166	+	Intron	DEL	T	-	-	rs72399911		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56562166delT	uc001skb.2	-						SMARCC2_uc001skd.2_Intron|SMARCC2_uc001ska.2_Intron|SMARCC2_uc001skc.2_Intron|SMARCC2_uc010sqf.1_Intron	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)			ttcttttttcttttttttttt	0.104													4	3	---	---	---	---	
MON2	23041	broad.mit.edu	37	12	62861377	62861377	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62861377delT	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srd.1_Intron	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		CACTAGCCTATTCTGGCCTTT	0.433													4	2	---	---	---	---	
MDM2	4193	broad.mit.edu	37	12	69217911	69217912	+	Intron	DEL	AC	-	-	rs141572036		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69217911_69217912delAC	uc001sui.2	+						MDM2_uc009zri.2_Intron|MDM2_uc009zqx.2_Intron|MDM2_uc009zqw.2_Intron|MDM2_uc001suk.2_Intron|MDM2_uc009zqy.1_Intron|MDM2_uc001sun.3_Intron|MDM2_uc009zqz.2_Intron|MDM2_uc009zra.2_Intron|MDM2_uc001sum.1_Intron|MDM2_uc009zrd.2_Intron|MDM2_uc009zrc.2_Intron|MDM2_uc009zre.2_Intron|MDM2_uc009zrf.2_Intron|MDM2_uc001suo.2_Intron|MDM2_uc009zrg.2_Intron|MDM2_uc009zrh.2_Intron	NM_002392	NP_002383	Q00987	MDM2_HUMAN	mouse double minute 2 homolog isoform MDM2						cellular response to hypoxia|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|establishment of protein localization|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein complex assembly|protein destabilization|protein localization to nucleus|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to antibiotic|synaptic transmission	cytosol|endocytic vesicle membrane|insoluble fraction|nucleolus|nucleoplasm|plasma membrane|protein complex	enzyme binding|identical protein binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|central_nervous_system(1)	3	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			AATTTATCTAACAGTCTTTTAA	0.317			A		sarcoma|glioma|colorectal|other								4	2	---	---	---	---	
ZDHHC17	23390	broad.mit.edu	37	12	77239826	77239826	+	Intron	DEL	T	-	-	rs57863212		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77239826delT	uc001syk.1	+							NM_015336	NP_056151	Q8IUH5	ZDH17_HUMAN	huntingtin interacting protein 14						lipoprotein transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|protein binding|protein-cysteine S-palmitoleyltransferase activity|signal transducer activity|zinc ion binding				0						GGAGGCAAAATTTTTTTTTTC	0.363													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	88718691	88718692	+	IGR	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88718691_88718692insA								TMTC3 (125028 upstream) : KITLG (167877 downstream)																							TTTTCTTATTTAAAAAATGCCT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106427085	106427086	+	IGR	DEL	CT	-	-	rs112934836		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106427085_106427086delCT								C12orf75 (661790 upstream) : NUAK1 (30039 downstream)																							TGACCATGGCCTCTCTGTCTGG	0.470													3	3	---	---	---	---	
MYO1H	283446	broad.mit.edu	37	12	109849410	109849411	+	Intron	INS	-	TGGCATTAAGC	TGGCATTAAGC	rs146395725	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109849410_109849411insTGGCATTAAGC	uc010sxn.1	+							NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H							myosin complex	motor activity				0						GAAAACGAGGTTGGTCATAGTA	0.441													4	5	---	---	---	---	
VPS29	51699	broad.mit.edu	37	12	110931168	110931168	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110931168delT	uc001tqy.2	-						VPS29_uc001tqw.2_Intron|VPS29_uc001tqx.2_Intron|VPS29_uc001tqz.2_Intron	NM_016226	NP_057310	Q9UBQ0	VPS29_HUMAN	vacuolar protein sorting 29 isoform 1						protein transport	endosome membrane	metal ion binding|phosphoserine phosphatase activity				0						CATTTATACAttttttttttt	0.144													5	3	---	---	---	---	
PPTC7	160760	broad.mit.edu	37	12	110975107	110975107	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110975107delA	uc001trh.1	-							NM_139283	NP_644812	Q8NI37	PPTC7_HUMAN	T-cell activation protein phosphatase 2C								metal ion binding|phosphoprotein phosphatase activity				0						ACTGAAGCTTAAAAAAAAAAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116774548	116774548	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116774548delA								MED13L (59557 upstream) : NCRNA00173 (196679 downstream)																							tcaaacaaacaaaaaaaaGAT	0.224													3	3	---	---	---	---	
COQ5	84274	broad.mit.edu	37	12	120960838	120960838	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120960838delA	uc001tyn.2	-						COQ5_uc001tyo.2_Intron|COQ5_uc010szj.1_Intron	NM_032314	NP_115690	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase						ubiquinone biosynthetic process	mitochondrion	methyltransferase activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGATTCTTATAAAAAAAAAAG	0.249													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	124638082	124638082	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124638082delA								ZNF664 (138115 upstream) : FAM101A (135628 downstream)																							AATCCTATGTAAAAGGACCAG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127039813	127039814	+	IGR	INS	-	TGGC	TGGC			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127039813_127039814insTGGC								LOC100128554 (82483 upstream) : None (None downstream)																							atggtgggatgtggcttcttta	0.054													4	2	---	---	---	---	
TMEM132C	92293	broad.mit.edu	37	12	128901436	128901436	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128901436delT	uc001uhs.3	+							NM_001136103	NP_001129575	Q8N3T6	T132C_HUMAN	transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1						TCATGAACTCTTACATCTTTT	0.413													4	2	---	---	---	---	
GALNT9	50614	broad.mit.edu	37	12	132685940	132685941	+	Intron	INS	-	GGCCCCATCC	GGCCCCATCC	rs141720371	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132685940_132685941insGGCCCCATCC	uc001ukc.3	-						GALNT9_uc009zyr.2_Intron|GALNT9_uc001ukb.2_Intron|GALNT9_uc001uka.2_Intron	NM_001122636	NP_001116108	Q9HCQ5	GALT9_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		TCAGATGCTGAGGCCCCATCCA	0.629													2	4	---	---	---	---	
MTUS2	23281	broad.mit.edu	37	13	30068622	30068622	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30068622delT	uc001usl.3	+						MTUS2_uc001usm.3_Intron|MTUS2_uc010aau.2_Intron|MTUS2_uc010tdq.1_5'Flank	NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						TGTTGTTTTGTTTTTTTAATG	0.398													4	2	---	---	---	---	
TSC22D1	8848	broad.mit.edu	37	13	45038637	45038637	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45038637delT	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		TGATATAGTCTTTTTTTTTTC	0.274													4	3	---	---	---	---	
CPB2	1361	broad.mit.edu	37	13	46632101	46632102	+	Intron	INS	-	A	A	rs75807983	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46632101_46632102insA	uc001vaw.2	-						uc001vau.1_Intron|uc001vav.1_Intron|CPB2_uc001vax.2_Intron	NM_001872	NP_001863	Q96IY4	CBPB2_HUMAN	plasma carboxypeptidase B2 isoform a						blood coagulation|fibrinolysis|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		GCCCACGTGCTGAATAAAGTGT	0.426													5	4	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52754797	52754797	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52754797delA	uc001vgk.2	-						THSD1P1_uc001vgm.1_Intron|THSD1P1_uc010adx.1_Intron|THSD1P1_uc010ady.1_Intron|THSD1P1_uc001vgl.1_Intron					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						TTCCTAAGACaaaaaaaaaaa	0.234													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	55078713	55078714	+	IGR	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55078713_55078714insT								MIR1297 (192530 upstream) : None (None downstream)																							atcctcctacatttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	79557449	79557450	+	IGR	DEL	AG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79557449_79557450delAG								RNF219 (322749 upstream) : RBM26 (336650 downstream)																							CACTGAAGAAAGAGAGAGAGAG	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	81011451	81011452	+	IGR	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81011451_81011452insA								SPRY2 (96365 upstream) : None (None downstream)																							AATTTTCAGATATAAAAGTTTT	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	89970720	89970721	+	IGR	INS	-	AAAC	AAAC	rs137981916	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89970720_89970721insAAAC								None (None upstream) : MIR622 (912715 downstream)																							tctgtctcaaaaaacaaacaaa	0.084													6	3	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	101936112	101936112	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101936112delA	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Intron|NALCN_uc001vpa.2_Intron	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGTGTATGTTAAAAAAAAAAA	0.348													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107042178	107042180	+	IGR	DEL	TAT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107042178_107042180delTAT								DAOA (898796 upstream) : EFNB2 (99918 downstream)																							CATATAATGGTATTATTATTGCC	0.468													4	2	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	107857716	107857716	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107857716delA	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						CCAAACATTTAAAAAAAAAAT	0.408											OREG0022505	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
CARKD	55739	broad.mit.edu	37	13	111274384	111274384	+	Intron	DEL	A	-	-	rs140560266		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111274384delA	uc001vrb.2	+						CARKD_uc010tji.1_Intron|CARKD_uc010tjj.1_Intron|CARKD_uc001vqz.2_Intron|CARKD_uc001vra.2_Intron|CARKD_uc010tjk.1_Intron|CARKD_uc010tjl.1_Intron|CARKD_uc001vrc.2_Intron			Q8IW45	CARKD_HUMAN	RecName: Full=Carbohydrate kinase domain-containing protein; Flags: Precursor;											skin(1)	1						ctcaaaaaagaaaaaaaaaaT	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19408019	19408019	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19408019delA								OR11H12 (29447 upstream) : POTEG (145346 downstream)																							CTGTGGAGCCAAAAAAAAAAT	0.393													4	2	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	47424204	47424204	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47424204delA	uc001wwj.3	-						MDGA2_uc001wwi.3_Intron|MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						GATGGGACATAATGGGGTATA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51662138	51662138	+	IGR	DEL	G	-	-	rs35178236		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51662138delG								TRIM9 (99716 upstream) : TMX1 (44748 downstream)																							ctcaccacttgtctggtatct	0.000													1	6	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	78734007	78734007	+	Intron	DEL	A	-	-	rs34095466		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78734007delA	uc001xum.1	+									Q9Y4C0	NRX3A_HUMAN	Homo sapiens mRNA for KIAA0743 protein, partial cds.						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		actgtctcttaaaaaaaataa	0.194													4	4	---	---	---	---	
SMEK1	55671	broad.mit.edu	37	14	91937518	91937518	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91937518delT	uc001xzn.2	-						SMEK1_uc001xzm.2_Intron|SMEK1_uc001xzo.2_Intron|SMEK1_uc010atz.2_Intron|SMEK1_uc001xzp.1_Intron	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		ggtgctttacttttttttatt	0.075													4	2	---	---	---	---	
C14orf64	388011	broad.mit.edu	37	14	98425566	98425566	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98425566delG	uc001yfw.2	-						C14orf64_uc001yfx.2_Intron|C14orf64_uc001yfy.2_RNA|C14orf64_uc010avq.2_RNA	NR_015430				Homo sapiens cDNA FLJ34349 fis, clone FEBRA2011063.												0						gcactagagtgggaattcaga	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	104694369	104694369	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104694369delG								KIF26A (47135 upstream) : C14orf180 (351687 downstream)																							aggctactgtgggggctcaga	0.214													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106500393	106500393	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106500393delT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						GAACATATGCttttttttttg	0.244													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106573151	106573151	+	Intron	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106573151delC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						TGCTCAGTGTCCCGGGCGCCC	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20107044	20107044	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20107044delA								None (None upstream) : GOLGA6L6 (630050 downstream)																							GCCAATAAGGAAAAAAAAAGC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20121367	20121369	+	IGR	DEL	ATT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20121367_20121369delATT								None (None upstream) : GOLGA6L6 (615725 downstream)																							attacctgtcattgttgtacagc	0.069													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20557542	20557542	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20557542delG								None (None upstream) : GOLGA6L6 (179552 downstream)																							tctggaggctgggggcagatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20591212	20591214	+	Intron	DEL	AGA	-	-	rs141743877		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20591212_20591214delAGA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		TCTCAATGTCAGAAGAAGTATAA	0.300													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21918463	21918464	+	IGR	DEL	CA	-	-	rs150921370		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21918463_21918464delCA								NF1P1 (783838 upstream) : LOC646214 (14050 downstream)																							tttatttactcacagttccaga	0.074													4	6	---	---	---	---	
SCG5	6447	broad.mit.edu	37	15	32986510	32986510	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32986510delT	uc001zha.2	+						SCG5_uc001zgz.2_Intron	NM_001144757	NP_001138229	P05408	7B2_HUMAN	secretogranin V isoform 1						intracellular protein transport|neuropeptide signaling pathway|peptide hormone processing|regulation of hormone secretion	extracellular region|stored secretory granule	enzyme inhibitor activity|GTP binding|unfolded protein binding				0		all_lung(180;7.32e-08)		all cancers(64;6.48e-17)|Epithelial(43;1.23e-11)|GBM - Glioblastoma multiforme(186;1.39e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0212)		AGATAGATTCTCCTCAAAGTT	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	36474462	36474462	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36474462delA								ATPBD4 (636058 upstream) : C15orf41 (397350 downstream)																							AGGATGTTGGAAAAAAAAAAG	0.388													5	3	---	---	---	---	
DNAJC17	55192	broad.mit.edu	37	15	41099112	41099112	+	Intron	DEL	G	-	-	rs34110073		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41099112delG	uc001zms.1	-						DNAJC17_uc010bbz.1_Intron|DNAJC17_uc010bca.1_Intron|DNAJC17_uc010bcb.1_Intron|ZFYVE19_uc001zmt.1_5'Flank|ZFYVE19_uc001zmu.1_5'Flank|ZFYVE19_uc001zmv.1_5'Flank|ZFYVE19_uc001zmw.1_5'Flank|ZFYVE19_uc001zmx.1_5'Flank|ZFYVE19_uc010bcc.1_5'Flank	NM_018163	NP_060633	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17						protein folding		heat shock protein binding|nucleotide binding|RNA binding|unfolded protein binding				0		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		ACATTGGCAAGGGGGCATGAA	0.448													3	3	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62160644	62160644	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62160644delA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						TTCTGCACACAAAAAAAAGCT	0.294													3	3	---	---	---	---	
CSNK1G1	53944	broad.mit.edu	37	15	64551058	64551058	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64551058delA	uc002anf.2	-						CSNK1G1_uc002ane.2_Intron|CSNK1G1_uc002ang.1_Intron|CSNK1G1_uc002anh.1_Intron|CSNK1G1_uc002anj.2_Intron	NM_022048	NP_071331	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0						TAAGTTAGAGAAAAAAACAGT	0.269													4	2	---	---	---	---	
CORO2B	10391	broad.mit.edu	37	15	69020047	69020047	+	3'UTR	DEL	T	-	-	rs71747415		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69020047delT	uc002arj.3	+	12					CORO2B_uc010bic.2_3'UTR|CORO2B_uc002ark.2_3'UTR	NM_006091	NP_006082	Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6						TTTCTGGAGCTTTTTTTTTTC	0.463													3	3	---	---	---	---	
NOX5	79400	broad.mit.edu	37	15	69341533	69341533	+	Intron	DEL	T	-	-	rs34467340		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69341533delT	uc002ars.1	+						NOX5_uc002arp.1_Intron|NOX5_uc002arq.1_Intron|NOX5_uc010bid.1_Intron|NOX5_uc002arr.1_Intron|NOX5_uc010bie.1_Intron|NOX5_uc010bif.1_Intron	NM_024505	NP_078781	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5						angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2						ACCCAGAGTCttttttttttt	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	77892636	77892636	+	IGR	DEL	G	-	-	rs73450935	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77892636delG								HMG20A (114693 upstream) : LINGO1 (12733 downstream)																							AGCTCCAGGTGGAGATAGACA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88941029	88941029	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88941029delC								NTRK3 (141368 upstream) : MRPL46 (61679 downstream)																							AGCTCGGCCACCCCCAGGGCA	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95217770	95217770	+	IGR	DEL	T	-	-	rs71841657		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95217770delT								MCTP2 (190590 upstream) : LOC145820 (758552 downstream)																							CTTCTTTGACTTTTTTTTTTT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	95779694	95779694	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95779694delC								MCTP2 (752514 upstream) : LOC145820 (196628 downstream)																							ATAGCCACGGCCCACACCTTG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98897136	98897136	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98897136delG								ARRDC4 (380069 upstream) : FAM169B (83255 downstream)																							agacatcagtgggcaaaagag	0.045													4	2	---	---	---	---	
ABCA17P	650655	broad.mit.edu	37	16	2408028	2408028	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2408028delT	uc002cqa.1	+						ABCA17P_uc002cqb.1_Intron|ABCA17P_uc002cqc.1_Intron					Homo sapiens cDNA FLJ37881 fis, clone BRSTN2000367.												0						gtcagcttccttttttgctgt	0.000													4	2	---	---	---	---	
PDXDC1	23042	broad.mit.edu	37	16	15131655	15131656	+	Intron	DEL	AA	-	-	rs34434940		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15131655_15131656delAA	uc002ddc.2	+							NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	ATTACCGACCAAAAAAAAAACT	0.347													4	2	---	---	---	---	
GSG1L	146395	broad.mit.edu	37	16	28062830	28062830	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28062830delG	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1							integral to membrane				ovary(1)	1						gaagtgttacgaaaaaaaaaa	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31577342	31577342	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31577342delG								AHSP (37219 upstream) : CSDAP1 (1746 downstream)																							GATATCTGAAGGGTTCAAATA	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32817831	32817833	+	IGR	DEL	CAA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32817831_32817833delCAA								TP53TG3B (128953 upstream) : SLC6A10P (70964 downstream)																							atcatttcatcaattcatcattt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32848034	32848034	+	IGR	DEL	A	-	-	rs75274373		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32848034delA								TP53TG3B (159156 upstream) : SLC6A10P (40763 downstream)																							tatttctttcattaaaaaatt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33518778	33518779	+	IGR	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33518778_33518779insA								SLC6A10P (622315 upstream) : MIR1826 (446729 downstream)																							aggtggccttttgtgcctggct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49097345	49097346	+	IGR	DEL	CT	-	-	rs72008483		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49097345_49097346delCT								N4BP1 (453225 upstream) : CBLN1 (214865 downstream)																							ACAGTGAAGACTCTGACTGGCT	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64711779	64711779	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64711779delG								None (None upstream) : CDH11 (268906 downstream)																							gtaaggcggtggagatttgct	0.000													4	2	---	---	---	---	
PDPR	55066	broad.mit.edu	37	16	70177798	70177799	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70177798_70177799insT	uc002eyf.1	+						CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron|PDPR_uc002eyg.1_Intron|PDPR_uc002eyh.2_5'Flank|PDPR_uc010vls.1_5'Flank	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory						glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		tgtcttttttcttttttttttt	0.178													4	3	---	---	---	---	
AARS	16	broad.mit.edu	37	16	70298635	70298635	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70298635delT	uc002eyn.1	-						AARS_uc010vlu.1_Intron	NM_001605	NP_001596	P49588	SYAC_HUMAN	alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)	ttcctacaaattttttttttt	0.134													4	3	---	---	---	---	
PKD1L3	342372	broad.mit.edu	37	16	72003578	72003578	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72003578delA	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0						GAACCAAAGGAAAAAAAAATA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77078584	77078585	+	IGR	INS	-	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77078584_77078585insC								CNTNAP4 (485449 upstream) : MON1B (146251 downstream)																							cacccatgctgccctttttgtg	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	81082277	81082277	+	IGR	DEL	C	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81082277delC								ATMIN (1326 upstream) : C16orf46 (4826 downstream)																							tgcatgaagaccacactacta	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	81082280	81082281	+	IGR	INS	-	T	T	rs35874135		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81082280_81082281insT								ATMIN (1329 upstream) : C16orf46 (4822 downstream)																							atgaagaccacactactactgt	0.074													4	2	---	---	---	---	
PKD1L2	114780	broad.mit.edu	37	16	81155069	81155069	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81155069delA	uc002fgh.1	-						PKD1L2_uc002fgf.1_Intron|PKD1L2_uc002fgg.1_Intron	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a						neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						actccatctcaaaaaaaaaaa	0.239													5	4	---	---	---	---	
CMIP	80790	broad.mit.edu	37	16	81615915	81615915	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81615915delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0						CCTTGGAATATTTTTTTTGCC	0.413													4	2	---	---	---	---	
KIAA0182	23199	broad.mit.edu	37	16	85703987	85703987	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85703987delT	uc002fix.2	+						KIAA0182_uc002fiw.2_Intron|KIAA0182_uc002fiy.2_Intron|KIAA0182_uc002fiz.2_Intron|KIAA0182_uc010cho.2_Intron	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1								protein binding			large_intestine(3)|ovary(1)|skin(1)	5						CATCCTTTGattttttttttc	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	3203431	3203431	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3203431delT								OR3A1 (7555 upstream) : OR3A4 (10108 downstream)																							CCCTTCCCTCTTTTTTTTTTT	0.254													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6622820	6622820	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6622820delA								SLC13A5 (6080 upstream) : XAF1 (35974 downstream)																							TTTGATTGCTAAAAAAGGCAG	0.418													4	2	---	---	---	---	
MAP2K4	6416	broad.mit.edu	37	17	11962347	11962348	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11962347_11962348insT	uc002gnj.2	+						MAP2K4_uc002gnk.2_Intron	NM_003010	NP_003001	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4						cellular response to mechanical stimulus|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|JUN kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			large_intestine(14)|breast(12)|lung(8)|ovary(8)|pancreas(8)|stomach(2)|central_nervous_system(1)|biliary_tract(1)|testis(1)|endometrium(1)|urinary_tract(1)|skin(1)	58		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TAAAAAAAGGATTTTTGGGGGG	0.282			D|Mis|N		pancreatic|breast|colorectal								4	2	---	---	---	---	
COX10	1352	broad.mit.edu	37	17	13984190	13984190	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13984190delT	uc002gof.3	+						COX10_uc010vvs.1_Intron|COX10_uc010vvt.1_Intron	NM_001303	NP_001294	Q12887	COX10_HUMAN	heme A:farnesyltransferase precursor						heme a biosynthetic process|heme O biosynthetic process|respiratory chain complex IV assembly	integral to membrane|mitochondrial membrane	protoheme IX farnesyltransferase activity				0		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		tatgtatttgtttttttcatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21241974	21241974	+	IGR	DEL	C	-	-	rs112465033		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21241974delC								MAP2K3 (23425 upstream) : KCNJ12 (37725 downstream)																							AGTGAGTTCGCTTGTTCGGCT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21520240	21520241	+	IGR	INS	-	A	A			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21520240_21520241insA								C17orf51 (42509 upstream) : FAM27L (305129 downstream)																							aagaaaaacttaccactgctag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21544829	21544829	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21544829delT								C17orf51 (67098 upstream) : FAM27L (280541 downstream)																							ctgtttttgattttttttttc	0.000													11	5	---	---	---	---	
HDAC5	10014	broad.mit.edu	37	17	42191166	42191166	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42191166delG	uc002ifd.1	-						HDAC5_uc002ife.1_Intron|HDAC5_uc002iff.1_Intron|HDAC5_uc010czp.1_Intron|HDAC5_uc002ifh.2_Intron	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1						B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		CAAAGGCTGTGGGGATGGGGG	0.552													4	2	---	---	---	---	
NFE2L1	4779	broad.mit.edu	37	17	46133539	46133539	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46133539delT	uc002imz.3	+						NFE2L1_uc002ina.3_Intron|NFE2L1_uc002inb.3_Intron|NFE2L1_uc010wle.1_Intron|NFE2L1_uc010wlf.1_Intron|NFE2L1_uc002inc.1_Intron	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1						anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1						CTAGTGGCTCTTTTTTTTTGT	0.517													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	48057601	48057601	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48057601delA								DLX4 (5279 upstream) : DLX3 (9775 downstream)																							AGCTTCCTCCAAACATCAAGC	0.562													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53776878	53776878	+	IGR	DEL	T	-	-	rs76490471		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53776878delT								MMD (277537 upstream) : TMEM100 (20112 downstream)																							GCAGAATTGATTTTTTTTTCC	0.463													6	4	---	---	---	---	
HSF5	124535	broad.mit.edu	37	17	56500056	56500056	+	Intron	DEL	T	-	-	rs112627859		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56500056delT	uc002iwi.1	-							NM_001080439	NP_001073908	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTCAGTTGCCttttttttttt	0.224													4	2	---	---	---	---	
HSF5	124535	broad.mit.edu	37	17	56554229	56554230	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56554229_56554230insT	uc002iwi.1	-							NM_001080439	NP_001073908	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GCTTCTTGCTGTTTTTTTTTTC	0.426													6	3	---	---	---	---	
MARCH10	162333	broad.mit.edu	37	17	60871506	60871507	+	Intron	INS	-	CAC	CAC	rs148676242	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60871506_60871507insCAC	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190								ligase activity|zinc ion binding				0						accaaaacagtcaccaccacca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	63289504	63289505	+	IGR	DEL	AA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63289504_63289505delAA								RGS9 (65685 upstream) : AXIN2 (235180 downstream)																							TTAAGTTTGTAAAGTACTTGCC	0.342													4	2	---	---	---	---	
AXIN2	8313	broad.mit.edu	37	17	63532780	63532780	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63532780delA	uc002jfi.2	-						AXIN2_uc002jfh.2_Intron	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2						cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2						AGAGAGAGTTAAAAAAAAAAC	0.383									Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				6	3	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75372128	75372128	+	Intron	DEL	G	-	-	rs76223580		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75372128delG	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_5'Flank	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			TTCCGAATCAGGGTAGAGAAA	0.552													2	6	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78796591	78796592	+	Intron	INS	-	GTGC	GTGC			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78796591_78796592insGTGC	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						cctgtatgtgtgtgcgtgtatt	0.119													4	2	---	---	---	---	
SECTM1	6398	broad.mit.edu	37	17	80282979	80282980	+	Intron	DEL	TG	-	-	rs5822518		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80282979_80282980delTG	uc002keo.2	-						SECTM1_uc002ken.2_Intron|SECTM1_uc002kep.2_Intron	NM_003004	NP_002995	Q8WVN6	SCTM1_HUMAN	secreted and transmembrane 1 precursor						immune response|mesoderm development|positive regulation of I-kappaB kinase/NF-kappaB cascade	extracellular space|Golgi apparatus|integral to membrane|plasma membrane	cytokine activity|signal transducer activity				0	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)			tgtgtgtgtatgtgtgtgtgtg	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	4750310	4750310	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4750310delT								DLGAP1 (295044 upstream) : LOC642597 (393362 downstream)																							GCGTACCTTCTTTTTTTCTTT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10068947	10068947	+	IGR	DEL	A	-	-	rs72069635		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10068947delA								VAPA (108930 upstream) : APCDD1 (385678 downstream)																							TGCCTCAGGTAAAAAAAATAA	0.527													4	2	---	---	---	---	
ROCK1	6093	broad.mit.edu	37	18	18560201	18560201	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18560201delA	uc002kte.2	-							NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)					tacatgggttaaaaaaaaaac	0.000													7	4	---	---	---	---	
ASXL3	80816	broad.mit.edu	37	18	31238058	31238059	+	Intron	DEL	GA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31238058_31238059delGA	uc010dmg.1	+						ASXL3_uc002kxq.2_Intron	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						GTCAGTCTTTGATATTTATTGG	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	36604354	36604356	+	IGR	DEL	TAA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36604354_36604356delTAA								None (None upstream) : LOC647946 (182532 downstream)																							TAAAAAATGTTAATAATAGATAT	0.241													4	2	---	---	---	---	
ST8SIA5	29906	broad.mit.edu	37	18	44294295	44294295	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44294295delT	uc002lcj.1	-						ST8SIA5_uc002lci.1_Intron|ST8SIA5_uc010xcy.1_Intron|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Intron	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3						TCCAACTCCCTTTTCTTTCCT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	45095247	45095248	+	Intron	INS	-	AG	AG	rs142550018	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45095247_45095248insAG	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																		cacacacacacagagagagaga	0.332													4	2	---	---	---	---	
ATP8B1	5205	broad.mit.edu	37	18	55344784	55344787	+	Intron	DEL	CCTT	-	-	rs111967490		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55344784_55344787delCCTT	uc002lgw.2	-						uc002lgv.1_Intron	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1						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)				GCTAAACACACCTTCCTTCCTTCC	0.426									Byler_disease				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62903303	62903303	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62903303delT								None (None upstream) : CDH7 (514185 downstream)																							TTTCTATGTGTTTTTTTCCTA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	74864794	74864794	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74864794delG								MBP (20020 upstream) : GALR1 (97214 downstream)																							GGTTAGTTATGTTTTTAAAAT	0.318													4	2	---	---	---	---	
CCDC94	55702	broad.mit.edu	37	19	4247436	4247437	+	Intron	INS	-	T	T	rs146043960	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4247436_4247437insT	uc002lzv.3	+							NM_018074	NP_060544	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94												0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)		ACCAGATAGGGTTTTTTTTCTG	0.614													4	6	---	---	---	---	
DENND1C	79958	broad.mit.edu	37	19	6469043	6469043	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6469043delT	uc002mfe.2	-						DENND1C_uc002mfb.2_Intron|DENND1C_uc002mfc.2_Intron|DENND1C_uc002mfd.2_Intron|DENND1C_uc010xje.1_Intron	NM_024898	NP_079174	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1						TTAGTTAGtcttttttttttt	0.264													5	5	---	---	---	---	
FCER2	2208	broad.mit.edu	37	19	7757517	7757522	+	Intron	DEL	CCATCG	-	-	rs35227229		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7757517_7757522delCCATCG	uc002mhn.2	-						FCER2_uc010xjs.1_Intron|FCER2_uc010xjt.1_Intron|FCER2_uc002mhm.2_Intron	NM_002002	NP_001993	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor						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						GTCACTAACACCATCGCCATCAGCAC	0.500													3	3	---	---	---	---	
ZNF440	126070	broad.mit.edu	37	19	11930872	11930872	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11930872delA	uc002msp.1	+							NM_152357	NP_689570	Q8IYI8	ZN440_HUMAN	zinc finger protein 440						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ACATGAGAGGAAAGCAGAGAA	0.403													4	2	---	---	---	---	
COPE	11316	broad.mit.edu	37	19	19010934	19010934	+	Intron	DEL	C	-	-	rs66650132		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19010934delC	uc002nkk.2	-						COPE_uc002nkl.2_Intron|COPE_uc002nkm.2_Intron|COPE_uc002nkn.2_Intron	NM_007263	NP_009194	O14579	COPE_HUMAN	epsilon subunit of coatomer protein complex						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	binding|structural molecule activity				0						GATGGGCCTGCCCCCTGGAGA	0.662													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29578018	29578018	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29578018delT								LOC148145 (117963 upstream) : UQCRFS1 (120149 downstream)																							AATGAGCTACTTTTTTTTTTT	0.363													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29830415	29830417	+	Intron	DEL	GGA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29830415_29830417delGGA	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		aaggggaagtggaggaggaggag	0.163													4	2	---	---	---	---	
ANKRD27	84079	broad.mit.edu	37	19	33113679	33113679	+	Intron	DEL	T	-	-	rs77974943		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33113679delT	uc002ntn.1	-							NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)						early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)					TTCTCATTCAttttttttttc	0.244													9	5	---	---	---	---	
CEACAM4	1089	broad.mit.edu	37	19	42133518	42133519	+	5'Flank	INS	-	C	C	rs144762122	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42133518_42133519insC	uc002orh.1	-						CEACAM4_uc010xwd.1_5'Flank	NM_001817	NP_001808	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion							integral to plasma membrane|membrane fraction					0						TCACCCCTCTGCCCCTCCCCTC	0.584													2	4	---	---	---	---	
ZNF230	7773	broad.mit.edu	37	19	44513655	44513655	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44513655delA	uc002oyb.1	+							NM_006300	NP_006291	Q9UIE0	ZN230_HUMAN	zinc finger protein 230						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				ctgcctcttgactacatctgt	0.045													3	3	---	---	---	---	
ZNF235	9310	broad.mit.edu	37	19	44794347	44794348	+	Intron	INS	-	AA	AA			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44794347_44794348insAA	uc002oza.3	-						ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF235_uc002ozb.3_Intron|ZNF235_uc010xwx.1_Intron	NM_004234	NP_004225	Q14590	ZN235_HUMAN	zinc finger protein 93 homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)				ATATGCCATCCAGAAACCAGTC	0.520													4	2	---	---	---	---	
DHDH	27294	broad.mit.edu	37	19	49442536	49442536	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49442536delA	uc002ple.1	+							NM_014475	NP_055290	Q9UQ10	DHDH_HUMAN	dimeric dihydrodiol dehydrogenase						carbohydrate metabolic process		binding|D-xylose 1-dehydrogenase (NADP+) activity|electron carrier activity|NAD(P)+ transhydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		atctctattcaaaaaaaaaag	0.224													4	2	---	---	---	---	
ZNF766	90321	broad.mit.edu	37	19	52780712	52780712	+	Intron	DEL	A	-	-	rs79554348		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52780712delA	uc002pyr.1	+						ZNF766_uc002pys.1_Intron|ZNF766_uc002pyt.1_5'UTR	NM_001010851	NP_001010851	Q5HY98	ZN766_HUMAN	zinc finger protein 766						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00236)|OV - Ovarian serous cystadenocarcinoma(262;0.00871)		actccgtctcaaaaaaaaaca	0.194													4	2	---	---	---	---	
ZNF320	162967	broad.mit.edu	37	19	53391576	53391577	+	Intron	INS	-	GA	GA			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53391576_53391577insGA	uc002qag.2	-						ZNF320_uc010eqi.1_Intron|ZNF320_uc002qah.2_Intron|ZNF320_uc002qai.2_Intron	NM_207333	NP_997216	A2RRD8	ZN320_HUMAN	zinc finger protein 320						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)		AATGAGAAGAGGAGAGGGGAAA	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54533477	54533477	+	IGR	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54533477delG								CACNG6 (17559 upstream) : VSTM1 (10608 downstream)																							GCAAGAGAGTGGGGGAAGCAG	0.279											OREG0025669	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
TMC4	147798	broad.mit.edu	37	19	54672527	54672528	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54672527_54672528insT	uc010erf.2	-						TMC4_uc002qdo.2_Intron	NM_001145303	NP_001138775	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4 isoform 1							integral to membrane				pancreas(1)	1	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					tcttttctttctttctttcttt	0.243													4	3	---	---	---	---	
TMC4	147798	broad.mit.edu	37	19	54672531	54672532	+	Intron	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54672531_54672532insT	uc010erf.2	-						TMC4_uc002qdo.2_Intron	NM_001145303	NP_001138775	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4 isoform 1							integral to membrane				pancreas(1)	1	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					ttctttctttctttcttttctt	0.228													2	5	---	---	---	---	
TMC4	147798	broad.mit.edu	37	19	54672540	54672541	+	Intron	INS	-	T	T	rs12984490		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54672540_54672541insT	uc010erf.2	-						TMC4_uc002qdo.2_Intron	NM_001145303	NP_001138775	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4 isoform 1							integral to membrane				pancreas(1)	1	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					tctttcttttctttctttcttt	0.203													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	57172646	57172647	+	IGR	INS	-	C	C	rs138763827	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57172646_57172647insC								ZNF71 (37104 upstream) : ZNF835 (2308 downstream)																							TAGGGCTGGTGTGGGATGTTCA	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	60522	60523	+	IGR	INS	-	C	C	rs150241001	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60522_60523insC								None (None upstream) : DEFB125 (7828 downstream)																							aagcactttgtcccccctggca	0.000													4	2	---	---	---	---	
KIF16B	55614	broad.mit.edu	37	20	16254307	16254310	+	Intron	DEL	TCAA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16254307_16254310delTCAA	uc002wpg.1	-						KIF16B_uc002wpe.1_Intron|KIF16B_uc002wpf.1_Intron|KIF16B_uc010gch.1_Intron	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						agaccctgtctcaatcaatcaatc	0.127													4	2	---	---	---	---	
TMEM90B	79953	broad.mit.edu	37	20	24478875	24478875	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24478875delT	uc002wtw.1	+							NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B						response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0						catcacttcatcactattcat	0.000													4	2	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25829628	25829629	+	Intron	INS	-	AA	AA	rs141949476	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25829628_25829629insAA	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						ctgcaattgacagaggtagtgg	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26202318	26202318	+	IGR	DEL	T	-	-	rs77929867		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26202318delT								MIR663 (13404 upstream) : None (None downstream)																							aattacagaatctttatatct	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29455644	29455645	+	IGR	INS	-	T	T			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29455644_29455645insT								None (None upstream) : FRG1B (156234 downstream)																							catttgggtgattttttttgtt	0.035													4	2	---	---	---	---	
HM13	81502	broad.mit.edu	37	20	30110358	30110358	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30110358delA	uc002wwe.2	+						HM13_uc002wwc.2_Intron|HM13_uc002wwd.2_Intron|HM13_uc002wwb.1_Intron	NM_030789	NP_110416	Q8TCT9	HM13_HUMAN	minor histocompatibility antigen 13 isoform 1						membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			aaaaaaaaacaaaaaaaaaaa	0.224													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36034550	36034551	+	IGR	DEL	GT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36034550_36034551delGT								SRC (731 upstream) : BLCAP (111269 downstream)																							CAGGGGGCGGgtgtgtgtgtgt	0.406													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39550206	39550207	+	IGR	DEL	AA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39550206_39550207delAA								MAFB (232330 upstream) : TOP1 (107255 downstream)																							accttgtctcaaaaaaaaagaa	0.000													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	40804324	40804325	+	Intron	INS	-	A	A	rs148852982	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40804324_40804325insA	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron|PTPRT_uc010ggi.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				tatctcaaaggaaaaaaccaga	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42006415	42006416	+	IGR	DEL	TA	-	-	rs140779029		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42006415_42006416delTA								PTPRT (187858 upstream) : SFRS6 (80088 downstream)																							ttccatcatgtatatatagaga	0.079													4	3	---	---	---	---	
PKIG	11142	broad.mit.edu	37	20	43199398	43199398	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43199398delA	uc002xmg.2	+						PKIG_uc002xmh.2_Intron|PKIG_uc002xmi.2_Intron	NM_181805	NP_861521	Q9Y2B9	IPKG_HUMAN	cAMP-dependent protein kinase inhibitor gamma								cAMP-dependent protein kinase inhibitor activity|protein binding				0		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.001)|COAD - Colon adenocarcinoma(18;0.00189)			aatgaacaacaaaaaaaagtg	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51288221	51288221	+	IGR	DEL	T	-	-	rs5841905		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51288221delT								ZFP64 (479697 upstream) : TSHZ2 (300656 downstream)																							TCTGTCTTGCTTTTAGGTCCT	0.328													4	2	---	---	---	---	
BMP7	655	broad.mit.edu	37	20	55822044	55822045	+	Intron	INS	-	A	A	rs142598200	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55822044_55822045insA	uc010gip.1	-						BMP7_uc010giq.1_Intron|BMP7_uc002xyc.2_Intron	NM_001719	NP_001710	P18075	BMP7_HUMAN	bone morphogenetic protein 7 precursor						BMP signaling pathway|cartilage development|cellular response to hypoxia|epithelial to mesenchymal transition|growth|mesonephros development|negative regulation of glomerular mesangial cell proliferation|negative regulation of MAP kinase activity|negative regulation of mitosis|negative regulation of neuron differentiation|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of phosphorylation|negative regulation of striated muscle cell apoptosis|negative regulation of transcription, DNA-dependent|ossification|pathway-restricted SMAD protein phosphorylation|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein localization to nucleus|regulation of removal of superoxide radicals|SMAD protein signal transduction|steroid hormone mediated signaling pathway|ureteric bud development	extracellular space	cytokine activity|growth factor activity			skin(1)	1	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			gactccatctcaaaaaaaaacc	0.059													1	5	---	---	---	---	
NTSR1	4923	broad.mit.edu	37	20	61365653	61365653	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61365653delA	uc002ydf.2	+							NM_002531	NP_002522	P30989	NTR1_HUMAN	neurotensin receptor 1							endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled			skin(2)|lung(1)|central_nervous_system(1)	4	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			CCTTCCCCGCAAAAAAAAAAA	0.597													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10141190	10141191	+	IGR	DEL	AA	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10141190_10141191delAA								None (None upstream) : TPTE (765552 downstream)																							aaatatgtctaaaatgtaaaaa	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10751134	10751134	+	IGR	DEL	A	-	-	rs111508745		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10751134delA								None (None upstream) : TPTE (155609 downstream)																							ccctatggtgaaaaacgaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10756265	10756270	+	IGR	DEL	ATCTTC	-	-	rs139653617		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10756265_10756270delATCTTC								None (None upstream) : TPTE (150473 downstream)																							aaaatgaaatatcttcacataaaaat	0.000													4	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11037534	11037535	+	Intron	INS	-	C	C	rs140499714		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11037534_11037535insC	uc002yit.1	-						TPTE_uc002yis.1_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)		ACAAAACAAAAAATACTTACTG	0.272													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11045983	11045983	+	Intron	DEL	A	-	-	rs111961463		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11045983delA	uc002yit.1	-							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)		TTCAAGTATCAAAACATTTAT	0.244													8	6	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11048496	11048497	+	Intron	DEL	AT	-	-	rs149081695		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11048496_11048497delAT	uc002yit.1	-							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)		AAAAAGtcacatgttttatctc	0.188													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11051168	11051168	+	Intron	DEL	T	-	-	rs139496343		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11051168delT	uc002yit.1	-							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)		agaccttttgtttttatttac	0.100													4	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11052792	11052794	+	Intron	DEL	TAC	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11052792_11052794delTAC	uc002yit.1	-							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)		aaacttctgttacataatcattt	0.000													7	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11071049	11071050	+	Intron	INS	-	G	G	rs112958643		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11071049_11071050insG	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)		ctctatattcagggaaaaaaag	0.000													11	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11074104	11074106	+	Intron	DEL	TAG	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11074104_11074106delTAG	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)		gaaaacaacttagaacatgagtg	0.000													3	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11076555	11076557	+	Intron	DEL	TAA	-	-	rs151275384		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11076555_11076557delTAA	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)		tctaatttgttaataataatata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11175282	11175283	+	IGR	INS	-	G	G	rs56073885		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11175282_11175283insG								BAGE (76345 upstream) : None (None downstream)																							GATCATCTGTAGTGTACGGTGG	0.391													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14362686	14362687	+	IGR	DEL	GT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14362686_14362687delGT								None (None upstream) : C21orf99 (47800 downstream)																							tacaaaaatagtgtttccaaac	0.000													4	2	---	---	---	---	
USP25	29761	broad.mit.edu	37	21	17150601	17150601	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17150601delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		ATTTCTTTCATTTTTTTTCTT	0.224													4	2	---	---	---	---	
C21orf91	54149	broad.mit.edu	37	21	19151351	19151351	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19151351delT	uc002ykm.2	-						C21orf91_uc002ykn.2_Intron			Q9NYK6	EURL_HUMAN	Homo sapiens partial mRNA; ID YG81-6.											ovary(1)	1				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)		atcacacagattttcctattt	0.010													4	2	---	---	---	---	
NCAM2	4685	broad.mit.edu	37	21	22582015	22582018	+	Intron	DEL	TGTC	-	-	rs143409689		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22582015_22582018delTGTC	uc002yld.1	+						NCAM2_uc011acb.1_Intron|NCAM2_uc011acc.1_Intron	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AAGCTCTGATTGTCTGCTCTGTGT	0.363													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26159393	26159393	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26159393delT								None (None upstream) : NCRNA00158 (598741 downstream)																							cagatcaccatttttttcact	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29204085	29204086	+	IGR	DEL	TT	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29204085_29204086delTT								NCRNA00113 (80533 upstream) : C21orf94 (181596 downstream)																							CAATTTTTAATTTACAAAATAG	0.233													4	2	---	---	---	---	
URB1	9875	broad.mit.edu	37	21	33714065	33714065	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33714065delT	uc002ypn.2	-							NM_014825	NP_055640	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0						GCAATGATTATTTTTTTTTAA	0.264													5	3	---	---	---	---	
CLDN14	23562	broad.mit.edu	37	21	37840019	37840019	+	5'Flank	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37840019delT	uc002yvk.1	-						CLDN14_uc002yvn.1_Intron|CLDN14_uc002yvo.1_Intron|CLDN14_uc002yvl.1_Intron|CLDN14_uc002yvm.1_Intron	NM_012130	NP_036262	O95500	CLD14_HUMAN	claudin 14						calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0						CTTACTCTCCTTAACCCTCAG	0.507													4	2	---	---	---	---	
CLDN14	23562	broad.mit.edu	37	21	37840189	37840189	+	5'Flank	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37840189delG	uc002yvk.1	-						CLDN14_uc002yvn.1_Intron|CLDN14_uc002yvo.1_Intron|CLDN14_uc002yvl.1_Intron|CLDN14_uc002yvm.1_Intron	NM_012130	NP_036262	O95500	CLD14_HUMAN	claudin 14						calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0						GCGGGGAGCTGGGGCACAAGC	0.562													4	2	---	---	---	---	
HLCS	3141	broad.mit.edu	37	21	38182786	38182786	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38182786delT	uc010gnb.2	-						HLCS_uc002yvs.2_Intron	NM_000411	NP_000402	P50747	BPL1_HUMAN	holocarboxylase synthetase						cell proliferation|histone biotinylation|response to biotin	chromatin|cytosol|mitochondrion|nuclear lamina|nuclear matrix	ATP binding|biotin binding|biotin-[acetyl-CoA-carboxylase] ligase activity|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity|enzyme binding			ovary(2)|breast(1)|kidney(1)|liver(1)	5		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	CTGAGCTTACTTGGTGCAGCT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40059264	40059265	+	IGR	INS	-	C	C			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40059264_40059265insC								ERG (25560 upstream) : NCRNA00114 (51614 downstream)																							GGTCCATTCTGCCTTTTTCACC	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	41380768	41380768	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41380768delT								PCP4 (79448 upstream) : DSCAM (3575 downstream)																							aaccctaaacttttTtttttc	0.000													1	6	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41846918	41846918	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41846918delA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TCTCTCCAGGAAAAAAAAAAG	0.537													3	3	---	---	---	---	
MX1	4599	broad.mit.edu	37	21	42814056	42814056	+	Intron	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42814056delA	uc002yzh.2	+						MX1_uc002yzi.2_Intron|MX1_uc010goq.2_Intron	NM_001144925	NP_001138397	P20591	MX1_HUMAN	myxovirus resistance protein 1						induction of apoptosis|response to virus|type I interferon-mediated signaling pathway	cytosol	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				TACTGCCAAGAAAAAAAAAAC	0.199													3	3	---	---	---	---	
C2CD2	25966	broad.mit.edu	37	21	43341863	43341864	+	Intron	INS	-	TG	TG	rs146559735	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43341863_43341864insTG	uc002yzw.2	-						C2CD2_uc002yzu.2_5'Flank|C2CD2_uc002yzv.2_Intron|C2CD2_uc002yzx.1_Intron	NM_015500	NP_056315	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2 isoform							cytosol|extracellular region|nucleus				ovary(1)	1						TTATAAAtgtatgtgtgtgtgt	0.297													3	9	---	---	---	---	
PDE9A	5152	broad.mit.edu	37	21	44179492	44179493	+	Intron	INS	-	GT	GT	rs146620339	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44179492_44179493insGT	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron|PDE9A_uc002zch.2_Intron|PDE9A_uc010gpf.1_Intron	NM_002606	NP_002597	O76083	PDE9A_HUMAN	phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2						tgtgtgggagcgtgtgtgtgtg	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17237155	17237155	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17237155delT								psiTPTE22 (57634 upstream) : XKR3 (27158 downstream)																							TAGTTACTTATTTTTATGACt	0.030													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20775034	20775035	+	IGR	INS	-	GTA	GTA	rs148634036	by1000genomes	TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20775034_20775035insGTA								ZNF74 (12283 upstream) : SCARF2 (3840 downstream)																							CTCCTGTGTGTGTAGGAGTTTG	0.342													6	4	---	---	---	---	
LOC644165	644165	broad.mit.edu	37	22	25043061	25043062	+	Intron	INS	-	CCGG	CCGG	rs71688733		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25043061_25043062insCCGG	uc011ajv.1	+						POM121L10P_uc003aaz.3_RNA|POM121L10P_uc003abc.2_RNA	NR_024494				Homo sapiens cDNA FLJ57042 complete cds, moderately similar to Breakpoint cluster region protein (EC 2.7.11.1).												0						CTACCGCGTGTCCGGTGTGGCC	0.653													9	5	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26165827	26165827	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26165827delT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_5'Flank	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						ttATGTAGTAttttttttttt	0.065													5	4	---	---	---	---	
CTPS2	56474	broad.mit.edu	37	X	16608663	16608663	+	Intron	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16608663delT	uc004cxk.2	-						CTPS2_uc004cxl.2_Intron|CTPS2_uc004cxm.2_Intron	NM_001144002	NP_001137474	Q9NRF8	PYRG2_HUMAN	cytidine triphosphate synthase II						glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine nucleotide biosynthetic process	cytosol	ATP binding|CTP synthase activity			ovary(1)	1	Hepatocellular(33;0.0997)					TGTACTTATATTTTTTTTTTC	0.363													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	19507265	19507265	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19507265delT								MAP3K15 (6871 upstream) : SH3KBP1 (44819 downstream)																							GCAGTAAGAATTTTTTTTAAT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	35041277	35041277	+	IGR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35041277delA								FAM47B (78243 upstream) : MAGEB16 (775182 downstream)																							atatagggttaaaaaaaaaaa	0.000													8	5	---	---	---	---	
GAGE1	2543	broad.mit.edu	37	X	49369421	49369421	+	Intron	DEL	G	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49369421delG	uc004dok.1	+						GAGE1_uc004doj.2_Intron|GAGE1_uc004dol.1_Intron	NM_001468	NP_001459	Q13065	GAGE1_HUMAN	G antigen 1 isoform 1						cellular defense response						0	Ovarian(276;0.236)					TGGtttgtttgtttgtttgcg	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61794673	61794673	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61794673delT								None (None upstream) : SPIN4 (772435 downstream)																							tgaacctttcttttgattcag	0.000													4	2	---	---	---	---	
COL4A6	1288	broad.mit.edu	37	X	107399432	107399432	+	3'UTR	DEL	A	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107399432delA	uc004enw.3	-	45					COL4A6_uc004env.3_3'UTR|COL4A6_uc011msn.1_3'UTR|COL4A6_uc010npk.2_3'UTR|COL4A6_uc011msm.1_Intron|COL4A6_uc010npj.2_3'UTR	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						CTGGCCCAGGAAAAAAGGCTG	0.473									Alport_syndrome_with_Diffuse_Leiomyomatosis				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9931364	9931364	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9931364delT								TTTY22 (280510 upstream) : None (None downstream)																							aaggtaaaagtttttttttcc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13430915	13430916	+	IGR	INS	-	A	A	rs113579599		TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13430915_13430916insA								None (None upstream) : None (None downstream)																							ACTTTAAACTTGGAAAAAATTG	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59010884	59010884	+	IGR	DEL	T	-	-			TCGA-B2-5641-01A-01D-1534-10	TCGA-B2-5641-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59010884delT								None (None upstream) : None (None downstream)																							ggaataactgttgatgcagta	0.000													4	2	---	---	---	---	
