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
TAS1R1	80835	broad.mit.edu	37	1	6637114	6637114	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6637114C>A	uc001ant.2	+	5	1578	c.1578C>A	c.(1576-1578)ACC>ACA	p.T526T	TAS1R1_uc001anu.2_Silent_p.T272T|TAS1R1_uc001anv.2_Silent_p.T272T|TAS1R1_uc001anw.2_Intron|ZBTB48_uc009vmc.1_5'Flank|ZBTB48_uc001anx.2_5'Flank|ZBTB48_uc009vmd.1_5'Flank	NM_138697	NP_619642	Q7RTX1	TS1R1_HUMAN	sweet taste receptor T1r isoform b	526	Extracellular (Potential).				sensory perception of umami taste	plasma membrane	protein heterodimerization activity|taste receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		GGGCTGGGACCTTCCTCAACA	0.617													4	19	---	---	---	---	PASS
PINK1	65018	broad.mit.edu	37	1	20975099	20975099	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20975099G>C	uc001bdm.2	+	6	1319	c.1225G>C	c.(1225-1227)GGA>CGA	p.G409R	PINK1_uc001bdn.2_Missense_Mutation_p.G102R	NM_032409	NP_115785	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1 precursor	409	Protein kinase.|Cytoplasmic (Potential).		G -> V (in PARK6).		cell death|intracellular protein kinase cascade|mitochondrion degradation|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of release of cytochrome c from mitochondria|regulation of protein complex assembly|regulation of protein ubiquitination|response to stress	cytosol|integral to membrane|mitochondrial outer membrane	ATP binding|C3HC4-type RING finger domain binding|calcium-dependent protein kinase activity|magnesium ion binding|protein serine/threonine kinase activity|ubiquitin protein ligase binding			ovary(2)|central_nervous_system(1)	3		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGATCGGGGCGGAAACGGCTG	0.627													5	28	---	---	---	---	PASS
CATSPER4	378807	broad.mit.edu	37	1	26524860	26524860	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26524860C>A	uc010oez.1	+	6	762	c.762C>A	c.(760-762)CTC>CTA	p.L254L	CATSPER4_uc010oey.1_Silent_p.L76L|CATSPER4_uc009vsf.2_RNA	NM_198137	NP_937770	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	254					cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		TGTACACCCTCTTCATCTGCA	0.522													6	104	---	---	---	---	PASS
GRIK3	2899	broad.mit.edu	37	1	37356697	37356697	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37356697C>A	uc001caz.2	-	2	251	c.116G>T	c.(115-117)GGA>GTA	p.G39V	GRIK3_uc001cba.1_Missense_Mutation_p.G39V	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	39	Extracellular (Potential).				negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)	GAAGATTCCTCCTGTGAAAGA	0.502													5	89	---	---	---	---	PASS
RAVER2	55225	broad.mit.edu	37	1	65296547	65296547	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65296547G>T	uc001dbs.1	+	12	1994	c.1916G>T	c.(1915-1917)CGA>CTA	p.R639L	RAVER2_uc001dbt.1_Missense_Mutation_p.R531L|RAVER2_uc010opb.1_Missense_Mutation_p.R364L	NM_018211	NP_060681	Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	652						cytoplasm|nucleus	nucleotide binding|RNA binding			large_intestine(1)	1						AATGAAAAGCGAGGCTCATCA	0.358													4	106	---	---	---	---	PASS
COL24A1	255631	broad.mit.edu	37	1	86523649	86523649	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86523649C>A	uc001dlj.2	-	10	1858	c.1816G>T	c.(1816-1818)GGA>TGA	p.G606*	COL24A1_uc010osd.1_5'UTR|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA|COL24A1_uc009wcq.2_Nonsense_Mutation_p.G606*	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	606	Collagen-like 2.				cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		CCTTCTGGTCCAGCTAAACCC	0.333													5	31	---	---	---	---	PASS
TARS2	80222	broad.mit.edu	37	1	150477118	150477118	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150477118G>T	uc001euq.2	+	15	1736	c.1729G>T	c.(1729-1731)GCC>TCC	p.A577S	TARS2_uc001eur.2_Missense_Mutation_p.A495S|TARS2_uc009wlt.2_Missense_Mutation_p.A203S|TARS2_uc009wls.2_Missense_Mutation_p.A447S	NM_025150	NP_079426	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial	577					threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GCAGGCGGGTGCCCTGGAGCG	0.527													5	102	---	---	---	---	PASS
DENND4B	9909	broad.mit.edu	37	1	153914391	153914391	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153914391G>T	uc001fdd.1	-	6	1410	c.1009C>A	c.(1009-1011)CTT>ATT	p.L337I		NM_014856	NP_055671	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	337	DENN.									ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TAGCGGTAAAGGAAGGTGAGG	0.667													5	28	---	---	---	---	PASS
NES	10763	broad.mit.edu	37	1	156640754	156640754	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156640754C>A	uc001fpq.2	-	4	3359	c.3226G>T	c.(3226-3228)GAC>TAC	p.D1076Y		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	1076	Tail.				brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GAGGCTTGGTCACCCCCTGGG	0.692													5	17	---	---	---	---	PASS
CD1B	910	broad.mit.edu	37	1	158298754	158298754	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158298754A>T	uc001frx.2	-	5	1045	c.937T>A	c.(937-939)TTG>ATG	p.L313M	CD1B_uc001frw.2_Missense_Mutation_p.L151M	NM_001764	NP_001755	P29016	CD1B_HUMAN	CD1B antigen precursor	313	Helical; (Potential).				antigen processing and presentation|immune response	endosome membrane|integral to membrane|lysosomal membrane|plasma membrane	protein binding			ovary(2)	2	all_hematologic(112;0.0378)					AAAAGGAGCAAGGAAGGCACT	0.428													13	61	---	---	---	---	PASS
MNDA	4332	broad.mit.edu	37	1	158812030	158812030	+	Silent	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158812030G>C	uc001fsz.1	+	2	287	c.87G>C	c.(85-87)CTG>CTC	p.L29L		NM_002432	NP_002423	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	29	DAPIN.				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)					AGTCCTTACTGGCCTATGATT	0.333													6	48	---	---	---	---	PASS
MNDA	4332	broad.mit.edu	37	1	158812031	158812031	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158812031G>A	uc001fsz.1	+	2	288	c.88G>A	c.(88-90)GCC>ACC	p.A30T		NM_002432	NP_002423	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	30	DAPIN.				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)					GTCCTTACTGGCCTATGATTT	0.328													6	48	---	---	---	---	PASS
FCER1A	2205	broad.mit.edu	37	1	159275872	159275872	+	Silent	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159275872G>A	uc001ftq.2	+	5	525	c.426G>A	c.(424-426)AAG>AAA	p.K142K		NM_002001	NP_001992	P12319	FCERA_HUMAN	Fc fragment of IgE, high affinity I, receptor	142	Ig-like 2.|Extracellular (Potential).					integral to plasma membrane				lung(2)|skin(2)|prostate(1)	5	all_hematologic(112;0.0429)				Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043)	ATGTGTACAAGGTGATCTATT	0.502													13	54	---	---	---	---	PASS
GPR161	23432	broad.mit.edu	37	1	168056836	168056836	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168056836C>A	uc001gfc.2	-	7	1625	c.1311G>T	c.(1309-1311)GTG>GTT	p.V437V	GPR161_uc001gfb.2_Silent_p.V305V|GPR161_uc010pll.1_Silent_p.V347V|GPR161_uc010plm.1_Silent_p.V323V|GPR161_uc009wvo.2_Silent_p.V454V|GPR161_uc001gfd.2_Silent_p.V437V|GPR161_uc010pln.1_Silent_p.V457V	NM_153832	NP_722561	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161 isoform 2	437	Cytoplasmic (Potential).				multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)					TGATTTGTTCCACTTCATCCT	0.483													6	119	---	---	---	---	PASS
NCF2	4688	broad.mit.edu	37	1	183546848	183546848	+	Intron	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183546848G>A	uc001gqj.3	-						NCF2_uc010pod.1_Intron|NCF2_uc010poe.1_Intron|NCF2_uc001gqk.3_Intron	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						CATATCTGCAGGACAGAGGGA	0.448													6	42	---	---	---	---	PASS
NCF2	4688	broad.mit.edu	37	1	183559390	183559390	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183559390G>T	uc001gqj.3	-	1	350	c.75C>A	c.(73-75)GCC>GCA	p.A25A	NCF2_uc010pod.1_Silent_p.A25A|NCF2_uc010poe.1_Silent_p.A25A|NCF2_uc001gqk.3_Silent_p.A25A	NM_000433	NP_000424	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	25					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						AGGCATCCAGGGCTCCCTTCC	0.552													13	82	---	---	---	---	PASS
EDEM3	80267	broad.mit.edu	37	1	184695505	184695505	+	Missense_Mutation	SNP	T	C	C	rs142115161		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184695505T>C	uc010pok.1	-	7	892	c.631A>G	c.(631-633)ATC>GTC	p.I211V	EDEM3_uc010pol.1_RNA|EDEM3_uc010pom.1_Missense_Mutation_p.I211V|EDEM3_uc001gqy.2_Missense_Mutation_p.I134V	NM_025191	NP_079467	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like	211					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			skin(1)	1						GGTTTTCTGATGCCAAACTTT	0.368													11	39	---	---	---	---	PASS
C1orf25	81627	broad.mit.edu	37	1	185089505	185089505	+	Intron	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185089505G>T	uc001grf.3	-						C1orf25_uc010pon.1_Intron	NM_030934	NP_112196	Q7Z2T5	TRM1L_HUMAN	N2,N2-dimethylguanosine tRNA							intracellular	RNA binding|tRNA (guanine-N2-)-methyltransferase activity|zinc ion binding				0						TCATTCACTGGGTGTCTTACT	0.284													4	34	---	---	---	---	PASS
LHX9	56956	broad.mit.edu	37	1	197898339	197898339	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197898339A>T	uc001guk.1	+	5	1581	c.1144A>T	c.(1144-1146)AGC>TGC	p.S382C	LHX9_uc001gui.1_Missense_Mutation_p.S373C|LHX9_uc001guj.1_Intron	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN	LIM homeobox 9 isoform 1	382					motor axon guidance|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1						TAACATGGACAGCCACGAATC	0.428													7	75	---	---	---	---	PASS
PTPRC	5788	broad.mit.edu	37	1	198668711	198668711	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198668711C>G	uc001gur.1	+	5	491	c.311C>G	c.(310-312)ACG>AGG	p.T104R	PTPRC_uc001gus.1_Missense_Mutation_p.T104R|PTPRC_uc001gut.1_Intron|PTPRC_uc009wze.1_Missense_Mutation_p.T40R|PTPRC_uc009wzf.1_Missense_Mutation_p.T40R|PTPRC_uc010ppg.1_Missense_Mutation_p.T40R|PTPRC_uc001guu.1_Missense_Mutation_p.T147R|PTPRC_uc001guv.1_RNA|PTPRC_uc001guw.1_RNA	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	104	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12						TCAGTACAGACGCCTCACCTT	0.502											OREG0014061	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	96	---	---	---	---	PASS
PPP1R15B	84919	broad.mit.edu	37	1	204375323	204375323	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204375323T>C	uc001hav.3	-	2	2444	c.2039A>G	c.(2038-2040)GAA>GGA	p.E680G		NM_032833	NP_116222	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	680					regulation of translation					ovary(1)|pancreas(1)	2	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)			AATAGCATCTTCTGTTTCTTG	0.388													6	58	---	---	---	---	PASS
CTSE	1510	broad.mit.edu	37	1	206331207	206331207	+	3'UTR	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206331207C>A	uc001hdu.2	+	9					CTSE_uc001hdv.2_Silent_p.A357A|CTSE_uc010prs.1_Silent_p.A282A	NM_001910	NP_001901	P14091	CATE_HUMAN	cathepsin E isoform a preproprotein						antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)			GTGTCTGTGCCTGCCTGTCTG	0.488													5	39	---	---	---	---	PASS
ACBD3	64746	broad.mit.edu	37	1	226334402	226334402	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226334402G>T	uc001hpy.2	-	8	1543	c.1496C>A	c.(1495-1497)CCA>CAA	p.P499Q		NM_022735	NP_073572	Q9H3P7	GCP60_HUMAN	acyl-Coenzyme A binding domain containing 3	499	GOLD.				steroid biosynthetic process|transport	Golgi membrane|integral to membrane|mitochondrion	fatty-acyl-CoA binding|protein binding				0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)		TCCTCTCCCTGGATATTGATG	0.443													5	97	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237755079	237755079	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237755079C>T	uc001hyl.1	+	32	4321	c.4201C>T	c.(4201-4203)CAT>TAT	p.H1401Y		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1401	Cytoplasmic (By similarity).|B30.2/SPRY 3.|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CAGCACAAGCCATTCTGCAAG	0.388													6	30	---	---	---	---	PASS
MAP1LC3C	440738	broad.mit.edu	37	1	242161882	242161882	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242161882G>A	uc001hzk.2	-	3	230	c.155C>T	c.(154-156)CCG>CTG	p.P52L		NM_001004343	NP_001004343	Q9BXW4	MLP3C_HUMAN	microtubule-associated protein 1 light chain 3	52					autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule	protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TTTGTCCAGCGGGGGCAGGAA	0.582											OREG0014354	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	42	---	---	---	---	PASS
OR2W5	441932	broad.mit.edu	37	1	247655381	247655381	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247655381G>T	uc001icz.1	+	1	952	c.952G>T	c.(952-954)GGA>TGA	p.G318*		NM_001004698	NP_001004698	A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W,	318					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|skin(1)	3	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			CTCAACGAGGGGAACACTCTA	0.498													9	36	---	---	---	---	PASS
OR6F1	343169	broad.mit.edu	37	1	247875729	247875729	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247875729G>C	uc001idj.1	-	1	329	c.329C>G	c.(328-330)ACA>AGA	p.T110R		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	110	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			GAAGTACTCTGTGCAGCCTAA	0.502													4	60	---	---	---	---	PASS
OR2T33	391195	broad.mit.edu	37	1	248436338	248436338	+	Missense_Mutation	SNP	G	C	C	rs147622928		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248436338G>C	uc010pzi.1	-	1	779	c.779C>G	c.(778-780)CCC>CGC	p.P260R		NM_001004695	NP_001004695	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T,	260	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			ATGGGATTTGGGTCTCATATA	0.478													14	77	---	---	---	---	PASS
OR2T1	26696	broad.mit.edu	37	1	248569858	248569858	+	Missense_Mutation	SNP	G	T	T	rs141385938	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248569858G>T	uc010pzm.1	+	1	563	c.563G>T	c.(562-564)CGC>CTC	p.R188L		NM_030904	NP_112166	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T,	188	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTCATGAGCCGCCGGGTCTGT	0.542													11	51	---	---	---	---	PASS
OTOF	9381	broad.mit.edu	37	2	26699098	26699098	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26699098G>T	uc002rhk.2	-	23	2891	c.2764C>A	c.(2764-2766)CGC>AGC	p.R922S	OTOF_uc010yla.1_5'Flank|OTOF_uc002rhh.2_Missense_Mutation_p.R175S|OTOF_uc002rhi.2_Missense_Mutation_p.R232S|OTOF_uc002rhj.2_Missense_Mutation_p.R175S	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	922	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AACTCCTTGCGCTGTTTGCTG	0.677													3	26	---	---	---	---	PASS
THADA	63892	broad.mit.edu	37	2	43732780	43732780	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43732780A>T	uc002rsw.3	-	24	3954	c.3602T>A	c.(3601-3603)ATA>AAA	p.I1201K	THADA_uc010far.2_Missense_Mutation_p.I470K|THADA_uc002rsx.3_Missense_Mutation_p.I1201K|THADA_uc002rsy.3_RNA|THADA_uc010fas.1_RNA|THADA_uc002rsz.2_Missense_Mutation_p.I910K|THADA_uc010fat.1_Missense_Mutation_p.I348K|THADA_uc002rta.2_Missense_Mutation_p.I911K	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1201							binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				TGTACTCTGTATGTCATCTGT	0.328													3	9	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	80085310	80085310	+	Intron	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80085310G>C	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						AAAATTGTACGTATGTAGAAC	0.463													4	38	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	80620402	80620402	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80620402G>T	uc010ysh.1	+	7	1128	c.1123G>T	c.(1123-1125)GAT>TAT	p.D375Y	CTNNA2_uc010yse.1_Missense_Mutation_p.D375Y|CTNNA2_uc010ysf.1_Missense_Mutation_p.D375Y|CTNNA2_uc010ysg.1_Missense_Mutation_p.D375Y|CTNNA2_uc010ysi.1_Missense_Mutation_p.D7Y	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	375					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						GAAAACAAGAGATCTAAGGAG	0.333													7	79	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90121879	90121879	+	RNA	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90121879A>T	uc010fhm.2	+	16		c.1748A>T								Parts of antibodies, mostly variable regions.																		TCCATCTGCCATGTCTGCATC	0.448													13	263	---	---	---	---	PASS
TBC1D8	11138	broad.mit.edu	37	2	101706829	101706829	+	Intron	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101706829T>A	uc010fiv.2	-						TBC1D8_uc010yvw.1_Intron	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						CAGGCGACCTTCAAAAGAAAA	0.552													12	37	---	---	---	---	PASS
MFSD9	84804	broad.mit.edu	37	2	103343376	103343376	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103343376T>C	uc002tcb.2	-	4	423	c.355A>G	c.(355-357)AGT>GGT	p.S119G	MFSD9_uc010fja.2_RNA	NM_032718	NP_116107	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing	119	Helical; (Potential).				transmembrane transport	integral to membrane|plasma membrane	transporter activity			ovary(2)|breast(2)	4						CCCAGAGCACTGAGTAGAATG	0.483													7	85	---	---	---	---	PASS
R3HDM1	23518	broad.mit.edu	37	2	136432940	136432940	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136432940G>T	uc002tuo.2	+	19	2456	c.2086G>T	c.(2086-2088)GGA>TGA	p.G696*	R3HDM1_uc010fni.2_Nonsense_Mutation_p.G695*|R3HDM1_uc002tup.2_Nonsense_Mutation_p.G641*|R3HDM1_uc010zbh.1_Nonsense_Mutation_p.G444*	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	696							nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)		AAACTACCAAGGAATAGTTGG	0.413													5	68	---	---	---	---	PASS
UBXN4	23190	broad.mit.edu	37	2	136537802	136537802	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136537802G>T	uc002tur.2	+	12	1546	c.1235G>T	c.(1234-1236)TGG>TTG	p.W412L	UBXN4_uc002tus.2_Missense_Mutation_p.W178L|UBXN4_uc002tut.2_Missense_Mutation_p.W48L	NM_014607	NP_055422	Q92575	UBXN4_HUMAN	UBX domain containing 2	412	Cytoplasmic (Potential).				response to unfolded protein	endoplasmic reticulum membrane|nuclear envelope	protein binding			skin(2)	2						GGAGACATTTGGACCTTGTTG	0.413													5	64	---	---	---	---	PASS
MMADHC	27249	broad.mit.edu	37	2	150443600	150443600	+	Intron	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150443600C>A	uc002txb.2	-						MMADHC_uc002txc.2_Intron|MMADHC_uc010fnu.2_Intron	NM_015702	NP_056517	Q9H3L0	MMAD_HUMAN	methylmalonic aciduria (cobalamin deficiency)							mitochondrion				central_nervous_system(1)|skin(1)	2						ATAATTTACTCACATTGGCCA	0.378													4	44	---	---	---	---	PASS
IFIH1	64135	broad.mit.edu	37	2	163174569	163174569	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163174569G>T	uc002uce.2	-	1	471	c.249C>A	c.(247-249)CTC>CTA	p.L83L	IFIH1_uc002ucf.2_Silent_p.L83L	NM_022168	NP_071451	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	83	CARD 1.				detection of virus|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|regulation of apoptosis	cytosol|nucleus	ATP binding|DNA binding|double-stranded RNA binding|helicase activity|protein binding|ribonucleoprotein binding|zinc ion binding			ovary(1)	1						CGGTTCTCCGGAGGGCCTCCA	0.592													5	50	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179583529	179583529	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179583529G>T	uc010zfg.1	-	81	20890	c.20666C>A	c.(20665-20667)ACA>AAA	p.T6889K	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.T3550K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7816							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)			CTCCAGTTCTGTGACAAAATC	0.478													9	72	---	---	---	---	PASS
TRAK2	66008	broad.mit.edu	37	2	202245669	202245669	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202245669G>T	uc002uyb.3	-	16	2788	c.2342C>A	c.(2341-2343)CCA>CAA	p.P781Q		NM_015049	NP_055864	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	781				Missing (in Ref. 2).		early endosome|plasma membrane	GABA receptor binding				0						TGAGTGAGATGGTGAATTTGG	0.522													6	94	---	---	---	---	PASS
ALS2	57679	broad.mit.edu	37	2	202590178	202590178	+	Splice_Site	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202590178C>A	uc002uyo.2	-	20	3605	c.3249_splice	c.e20-1	p.G1083_splice	ALS2_uc002uyp.3_Splice_Site_p.G1083_splice|ALS2_uc010ftl.2_Splice_Site	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1						cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						TTCTCCATACCTGCCATGAAA	0.363													5	83	---	---	---	---	PASS
DYTN	391475	broad.mit.edu	37	2	207527889	207527889	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207527889C>T	uc002vbr.1	-	11	1488	c.1371G>A	c.(1369-1371)GAG>GAA	p.E457E		NM_001093730	NP_001087199	A2CJ06	DYTN_HUMAN	dystrotelin	457						plasma membrane	zinc ion binding			ovary(1)|central_nervous_system(1)	2				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GCAAAGTGGTCTCTGGTGATT	0.488													5	57	---	---	---	---	PASS
C2orf67	151050	broad.mit.edu	37	2	211018789	211018789	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211018789C>A	uc002vds.2	-	2	726	c.518G>T	c.(517-519)TGG>TTG	p.W173L	C2orf67_uc002vdt.2_Missense_Mutation_p.W173L|C2orf67_uc002vdw.2_Missense_Mutation_p.W173L|C2orf67_uc002vdy.1_Missense_Mutation_p.W173L|C2orf67_uc002vdv.2_Missense_Mutation_p.W173L|C2orf67_uc002vdx.1_Missense_Mutation_p.W173L	NM_152519	NP_689732	A0AUZ9	CB067_HUMAN	hypothetical protein LOC151050	173										ovary(3)	3		Renal(323;0.202)		Epithelial(149;0.00435)|Lung(261;0.0529)|LUSC - Lung squamous cell carcinoma(261;0.0551)|all cancers(144;0.0696)		CTCTTGATACCATTTACAGTT	0.338													6	64	---	---	---	---	PASS
UGT1A1	54658	broad.mit.edu	37	2	234669706	234669706	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234669706G>C	uc002vvb.2	+	1	788	c.773G>C	c.(772-774)AGT>ACT	p.S258T	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A5_uc002vuw.2_Intron|UGT1A4_uc010zna.1_Intron|UGT1A4_uc002vux.2_Intron|UGT1A3_uc010znb.1_Intron|UGT1A3_uc002vuy.2_Intron|UGT1A9_uc002vva.2_Intron|UGT1A1_uc010znc.1_Missense_Mutation_p.S258T	NM_000463	NP_000454	P22309	UD11_HUMAN	UDP glycosyltransferase 1 family, polypeptide A1	258					bilirubin conjugation|digestion|estrogen metabolic process|flavone metabolic process|heme catabolic process	endoplasmic reticulum membrane|microsome	enzyme binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding|steroid binding			central_nervous_system(1)|skin(1)	2		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Adenine(DB00173)|Diclofenac(DB00586)|Estradiol(DB00783)|Ezetimibe(DB00973)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Rifampin(DB01045)|Troglitazone(DB00197)	CTGTTTAGAAGTGACTTTGTG	0.468													4	68	---	---	---	---	PASS
MLPH	79083	broad.mit.edu	37	2	238419719	238419719	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238419719C>A	uc002vwt.2	+	4	647	c.420C>A	c.(418-420)TCC>TCA	p.S140S	MLPH_uc002vws.2_Silent_p.S140S|MLPH_uc010fyt.1_Silent_p.S140S|MLPH_uc002vwu.2_Silent_p.S140S|MLPH_uc002vwv.2_Silent_p.S140S|MLPH_uc002vww.2_Silent_p.S116S	NM_024101	NP_077006	Q9BV36	MELPH_HUMAN	melanophilin isoform 1	140							metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		TCATCCGGTCCCTCCACGGGC	0.522													7	177	---	---	---	---	PASS
CNTN4	152330	broad.mit.edu	37	3	2787299	2787299	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2787299C>A	uc003bpc.2	+	5	497	c.276C>A	c.(274-276)ACC>ACA	p.T92T	CNTN4_uc003bpb.1_5'UTR|CNTN4_uc003bpd.1_Silent_p.T92T	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	92	Ig-like C2-type 1.				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	p.K92N(1)		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)		CCAATAAAACCCAAGATGCTG	0.413													5	68	---	---	---	---	PASS
VILL	50853	broad.mit.edu	37	3	38047298	38047298	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38047298G>T	uc003chj.2	+	17	2252	c.1966G>T	c.(1966-1968)GGG>TGG	p.G656W	VILL_uc003chl.2_Missense_Mutation_p.G656W	NM_015873	NP_056957	O15195	VILL_HUMAN	villin-like protein	656	Gelsolin-like 6.				actin filament capping|cytoskeleton organization	actin cytoskeleton	actin binding|structural constituent of cytoskeleton				0				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		CCTGTGGCTTGGGGAAGCTGC	0.647													4	18	---	---	---	---	PASS
IMPG2	50939	broad.mit.edu	37	3	100964871	100964871	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100964871C>G	uc003duq.1	-	12	1521	c.1318G>C	c.(1318-1320)GGT>CGT	p.G440R	IMPG2_uc011bhe.1_Missense_Mutation_p.G303R	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	440	Extracellular (Potential).				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						GAGGGAGGACCAGAGCTGAAA	0.493													8	43	---	---	---	---	PASS
DZIP3	9666	broad.mit.edu	37	3	108394691	108394691	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108394691G>A	uc003dxd.2	+	25	3174	c.2752G>A	c.(2752-2754)GAT>AAT	p.D918N	DZIP3_uc003dxf.1_Missense_Mutation_p.D918N|DZIP3_uc011bhm.1_Missense_Mutation_p.D369N	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	918	Potential.				protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						CATTGTGGCAGATGTTAGAAA	0.363													6	16	---	---	---	---	PASS
DPPA4	55211	broad.mit.edu	37	3	109049388	109049388	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109049388G>A	uc003dxq.3	-	5	717	c.662C>T	c.(661-663)TCT>TTT	p.S221F	DPPA4_uc011bho.1_Intron|DPPA4_uc011bhp.1_Missense_Mutation_p.S221F	NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	221						nucleus	protein binding			upper_aerodigestive_tract(1)	1						CTCTTGTGGAGATTCCACTGC	0.473													4	36	---	---	---	---	PASS
FAM162A	26355	broad.mit.edu	37	3	122128637	122128637	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122128637C>A	uc003eez.2	+	5	514	c.424C>A	c.(424-426)CGT>AGT	p.R142S		NM_014367	NP_055182	Q96A26	F162A_HUMAN	growth and transformation-dependent protein	142						integral to membrane				ovary(1)	1						AAAGAAAGCTCGTCTGAAAGA	0.433													5	107	---	---	---	---	PASS
EPHB1	2047	broad.mit.edu	37	3	134851685	134851685	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134851685G>A	uc003eqt.2	+	5	1311	c.1091G>A	c.(1090-1092)CGG>CAG	p.R364Q	EPHB1_uc010htz.1_RNA|EPHB1_uc011bly.1_3'UTR|EPHB1_uc003equ.2_5'UTR	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	364	Extracellular (Potential).|Fibronectin type-III 1.					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding	p.R364L(2)		lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						AAAAAGTGCCGGGCAGACCGC	0.602													4	35	---	---	---	---	PASS
P2RY13	53829	broad.mit.edu	37	3	151046127	151046127	+	Silent	SNP	A	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151046127A>G	uc003eyv.2	-	2	738	c.717T>C	c.(715-717)TAT>TAC	p.Y239Y	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_176894	NP_795713	Q9BPV8	P2Y13_HUMAN	purinergic receptor P2Y, G-protein coupled, 13	239	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(3)|lung(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0189)|Lung(72;0.0278)			TGGACTTTCTATAAGAATCAT	0.318													5	60	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164905718	164905718	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164905718G>T	uc003fej.3	-	2	3345	c.2901C>A	c.(2899-2901)CTC>CTA	p.L967L	SLITRK3_uc003fek.2_Silent_p.L967L	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	967	Cytoplasmic (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						CCAGGACTTCGAGGTAATCCG	0.388										HNSCC(40;0.11)			5	145	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164907242	164907242	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164907242C>G	uc003fej.3	-	2	1821	c.1377G>C	c.(1375-1377)AAG>AAC	p.K459N	SLITRK3_uc003fek.2_Missense_Mutation_p.K459N	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	459	LRR 9.|Extracellular (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						GGAAGAGGCTCTTTAAGTTGG	0.433										HNSCC(40;0.11)			4	49	---	---	---	---	PASS
FNDC3B	64778	broad.mit.edu	37	3	172052809	172052809	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172052809G>T	uc003fhy.2	+	15	1889	c.1717G>T	c.(1717-1719)GGA>TGA	p.G573*	FNDC3B_uc003fhz.3_Nonsense_Mutation_p.G573*|FNDC3B_uc003fia.2_Nonsense_Mutation_p.G504*	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	573	Fibronectin type-III 4.					endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		TGACAGGCCTGGACCTCCTAC	0.453													7	199	---	---	---	---	PASS
PIK3CA	5290	broad.mit.edu	37	3	178921477	178921477	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178921477G>T	uc003fjk.2	+	5	1116	c.959G>T	c.(958-960)GGA>GTA	p.G320V		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	320					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			TATATGAATGGAGAAACATCT	0.358		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			5	83	---	---	---	---	PASS
MFN1	55669	broad.mit.edu	37	3	179069752	179069752	+	Silent	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179069752A>T	uc003fjs.2	+	3	303	c.177A>T	c.(175-177)GGA>GGT	p.G59G	MFN1_uc010hxb.2_RNA|MFN1_uc003fjt.2_Silent_p.G87G	NM_033540	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	59	Cytoplasmic (Potential).				mitochondrial fusion	integral to membrane|mitochondrial outer membrane	GTP binding|GTPase activity			ovary(2)|large_intestine(1)	3	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			AAATGCAAGGATATAAAGACA	0.353													35	111	---	---	---	---	PASS
PCDH7	5099	broad.mit.edu	37	4	31144376	31144376	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31144376G>T	uc011bxx.1	+	3	4657	c.3649G>T	c.(3649-3651)GAG>TAG	p.E1217*	PCDH7_uc011bxw.1_Nonsense_Mutation_p.E1170*	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	Error:Variant_position_missing_in_O60245_after_alignment					homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						CAGCAAAAATGAGGAAGCCAA	0.463													6	128	---	---	---	---	PASS
CEP135	9662	broad.mit.edu	37	4	56832003	56832003	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56832003A>T	uc003hbi.2	+	8	1256	c.1022A>T	c.(1021-1023)GAT>GTT	p.D341V	CEP135_uc003hbj.2_Missense_Mutation_p.D47V|CEP135_uc010igz.1_Missense_Mutation_p.D171V	NM_025009	NP_079285	Q66GS9	CP135_HUMAN	centrosome protein 4	341	Potential.				centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	Glioma(25;0.08)|all_neural(26;0.101)					GAGACTGCTGATAAAGAGCTT	0.363													9	25	---	---	---	---	PASS
AP1AR	55435	broad.mit.edu	37	4	113189328	113189328	+	Silent	SNP	A	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113189328A>G	uc003iaj.3	+	10	1025	c.672A>G	c.(670-672)GAA>GAG	p.E224E	AP1AR_uc003iak.3_Silent_p.E191E	NM_018569	NP_061039	Q63HQ0	AP1AR_HUMAN	adaptor-related protein complex 1 associated	224					protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0						CAATGAGAGAACGTTCCAAAA	0.363													4	35	---	---	---	---	PASS
GUCY1A3	2982	broad.mit.edu	37	4	156632319	156632319	+	Silent	SNP	G	T	T	rs1049509		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156632319G>T	uc003iov.2	+	7	1538	c.1002G>T	c.(1000-1002)ACG>ACT	p.T334T	GUCY1A3_uc003iou.2_Silent_p.T334T|GUCY1A3_uc010iqc.2_Silent_p.T334T|GUCY1A3_uc003iow.2_Silent_p.T334T|GUCY1A3_uc010iqd.2_Silent_p.T333T|GUCY1A3_uc003iox.2_Silent_p.T334T|GUCY1A3_uc003ioz.2_Silent_p.T99T|GUCY1A3_uc003ioy.2_Silent_p.T334T|GUCY1A3_uc010iqe.2_Silent_p.T99T|GUCY1A3_uc003ipa.2_Intron|GUCY1A3_uc003ipb.2_Silent_p.T334T	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A	334					blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		TCAACCAGACGTTTAGCGGGA	0.388													11	62	---	---	---	---	PASS
WDR17	116966	broad.mit.edu	37	4	177094441	177094441	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177094441A>T	uc003iuj.2	+	27	3541	c.3385A>T	c.(3385-3387)ACT>TCT	p.T1129S	WDR17_uc003iuk.2_Missense_Mutation_p.T1105S|WDR17_uc003ium.3_Missense_Mutation_p.T1090S|WDR17_uc003iul.1_Intron|WDR17_uc003iun.2_Missense_Mutation_p.T340S	NM_170710	NP_733828	Q8IZU2	WDR17_HUMAN	WD repeat domain 17 isoform 1	1129										ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		CTCAGACTGGACTTTGGATAC	0.318													4	23	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183603016	183603016	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183603016G>T	uc003ivd.1	+	10	1921	c.1884G>T	c.(1882-1884)GGG>GGT	p.G628G	ODZ3_uc003ive.1_Silent_p.G34G	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	628	EGF-like 4.|Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		GTATCCACGGGGAATGTCACT	0.448													5	26	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183675766	183675766	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183675766C>A	uc003ivd.1	+	21	4283	c.4246C>A	c.(4246-4248)CTG>ATG	p.L1416M	ODZ3_uc003ive.1_Missense_Mutation_p.L829M	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	1416	Extracellular (Potential).|NHL 4.				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		CAGTGGGGTCCTGTACATTAC	0.502													4	35	---	---	---	---	PASS
ACSL1	2180	broad.mit.edu	37	4	185687866	185687866	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185687866G>T	uc003iww.2	-	13	1467	c.1173C>A	c.(1171-1173)GAC>GAA	p.D391E	ACSL1_uc011ckm.1_Missense_Mutation_p.D220E|ACSL1_uc003iwt.1_Missense_Mutation_p.D391E|ACSL1_uc003iwu.1_Missense_Mutation_p.D391E|ACSL1_uc011ckn.1_Missense_Mutation_p.D357E|ACSL1_uc003iws.1_5'UTR	NM_001995	NP_001986	P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	391	Cytoplasmic (Potential).				digestion|fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|regulation of fatty acid oxidation|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			ovary(2)	2		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TGGAGGCAAAGTCCAAGAGCC	0.423													4	76	---	---	---	---	PASS
UFSP2	55325	broad.mit.edu	37	4	186343691	186343691	+	Silent	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186343691G>C	uc003ixo.2	-	2	147	c.30C>G	c.(28-30)CTC>CTG	p.L10L	UFSP2_uc003ixq.2_5'UTR|UFSP2_uc003ixp.2_RNA	NM_018359	NP_060829	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	10						endoplasmic reticulum|nucleus	small conjugating protein-specific protease activity				0		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)		TTATTCTGAAGAGTATATCCA	0.294													4	32	---	---	---	---	PASS
ADAMTS16	170690	broad.mit.edu	37	5	5240017	5240017	+	Silent	SNP	C	G	G	rs72647759		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5240017C>G	uc003jdl.2	+	16	2640	c.2502C>G	c.(2500-2502)ACC>ACG	p.T834T	ADAMTS16_uc003jdk.1_Silent_p.T834T	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	834	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						CTGGACCAACCAACGAGACAC	0.507													18	104	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24509935	24509935	+	Intron	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24509935A>T	uc003jgr.1	-						CDH10_uc011cnu.1_Intron	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		GTGGCTGTATAAAAAAATAAA	0.373										HNSCC(23;0.051)			6	34	---	---	---	---	PASS
CDH10	1008	broad.mit.edu	37	5	24537668	24537668	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24537668C>A	uc003jgr.1	-	3	679	c.347G>T	c.(346-348)CGA>CTA	p.R116L	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	116	Cadherin 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)		CCTATCAATTCGCCTTGTGGC	0.398										HNSCC(23;0.051)			4	87	---	---	---	---	PASS
MIR1274A	100302199	broad.mit.edu	37	5	41475802	41475802	+	RNA	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41475802C>A	hsa-mir-1274a|MI0006410	+			c.69C>A			PLCXD3_uc003jmm.1_Intron																	0						ttgagaccatcactacgacag	0.060													13	124	---	---	---	---	PASS
SEC24A	10802	broad.mit.edu	37	5	133996855	133996855	+	Silent	SNP	A	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133996855A>G	uc003kzs.2	+	2	432	c.144A>G	c.(142-144)CAA>CAG	p.Q48Q	SEC24A_uc011cxu.1_5'UTR	NM_021982	NP_068817	O95486	SC24A_HUMAN	SEC24 related gene family, member A	48					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAGTGAGCCAAGGATACAATT	0.418													42	246	---	---	---	---	PASS
PCDHA5	56143	broad.mit.edu	37	5	140202419	140202419	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140202419C>A	uc003lhl.2	+	1	1059	c.1059C>A	c.(1057-1059)ACC>ACA	p.T353T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Silent_p.T353T|PCDHA5_uc003lhj.1_Silent_p.T353T	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	353	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCATAACCACCCTTTTCCTGC	0.498													5	59	---	---	---	---	PASS
PCDHA13	56136	broad.mit.edu	37	5	140262130	140262130	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140262130G>T	uc003lif.2	+	1	277	c.277G>T	c.(277-279)GAG>TAG	p.E93*	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Nonsense_Mutation_p.E93*|PCDHA13_uc003lid.2_Nonsense_Mutation_p.E93*	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	93	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATCGACCGCGAGGAGCTGTG	0.587													5	140	---	---	---	---	PASS
PCDHAC2	56134	broad.mit.edu	37	5	140347837	140347837	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140347837C>A	uc003lii.2	+	1	1726	c.1486C>A	c.(1486-1488)CCA>ACA	p.P496T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron|PCDHAC2_uc011dag.1_Missense_Mutation_p.P496T	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1	496	Cadherin 5.|Extracellular (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)			AGCCACAGACCCAGATGAAAA	0.502													16	77	---	---	---	---	PASS
PCDHB16	57717	broad.mit.edu	37	5	140564189	140564189	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140564189G>T	uc003liv.2	+	1	3210	c.2055G>T	c.(2053-2055)TCG>TCT	p.S685S	PCDHB9_uc003liw.1_5'Flank	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	685	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGCCAACTCGCTCACTGTCT	0.692													4	39	---	---	---	---	PASS
PCDHB16	57717	broad.mit.edu	37	5	140564195	140564195	+	Silent	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140564195T>C	uc003liv.2	+	1	3216	c.2061T>C	c.(2059-2061)ACT>ACC	p.T687T	PCDHB9_uc003liw.1_5'Flank	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	687	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACTCGCTCACTGTCTACCTGG	0.692													6	49	---	---	---	---	PASS
GRPEL2	134266	broad.mit.edu	37	5	148730657	148730657	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148730657G>T	uc003lqj.2	+	4	616	c.490G>T	c.(490-492)GAG>TAG	p.E164*	GRPEL2_uc011dca.1_3'UTR	NM_152407	NP_689620	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial precursor	164					protein folding	mitochondrial matrix	adenyl-nucleotide exchange factor activity|chaperone binding|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCATGGCCTGGAGAAACTGAC	0.517													7	151	---	---	---	---	PASS
PCYOX1L	78991	broad.mit.edu	37	5	148747746	148747746	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148747746C>T	uc003lqk.2	+	6	1076	c.1014C>T	c.(1012-1014)CAC>CAT	p.H338H	PCYOX1L_uc003lql.2_Silent_p.H321H|PCYOX1L_uc010jgz.2_Silent_p.H262H|PCYOX1L_uc003lqm.2_Silent_p.H220H|PCYOX1L_uc003lqn.2_Silent_p.H248H	NM_024028	NP_076933	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like precursor	338				H -> P (in Ref. 7; BAC03391).	prenylcysteine catabolic process	extracellular region	oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTTGGTCCACGGCTACCTCA	0.552											OREG0016912	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	123	---	---	---	---	PASS
PDGFRB	5159	broad.mit.edu	37	5	149511557	149511557	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149511557G>T	uc003lro.2	-	8	1697	c.1228C>A	c.(1228-1230)CAG>AAG	p.Q410K	PDGFRB_uc010jhd.2_Missense_Mutation_p.Q249K	NM_002609	NP_002600	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor beta	410	Extracellular (Potential).				aorta morphogenesis|cardiac myofibril assembly|hemopoiesis|metanephric glomerular capillary formation|metanephric glomerular mesangial cell proliferation involved in metanephros development|peptidyl-tyrosine phosphorylation|positive regulation of calcium ion import|positive regulation of chemotaxis|positive regulation of DNA biosynthetic process|positive regulation of ERK1 and ERK2 cascade|positive regulation of MAP kinase activity|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|protein autophosphorylation|regulation of actin cytoskeleton organization|retina vasculature development in camera-type eye|smooth muscle cell chemotaxis	apical plasma membrane|cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|vascular endothelial growth factor receptor activity			central_nervous_system(4)|lung(4)|breast(3)|stomach(2)|prostate(2)|large_intestine(1)|ovary(1)	17		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATCTGTAGCTGGAAGGAGAGC	0.423			T	ETV6|TRIP11|HIP1|RAB5EP|H4|NIN|HCMOGT-1|PDE4DIP	MPD|AML|CMML|CML								4	25	---	---	---	---	PASS
FABP6	2172	broad.mit.edu	37	5	159640821	159640821	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159640821G>C	uc003lxx.1	+	3	276	c.130G>C	c.(130-132)GGA>CGA	p.G44R	FABP6_uc003lxz.1_Missense_Mutation_p.G44R	NM_001130958	NP_001124430	P51161	FABP6_HUMAN	gastrotropin isoform 1	Error:Variant_position_missing_in_P51161_after_alignment					bile acid and bile salt transport|bile acid metabolic process|negative regulation of cell proliferation	cytosol	transporter activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GACACATAAAGGAAAGGTATG	0.478													9	42	---	---	---	---	PASS
ATP10B	23120	broad.mit.edu	37	5	160025766	160025766	+	Intron	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160025766G>A	uc003lym.1	-						ATP10B_uc010jit.1_Intron	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGGCTGCCCGATCTCCTTAC	0.517													38	249	---	---	---	---	PASS
OR2J3	442186	broad.mit.edu	37	6	29080293	29080293	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29080293T>G	uc011dll.1	+	1	626	c.626T>G	c.(625-627)TTT>TGT	p.F209C		NM_001005216	NP_001005216	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J,	209	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AGCTCCATATTTGTTCTCATA	0.448													5	60	---	---	---	---	PASS
MAS1L	116511	broad.mit.edu	37	6	29454983	29454983	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29454983C>A	uc011dlq.1	-	1	697	c.697G>T	c.(697-699)GCT>TCT	p.A233S		NM_052967	NP_443199	P35410	MAS1L_HUMAN	MAS1 oncogene-like	233	Helical; Name=5; (Potential).					cytoplasm|integral to membrane|nucleus|plasma membrane	G-protein coupled receptor activity			ovary(7)|lung(2)	9						GAAAGGATAGCATGGAAGAGC	0.443													5	47	---	---	---	---	PASS
LY6G5B	58496	broad.mit.edu	37	6	31638749	31638749	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31638749G>T	uc003nvt.1	+	1	22	c.22G>T	c.(22-24)GGT>TGT	p.G8C	CSNK2B_uc003nvs.1_Intron	NM_021221	NP_067044	Q8NDX9	LY65B_HUMAN	lymphocyte antigen 6 complex G5B precursor	8						extracellular region					0						TATGCTTGTAGGTGTGCTGGT	0.572													6	149	---	---	---	---	PASS
COL11A2	1302	broad.mit.edu	37	6	33146896	33146896	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33146896C>A	uc003ocx.1	-	16	1793	c.1565G>T	c.(1564-1566)AGA>ATA	p.R522I	COL11A2_uc010jul.1_5'Flank|COL11A2_uc003ocy.1_Missense_Mutation_p.R436I|COL11A2_uc003ocz.1_Missense_Mutation_p.R415I	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	522	Triple-helical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						CTGAGGTCCTCTGGGGCCCTG	0.652													4	16	---	---	---	---	PASS
CYP39A1	51302	broad.mit.edu	37	6	46593145	46593145	+	Intron	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46593145G>T	uc003oyf.1	-						CYP39A1_uc011dwa.1_Intron|CYP39A1_uc010jzd.1_Intron	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,						bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1						TATATAATAAGGTTTAGTACC	0.343													5	46	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51890462	51890462	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51890462G>T	uc003pah.1	-	32	4422	c.4146C>A	c.(4144-4146)CTC>CTA	p.L1382L	PKHD1_uc003pai.2_Silent_p.L1382L	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1382	IPT/TIG 8; atypical.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					CAAATTGCTGGAGCACCACAG	0.512													16	66	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54735295	54735295	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54735295A>T	uc003pck.2	+	2	367	c.251A>T	c.(250-252)GAT>GTT	p.D84V		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	84										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					GATTCCTGTGATGATACCTTA	0.433													5	91	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64404570	64404570	+	Silent	SNP	C	A	A	rs139681301		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64404570C>A	uc003pep.1	+	5	2622	c.2596C>A	c.(2596-2598)CGG>AGG	p.R866R	PHF3_uc010kaf.1_Silent_p.R866R|PHF3_uc003pem.2_Silent_p.R819R|PHF3_uc010kag.1_Silent_p.R778R|PHF3_uc010kah.1_Silent_p.R680R|PHF3_uc003pen.2_Silent_p.R778R|PHF3_uc011dxs.1_Silent_p.R135R	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	866					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			AGTTTTACCTCGGAGATCCTC	0.403													5	188	---	---	---	---	PASS
CD109	135228	broad.mit.edu	37	6	74477846	74477846	+	Silent	SNP	A	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74477846A>G	uc003php.2	+	14	1991	c.1566A>G	c.(1564-1566)GAA>GAG	p.E522E	CD109_uc010kaz.2_Silent_p.E522E|CD109_uc003phq.2_Silent_p.E522E|CD109_uc010kba.2_Silent_p.E445E	NM_133493	NP_598000	Q6YHK3	CD109_HUMAN	CD109 antigen isoform 1 precursor	522						anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4						TAACACCAGAAAATTCTTGGA	0.338													5	54	---	---	---	---	PASS
C6orf174	387104	broad.mit.edu	37	6	127765317	127765317	+	3'UTR	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127765317A>T	uc003qbd.2	-	12					C6orf174_uc003qbc.2_Silent_p.P674P|C6orf174_uc003qba.2_Silent_p.P85P|C6orf174_uc003qbb.2_Silent_p.P557P|KIAA0408_uc011ebs.1_Silent_p.P674P	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor							integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)		TCCGCAAGGCAGGGGGTGCAG	0.498													7	23	---	---	---	---	PASS
SAMD3	154075	broad.mit.edu	37	6	130505284	130505284	+	Missense_Mutation	SNP	C	A	A	rs41285308	byFrequency	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130505284C>A	uc003qbv.2	-	8	944	c.618G>T	c.(616-618)CAG>CAT	p.Q206H	SAMD3_uc003qbx.2_Missense_Mutation_p.Q206H|SAMD3_uc003qbw.2_Missense_Mutation_p.Q206H|SAMD3_uc010kfg.1_Missense_Mutation_p.Q206H|SAMD3_uc003qby.2_Missense_Mutation_p.Q206H|SAMD3_uc003qbz.1_Missense_Mutation_p.Q165H	NM_001017373	NP_001017373	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3 isoform	206										ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		AAGGGTGGGCCTGCAGCAGGG	0.473													10	29	---	---	---	---	PASS
ENPP3	5169	broad.mit.edu	37	6	132014691	132014691	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132014691C>T	uc003qcu.3	+	16	1686	c.1339C>T	c.(1339-1341)CGA>TGA	p.R447*	ENPP3_uc010kfq.2_RNA|ENPP3_uc003qcv.2_Nonsense_Mutation_p.R447*	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	447	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		TTTGCCAAAGCGACTGCACTA	0.393													10	80	---	---	---	---	PASS
SLC35D3	340146	broad.mit.edu	37	6	137245645	137245645	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137245645C>T	uc003qhe.2	+	2	1227	c.1062C>T	c.(1060-1062)GGC>GGT	p.G354G		NM_001008783	NP_001008783	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	354					carbohydrate transport	integral to membrane				ovary(1)|central_nervous_system(1)	2	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		CAGCAGGTGGCCCCGCTCAGG	0.652													6	11	---	---	---	---	PASS
RAB32	10981	broad.mit.edu	37	6	146870640	146870640	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146870640G>T	uc003qln.1	+	2	471	c.291G>T	c.(289-291)AAG>AAT	p.K97N		NM_006834	NP_006825	Q13637	RAB32_HUMAN	RAB32, member RAS oncogene family	97					protein transport|small GTPase mediated signal transduction	mitochondrion	GTP binding				0		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.68e-09)|GBM - Glioblastoma multiforme(68;0.00608)		TATACTACAAGGAAGCTGTTG	0.358													5	51	---	---	---	---	PASS
PDE10A	10846	broad.mit.edu	37	6	165756886	165756886	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165756886C>A	uc003qun.2	-	20	2302	c.2061G>T	c.(2059-2061)TGG>TGT	p.W687C	PDE10A_uc011egj.1_RNA|PDE10A_uc011egk.1_Missense_Mutation_p.W617C|PDE10A_uc003quo.2_Missense_Mutation_p.W697C	NM_006661	NP_006652	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 2	687					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	ATACCTCAGCCCAGAATTCTG	0.368													7	49	---	---	---	---	PASS
MLLT4	4301	broad.mit.edu	37	6	168347398	168347398	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168347398C>T	uc003qwd.2	+	26	3488	c.3346C>T	c.(3346-3348)CGT>TGT	p.R1116C	MLLT4_uc003qwb.1_Missense_Mutation_p.R1101C|MLLT4_uc003qwc.1_Missense_Mutation_p.R1117C|MLLT4_uc003qwg.1_Missense_Mutation_p.R426C	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	1117					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)		TTCAGATCGTCGTGGCTCAGG	0.393			T	MLL	AL								9	57	---	---	---	---	PASS
RALA	5898	broad.mit.edu	37	7	39730195	39730195	+	Intron	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39730195T>A	uc003thd.2	+							NM_005402	NP_005393	P11233	RALA_HUMAN	ras related v-ral simian leukemia viral oncogene						actin cytoskeleton reorganization|cell cycle|chemotaxis|cytokinesis|exocytosis|interspecies interaction between organisms|membrane raft localization|nerve growth factor receptor signaling pathway|positive regulation of filopodium assembly|Ras protein signal transduction|regulation of exocytosis	cell surface|cleavage furrow|cytosol|midbody|plasma membrane	Edg-2 lysophosphatidic acid receptor binding|GTP binding|GTPase activity			lung(1)|skin(1)	2						TTCAGGTATGTCCTAGAGTAA	0.403													7	22	---	---	---	---	PASS
POM121	9883	broad.mit.edu	37	7	72398919	72398919	+	Intron	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72398919G>T	uc003twk.2	+						POM121_uc003twj.2_Intron|POM121_uc010lam.1_Intron	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)				TTGATTTGTCGCAGGCGCCAT	0.443													20	158	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86493636	86493636	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86493636C>A	uc003uid.2	+	6	3704	c.2605C>A	c.(2605-2607)CGG>AGG	p.R869R	GRM3_uc010lef.2_Missense_Mutation_p.A511E|GRM3_uc010leg.2_Silent_p.R741R|GRM3_uc010leh.2_Silent_p.R461R	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	869	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GTGCAATGGGCGGGAAGTCCT	0.433													33	89	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	100551669	100551669	+	RNA	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100551669C>A	uc003uxk.1	+	1		c.920C>A			uc003uxl.1_Silent_p.A40A					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																		TGACGTCAGCCACTGGGACCC	0.483													86	301	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100686777	100686777	+	Missense_Mutation	SNP	C	A	A	rs138142210	byFrequency	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100686777C>A	uc003uxp.1	+	3	12133	c.12080C>A	c.(12079-12081)ACG>AAG	p.T4027K	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	4027	Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					TCTGCATCAACGCTTTCTGCA	0.537													29	99	---	---	---	---	PASS
CLDN15	24146	broad.mit.edu	37	7	100880666	100880666	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100880666G>T	uc003uyg.1	-	1	451	c.197C>A	c.(196-198)CCG>CAG	p.P66Q	CLDN15_uc003uyh.1_Missense_Mutation_p.P66Q|CLDN15_uc003uyi.2_Missense_Mutation_p.P66Q	NM_014343	NP_055158	P56746	CLD15_HUMAN	claudin 15	66	Extracellular (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	Lung NSC(181;0.168)|all_lung(186;0.215)					CAGCATGGACGGGAACTCCCA	0.637													3	15	---	---	---	---	PASS
CADPS2	93664	broad.mit.edu	37	7	122303469	122303469	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122303469C>A	uc010lkp.2	-	3	771	c.608G>T	c.(607-609)TGG>TTG	p.W203L	CADPS2_uc010lkq.2_Missense_Mutation_p.W203L	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	203					exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						TTTGGCTATCCATGAGCTCAA	0.413													5	62	---	---	---	---	PASS
RNF133	168433	broad.mit.edu	37	7	122338498	122338498	+	Nonsense_Mutation	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122338498T>A	uc003vkj.1	-	1	711	c.475A>T	c.(475-477)AAA>TAA	p.K159*	CADPS2_uc010lkp.2_Intron|CADPS2_uc010lkq.2_Intron	NM_139175	NP_631914	Q8WVZ7	RN133_HUMAN	ring finger protein 133	159	PA.					endoplasmic reticulum membrane|integral to membrane	ligase activity|zinc ion binding			skin(1)	1						TCCGTGCCTTTTAAGTTACCA	0.423													14	73	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	132193312	132193312	+	Silent	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132193312G>C	uc003vra.3	-	2	370	c.141C>G	c.(139-141)CCC>CCG	p.P47P	PLXNA4_uc003vrc.2_Silent_p.P47P|PLXNA4_uc003vrb.2_Silent_p.P47P	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	47	Extracellular (Potential).|Sema.					integral to membrane|intracellular|plasma membrane				ovary(1)	1						AACCCTCGGCGGGCTCTCCTC	0.587													9	26	---	---	---	---	PASS
EXOC4	60412	broad.mit.edu	37	7	133314881	133314881	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133314881C>A	uc003vrk.2	+	10	1536	c.1501C>A	c.(1501-1503)CAC>AAC	p.H501N	EXOC4_uc011kpo.1_Missense_Mutation_p.H400N|EXOC4_uc003vrl.2_Missense_Mutation_p.H111N|EXOC4_uc011kpp.1_Missense_Mutation_p.H33N	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a	501					vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)				CGTCATATTCCACCCATTACT	0.383													5	77	---	---	---	---	PASS
OR2A12	346525	broad.mit.edu	37	7	143793122	143793122	+	Silent	SNP	A	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143793122A>C	uc011kty.1	+	1	922	c.922A>C	c.(922-924)AGA>CGA	p.R308R		NM_001004135	NP_001004135	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A,	308	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	Melanoma(164;0.0783)					TTGGAAACAGAGATCAATGTG	0.423													6	135	---	---	---	---	PASS
CUL1	8454	broad.mit.edu	37	7	148495745	148495745	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148495745G>T	uc010lpg.2	+	20	2638	c.2112G>T	c.(2110-2112)GAG>GAT	p.E704D	CUL1_uc003wey.2_Missense_Mutation_p.E704D|CUL1_uc003wez.2_Missense_Mutation_p.E594D|CUL1_uc003wfa.2_Missense_Mutation_p.E365D	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	704					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			AAAACATCGAGGAAGACCGCA	0.483													7	179	---	---	---	---	PASS
UBE3C	9690	broad.mit.edu	37	7	156974359	156974359	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156974359G>T	uc010lqs.2	+	7	1076	c.764G>T	c.(763-765)GGT>GTT	p.G255V	UBE3C_uc003wnf.2_Missense_Mutation_p.G212V|UBE3C_uc003wng.2_Missense_Mutation_p.G255V	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	255					protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		TGTCCGGAAGGTGCGAGGTGA	0.338													8	75	---	---	---	---	PASS
SNTG1	54212	broad.mit.edu	37	8	51449319	51449319	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51449319C>A	uc010lxy.1	+	12	1002	c.631C>A	c.(631-633)CTA>ATA	p.L211I	SNTG1_uc003xqs.1_Missense_Mutation_p.L211I|SNTG1_uc010lxz.1_Missense_Mutation_p.L211I|SNTG1_uc011ldl.1_RNA	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	211					cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				ACTGATCCCTCTACTTCATTC	0.483													6	148	---	---	---	---	PASS
CPA6	57094	broad.mit.edu	37	8	68423884	68423884	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68423884G>T	uc003xxq.3	-	4	580	c.324C>A	c.(322-324)CTC>CTA	p.L108L	CPA6_uc003xxr.3_5'UTR|CPA6_uc003xxs.2_Silent_p.L108L	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor	108					proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			GATCTTCTATGAGGACCCTGA	0.383													6	125	---	---	---	---	PASS
PREX2	80243	broad.mit.edu	37	8	69009359	69009359	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69009359G>T	uc003xxv.1	+	22	2503	c.2476G>T	c.(2476-2478)GAC>TAC	p.D826Y	PREX2_uc003xxu.1_Missense_Mutation_p.D826Y|PREX2_uc011lez.1_Missense_Mutation_p.D761Y	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	826					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						GTATGAGTACGACAGCACAGC	0.458													12	78	---	---	---	---	PASS
C8orf34	116328	broad.mit.edu	37	8	69351818	69351818	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69351818C>A	uc010lyz.2	+	2	203	c.154C>A	c.(154-156)CGT>AGT	p.R52S	C8orf34_uc010lyx.1_Missense_Mutation_p.R52S|C8orf34_uc010lyy.1_Missense_Mutation_p.R52S|C8orf34_uc003xyb.2_Missense_Mutation_p.R27S	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	52					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			ACAAGGGAACCGTGGACAACT	0.403													8	35	---	---	---	---	PASS
SLCO5A1	81796	broad.mit.edu	37	8	70744099	70744099	+	Silent	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70744099C>G	uc003xyl.2	-	2	1517	c.810G>C	c.(808-810)GCG>GCC	p.A270A	SLCO5A1_uc010lzb.2_Silent_p.A270A|SLCO5A1_uc011lfa.1_RNA|SLCO5A1_uc003xyk.2_Silent_p.A270A|SLCO5A1_uc010lzc.2_Silent_p.A270A	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	270	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)			TGAGAATCTGCGCGCAAATGA	0.502													10	66	---	---	---	---	PASS
KIAA1429	25962	broad.mit.edu	37	8	95523407	95523407	+	Intron	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95523407T>A	uc003ygo.1	-						KIAA1429_uc003ygp.2_Silent_p.S1132S|KIAA1429_uc010maz.1_Intron	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1						mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TATATGGAAGTGATACCTGAG	0.383													6	31	---	---	---	---	PASS
FBXO43	286151	broad.mit.edu	37	8	101153374	101153374	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101153374C>A	uc003yjd.2	-	2	1821	c.1108G>T	c.(1108-1110)GAC>TAC	p.D370Y	FBXO43_uc003yje.2_Missense_Mutation_p.D336Y|FBXO43_uc010mbp.1_Missense_Mutation_p.D370Y	NM_001029860	NP_001025031	Q4G163	FBX43_HUMAN	F-box protein 43 isoform b	370					meiosis		zinc ion binding			kidney(1)|skin(1)	2	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			CTTATGGTGTCCCCAACTTTG	0.463													20	64	---	---	---	---	PASS
PKHD1L1	93035	broad.mit.edu	37	8	110453071	110453071	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110453071C>T	uc003yne.2	+	33	4193	c.4089C>T	c.(4087-4089)ACC>ACT	p.T1363T		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	1363	Extracellular (Potential).|IPT/TIG 7.				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)			CTGAGAATACCGTGCTGTTAG	0.383										HNSCC(38;0.096)			12	129	---	---	---	---	PASS
ASAP1	50807	broad.mit.edu	37	8	131067058	131067058	+	Intron	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131067058G>T	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						CAATCTGCAGGGAGAAAAGAG	0.557													5	51	---	---	---	---	PASS
ZFAT	57623	broad.mit.edu	37	8	135621002	135621002	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135621002G>A	uc003yup.2	-	5	930	c.755C>T	c.(754-756)ACA>ATA	p.T252I	ZFAT_uc003yun.2_Missense_Mutation_p.T240I|ZFAT_uc003yuo.2_Missense_Mutation_p.T240I|ZFAT_uc010meh.2_Missense_Mutation_p.T240I|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Missense_Mutation_p.T240I|ZFAT_uc010mej.2_Missense_Mutation_p.T190I|ZFAT_uc003yur.2_Missense_Mutation_p.T240I	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	252					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CTCATAAGGTGTCTGCTGAAT	0.512													8	105	---	---	---	---	PASS
DENND3	22898	broad.mit.edu	37	8	142178277	142178277	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142178277G>T	uc003yvy.2	+	13	1966	c.1688G>T	c.(1687-1689)CGA>CTA	p.R563L	DENND3_uc010mep.2_Missense_Mutation_p.R524L|DENND3_uc003yvz.1_Missense_Mutation_p.R247L	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	563										ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TTGTACCTCCGAGGGCTCGTT	0.532													4	84	---	---	---	---	PASS
ELAVL2	1993	broad.mit.edu	37	9	23701384	23701384	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23701384G>C	uc003zpu.2	-	5	981	c.706C>G	c.(706-708)CGT>GGT	p.R236G	ELAVL2_uc003zps.2_Missense_Mutation_p.R236G|ELAVL2_uc003zpt.2_Missense_Mutation_p.R236G|ELAVL2_uc003zpv.2_Missense_Mutation_p.R236G|ELAVL2_uc003zpw.2_Missense_Mutation_p.R236G	NM_004432	NP_004423	Q12926	ELAV2_HUMAN	ELAV (embryonic lethal, abnormal vision,	236					regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		TACCTAAAACGCTGTGCCTGC	0.458													30	182	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79323950	79323950	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79323950G>C	uc010mpk.2	-	8	3364	c.3240C>G	c.(3238-3240)GAC>GAG	p.D1080E		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1080					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						TGCTGGGGTCGTCGTAACTGG	0.512													18	89	---	---	---	---	PASS
HEMGN	55363	broad.mit.edu	37	9	100693232	100693232	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100693232C>A	uc004axy.2	-	3	553	c.445G>T	c.(445-447)GAG>TAG	p.E149*	HEMGN_uc004axz.2_Nonsense_Mutation_p.E149*	NM_197978	NP_932095	Q9BXL5	HEMGN_HUMAN	hemogen	149					cell differentiation|multicellular organismal development					ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)				TCTTGGTACTCAGAAAAATTC	0.378													5	93	---	---	---	---	PASS
CEP110	11064	broad.mit.edu	37	9	123875857	123875857	+	Silent	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123875857A>T	uc004bkx.1	+	8	1231	c.1200A>T	c.(1198-1200)ACA>ACT	p.T400T	CEP110_uc004bkw.2_Silent_p.T400T|CEP110_uc004bky.1_Silent_p.T4T	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa	400					cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						TGTTTGCCACAGAGAGTTATA	0.378													13	92	---	---	---	---	PASS
CEL	1056	broad.mit.edu	37	9	135941993	135941993	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135941993C>T	uc010naa.1	+	5	640	c.624C>T	c.(622-624)CCC>CCT	p.P208P		NM_001807	NP_001798	P19835	CEL_HUMAN	carboxyl ester lipase precursor	205					cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification	cytosol|extracellular space	acylglycerol lipase activity|carboxylesterase activity|heparin binding|sterol esterase activity|triglyceride lipase activity			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		GGGGGGACCCCAACAACATCA	0.642													12	65	---	---	---	---	PASS
LYZL2	119180	broad.mit.edu	37	10	30915048	30915048	+	Missense_Mutation	SNP	T	A	A	rs143775752	byFrequency	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30915048T>A	uc001ivk.2	-	3	435	c.422A>T	c.(421-423)CAC>CTC	p.H141L		NM_183058	NP_898881	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	95					cell wall macromolecule catabolic process	extracellular region	lysozyme activity				0		Prostate(175;0.151)				GCAGGCGACGTGGCAGTGGTT	0.557													6	75	---	---	---	---	PASS
ZEB1	6935	broad.mit.edu	37	10	31791294	31791294	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31791294A>T	uc001ivs.3	+	4	401	c.338A>T	c.(337-339)GAG>GTG	p.E113V	ZEB1_uc001ivr.3_5'UTR|ZEB1_uc010qee.1_5'UTR|ZEB1_uc010qef.1_5'UTR|ZEB1_uc009xlh.1_RNA|ZEB1_uc009xli.1_RNA|ZEB1_uc009xlj.1_Intron|ZEB1_uc010qeg.1_Intron|ZEB1_uc009xlk.1_5'UTR|ZEB1_uc001ivt.3_5'UTR|ZEB1_uc001ivu.3_Missense_Mutation_p.E114V|ZEB1_uc001ivv.3_Missense_Mutation_p.E93V|ZEB1_uc010qeh.1_Missense_Mutation_p.E46V|ZEB1_uc009xll.2_RNA|ZEB1_uc009xlm.1_RNA|ZEB1_uc009xln.1_RNA|ZEB1_uc009xlo.1_Missense_Mutation_p.E96V|ZEB1_uc009xlp.2_Missense_Mutation_p.E97V	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	113					cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				GATGAATGCGAGTCAGATGCA	0.338													5	26	---	---	---	---	PASS
TMEM72	643236	broad.mit.edu	37	10	45430487	45430487	+	Missense_Mutation	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45430487G>A	uc001jbn.2	+	5	930	c.733G>A	c.(733-735)GAG>AAG	p.E245K	uc001jbk.1_Intron|uc001jbl.2_Intron|TMEM72_uc009xmm.1_Missense_Mutation_p.E127K	NM_001123376	NP_001116848	A0PK05	TMM72_HUMAN	transmembrane protein 72	245						integral to membrane					0						TGGGGACAGTGAGCCAGAGGA	0.602													15	56	---	---	---	---	PASS
C10orf25	220979	broad.mit.edu	37	10	45495868	45495868	+	Intron	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45495868G>A	uc001jbv.1	-						C10orf25_uc010qff.1_Intron|ZNF22_uc001jbw.2_5'Flank	NM_001039380	NP_001034469	Q5T742	CJ025_HUMAN	hypothetical protein LOC220979 precursor							extracellular region					0						GAGGAGCCTGGAAGGAATAAG	0.199													4	16	---	---	---	---	PASS
FRMPD2	143162	broad.mit.edu	37	10	49457087	49457087	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49457087C>A	uc001jgi.2	-	3	393	c.286G>T	c.(286-288)GAT>TAT	p.D96Y	FRMPD2_uc001jgh.2_Missense_Mutation_p.D87Y|FRMPD2_uc001jgj.2_Missense_Mutation_p.D96Y	NM_001018071	NP_001018081	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2 isoform 3	96	KIND.				tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)		GGCTGCTCATCCTCACTCTGT	0.567													5	39	---	---	---	---	PASS
SLC18A3	6572	broad.mit.edu	37	10	50820303	50820303	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50820303G>T	uc001jhw.2	+	1	1957	c.1517G>T	c.(1516-1518)GGC>GTC	p.G506V	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank|CHAT_uc001jia.2_5'Flank|CHAT_uc001jhz.2_5'Flank|CHAT_uc010qgs.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	506	Cytoplasmic (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(2)	2						CCTGTGTCTGGCCAGGACGGC	0.652													5	29	---	---	---	---	PASS
A1CF	29974	broad.mit.edu	37	10	52595861	52595861	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52595861C>A	uc001jjj.2	-	6	765	c.577G>T	c.(577-579)GCC>TCC	p.A193S	A1CF_uc010qhn.1_Missense_Mutation_p.A201S|A1CF_uc001jji.2_Missense_Mutation_p.A193S|A1CF_uc001jjh.2_Missense_Mutation_p.A201S|A1CF_uc010qho.1_Missense_Mutation_p.A201S|A1CF_uc009xov.2_Missense_Mutation_p.A193S	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 2	193	RRM 2.				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1						CTCGCCATGGCAGCTGCTCGA	0.498													5	63	---	---	---	---	PASS
RUFY2	55680	broad.mit.edu	37	10	70161474	70161474	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70161474A>T	uc001job.2	-	3	631	c.304T>A	c.(304-306)TAC>AAC	p.Y102N	RUFY2_uc001jnz.1_RNA|RUFY2_uc001joc.2_Missense_Mutation_p.Y67N|RUFY2_uc010qiw.1_Missense_Mutation_p.Y9N|RUFY2_uc001jod.1_Missense_Mutation_p.Y67N|RUFY2_uc009xpv.1_5'UTR|RUFY2_uc001joe.1_Missense_Mutation_p.Y67N	NM_017987	NP_060457	Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain-containing 2 isoform a	116	RUN.					nucleus	metal ion binding			ovary(1)	1						GTTTTGTTGTAACTCAAAAAT	0.373													6	41	---	---	---	---	PASS
CBARA1	10367	broad.mit.edu	37	10	74267937	74267937	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74267937T>C	uc001jtb.1	-	7	767	c.634A>G	c.(634-636)ATT>GTT	p.I212V	CBARA1_uc010qjw.1_5'UTR|CBARA1_uc010qjx.1_Intron|CBARA1_uc009xqo.1_RNA	NM_006077	NP_006068	Q9BPX6	MICU1_HUMAN	calcium binding atopy-related autoantigen 1	210					calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1						GTGAGGAAAATGTAGTCTGAA	0.328													3	9	---	---	---	---	PASS
RPP30	10556	broad.mit.edu	37	10	92631758	92631758	+	Silent	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92631758A>T	uc009xtx.2	+	1	50	c.15A>T	c.(13-15)GCA>GCT	p.A5A	RPP30_uc001khd.2_Silent_p.A5A|RPP30_uc010qnj.1_Silent_p.A5A	NM_006413	NP_006404	P78346	RPP30_HUMAN	ribonuclease P/MRP 30kDa subunit isoform b	5					tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0						CGGTGTTTGCAGATTTGGACC	0.652													8	114	---	---	---	---	PASS
SORCS1	114815	broad.mit.edu	37	10	108432656	108432656	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108432656C>G	uc001kym.2	-	15	2036	c.2028G>C	c.(2026-2028)GAG>GAC	p.E676D	SORCS1_uc001kyl.2_Missense_Mutation_p.E676D|SORCS1_uc009xxs.2_Missense_Mutation_p.E676D|SORCS1_uc001kyn.1_Missense_Mutation_p.E676D|SORCS1_uc001kyo.2_Missense_Mutation_p.E676D	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	676	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GTCTGTAGTCCTCTTCGGCAC	0.507													4	30	---	---	---	---	PASS
TACC2	10579	broad.mit.edu	37	10	123842522	123842522	+	Silent	SNP	C	A	A	rs146425124	byFrequency	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123842522C>A	uc001lfv.2	+	4	867	c.507C>A	c.(505-507)GCC>GCA	p.A169A	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Silent_p.A169A|TACC2_uc010qtv.1_Silent_p.A169A	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	169						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				AGATTGCTGCCGTCCCCAGTG	0.587													3	14	---	---	---	---	PASS
C10orf137	26098	broad.mit.edu	37	10	127418024	127418024	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127418024A>G	uc001liq.1	+	8	1285	c.992A>G	c.(991-993)TAC>TGC	p.Y331C	C10orf137_uc001lin.2_Missense_Mutation_p.Y297C|C10orf137_uc001lio.1_Missense_Mutation_p.Y297C|C10orf137_uc001lip.1_Missense_Mutation_p.T30A	NM_015608	NP_056423	Q3B7T1	EDRF1_HUMAN	erythroid differentiation-related factor 1	331					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	binding			ovary(5)|large_intestine(3)|lung(2)	10		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GGAGGCAGATACCCAGCAGTC	0.398													5	62	---	---	---	---	PASS
JAKMIP3	282973	broad.mit.edu	37	10	133978215	133978215	+	Silent	SNP	A	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133978215A>G	uc001lkx.3	+	20	2460	c.2460A>G	c.(2458-2460)AGA>AGG	p.R820R	JAKMIP3_uc009yba.1_Silent_p.R257R	NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		CTCAGAAGAGACAAATAAAGG	0.418													11	74	---	---	---	---	PASS
OR52E6	390078	broad.mit.edu	37	11	5862634	5862634	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5862634A>T	uc010qzq.1	-	1	494	c.494T>A	c.(493-495)CTC>CAC	p.L165H	TRIM5_uc001mbq.1_Intron	NM_001005167	NP_001005167	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAACCTTAAGAGGAGAAACAC	0.493													25	128	---	---	---	---	PASS
FAM160A2	84067	broad.mit.edu	37	11	6245017	6245017	+	Silent	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6245017T>A	uc001mcl.3	-	3	959	c.600A>T	c.(598-600)CCA>CCT	p.P200P	FAM160A2_uc001mck.3_Silent_p.P200P|FAM160A2_uc001mcm.2_Silent_p.P200P	NM_001098794	NP_001092264	Q8N612	F16A2_HUMAN	hypothetical protein LOC84067 isoform 2	200					early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding			skin(2)	2						GCTCAGGAGGTGGCTGCAGGA	0.602													14	74	---	---	---	---	PASS
WEE1	7465	broad.mit.edu	37	11	9608129	9608129	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9608129C>A	uc001mhs.2	+	9	1857	c.1604C>A	c.(1603-1605)CCA>CAA	p.P535Q	WEE1_uc001mht.2_Missense_Mutation_p.P321Q	NM_003390	NP_003381	P30291	WEE1_HUMAN	WEE1 tyrosine kinase isoform 1	535	Protein kinase.				blood coagulation|cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|S phase of mitotic cell cycle	nucleoplasm	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	5				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		CCTCGGATACCACAAGTGCTT	0.413													5	83	---	---	---	---	PASS
SERGEF	26297	broad.mit.edu	37	11	18014479	18014479	+	Silent	SNP	T	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18014479T>G	uc001mnm.2	-	7	764	c.684A>C	c.(682-684)ACA>ACC	p.T228T	SERGEF_uc009yhd.2_RNA|SERGEF_uc001mnn.2_Silent_p.T228T|SERGEF_uc010rcz.1_Silent_p.T114T|SERGEF_uc001mno.1_Silent_p.T114T	NM_012139	NP_036271	Q9UGK8	SRGEF_HUMAN	deafness locus associated putative guanine	228	RCC1 4.				negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1						GGTACCTACCTGTTAATGAAG	0.338													8	38	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	30928154	30928154	+	RNA	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30928154C>G	uc001mss.1	-	8		c.1140G>C			uc009yjk.1_Missense_Mutation_p.C794S|uc009yjj.1_RNA					Homo sapiens mRNA for KIAA1493 protein, partial cds.																		GCCTGAAATACAGAGGAATGG	0.463													7	22	---	---	---	---	PASS
C11orf41	25758	broad.mit.edu	37	11	33565038	33565038	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33565038C>T	uc001mup.3	+	1	1162	c.1038C>T	c.(1036-1038)GGC>GGT	p.G346G	C11orf41_uc001mun.1_Silent_p.G346G	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	346						integral to membrane				ovary(2)	2						CATCTCTTGGCTTTTCCAGCA	0.537											OREG0020868	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	24	113	---	---	---	---	PASS
SPRYD5	84767	broad.mit.edu	37	11	55655543	55655543	+	Silent	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55655543T>A	uc010rip.1	+	4	635	c.543T>A	c.(541-543)GCT>GCA	p.A181A	SPRYD5_uc010riq.1_Silent_p.A38A	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	181						intracellular	zinc ion binding				0		all_epithelial(135;0.226)				CAATCAGAGCTGAATATCAGA	0.393													5	28	---	---	---	---	PASS
OR5T1	390155	broad.mit.edu	37	11	56043875	56043875	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56043875G>T	uc001nio.1	+	1	761	c.761G>T	c.(760-762)GGA>GTA	p.G254V		NM_001004745	NP_001004745	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T,	254	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(21;0.00448)					TCTACATGTGGAGCTCACCTA	0.438													12	140	---	---	---	---	PASS
OR5M10	390167	broad.mit.edu	37	11	56344723	56344723	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56344723G>C	uc001niz.1	-	1	475	c.475C>G	c.(475-477)CAG>GAG	p.Q159E		NM_001004741	NP_001004741	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M,	159	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						AGCAGTGTCTGAGAGAGCCCA	0.468													4	149	---	---	---	---	PASS
FAM111B	374393	broad.mit.edu	37	11	58892347	58892347	+	Silent	SNP	A	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58892347A>G	uc001nnl.2	+	4	1020	c.777A>G	c.(775-777)GTA>GTG	p.V259V	FAM111B_uc001nnm.2_Silent_p.V229V|FAM111B_uc010rko.1_Silent_p.V229V	NM_198947	NP_945185	Q6SJ93	F111B_HUMAN	hypothetical protein LOC374393 isoform a	259							catalytic activity			ovary(2)	2						TGGATGAAGTATCTGGAAAAG	0.338													7	46	---	---	---	---	PASS
PPFIA1	8500	broad.mit.edu	37	11	70118486	70118486	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70118486G>T	uc001opo.2	+	2	406	c.208G>T	c.(208-210)GAG>TAG	p.E70*	PPFIA1_uc001opn.1_Nonsense_Mutation_p.E70*|PPFIA1_uc001opp.2_RNA	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b	70	Potential.				cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			GAAGTTACACGAGGTTGGTCA	0.458													5	99	---	---	---	---	PASS
C11orf30	56946	broad.mit.edu	37	11	76171008	76171008	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76171008G>T	uc001oxl.2	+	6	593	c.450G>T	c.(448-450)ACG>ACT	p.T150T	C11orf30_uc001oxk.2_3'UTR|C11orf30_uc009yuj.1_Silent_p.T165T|C11orf30_uc010rsa.1_Intron|C11orf30_uc001oxm.2_Silent_p.T151T|C11orf30_uc010rsb.1_Silent_p.T165T|C11orf30_uc010rsc.1_Silent_p.T165T|C11orf30_uc001oxn.2_Silent_p.T151T|C11orf30_uc010rsd.1_Silent_p.T164T	NM_020193	NP_064578	Q7Z589	EMSY_HUMAN	EMSY protein	150	Interaction with BRCA2.				chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6						CAAGTACCACGTCAACCCCAA	0.443													6	106	---	---	---	---	PASS
C11orf82	220042	broad.mit.edu	37	11	82644903	82644903	+	Silent	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82644903T>C	uc001ozt.2	+	6	2767	c.2523T>C	c.(2521-2523)GGT>GGC	p.G841G	C11orf82_uc010rsr.1_Silent_p.G540G|C11orf82_uc010rss.1_Silent_p.G540G|C11orf82_uc009yvd.2_Intron	NM_145018	NP_659455	Q8IXT1	NOXIN_HUMAN	nitric oxide-inducible gene protein	841					apoptosis|cell cycle arrest	cytoplasm|nucleus				ovary(2)	2						TTGTATCTGGTGTTTCACAAC	0.403													6	54	---	---	---	---	PASS
CHORDC1	26973	broad.mit.edu	37	11	89935578	89935578	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89935578C>G	uc001pdg.2	-	11	1404	c.994G>C	c.(994-996)GAT>CAT	p.D332H	CHORDC1_uc009yvz.2_Missense_Mutation_p.D313H	NM_012124	NP_036256	Q9UHD1	CHRD1_HUMAN	cysteine and histidine-rich domain-containing	332					chaperone-mediated protein folding|regulation of response to stress|response to stress		Hsp90 protein binding|identical protein binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.00915)				CCCACTCAATCTGTTGTGGCA	0.398													4	28	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92495063	92495063	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92495063C>A	uc001pdj.3	+	4	3728	c.3711C>A	c.(3709-3711)ACC>ACA	p.T1237T		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1237	Cadherin 11.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AACAGTCAACCATTTGGGTGG	0.438										TCGA Ovarian(4;0.039)			7	170	---	---	---	---	PASS
FAT3	120114	broad.mit.edu	37	11	92534954	92534954	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92534954G>T	uc001pdj.3	+	9	8792	c.8775G>T	c.(8773-8775)GCG>GCT	p.A2925A		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2925	Cadherin 27.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CAGTCTTCGCGCAGGAAGTGT	0.567										TCGA Ovarian(4;0.039)			4	79	---	---	---	---	PASS
GRAMD1B	57476	broad.mit.edu	37	11	123477373	123477373	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123477373G>T	uc001pyx.2	+	10	1280	c.951G>T	c.(949-951)AAG>AAT	p.K317N	GRAMD1B_uc001pyw.2_Missense_Mutation_p.K324N|GRAMD1B_uc010rzw.1_Missense_Mutation_p.K277N|GRAMD1B_uc010rzx.1_Missense_Mutation_p.K277N|GRAMD1B_uc009zbe.1_Missense_Mutation_p.K313N|GRAMD1B_uc001pyy.2_5'Flank	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	317						integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CCCTGGAAAAGGAGCTCGCCA	0.562													4	17	---	---	---	---	PASS
TMEM225	338661	broad.mit.edu	37	11	123754822	123754822	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123754822C>T	uc001pzi.2	-	3	631	c.423G>A	c.(421-423)ATG>ATA	p.M141I		NM_001013743	NP_001013765	Q6GV28	TM225_HUMAN	transmembrane protein 225	141	Helical; (Potential).					integral to membrane				upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	3						AAGCAGTATACATGATCCAGG	0.448													6	70	---	---	---	---	PASS
OR10G4	390264	broad.mit.edu	37	11	123887173	123887173	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123887173G>T	uc010sac.1	+	1	892	c.892G>T	c.(892-894)GTG>TTG	p.V298L		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	298	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		GAAGAAAGCTGTGTTGAAACT	0.393													10	52	---	---	---	---	PASS
GALNT8	26290	broad.mit.edu	37	12	4874599	4874599	+	Missense_Mutation	SNP	G	T	T	rs144271473	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4874599G>T	uc001qne.1	+	10	1740	c.1648G>T	c.(1648-1650)GCC>TCC	p.A550S		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	550	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(1)|skin(1)	4						GATTGCAGAGGCCAGTGCTAG	0.458													6	41	---	---	---	---	PASS
CD163	9332	broad.mit.edu	37	12	7647710	7647710	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7647710C>T	uc001qsz.3	-	6	1515	c.1387G>A	c.(1387-1389)GAT>AAT	p.D463N	CD163_uc001qta.3_Missense_Mutation_p.D463N|CD163_uc009zfw.2_Missense_Mutation_p.D463N	NM_004244	NP_004235	Q86VB7	C163A_HUMAN	CD163 antigen isoform a	463	SRCR 4.|Extracellular (Potential).				acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity			ovary(6)|pancreas(1)|skin(1)	8						TCATAGTGATCACAGGTAAGT	0.398													16	98	---	---	---	---	PASS
MFAP5	8076	broad.mit.edu	37	12	8803091	8803091	+	Intron	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8803091C>T	uc001qut.1	-						MFAP5_uc001qus.2_Intron|MFAP5_uc009zge.1_Intron	NM_003480	NP_003471	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5 precursor							microfibril	extracellular matrix structural constituent			breast(1)	1	Lung SC(5;0.184)					ATTCTGGGATCCCTTACCTGG	0.448													6	34	---	---	---	---	PASS
CMAS	55907	broad.mit.edu	37	12	22218072	22218072	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22218072G>T	uc001rfm.2	+	8	1211	c.1132G>T	c.(1132-1134)GAA>TAA	p.E378*	CMAS_uc001rfn.2_RNA	NM_018686	NP_061156	Q8NFW8	NEUA_HUMAN	cytidine monophospho-N-acetylneuraminic acid	378					lipopolysaccharide biosynthetic process	nucleus	N-acylneuraminate cytidylyltransferase activity			ovary(1)|pancreas(1)|skin(1)	3						AGTGTCTGATGAAGAGTGCTT	0.423													16	113	---	---	---	---	PASS
C12orf40	283461	broad.mit.edu	37	12	40114794	40114794	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40114794C>A	uc001rmc.2	+	13	1867	c.1700C>A	c.(1699-1701)CCA>CAA	p.P567Q	C12orf40_uc009zjv.1_Intron	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	567										ovary(6)	6						GATCAGTTTCCACAGTTGCAG	0.388													6	61	---	---	---	---	PASS
GXYLT1	283464	broad.mit.edu	37	12	42512879	42512879	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42512879C>G	uc001rms.3	-	3	634	c.409G>C	c.(409-411)GCT>CCT	p.A137P	GXYLT1_uc001rmt.3_Missense_Mutation_p.A106P	NM_173601	NP_775872	Q4G148	GXLT1_HUMAN	glycosyltransferase 8 domain containing 3	137	Lumenal (Potential).				O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0						AAAATGATAGCTGACTTCAAC	0.373													4	66	---	---	---	---	PASS
BIN2	51411	broad.mit.edu	37	12	51696919	51696919	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51696919C>A	uc001ryg.2	-	3	221	c.169G>T	c.(169-171)GGC>TGC	p.G57C	BIN2_uc009zlz.2_Missense_Mutation_p.G57C|BIN2_uc001ryh.2_Translation_Start_Site|BIN2_uc010sng.1_Missense_Mutation_p.G31C	NM_016293	NP_057377	Q9UBW5	BIN2_HUMAN	bridging integrator 2	57	BAR.					cytoplasm	protein binding			ovary(1)	1						AGCTTGTGGCCTTCTGCCTGA	0.418													5	44	---	---	---	---	PASS
ACVR1B	91	broad.mit.edu	37	12	52380615	52380615	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52380615G>C	uc001rzn.2	+	7	1192	c.1150G>C	c.(1150-1152)GAA>CAA	p.E384Q	ACVR1B_uc001rzl.2_Missense_Mutation_p.E384Q|ACVR1B_uc001rzm.2_Missense_Mutation_p.E384Q|ACVR1B_uc010snn.1_Missense_Mutation_p.E425Q	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor	384	Protein kinase.|Cytoplasmic (Potential).				G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway	cell surface	activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding			pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1)	9				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	CATGGCCCCTGAAGTACTTGA	0.393													10	67	---	---	---	---	PASS
KRT6B	3854	broad.mit.edu	37	12	52841120	52841120	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52841120A>T	uc001sak.2	-	9	1597	c.1549T>A	c.(1549-1551)TAT>AAT	p.Y517N		NM_005555	NP_005546	P04259	K2C6B_HUMAN	keratin 6B	517	Tail.				ectoderm development	keratin filament	structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.083)		CCACTGCCATAGGAGTAGCTG	0.632													5	35	---	---	---	---	PASS
HOXC5	3222	broad.mit.edu	37	12	54428081	54428081	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54428081C>A	uc001sew.2	+	2	549	c.474C>A	c.(472-474)TCC>TCA	p.S158S	HOXC5_uc001set.2_RNA|HOXC4_uc001seu.2_Intron	NM_018953	NP_061826	Q00444	HXC5_HUMAN	homeobox C5	158	Homeobox.				regulation of transcription from RNA polymerase II promoter	cell junction|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GCAAGCGGTCCCGAACCAGTT	0.597													7	116	---	---	---	---	PASS
NCKAP1L	3071	broad.mit.edu	37	12	54925091	54925091	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54925091C>A	uc001sgc.3	+	23	2633	c.2554C>A	c.(2554-2556)CTG>ATG	p.L852M	NCKAP1L_uc010sox.1_Missense_Mutation_p.L394M|NCKAP1L_uc010soy.1_Missense_Mutation_p.L802M	NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	852					actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4						CATGAAGTTCCTGAGTGAAAA	0.512													6	146	---	---	---	---	PASS
STAT2	6773	broad.mit.edu	37	12	56749145	56749145	+	Intron	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56749145G>T	uc001slc.2	-						STAT2_uc001sld.2_Intron|STAT2_uc010sqn.1_Intron	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription						interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3						TCTGCAGAGGGGAGAGGACCC	0.502													8	124	---	---	---	---	PASS
TPH2	121278	broad.mit.edu	37	12	72425388	72425388	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72425388T>A	uc009zrw.1	+	11	1527	c.1386T>A	c.(1384-1386)AGT>AGA	p.S462R	TPH2_uc001swy.2_Missense_Mutation_p.S372R	NM_173353	NP_775489	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	462					aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)|skin(1)	4					L-Tryptophan(DB00150)	ACACCAGAAGTATTGAAAATG	0.408													14	57	---	---	---	---	PASS
C12orf26	84190	broad.mit.edu	37	12	82780723	82780723	+	Missense_Mutation	SNP	G	T	T	rs149436881		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82780723G>T	uc001szq.2	+	2	422	c.401G>T	c.(400-402)CGA>CTA	p.R134L		NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190	134											0						GTAGCCCTTCGAGGAAATCAA	0.373													4	80	---	---	---	---	PASS
NT5DC3	51559	broad.mit.edu	37	12	104179133	104179133	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104179133C>A	uc010swe.1	-	12	1350	c.1309G>T	c.(1309-1311)GGC>TGC	p.G437C		NM_001031701	NP_001026871	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	437							hydrolase activity|metal ion binding			ovary(2)|skin(1)	3						TCCAATAAGCCAGTCAAGGTC	0.408													11	89	---	---	---	---	PASS
ALDH1L2	160428	broad.mit.edu	37	12	105420472	105420472	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105420472G>T	uc001tlc.2	-	22	2694	c.2567C>A	c.(2566-2568)GCC>GAC	p.A856D	ALDH1L2_uc009zuo.2_Missense_Mutation_p.A311D|ALDH1L2_uc009zup.2_RNA	NM_001034173	NP_001029345	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	856	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding			skin(1)	1						AACCCCTGAGGCCAAACCATA	0.373													5	89	---	---	---	---	PASS
NAA25	80018	broad.mit.edu	37	12	112481017	112481017	+	Splice_Site	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112481017T>A	uc001ttm.2	-	19	2271	c.2251_splice	c.e19-1	p.Y751_splice	NAA25_uc001ttn.3_Splice_Site|NAA25_uc009zvz.1_Splice_Site_p.Y723_splice|NAA25_uc009zwa.1_Splice_Site_p.Y751_splice	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3						GAAAGGATACTGGAAAAAAGG	0.358													9	61	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112744001	112744001	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112744001G>T	uc009zwc.2	-	1	38	c.20C>A	c.(19-21)CCC>CAC	p.P7H		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						GCTGCCAATGGGGAGGTGATT	0.498													4	20	---	---	---	---	PASS
VSIG10	54621	broad.mit.edu	37	12	118533522	118533522	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118533522G>T	uc001tws.2	-	2	511	c.177C>A	c.(175-177)AAC>AAA	p.N59K		NM_019086	NP_061959	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	59	Ig-like C2-type 1.|Extracellular (Potential).					integral to membrane					0						GCTCCGAGTTGTTCCGGTACC	0.557													3	32	---	---	---	---	PASS
C12orf43	64897	broad.mit.edu	37	12	121448635	121448635	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121448635C>A	uc001tzh.1	-	3	306	c.283G>T	c.(283-285)GAC>TAC	p.D95Y	C12orf43_uc009zxa.1_Missense_Mutation_p.D126Y|C12orf43_uc010szo.1_Missense_Mutation_p.D53Y|C12orf43_uc010szp.1_Missense_Mutation_p.D95Y|C12orf43_uc001tzi.1_Missense_Mutation_p.D95Y	NM_022895	NP_075046	Q96C57	CL043_HUMAN	hypothetical protein LOC64897	95											0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTTTACCTGTCCAGCAGGGCT	0.393													5	42	---	---	---	---	PASS
C12orf43	64897	broad.mit.edu	37	12	121448636	121448636	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121448636C>A	uc001tzh.1	-	3	305	c.282G>T	c.(280-282)CTG>CTT	p.L94L	C12orf43_uc009zxa.1_Silent_p.L125L|C12orf43_uc010szo.1_Silent_p.L52L|C12orf43_uc010szp.1_Silent_p.L94L|C12orf43_uc001tzi.1_Silent_p.L94L	NM_022895	NP_075046	Q96C57	CL043_HUMAN	hypothetical protein LOC64897	94											0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TTTACCTGTCCAGCAGGGCTC	0.398													6	41	---	---	---	---	PASS
NBEA	26960	broad.mit.edu	37	13	35770415	35770415	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35770415C>A	uc001uvb.2	+	31	5548	c.5342C>A	c.(5341-5343)CCT>CAT	p.P1781H	NBEA_uc010abi.2_Missense_Mutation_p.P437H	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	1781						cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GCTATTCTTCCTATGCAGTTT	0.368													5	59	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22934777	22934777	+	Intron	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22934777G>T	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_3'UTR|uc001wea.3_3'UTR					SubName: Full=Alpha-chain C region; Flags: Fragment;																		AGGGATAGAAGGATATAAAAA	0.368													4	34	---	---	---	---	PASS
PSMC6	5706	broad.mit.edu	37	14	53185722	53185722	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53185722C>T	uc010tqx.1	+	10	785	c.785C>T	c.(784-786)TCA>TTA	p.S262L	PSMC6_uc001wzy.2_5'Flank	NM_002806	NP_002797	P62333	PRS10_HUMAN	proteasome 26S ATPase subunit 6	248					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding, bridging			lung(1)	1	Breast(41;0.176)					GAGGGTACTTCAGCTGACAGA	0.348													5	71	---	---	---	---	PASS
PLEK2	26499	broad.mit.edu	37	14	67854081	67854081	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67854081C>T	uc001xjh.1	-	9	1079	c.1027G>A	c.(1027-1029)GCC>ACC	p.A343T		NM_016445	NP_057529	Q9NYT0	PLEK2_HUMAN	pleckstrin 2	343	PH 2.				actin cytoskeleton organization|intracellular signal transduction	cytoplasm|cytoskeleton|lamellipodium membrane				ovary(1)|pancreas(1)	2				all cancers(60;0.000728)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.00953)		ATCCACTCGGCTCGCTCAGCC	0.488													5	79	---	---	---	---	PASS
RBM25	58517	broad.mit.edu	37	14	73577735	73577735	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73577735G>T	uc001xno.2	+	15	2097	c.1889G>T	c.(1888-1890)AGT>ATT	p.S630I	RBM25_uc010ttu.1_Missense_Mutation_p.S630I|RBM25_uc001xnp.2_Missense_Mutation_p.S425I	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25	630	Necessary for nuclear speckle localization.				apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		TCCTCTGCCAGTGGCAATGCA	0.483													4	30	---	---	---	---	PASS
YLPM1	56252	broad.mit.edu	37	14	75269258	75269258	+	Splice_Site	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75269258G>A	uc001xqj.3	+	6	4525	c.4401_splice	c.e6-1	p.R1467_splice	YLPM1_uc001xql.3_Splice_Site	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		TTTGTTTGCAGGGAACAGAAA	0.358													4	67	---	---	---	---	PASS
KIAA1737	85457	broad.mit.edu	37	14	77579782	77579782	+	Silent	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77579782C>G	uc001xtd.2	+	4	500	c.321C>G	c.(319-321)TCC>TCG	p.S107S	KIAA1737_uc001xtc.1_Silent_p.S9S	NM_033426	NP_219494	Q9C0C6	K1737_HUMAN	KIAA1737 protein	107	Poly-Ser.										0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0284)		GCAGCTCATCCCAGCTCCAGT	0.517													5	55	---	---	---	---	PASS
DLK1	8788	broad.mit.edu	37	14	101200491	101200491	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101200491C>T	uc001yhs.3	+	5	563	c.410C>T	c.(409-411)CCC>CTC	p.P137L	DLK1_uc001yhu.3_Missense_Mutation_p.P137L	NM_003836	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog precursor	137	Extracellular (Potential).|EGF-like 4.				multicellular organismal development	extracellular space|integral to membrane|soluble fraction				ovary(2)|breast(1)|skin(1)	4		Melanoma(154;0.155)				TGCAGCTCCCCCTGCCAGCAC	0.647													4	24	---	---	---	---	PASS
MIR493	574450	broad.mit.edu	37	14	101335439	101335439	+	RNA	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101335439G>T	hsa-mir-493|MI0003132	+			c.43G>T																				0						tcattcattcgtttgcacatt	0.428													8	55	---	---	---	---	PASS
RTL1	388015	broad.mit.edu	37	14	101348215	101348215	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101348215C>T	uc010txj.1	-	1	2970	c.2911G>A	c.(2911-2913)GTC>ATC	p.V971I	MIR433_hsa-mir-433|MI0001723_5'Flank|uc001yig.3_5'Flank|MIR127_hsa-mir-127|MI0000472_5'Flank|MIR432_hsa-mir-432|MI0003133_5'Flank|uc010txk.1_5'Flank|MIR136_hsa-mir-136|MI0000475_5'Flank	NM_001134888	NP_001128360	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	971										pancreas(1)	1						AAGAAGAAGACCCAATGCCCG	0.557													14	120	---	---	---	---	PASS
AKT1	207	broad.mit.edu	37	14	105246551	105246551	+	Missense_Mutation	SNP	C	T	T	rs34409589		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105246551C>T	uc001ypk.2	-	3	603	c.49G>A	c.(49-51)GAG>AAG	p.E17K	INF2_uc010tyi.1_Intron|AKT1_uc001ypl.2_Missense_Mutation_p.E17K|AKT1_uc010axa.2_Missense_Mutation_p.E17K|AKT1_uc001ypm.2_Missense_Mutation_p.E17K|AKT1_uc001ypn.2_Missense_Mutation_p.E17K|AKT1_uc010tyk.1_5'Flank	NM_005163	NP_005154	P31749	AKT1_HUMAN	AKT1 kinase	17	PH.		E -> K (in breast cancer; also detected in colorectal and ovarian cancer; somatic mutation; alters the PH domain conformation; results in activation of the protein; alters the subcellular location of the protein to the plasma membrane).	E->K: Increase in basal ubiquitination, phosphorylation at T-308 and important increase in membrane recruitment. Decrease in ubiquitination, phosphorylation at T-308 as well as impaired association with the membrane; when associated with R-8.	activation of pro-apoptotic gene products|activation-induced cell death of T cells|endocrine pancreas development|G-protein coupled receptor protein signaling pathway|glucose metabolic process|glycogen biosynthetic process|induction of apoptosis by intracellular signals|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|mRNA metabolic process|negative regulation of fatty acid beta-oxidation|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|nitric oxide biosynthetic process|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of blood vessel endothelial cell migration|positive regulation of cell growth|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of establishment of protein localization in plasma membrane|positive regulation of fat cell differentiation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|positive regulation of nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein autophosphorylation|protein import into nucleus, translocation|regulation of neuron projection development|regulation of translation|response to fluid shear stress|response to heat|response to UV-A|T cell costimulation	cytosol|nucleoplasm|plasma membrane	enzyme binding|identical protein binding|nitric-oxide synthase regulator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein serine/threonine kinase activity	p.E17K(126)		breast(86)|urinary_tract(12)|thyroid(10)|lung(7)|endometrium(5)|large_intestine(4)|skin(4)|prostate(3)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|NS(1)	134		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	TTGATGTACTCCCCTACAGAC	0.612	E17K(KU1919_URINARY_TRACT)	1	Mis		breast|colorectal|ovarian|NSCLC								4	21	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106641592	106641592	+	RNA	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106641592C>G	uc010tyt.1	-	1021		c.24409G>C								Parts of antibodies, mostly variable regions.												0						GCCGTGTCGTCAGATCTCAGG	0.532													6	188	---	---	---	---	PASS
OR4M2	390538	broad.mit.edu	37	15	22368589	22368589	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22368589A>C	uc010tzu.1	+	1	14	c.14A>C	c.(13-15)AAT>ACT	p.N5T	LOC727924_uc001yua.2_RNA|LOC727924_uc001yub.1_Intron|OR4N4_uc001yuc.1_Intron	NM_001004719	NP_001004719	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M,	5	Extracellular (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)		GAAACTGCAAATTACACCAAG	0.328													5	132	---	---	---	---	PASS
OR4N4	283694	broad.mit.edu	37	15	22382889	22382889	+	Missense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22382889A>T	uc001yuc.1	+	7	1398	c.417A>T	c.(415-417)AGA>AGT	p.R139S	LOC727924_uc001yub.1_Intron|OR4N4_uc010tzv.1_Missense_Mutation_p.R139S	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	139	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)|skin(1)	5		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)		TGAACCCTAGAGCCTGCTATG	0.542													6	81	---	---	---	---	PASS
GABRB3	2562	broad.mit.edu	37	15	26866631	26866631	+	Silent	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26866631G>C	uc001zaz.2	-	4	433	c.291C>G	c.(289-291)CTC>CTG	p.L97L	GABRB3_uc010uae.1_Silent_p.L12L|GABRB3_uc001zba.2_Silent_p.L97L|GABRB3_uc001zbb.2_Silent_p.L153L|GABRB3_uc001zbc.2_RNA	NM_000814	NP_000805	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	97	Extracellular (Probable).				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			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	CAGAATAGGCGAGCCTTTTAT	0.428													3	32	---	---	---	---	PASS
OCA2	4948	broad.mit.edu	37	15	28235745	28235745	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28235745C>A	uc001zbh.3	-	10	1203	c.1093G>T	c.(1093-1095)GCA>TCA	p.A365S	OCA2_uc010ayv.2_Intron	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	365	Helical; (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		GCCAGTGCTGCCAGTGCTGCA	0.537									Oculocutaneous_Albinism				11	110	---	---	---	---	PASS
C15orf55	256646	broad.mit.edu	37	15	34648683	34648683	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34648683T>A	uc001zif.2	+	7	2545	c.2390T>A	c.(2389-2391)CTA>CAA	p.L797Q	C15orf55_uc010ucc.1_Missense_Mutation_p.L825Q|C15orf55_uc010ucd.1_Missense_Mutation_p.L815Q	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	797						cytoplasm|nucleus			BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	midline_organs(25)|ovary(2)|lung(2)|skin(1)	30		all_lung(180;2.78e-08)		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)		GCAGCTGCCCTAGAAAAGAGA	0.542			T	BRD3|BRD4	lethal midline carcinoma								9	43	---	---	---	---	PASS
PLA2G4D	283748	broad.mit.edu	37	15	42378498	42378498	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42378498C>T	uc001zox.2	-	4	395	c.300G>A	c.(298-300)GAG>GAA	p.E100E		NM_178034	NP_828848	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD	100	C2.				phospholipid catabolic process	cytoplasmic vesicle membrane|cytosol	metal ion binding|phospholipase A2 activity			large_intestine(1)|skin(1)	2		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		AGATGTCATCCTCCGTGACTG	0.512													10	40	---	---	---	---	PASS
LCMT2	9836	broad.mit.edu	37	15	43622597	43622597	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43622597C>A	uc001zrg.2	-	1	295	c.91G>T	c.(91-93)GGG>TGG	p.G31W	LCMT2_uc010udn.1_5'UTR|ADAL_uc001zrh.2_5'Flank|ADAL_uc010udo.1_5'Flank	NM_014793	NP_055608	O60294	LCMT2_HUMAN	leucine carboxyl methyltransferase 2	31					tRNA processing		methyltransferase activity|protein binding				0		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	TGCACGTACCCGCGCGCGGCC	0.716													3	12	---	---	---	---	PASS
ANKDD1A	348094	broad.mit.edu	37	15	65219162	65219162	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65219162C>A	uc002aoa.2	+	6	563	c.534C>A	c.(532-534)CTC>CTA	p.L178L	ANKDD1A_uc002anx.1_Silent_p.L174L|ANKDD1A_uc002any.2_Silent_p.L87L|ANKDD1A_uc002anz.2_Silent_p.L87L|ANKDD1A_uc002aob.2_Intron|ANKDD1A_uc002aoc.2_RNA|ANKDD1A_uc010bha.2_Silent_p.L87L	NM_182703	NP_874362	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	178	ANK 5.				signal transduction					ovary(1)	1						TGGACTTCCTCGTGGGCTCTG	0.612													4	60	---	---	---	---	PASS
TSPAN3	10099	broad.mit.edu	37	15	77348510	77348510	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77348510G>C	uc002bcj.2	-	2	368	c.151C>G	c.(151-153)CTC>GTC	p.L51V	TSPAN3_uc002bck.2_Missense_Mutation_p.L51V|TSPAN3_uc010ump.1_Intron|TSPAN3_uc010bkx.2_Intron	NM_005724	NP_005715	O60637	TSN3_HUMAN	transmembrane 4 superfamily member 8 isoform 1	51	Helical; (Potential).					integral to membrane					0				all cancers(203;1.14e-19)		GCAGGGATGAGCGTGTACACA	0.478													7	123	---	---	---	---	PASS
TSPAN3	10099	broad.mit.edu	37	15	77348511	77348511	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77348511C>A	uc002bcj.2	-	2	367	c.150G>T	c.(148-150)ACG>ACT	p.T50T	TSPAN3_uc002bck.2_Silent_p.T50T|TSPAN3_uc010ump.1_Intron|TSPAN3_uc010bkx.2_Intron	NM_005724	NP_005715	O60637	TSN3_HUMAN	transmembrane 4 superfamily member 8 isoform 1	50	Extracellular (Potential).					integral to membrane					0				all cancers(203;1.14e-19)		CAGGGATGAGCGTGTACACAT	0.473													7	123	---	---	---	---	PASS
PAQR4	124222	broad.mit.edu	37	16	3021766	3021766	+	Silent	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3021766G>A	uc002csj.3	+	3	973	c.639G>A	c.(637-639)GCG>GCA	p.A213A	PAQR4_uc002csk.3_Silent_p.A174A|PAQR4_uc002csl.3_Silent_p.A139A|PAQR4_uc010uwm.1_Silent_p.A144A	NM_152341	NP_689554	Q8N4S7	PAQR4_HUMAN	progestin and adipoQ receptor family member IV	213						integral to membrane	receptor activity				0						ACGCACTGGCGCTGCTTGGGG	0.657													5	29	---	---	---	---	PASS
MEFV	4210	broad.mit.edu	37	16	3293137	3293137	+	3'UTR	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3293137G>C	uc002cun.1	-	10						NM_000243	NP_000234	O15553	MEFV_HUMAN	Mediterranean fever protein						inflammatory response	cytoplasm|microtubule|microtubule associated complex|nucleus	actin binding|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|lung(1)	6					Colchicine(DB01394)	GCAGTGTTGGGCATTCAGTCA	0.393													5	26	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3832794	3832794	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3832794G>T	uc002cvv.2	-	6	1668	c.1464C>A	c.(1462-1464)CTC>CTA	p.L488L	CREBBP_uc002cvw.2_Silent_p.L450L	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	488					cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		AGGGGAGTCCGAGAGCAGCAT	0.557			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				4	51	---	---	---	---	PASS
GLYR1	84656	broad.mit.edu	37	16	4873817	4873817	+	Intron	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4873817C>A	uc002cxx.3	-						GLYR1_uc002cxy.2_Intron|GLYR1_uc002cxz.1_Intron|GLYR1_uc002cya.2_Intron|GLYR1_uc010uxv.1_Intron	NM_032569	NP_115958	Q49A26	GLYR1_HUMAN	cytokine-like nuclear factor n-pac						pentose-phosphate shunt	nucleus	coenzyme binding|DNA binding|methylated histone residue binding|phosphogluconate dehydrogenase (decarboxylating) activity				0						AGGAGAGCTCCTTACCTCGCT	0.517													6	136	---	---	---	---	PASS
GP2	2813	broad.mit.edu	37	16	20329643	20329643	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20329643C>A	uc002dgv.2	-	8	1209	c.1126G>T	c.(1126-1128)GTT>TTT	p.V376F	GP2_uc002dgw.2_Missense_Mutation_p.V373F|GP2_uc002dgx.2_Missense_Mutation_p.V229F|GP2_uc002dgy.2_Missense_Mutation_p.V226F	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform	376	ZP.					anchored to membrane|extracellular region|plasma membrane				ovary(3)|skin(1)	4						ACGGACTCAACAGACAGTTCA	0.527													23	128	---	---	---	---	PASS
ACSM1	116285	broad.mit.edu	37	16	20682918	20682918	+	Silent	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20682918G>A	uc002dhm.1	-	4	755	c.687C>T	c.(685-687)ACC>ACT	p.T229T	ACSM1_uc002dhn.1_RNA|ACSM1_uc010bwg.1_Silent_p.T229T	NM_052956	NP_443188	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member	229	ATP (By similarity).				benzoate metabolic process|butyrate metabolic process|energy derivation by oxidation of organic compounds|fatty acid oxidation|xenobiotic metabolic process	mitochondrial matrix	acyl-CoA ligase activity|ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			central_nervous_system(1)|skin(1)	2						GGAAGCCTGTGGTCCCACTGG	0.532													9	47	---	---	---	---	PASS
UBFD1	56061	broad.mit.edu	37	16	23569488	23569488	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23569488G>T	uc002dlv.2	+	2	445	c.243G>T	c.(241-243)GCG>GCT	p.A81A	EARS2_uc002dls.3_5'Flank|EARS2_uc002dlt.3_5'Flank|EARS2_uc002dlu.2_5'Flank	NM_019116	NP_061989	O14562	UBFD1_HUMAN	ubiquitin-binding protein homolog	81											0				GBM - Glioblastoma multiforme(48;0.0331)		GCGGCGGCGCGGGCAGGGAGC	0.682													4	18	---	---	---	---	PASS
KIAA0556	23247	broad.mit.edu	37	16	27789275	27789275	+	Missense_Mutation	SNP	A	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27789275A>C	uc002dow.2	+	27	4810	c.4786A>C	c.(4786-4788)AGC>CGC	p.S1596R	KIAA0556_uc010vco.1_Missense_Mutation_p.S98R	NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	1596										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						ACGGAAGCAGAGCGTTGTTGA	0.512													8	66	---	---	---	---	PASS
MYLK3	91807	broad.mit.edu	37	16	46782053	46782053	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46782053C>A	uc002eei.3	-	1	169	c.53G>T	c.(52-54)GGC>GTC	p.G18V	MYLK3_uc010vge.1_Intron	NM_182493	NP_872299	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	18					cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis	cytosol	ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	7		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GCAGGTCTTGCCCAACCCTGG	0.562													11	38	---	---	---	---	PASS
DPEP3	64180	broad.mit.edu	37	16	68010022	68010022	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68010022G>T	uc002evc.3	-	9	1373	c.1279C>A	c.(1279-1281)CTG>ATG	p.L427M	DPEP3_uc010cex.2_Missense_Mutation_p.L426M	NM_022357	NP_071752	Q9H4B8	DPEP3_HUMAN	dipeptidase 3 isoform a	402					meiosis	anchored to membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity			breast(3)	3		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0117)|Epithelial(162;0.0481)|all cancers(182;0.236)		AAGACCCGCAGCAGGTTTCCA	0.562													29	187	---	---	---	---	PASS
ADAT1	23536	broad.mit.edu	37	16	75634194	75634194	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75634194G>T	uc002feo.1	-	11	1531	c.1429C>A	c.(1429-1431)CAG>AAG	p.Q477K	ADAT1_uc002fep.1_Missense_Mutation_p.Q328K	NM_012091	NP_036223	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	477	A to I editase.				tRNA processing		metal ion binding|RNA binding|tRNA-specific adenosine deaminase activity			ovary(1)|skin(1)	2						CAGGCTTCCTGGTAAGAGGAC	0.512													5	70	---	---	---	---	PASS
TUSC5	286753	broad.mit.edu	37	17	1183600	1183600	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1183600G>C	uc002fsi.1	+	1	644	c.305G>C	c.(304-306)AGA>ACA	p.R102T		NM_172367	NP_758955	Q8IXB3	TUSC5_HUMAN	LOST1	102					response to biotic stimulus	integral to membrane				skin(2)	2				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GAAGCCCCCAGAGATTACCTC	0.627													6	31	---	---	---	---	PASS
SERPINF2	5345	broad.mit.edu	37	17	1657687	1657687	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1657687G>T	uc002ftk.1	+	10	1412	c.1335G>T	c.(1333-1335)AAG>AAT	p.K445N	SERPINF2_uc010vqr.1_Missense_Mutation_p.K381N	NM_000934	NP_000925	P08697	A2AP_HUMAN	alpha-2-antiplasmin isoform a precursor	445					acute-phase response|fibrinolysis|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Streptokinase(DB00086)	GGGAGCTCAAGGAACAGCAGG	0.607													6	69	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7578271	7578271	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578271T>C	uc002gim.2	-	6	772	c.578A>G	c.(577-579)CAT>CGT	p.H193R	TP53_uc002gig.1_Missense_Mutation_p.H193R|TP53_uc002gih.2_Missense_Mutation_p.H193R|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.H61R|TP53_uc010cng.1_Missense_Mutation_p.H61R|TP53_uc002gii.1_Missense_Mutation_p.H61R|TP53_uc010cnh.1_Missense_Mutation_p.H193R|TP53_uc010cni.1_Missense_Mutation_p.H193R|TP53_uc002gij.2_Missense_Mutation_p.H193R|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.H100R|TP53_uc002gio.2_Missense_Mutation_p.H61R|TP53_uc010vug.1_Missense_Mutation_p.H154R	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	193	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		H -> D (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.H193R(67)|p.H193L(31)|p.H193Y(26)|p.H193P(12)|p.0?(7)|p.H193D(7)|p.H193N(4)|p.A189_V197delAPPQHLIRV(4)|p.H193fs*16(3)|p.H193H(2)|p.P191fs*53(2)|p.K164_P219del(1)|p.P191fs*15(1)|p.P191fs*6(1)|p.H100L(1)|p.H61L(1)|p.H193_I195delHLI(1)|p.H193_I195>AP(1)|p.A189fs*53(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		TCGGATAAGATGCTGAGGAGG	0.562		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			5	16	---	---	---	---	PASS
MYH13	8735	broad.mit.edu	37	17	10216043	10216043	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10216043C>A	uc002gmk.1	-	31	4303	c.4213G>T	c.(4213-4215)GAG>TAG	p.E1405*		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1405	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						GTGTTCTCCTCTGCTTCCTGG	0.517													7	21	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10443358	10443358	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10443358G>T	uc010coi.2	-	12	1162	c.1034C>A	c.(1033-1035)ACT>AAT	p.T345N	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.T345N|MYH2_uc010coj.2_Missense_Mutation_p.T345N	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	345	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						TTCTTCATTAGTAAAGCCCAA	0.418													16	79	---	---	---	---	PASS
TEKT3	64518	broad.mit.edu	37	17	15207316	15207316	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15207316C>G	uc002gon.2	-	9	1597	c.1410G>C	c.(1408-1410)CAG>CAC	p.Q470H		NM_031898	NP_114104	Q9BXF9	TEKT3_HUMAN	tektin 3	470					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		TGCATTTTTCCTGGTCGATGT	0.562													8	34	---	---	---	---	PASS
ATAD5	79915	broad.mit.edu	37	17	29162429	29162429	+	Nonsense_Mutation	SNP	A	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29162429A>T	uc002hfs.1	+	2	1676	c.1330A>T	c.(1330-1332)AAA>TAA	p.K444*	ATAD5_uc002hft.1_Nonsense_Mutation_p.K341*	NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	444					response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TGATAATTCTAAAAAAATCAT	0.294													9	27	---	---	---	---	PASS
FZD2	2535	broad.mit.edu	37	17	42636019	42636019	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42636019C>T	uc002igx.1	+	1	1095	c.963C>T	c.(961-963)GGC>GGT	p.G321G		NM_001466	NP_001457	Q14332	FZD2_HUMAN	frizzled 2 precursor	321	Extracellular (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|positive regulation of cGMP metabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TGGTGCAGGGCACCAAGAAGG	0.617													14	30	---	---	---	---	PASS
HOXB2	3212	broad.mit.edu	37	17	46622226	46622226	+	Silent	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46622226C>A	uc002inm.2	-	1	168	c.48G>T	c.(46-48)CCG>CCT	p.P16P		NM_002145	NP_002136	P14652	HXB2_HUMAN	homeobox B2	16					blood circulation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CGGCGAGCGACGGCTGGCTGT	0.527													11	32	---	---	---	---	PASS
BPTF	2186	broad.mit.edu	37	17	65871037	65871037	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65871037G>C	uc002jgf.2	+	4	1826	c.1765G>C	c.(1765-1767)GAT>CAT	p.D589H	BPTF_uc002jge.2_Missense_Mutation_p.D589H|BPTF_uc010wqm.1_Missense_Mutation_p.D589H	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGACTCTAAAGATGCTGAGAA	0.388													5	184	---	---	---	---	PASS
TNRC6C	57690	broad.mit.edu	37	17	76099517	76099517	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76099517C>T	uc002jud.2	+	20	5195	c.4595C>T	c.(4594-4596)ACA>ATA	p.T1532I	TNRC6C_uc002juf.2_Missense_Mutation_p.T1568I	NM_018996	NP_061869	Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C isoform 2	1532	Sufficient for translational repression when tethered to a target mRNA.				gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			ACACTGCGGACATTGTGTTTG	0.473													10	34	---	---	---	---	PASS
ARHGAP28	79822	broad.mit.edu	37	18	6873571	6873571	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6873571G>T	uc010wzi.1	+	7	825	c.587G>T	c.(586-588)CGA>CTA	p.R196L	ARHGAP28_uc002knc.2_Missense_Mutation_p.R321L|ARHGAP28_uc002knd.2_Missense_Mutation_p.R214L|ARHGAP28_uc002kne.2_Missense_Mutation_p.R214L|ARHGAP28_uc002knf.2_Missense_Mutation_p.R205L			B4DXL2	B4DXL2_HUMAN	SubName: Full=Putative uncharacterized protein ARHGAP28;	196					signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)				GTAAAAGGACGAGGTAACTAA	0.358													6	94	---	---	---	---	PASS
PPP4R1	9989	broad.mit.edu	37	18	9557344	9557344	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9557344C>A	uc002koe.1	-	15	2183	c.2065G>T	c.(2065-2067)GAG>TAG	p.E689*	PPP4R1_uc002kof.2_Nonsense_Mutation_p.E106*|PPP4R1_uc010wzo.1_Nonsense_Mutation_p.E535*|PPP4R1_uc002kod.1_Nonsense_Mutation_p.E672*	NM_001042388	NP_001035847	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	689					protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity			skin(1)	1						ACTGCAAGCTCGTGGATGGAG	0.398													4	118	---	---	---	---	PASS
ASXL3	80816	broad.mit.edu	37	18	31323945	31323945	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31323945G>T	uc010dmg.1	+	12	4188	c.4133G>T	c.(4132-4134)GGG>GTG	p.G1378V	ASXL3_uc002kxq.2_Missense_Mutation_p.G1085V	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1378					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						GCCATACCTGGGAGTGAAGAA	0.502											OREG0024911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	103	---	---	---	---	PASS
GALNT1	2589	broad.mit.edu	37	18	33283583	33283583	+	Silent	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33283583C>T	uc010dmu.2	+	11	1562	c.1509C>T	c.(1507-1509)AAC>AAT	p.N503N	GALNT1_uc002kyz.3_Silent_p.N443N|GALNT1_uc002kzb.2_Silent_p.N503N	NM_020474	NP_065207	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	503	Lumenal (Potential).|Ricin B-type lectin.				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2						TAAAAGGCAACCAACTCTGGG	0.373													7	70	---	---	---	---	PASS
C18orf32	497661	broad.mit.edu	37	18	47010053	47010053	+	Silent	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47010053T>C	uc002ldk.1	-	2	278	c.66A>G	c.(64-66)CCA>CCG	p.P22P	C18orf32_uc002ldl.2_Silent_p.P22P|C18orf32_uc002ldm.1_Missense_Mutation_p.H199R	NM_001035005	NP_001030177	Q8TCD1	CR032_HUMAN	hypothetical protein LOC497661	22					positive regulation of I-kappaB kinase/NF-kappaB cascade		signal transducer activity				0						GGTATATATATGGCTCCAGGA	0.398													10	83	---	---	---	---	PASS
SERPINB4	6318	broad.mit.edu	37	18	61328424	61328424	+	Silent	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61328424G>A	uc002ljg.2	-	1	53	c.27C>T	c.(25-27)ACC>ACT	p.T9T	SERPINB3_uc002lji.2_Silent_p.T9T|SERPINB3_uc010dqa.2_Silent_p.T9T|SERPINB3_uc010dqb.2_Silent_p.T9T|SERPINB3_uc010dqc.2_Silent_p.T9T			P48594	SPB4_HUMAN	SubName: Full=Squamous cell carcinoma antigen 2;	9					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|lung(1)	3						ACATGAACTTGGTGTTGGCTT	0.413													14	115	---	---	---	---	PASS
MYO1F	4542	broad.mit.edu	37	19	8609217	8609217	+	Nonsense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8609217C>T	uc002mkg.2	-	14	1602	c.1488G>A	c.(1486-1488)TGG>TGA	p.W496*		NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF	496	Myosin head-like.					unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3						AGCCGGCGCTCCAGCTGTTGA	0.677													4	15	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9074998	9074998	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9074998G>T	uc002mkp.2	-	3	12652	c.12448C>A	c.(12448-12450)CCT>ACT	p.P4150T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4152	Thr-rich.|Extracellular (Potential).|Ser-rich.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						ACAGAGGGAGGGCTTGGCTGT	0.502													13	74	---	---	---	---	PASS
ZNF442	79973	broad.mit.edu	37	19	12460784	12460784	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12460784T>G	uc002mtr.1	-	6	2226	c.1615A>C	c.(1615-1617)ACT>CCT	p.T539P	ZNF442_uc010xmk.1_Missense_Mutation_p.T470P	NM_030824	NP_110451	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	539					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|breast(1)|kidney(1)	4						TTCTCTCCAGTGTGAATCCTT	0.383													9	59	---	---	---	---	PASS
PDE4C	5143	broad.mit.edu	37	19	18321932	18321932	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18321932T>C	uc010xqc.1	-	15	2426	c.1946A>G	c.(1945-1947)GAG>GGG	p.E649G	PDE4C_uc002nik.3_Missense_Mutation_p.E649G|PDE4C_uc002nil.3_Missense_Mutation_p.E649G|PDE4C_uc002nif.3_Missense_Mutation_p.E418G|PDE4C_uc002nig.3_Missense_Mutation_p.E364G|PDE4C_uc002nih.3_Missense_Mutation_p.E419G|PDE4C_uc010ebk.2_Missense_Mutation_p.E543G|PDE4C_uc002nii.3_Missense_Mutation_p.E617G|PDE4C_uc010ebl.2_Missense_Mutation_p.E363G	NM_001098819	NP_001092289	Q08493	PDE4C_HUMAN	phosphodiesterase 4C isoform PDE4C-2	649					signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|skin(2)|central_nervous_system(1)	5					Dyphylline(DB00651)	CCCGTCCCGCTCGGGGTTGGT	0.443													8	56	---	---	---	---	PASS
SFRS14	10147	broad.mit.edu	37	19	19135671	19135671	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19135671C>A	uc002nkx.2	-	3	1632	c.1486G>T	c.(1486-1488)GAG>TAG	p.E496*	SFRS14_uc002nkz.1_Nonsense_Mutation_p.E510*|SFRS14_uc002nla.1_Nonsense_Mutation_p.E496*|SFRS14_uc002nlb.2_Nonsense_Mutation_p.E496*|SFRS14_uc010xqk.1_Nonsense_Mutation_p.E265*	NM_014884	NP_055699	Q8IX01	SUGP2_HUMAN	splicing factor, arginine/serine-rich 14	496					mRNA processing|RNA splicing	nucleus	RNA binding				0			OV - Ovarian serous cystadenocarcinoma(5;3.05e-05)|Epithelial(12;0.00161)			AAGATTTTCTCCTGCCGGAAA	0.507													7	148	---	---	---	---	PASS
ZNF91	7644	broad.mit.edu	37	19	23544724	23544724	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23544724T>C	uc002nre.2	-	4	1170	c.1057A>G	c.(1057-1059)AAA>GAA	p.K353E	ZNF91_uc010xrj.1_Missense_Mutation_p.K321E	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	353	C2H2-type 8.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CCACATTCTTTACATTTGTAG	0.373													3	55	---	---	---	---	PASS
MAP4K1	11184	broad.mit.edu	37	19	39088220	39088220	+	Silent	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39088220G>A	uc002oix.1	-	23	1792	c.1684C>T	c.(1684-1686)CTG>TTG	p.L562L	MAP4K1_uc002oiw.1_Silent_p.L149L|MAP4K1_uc002oiy.1_Silent_p.L562L|MAP4K1_uc010xug.1_Silent_p.T203T	NM_007181	NP_009112	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase	562	CNH.				activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TGAGAATACAGGTGGGGGGTC	0.552													6	24	---	---	---	---	PASS
GRIK5	2901	broad.mit.edu	37	19	42566697	42566697	+	Nonsense_Mutation	SNP	G	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42566697G>A	uc002osj.1	-	4	486	c.451C>T	c.(451-453)CGA>TGA	p.R151*	GRIK5_uc010eib.1_Nonsense_Mutation_p.R70*	NM_002088	NP_002079	Q16478	GRIK5_HUMAN	glutamate receptor KA2 precursor	151	Extracellular (Potential).					cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity				0		Prostate(69;0.059)			L-Glutamic Acid(DB00142)	TTGAGGATTCGGGAGACCGCC	0.577													10	45	---	---	---	---	PASS
PSG3	5671	broad.mit.edu	37	19	43243198	43243198	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43243198G>T	uc002oue.2	-	2	240	c.108C>A	c.(106-108)GTC>GTA	p.V36V	PSG3_uc002ouf.2_RNA|PSG1_uc002oug.1_Intron|PSG3_uc010eil.2_Silent_p.V58V	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	36	Ig-like V-type.				defense response|female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				CTTCAATCGTGACTTGGGCAG	0.463													10	65	---	---	---	---	PASS
HIF3A	64344	broad.mit.edu	37	19	46842856	46842856	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46842856G>T	uc002peh.2	+	15	2016	c.1987G>T	c.(1987-1989)GCA>TCA	p.A663S	HIF3A_uc002pek.2_Missense_Mutation_p.A607S|HIF3A_uc010xxy.1_Missense_Mutation_p.A594S|HIF3A_uc002pel.2_Missense_Mutation_p.A661S	NM_152795	NP_690008	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	663					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CCAGCCAAGGGCAGGCTCAGC	0.622													8	32	---	---	---	---	PASS
ELSPBP1	64100	broad.mit.edu	37	19	48525518	48525518	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48525518G>T	uc002pht.2	+	6	761	c.606G>T	c.(604-606)AAG>AAT	p.K202N		NM_022142	NP_071425	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1 precursor	202	Fibronectin type-II 4.				single fertilization	extracellular region					0		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		AAGGATCAAAGGAGAACCTTG	0.458													5	76	---	---	---	---	PASS
SIGLEC7	27036	broad.mit.edu	37	19	51645698	51645698	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51645698G>T	uc002pvv.1	+	1	141	c.72G>T	c.(70-72)AAG>AAT	p.K24N	SIGLEC7_uc002pvw.1_Missense_Mutation_p.K24N|SIGLEC7_uc010eoq.1_RNA|SIGLEC7_uc010eor.1_Missense_Mutation_p.K24N	NM_014385	NP_055200	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7 isoform 1	24	Extracellular (Potential).				cell adhesion	integral to plasma membrane	receptor activity|sugar binding			large_intestine(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		GTAACCGGAAGGATTACTCGC	0.512													6	22	---	---	---	---	PASS
LILRA2	11027	broad.mit.edu	37	19	55087509	55087509	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55087509C>A	uc002qgg.3	+	6	1277	c.1188C>A	c.(1186-1188)TAC>TAA	p.Y396*	LILRA2_uc010ern.2_Nonsense_Mutation_p.Y396*|LILRA2_uc002qgf.2_Nonsense_Mutation_p.Y396*|LILRA2_uc010yfe.1_Nonsense_Mutation_p.Y396*|LILRA2_uc010yff.1_Nonsense_Mutation_p.Y384*|LILRA2_uc010ero.2_Nonsense_Mutation_p.Y384*|LILRA2_uc010yfg.1_Intron	NM_001130917	NP_001124389	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	396	Ig-like C2-type 4.|Extracellular (Potential).				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)		ACAGATGCTACAGCTCACTCA	0.602													14	99	---	---	---	---	PASS
NLRP7	199713	broad.mit.edu	37	19	55435122	55435122	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55435122C>A	uc002qih.3	-	10	3005	c.2929G>T	c.(2929-2931)GAC>TAC	p.D977Y	NLRP7_uc002qig.3_Missense_Mutation_p.D1006Y|NLRP7_uc002qii.3_Missense_Mutation_p.D1034Y|NLRP7_uc010esk.2_3'UTR|NLRP7_uc010esl.2_Missense_Mutation_p.D1062Y	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	977							ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)		CAAAAAAAGTCACAGCACGGA	0.473													13	67	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56382329	56382329	+	Missense_Mutation	SNP	T	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56382329T>A	uc002qmd.3	+	7	2913	c.2491T>A	c.(2491-2493)TTG>ATG	p.L831M	NLRP4_uc002qmf.2_Missense_Mutation_p.L756M|NLRP4_uc010etf.2_Missense_Mutation_p.L606M	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	831	LRR 5.						ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CTGCGAGGCCTTGAAACATCC	0.493													11	78	---	---	---	---	PASS
NLRP13	126204	broad.mit.edu	37	19	56423244	56423244	+	Nonsense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56423244C>A	uc010ygg.1	-	5	1964	c.1939G>T	c.(1939-1941)GAG>TAG	p.E647*		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	647							ATP binding			skin(4)|ovary(3)|pancreas(1)|lung(1)	9		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		AAGTCTTCCTCCTGGGACTCG	0.423													5	70	---	---	---	---	PASS
ZNF274	10782	broad.mit.edu	37	19	58723027	58723027	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58723027G>C	uc002qrq.1	+	9	1413	c.954G>C	c.(952-954)GAG>GAC	p.E318D	ZNF274_uc002qrr.1_Missense_Mutation_p.E286D|ZNF274_uc002qrs.1_Missense_Mutation_p.E213D|ZNF274_uc010eum.1_Missense_Mutation_p.E77D	NM_133502	NP_598009	Q96GC6	ZN274_HUMAN	zinc finger protein 274 isoform c	318	KRAB 2.				viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)		TGATGCTGGAGACCTTTGGGC	0.632													4	57	---	---	---	---	PASS
SLC27A5	10998	broad.mit.edu	37	19	59010941	59010941	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59010941C>A	uc002qtc.2	-	7	1695	c.1585G>T	c.(1585-1587)GTT>TTT	p.V529F	SLC27A5_uc002qtb.2_5'Flank	NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid	529	Cytoplasmic (Probable).				bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		TTGTAGTAAACGTCGCCCGAT	0.647													7	46	---	---	---	---	PASS
SEC23B	10483	broad.mit.edu	37	20	18516382	18516382	+	Missense_Mutation	SNP	A	G	G	rs150210442		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18516382A>G	uc002wqz.1	+	12	1843	c.1400A>G	c.(1399-1401)AAT>AGT	p.N467S	SEC23B_uc002wra.1_Missense_Mutation_p.N467S|SEC23B_uc002wrb.1_Missense_Mutation_p.N467S|SEC23B_uc010zsb.1_Missense_Mutation_p.N449S|SEC23B_uc002wrc.1_Missense_Mutation_p.N467S	NM_006363	NP_006354	Q15437	SC23B_HUMAN	Sec23 homolog B	467					ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1						GAAGTTGTCAATCAGGTGAGT	0.438													9	37	---	---	---	---	PASS
CST8	10047	broad.mit.edu	37	20	23472308	23472308	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23472308C>G	uc002wth.1	+	2	361	c.4C>G	c.(4-6)CCC>GCC	p.P2A		NM_005492	NP_005483	O60676	CST8_HUMAN	cystatin 8 precursor	2						extracellular region	cysteine-type endopeptidase inhibitor activity				0	Colorectal(13;0.0431)|Lung NSC(19;0.235)					AGGGACCATGCCCAGGTGCCG	0.612													14	66	---	---	---	---	PASS
ENTPD6	955	broad.mit.edu	37	20	25187731	25187731	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25187731G>T	uc002wuj.2	+	3	254	c.74G>T	c.(73-75)TGG>TTG	p.W25L	ENTPD6_uc010zsy.1_Missense_Mutation_p.W25L|ENTPD6_uc010gdj.1_5'UTR|ENTPD6_uc010zsz.1_Intron|ENTPD6_uc002wum.2_Missense_Mutation_p.W8L|ENTPD6_uc010zta.1_Missense_Mutation_p.W25L|ENTPD6_uc002wun.2_Missense_Mutation_p.W25L|ENTPD6_uc002wuk.2_Missense_Mutation_p.W24L|ENTPD6_uc002wul.2_Missense_Mutation_p.W24L|ENTPD6_uc010ztb.1_5'UTR|ENTPD6_uc010ztc.1_5'UTR|ENTPD6_uc002wuo.2_Intron|ENTPD6_uc010ztd.1_5'Flank	NM_001247	NP_001238	O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6	25	Cytoplasmic (Potential).					Golgi membrane|integral to membrane	nucleoside-diphosphatase activity				0						CACGGTCCTTGGCAAACAAGG	0.607													5	45	---	---	---	---	PASS
SNAI1	6615	broad.mit.edu	37	20	48600466	48600466	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48600466C>G	uc002xuz.2	+	2	258	c.188C>G	c.(187-189)TCT>TGT	p.S63C		NM_005985	NP_005976	O95863	SNAI1_HUMAN	snail 1 homolog	63					epithelial to mesenchymal transition|mesoderm formation|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|zinc ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			ATCTGGGACTCTGTCCTGGCG	0.652													8	33	---	---	---	---	PASS
DIDO1	11083	broad.mit.edu	37	20	61541126	61541126	+	Missense_Mutation	SNP	T	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61541126T>G	uc002ydr.1	-	4	1350	c.1086A>C	c.(1084-1086)GAA>GAC	p.E362D	DIDO1_uc002yds.1_Missense_Mutation_p.E362D|DIDO1_uc002ydt.1_Missense_Mutation_p.E362D|DIDO1_uc002ydu.1_Missense_Mutation_p.E362D|DIDO1_uc002ydv.1_Missense_Mutation_p.E362D|DIDO1_uc002ydw.1_Missense_Mutation_p.E362D|DIDO1_uc002ydx.1_Missense_Mutation_p.E362D|DIDO1_uc011aao.1_Missense_Mutation_p.E362D	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	362					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)					TCCCTTGGTCTTCGCTAGACT	0.458													23	154	---	---	---	---	PASS
RNF160	26046	broad.mit.edu	37	21	30304833	30304833	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30304833G>T	uc002ymr.2	-	28	5180	c.5167C>A	c.(5167-5169)CGG>AGG	p.R1723R		NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	1677							ligase activity|zinc ion binding				0						ATCCAGTTCCGCCACTGCTGA	0.378													5	172	---	---	---	---	PASS
SLC37A1	54020	broad.mit.edu	37	21	43959738	43959738	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43959738G>T	uc002zbi.2	+	7	879	c.467G>T	c.(466-468)GGA>GTA	p.G156V	SLC37A1_uc002zbj.2_Missense_Mutation_p.G156V	NM_018964	NP_061837	P57057	GLPT_HUMAN	solute carrier family 37 member 1	156					carbohydrate transport|transmembrane transport	integral to membrane					0						CACAGTTTCGGATTCTACGTG	0.522													6	51	---	---	---	---	PASS
KRTAP10-7	386675	broad.mit.edu	37	21	46021203	46021203	+	Missense_Mutation	SNP	C	T	T	rs672479		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46021203C>T	uc002zfn.3	+	2	692	c.667C>T	c.(667-669)CCT>TCT	p.P223S	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198689	NP_941962	P60409	KR107_HUMAN	keratin associated protein 10-7	228	30 X 5 AA repeats of C-C-X(3).					keratin filament					0						CACCTCCTCCCCCTGCCAGCA	0.652													8	84	---	---	---	---	PASS
CDC45	8318	broad.mit.edu	37	22	19471538	19471538	+	Intron	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19471538G>T	uc002zpr.2	+						CDC45_uc011agz.1_Intron|CDC45_uc011aha.1_Intron|CDC45_uc002zps.2_Intron|CDC45_uc002zpt.2_Intron	NM_003504	NP_003495	O75419	CDC45_HUMAN	CDC45-like						DNA replication checkpoint|DNA strand elongation involved in DNA replication|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	centrosome|nucleoplasm	protein binding			lung(1)	1						GGTGAGTTTGGGTCTCTCACA	0.453													5	52	---	---	---	---	PASS
MYO18B	84700	broad.mit.edu	37	22	26423089	26423089	+	Silent	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26423089G>T	uc003abz.1	+	43	7399	c.7149G>T	c.(7147-7149)CGG>CGT	p.R2383R	MYO18B_uc003aca.1_Silent_p.R2264R|MYO18B_uc010guy.1_Silent_p.R2265R|MYO18B_uc010guz.1_Silent_p.R2263R|MYO18B_uc011aka.1_Silent_p.R1537R|MYO18B_uc011akb.1_Silent_p.R1896R|MYO18B_uc010gva.1_Silent_p.R366R|MYO18B_uc010gvb.1_RNA	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2383						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						TGCGTCCTCGGAGGCGGTGTC	0.602													15	57	---	---	---	---	PASS
SEC14L2	23541	broad.mit.edu	37	22	30818328	30818328	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30818328G>T	uc003ahr.2	+	12	1317	c.1144G>T	c.(1144-1146)GAG>TAG	p.E382*	SEC14L2_uc011akx.1_Nonsense_Mutation_p.E328*|SEC14L2_uc003ahs.2_Nonsense_Mutation_p.E308*|SEC14L2_uc011aky.1_Nonsense_Mutation_p.E299*|SEC14L2_uc003aht.2_RNA|SEC14L2_uc003ahu.3_Intron|SEC14L2_uc010gvv.2_RNA|SEC14L2_uc010gvw.1_Intron|MTP18_uc010gvx.1_Intron|MTP18_uc003ahv.1_Intron|MTP18_uc010gvy.1_Intron	NM_012429	NP_036561	O76054	S14L2_HUMAN	SEC14-like 2 isoform 1	382	GOLD.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	phospholipid binding|transporter activity|vitamin E binding				0					Vitamin E(DB00163)	TTTCACTGTGGAGGTCCTGCT	0.522													6	59	---	---	---	---	PASS
FAM47C	442444	broad.mit.edu	37	X	37027657	37027657	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37027657C>G	uc004ddl.1	+	1	1188	c.1174C>G	c.(1174-1176)CCA>GCA	p.P392A		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	392										ovary(3)	3						TCCTCTCCGCCCAGAGACCCC	0.612													3	15	---	---	---	---	PASS
CACNA1F	778	broad.mit.edu	37	X	49067838	49067838	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49067838C>A	uc004dnb.2	-	36	4299	c.4237G>T	c.(4237-4239)GGT>TGT	p.G1413C	CACNA1F_uc010nip.2_Missense_Mutation_p.G1402C	NM_005183	NP_005174	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type,	1413	Phenylalkylamine binding (By similarity).|Extracellular (Potential).|IV.|Dihydropyridine binding (By similarity).				axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)	AAATTGCTACCACAGGTAAAC	0.537													4	31	---	---	---	---	PASS
HEPH	9843	broad.mit.edu	37	X	65392409	65392409	+	Missense_Mutation	SNP	C	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65392409C>G	uc011moz.1	+	3	449	c.389C>G	c.(388-390)CCT>CGT	p.P130R	HEPH_uc004dwn.2_Missense_Mutation_p.P130R|HEPH_uc004dwo.2_5'UTR|HEPH_uc010nkr.2_Missense_Mutation_p.P130R|HEPH_uc011mpa.1_Missense_Mutation_p.P130R	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	127	Extracellular (Potential).|Plastocyanin-like 1.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						ACCATCCACCCTCATGGTGTC	0.493													5	31	---	---	---	---	PASS
HEPH	9843	broad.mit.edu	37	X	65427122	65427122	+	Missense_Mutation	SNP	A	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65427122A>G	uc011moz.1	+	14	2446	c.2386A>G	c.(2386-2388)ACA>GCA	p.T796A	HEPH_uc004dwn.2_Missense_Mutation_p.T796A|HEPH_uc004dwo.2_Missense_Mutation_p.T526A|HEPH_uc010nkr.2_Missense_Mutation_p.T604A|HEPH_uc011mpa.1_Missense_Mutation_p.T796A|HEPH_uc010nks.2_Missense_Mutation_p.T85A	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	793	Extracellular (Potential).|Plastocyanin-like 5.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						CACTGATGGTACATTCAGGAT	0.468													5	15	---	---	---	---	PASS
HEPH	9843	broad.mit.edu	37	X	65427158	65427158	+	Nonsense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65427158G>T	uc011moz.1	+	14	2482	c.2422G>T	c.(2422-2424)GAA>TAA	p.E808*	HEPH_uc004dwn.2_Nonsense_Mutation_p.E808*|HEPH_uc004dwo.2_Nonsense_Mutation_p.E538*|HEPH_uc010nkr.2_Nonsense_Mutation_p.E616*|HEPH_uc011mpa.1_Nonsense_Mutation_p.E808*|HEPH_uc010nks.2_Nonsense_Mutation_p.E97*	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a	805	Extracellular (Potential).|Plastocyanin-like 5.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						TGGACCAGAAGAACACTTGGG	0.493													4	17	---	---	---	---	PASS
CYLC1	1538	broad.mit.edu	37	X	83128462	83128462	+	Missense_Mutation	SNP	T	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83128462T>C	uc004eei.1	+	4	767	c.746T>C	c.(745-747)ATG>ACG	p.M249T	CYLC1_uc004eeh.1_Missense_Mutation_p.M248T	NM_021118	NP_066941	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head	249					cell differentiation|multicellular organismal development|spermatogenesis	acrosomal matrix|cytoskeletal calyx	structural molecule activity			ovary(4)|skin(1)	5						GATTTCCTCATGTTAGTGGGA	0.313													4	15	---	---	---	---	PASS
CHRDL1	91851	broad.mit.edu	37	X	109924818	109924818	+	Missense_Mutation	SNP	G	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109924818G>C	uc004eou.3	-	10	1397	c.1048C>G	c.(1048-1050)CCT>GCT	p.P350A	CHRDL1_uc004eov.2_Missense_Mutation_p.P339A|CHRDL1_uc004eow.2_Missense_Mutation_p.P348A|CHRDL1_uc010nps.2_Missense_Mutation_p.P349A|CHRDL1_uc004eot.2_Missense_Mutation_p.P269A|CHRDL1_uc011mss.1_Missense_Mutation_p.P264A	NM_001143981	NP_001137453	Q9BU40	CRDL1_HUMAN	chordin-like 1 isoform 1 precursor	342					BMP signaling pathway|cell differentiation|nervous system development|ossification	extracellular region					0						TCATACACAGGCATCGTTTCT	0.453													6	43	---	---	---	---	PASS
ARHGAP36	158763	broad.mit.edu	37	X	130218636	130218636	+	Missense_Mutation	SNP	C	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130218636C>A	uc004evz.2	+	6	1130	c.785C>A	c.(784-786)TCC>TAC	p.S262Y	ARHGAP36_uc004ewa.2_Missense_Mutation_p.S250Y|ARHGAP36_uc004ewb.2_Missense_Mutation_p.S231Y|ARHGAP36_uc004ewc.2_Missense_Mutation_p.S126Y	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	262	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3						CTTGAATACTCCGTGCAGCGA	0.473													8	45	---	---	---	---	PASS
IGSF1	3547	broad.mit.edu	37	X	130417031	130417031	+	Missense_Mutation	SNP	C	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130417031C>T	uc004ewd.2	-	6	1113	c.875G>A	c.(874-876)GGA>GAA	p.G292E	IGSF1_uc004ewe.3_Missense_Mutation_p.G281E|IGSF1_uc004ewf.2_Missense_Mutation_p.G272E	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	292	Ig-like C2-type 3.|Extracellular (Potential).				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						GAGGTAATGTCCAGTATCTTG	0.398													4	31	---	---	---	---	PASS
F9	2158	broad.mit.edu	37	X	138623348	138623348	+	Missense_Mutation	SNP	G	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138623348G>T	uc004fas.1	+	4	420	c.391G>T	c.(391-393)GAT>TAT	p.D131Y	F9_uc004fat.1_Intron	NM_000133	NP_000124	P00740	FA9_HUMAN	coagulation factor IX preproprotein	131	EGF-like 2.				blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen|plasma membrane	calcium ion binding|serine-type endopeptidase activity			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Heparin(DB01109)|Menadione(DB00170)	CTGTGAATTAGGTAAGTAACT	0.338													4	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5716682	5716683	+	Intron	INS	-	G	G	rs138690198		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5716682_5716683insG	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																		tgttgagaggcaggcctaataa	0.059													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	12107339	12107340	+	IGR	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12107339_12107340delCA								MIIP (15233 upstream) : TNFRSF8 (16094 downstream)																							cacacacatgcacacacacaca	0.351													3	3	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15005780	15005781	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15005780_15005781insT	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						tttgttgggtcttttttttttt	0.000													4	2	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17232468	17232473	+	Intron	DEL	TGTTTT	-	-	rs66840727		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17232468_17232473delTGTTTT	uc009voy.1	+									Q5TZA2	CROCC_HUMAN	Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TGTGGTCAGCTGTTTTTGTTTTTGTG	0.451													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20185825	20185825	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20185825delC								RNF186 (44054 upstream) : OTUD3 (23063 downstream)																							cgcctgtaatcctagcacttt	0.124													4	2	---	---	---	---	
LOC284632	284632	broad.mit.edu	37	1	24537536	24537536	+	RNA	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24537536delT	uc010oei.1	+	3		c.1202delT				NR_027087				Homo sapiens hypothetical protein LOC284632, mRNA (cDNA clone IMAGE:4826835).												0						ACCCTCTTTCTTAACCAGACA	0.458													4	2	---	---	---	---	
C1orf201	90529	broad.mit.edu	37	1	24706438	24706439	+	Intron	INS	-	G	G	rs138697925	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24706438_24706439insG	uc001bjc.2	-						C1orf201_uc001bja.2_Intron|C1orf201_uc001bjb.2_Intron|C1orf201_uc001bjd.2_Intron|C1orf201_uc001bje.1_Intron|C1orf201_uc001bjf.2_Intron			Q5TH74	CA201_HUMAN	RecName: Full=UPF0490 protein C1orf201;											ovary(1)|breast(1)	2		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.0191)|all_lung(284;0.0251)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.056)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.48e-25)|Colorectal(126;7.29e-08)|COAD - Colon adenocarcinoma(152;3.85e-06)|GBM - Glioblastoma multiforme(114;0.000399)|BRCA - Breast invasive adenocarcinoma(304;0.00107)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00393)|READ - Rectum adenocarcinoma(331;0.0672)|Lung(427;0.145)		AAACTCTGGCAGTAACAATGAT	0.396													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	26716441	26716445	+	IGR	DEL	TTTTG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26716441_26716445delTTTTG								ZNF683 (17175 upstream) : LIN28A (20824 downstream)																							GGTTAGTGATttttgttttgttttg	0.293													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	27403512	27403512	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27403512delT								FAM46B (64179 upstream) : SLC9A1 (21789 downstream)																							cctcctttccttttttcccct	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	29695382	29695383	+	IGR	DEL	AA	-	-	rs113557140		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29695382_29695383delAA								PTPRU (42067 upstream) : None (None downstream)																							actctgtctcaaaaaaaaaaaa	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	33657014	33657014	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33657014delC								TRIM62 (9343 upstream) : ZNF362 (65160 downstream)																							TCCTTCCCTTCCCAAAGCAGG	0.383													4	2	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39664486	39664487	+	Intron	DEL	CT	-	-	rs149299832		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39664486_39664487delCT	uc010ois.1	+						MACF1_uc001cda.1_Intron	NM_012090	NP_036222	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			cagagcaagactctgtctcaag	0.104													0	7	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	41992788	41992789	+	Intron	DEL	CT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41992788_41992789delCT	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001cgy.2_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ctcacacaccctcttcctcaca	0.015													4	3	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42311091	42311096	+	Intron	DEL	CACACA	-	-	rs72326822		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42311091_42311096delCACACA	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				cacacacacgcacacacacacacaca	0.301													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	43540364	43540364	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43540364delG								SLC2A1 (115517 upstream) : FAM183A (73230 downstream)																							gtttttgtttgggatttgttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	44617374	44617374	+	IGR	DEL	A	-	-	rs803381	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44617374delA								KLF17 (16567 upstream) : DMAP1 (61751 downstream)																							CAGTGTATATATTTTTTTTTT	0.383													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58312494	58312495	+	Intron	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58312494_58312495delCA	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						cacgtgcgtgcacacacacaca	0.094													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58834227	58834228	+	Intron	INS	-	TCGT	TCGT	rs138081706	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58834227_58834228insTCGT	uc001cyt.1	-							NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						AGTATTTTTAATTGTTTGTTTT	0.208													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	61171665	61171665	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61171665delT	uc001czt.1	-											Homo sapiens cDNA FLJ39874 fis, clone SPLEN2015815.																		aagggcccaattttttttttt	0.000													4	2	---	---	---	---	
ROR1	4919	broad.mit.edu	37	1	64439906	64439906	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64439906delT	uc001dbj.2	+						ROR1_uc001dbi.3_Intron	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1						transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19						aattaaattcttactagctgt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	74210578	74210579	+	IGR	INS	-	AAC	AAC	rs145618167	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74210578_74210579insAAC								None (None upstream) : LRRIQ3 (281125 downstream)																							caaaagcaaagaacaacaacaa	0.000													3	4	---	---	---	---	
LRRIQ3	127255	broad.mit.edu	37	1	74645560	74645560	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74645560delT	uc001dfy.3	-						LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3											ovary(2)	2						TTTTCTCCAATTATTTCTTCA	0.284													4	2	---	---	---	---	
TNNI3K	51086	broad.mit.edu	37	1	74933950	74933950	+	Intron	DEL	A	-	-	rs3831092		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74933950delA	uc001dgf.1	+						TNNI3K_uc001dge.1_Intron	NM_015978	NP_057062	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform b							cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10						AAAGAAGAAGAAAAAAAAAAA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	85614089	85614089	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85614089delT								WDR63 (15269 upstream) : SYDE2 (9268 downstream)																							ATAAACCCTATCCATCATTAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88342448	88342448	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88342448delG								LMO4 (527845 upstream) : PKN2 (807474 downstream)																							ttgttgttgtgtgtgtgtgtg	0.000													6	3	---	---	---	---	
CCDC18	343099	broad.mit.edu	37	1	93662685	93662685	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93662685delA	uc001dpq.2	+							NM_206886	NP_996769	Q5T9S5	CCD18_HUMAN	sarcoma antigen NY-SAR-41											ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		aaaggaggacatcagaagaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96405478	96405478	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96405478delC								RWDD3 (692705 upstream) : PTBP2 (781697 downstream)																							TACTCCTCTTCCCTACTCTCT	0.388													4	2	---	---	---	---	
DBT	1629	broad.mit.edu	37	1	100712557	100712558	+	Intron	DEL	AC	-	-	rs57411954		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100712557_100712558delAC	uc001dta.2	-						DBT_uc010oug.1_Intron	NM_001918	NP_001909	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase						branched chain family amino acid catabolic process|fatty-acyl-CoA biosynthetic process	microtubule cytoskeleton|mitochondrial alpha-ketoglutarate dehydrogenase complex|mitochondrial nucleoid	acyltransferase activity|cofactor binding|dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity|protein binding			pancreas(1)	1		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		tggagttgagacagaaagcaca	0.000													4	2	---	---	---	---	
DCLRE1B	64858	broad.mit.edu	37	1	114451426	114451427	+	Intron	DEL	CA	-	-	rs35433996		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114451426_114451427delCA	uc001eeg.2	+						DCLRE1B_uc001eeh.2_Intron|DCLRE1B_uc001eei.2_Intron	NM_022836	NP_073747	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B (PSO2 homolog, S.						cell cycle checkpoint|DNA repair|protection from non-homologous end joining at telomere|telomeric 3' overhang formation|telomeric loop formation	centrosome|chromosome, telomeric region|nucleus	5'-3' exonuclease activity|protein binding				0	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		catacgcgtgcacacacacaca	0.287								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					4	3	---	---	---	---	
SPAG17	200162	broad.mit.edu	37	1	118691108	118691131	+	Intron	DEL	GCTGATTGGTCCATTTTACAGACT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118691108_118691131delGCTGATTGGTCCATTTTACAGACT	uc001ehk.2	-							NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17							cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		tttacagagcgctgattggtccattttacagactgctgattggt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142649332	142649333	+	Intron	INS	-	TT	TT	rs141768307	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142649332_142649333insTT	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		gacccagctaatttttttgtgt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142793187	142793188	+	Intron	INS	-	T	T	rs71249075		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142793187_142793188insT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		gaatgatttgattttttttttt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143516178	143516178	+	IGR	DEL	G	-	-	rs61824581		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143516178delG								None (None upstream) : LOC100286793 (131461 downstream)																							AAAAGAAAAAGTCATATTCCC	0.284													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144015779	144015780	+	Intron	DEL	AC	-	-	rs57828590		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144015779_144015780delAC	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		ctccagtcctactataacaaga	0.094													10	6	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144519342	144519343	+	Intron	INS	-	A	A	rs151085852	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144519342_144519343insA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|LOC728875_uc001eky.3_Intron|LOC728875_uc001ela.3_Intron|LOC728875_uc001ekz.3_Intron|uc001elb.3_RNA	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						ACCACTCATTGAAAAAAAAAAT	0.396													4	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144536015	144536016	+	Intron	INS	-	A	A	rs67192080		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144536015_144536016insA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						gtcaggagttcgagaccagcat	0.040													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	144596452	144596452	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144596452delG	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|uc001elc.2_RNA|NBPF9_uc009wif.1_Intron|uc001ele.2_RNA	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						ttgtagagatggggattcaac	0.000													6	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144942052	144942052	+	Intron	DEL	T	-	-	rs5008462		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144942052delT	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_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTGGTGGTACTTTTTTTGCTT	0.353			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145041738	145041738	+	Intron	DEL	T	-	-	rs11311233		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145041738delT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'Flank|PDE4DIP_uc001eln.3_5'Flank|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_5'Flank|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						ATGTGTTGCATTTTTTTCCCA	0.289													6	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145048529	145048529	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145048529delC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						aactgggaggcccccccccag	0.000													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145087200	145087200	+	Intron	DEL	G	-	-	rs58890996		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145087200delG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						tttgtcctttgtaatatggtg	0.000													7	5	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	147994684	147994685	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147994684_147994685insT	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						TTTTTTTGTTGTTTTTTTCCCC	0.371													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148850890	148850894	+	IGR	DEL	TCATT	-	-	rs145379788		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148850890_148850894delTCATT								NBPF16 (92579 upstream) : LOC645166 (77392 downstream)																							catcatttcatcatttcatttcatt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149222129	149222130	+	IGR	DEL	AG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149222129_149222130delAG								LOC645166 (269075 upstream) : LOC388692 (57346 downstream)																							agagagagacagagagagagag	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149259515	149259515	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149259515delT								LOC645166 (306461 upstream) : LOC388692 (19961 downstream)																							tagctagttgtttttagaccc	0.000													4	2	---	---	---	---	
PLEKHO1	51177	broad.mit.edu	37	1	150130387	150130387	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150130387delG	uc001ett.2	+						PLEKHO1_uc001etr.2_Intron|PLEKHO1_uc001ets.2_Intron|PLEKHO1_uc001etu.2_Intron	NM_016274	NP_057358	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O							cytoplasm|nucleus|plasma membrane				lung(1)	1	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTCGTGCCATGGGGAGCATCC	0.468													4	2	---	---	---	---	
CGN	57530	broad.mit.edu	37	1	151484666	151484667	+	Intron	DEL	GA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151484666_151484667delGA	uc009wmw.2	+							NM_020770	NP_065821	Q9P2M7	CING_HUMAN	cingulin							myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			TCTTCCTCTTGAGAGAGAGAGA	0.455													4	2	---	---	---	---	
SPRR3	6707	broad.mit.edu	37	1	152973161	152973162	+	5'Flank	DEL	TC	-	-	rs71956308		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152973161_152973162delTC	uc001fax.3	+						SPRR3_uc001faz.3_5'Flank|SPRR3_uc001fay.2_5'Flank	NM_005416	NP_005407	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3						keratinization|peptide cross-linking|wound healing	cytoplasm	protein binding|structural molecule activity			skin(1)	1	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			tttctttccttctctctctctc	0.099													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	159744140	159744141	+	IGR	INS	-	G	G	rs137879985	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159744140_159744141insG								CRP (59761 upstream) : DUSP23 (6618 downstream)																							AAGGAGGTTTTGGGGGATGGGA	0.520													3	3	---	---	---	---	
SLAMF8	56833	broad.mit.edu	37	1	159803597	159803598	+	Intron	INS	-	C	C	rs141014631	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159803597_159803598insC	uc001fue.3	+							NM_020125	NP_064510	Q9P0V8	SLAF8_HUMAN	SLAM family member 8 precursor							integral to membrane					0	all_hematologic(112;0.0597)					tacatttacttccccactgaat	0.000													2	4	---	---	---	---	
F5	2153	broad.mit.edu	37	1	169533094	169533097	+	Intron	DEL	TCTT	-	-	rs143022586		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169533094_169533097delTCTT	uc001ggg.1	-						F5_uc010plr.1_Intron	NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	ttctattctctctttcacttctca	0.000													6	5	---	---	---	---	
TNFSF4	7292	broad.mit.edu	37	1	173174042	173174043	+	Intron	DEL	AC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173174042_173174043delAC	uc001giw.2	-						TNFSF4_uc001giv.2_Intron	NM_003326	NP_003317	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily,						acute inflammatory response|cellular response to lipopolysaccharide|cellular response to prostaglandin E stimulus|chemokine (C-C motif) ligand 11 production|defense response to nematode|interleukin-4-dependent isotype switching to IgE isotypes|memory T cell activation|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of regulatory T cell differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of T-helper 1 cell differentiation|negative regulation of transcription, DNA-dependent|positive regulation of alpha-beta T cell proliferation|positive regulation of B cell activation|positive regulation of immunoglobulin mediated immune response|positive regulation of immunoglobulin secretion|positive regulation of inflammatory response|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-6 production|positive regulation of memory T cell differentiation|positive regulation of T cell cytokine production|positive regulation of T-helper 2 cell differentiation|positive regulation of type 2 immune response|response to virus|signal transduction|T-helper 2 cell activation	cell surface|extracellular space|integral to plasma membrane	cytokine activity			central_nervous_system(1)	1						acacacagaaacacacacacac	0.228													3	4	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175514551	175514552	+	Intron	DEL	AG	-	-	rs142112243		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175514551_175514552delAG	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					agaaatatatagagagaaacag	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177822827	177822828	+	IGR	INS	-	CA	CA	rs9425813		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177822827_177822828insCA								FAM5B (571270 upstream) : SEC16B (74661 downstream)																							CTGAGcacatgcacacacacac	0.381													4	3	---	---	---	---	
RASAL2	9462	broad.mit.edu	37	1	178234923	178234923	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178234923delC	uc001glq.2	+						RASAL2_uc009wxb.2_Intron	NM_170692	NP_733793	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 2						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						agacacttcacctgcaaacag	0.000													4	2	---	---	---	---	
QSOX1	5768	broad.mit.edu	37	1	180144291	180144292	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180144291_180144292insA	uc001gnz.2	+						QSOX1_uc001gny.2_Intron|QSOX1_uc001goa.2_Intron	NM_002826	NP_002817	O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1 isoform a						cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2						gactctgtctcaaaaaaaaaaa	0.000													2	5	---	---	---	---	
CACNA1E	777	broad.mit.edu	37	1	181519854	181519854	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181519854delT	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						AAATAAATGCTTTTTTTTTTT	0.408													3	3	---	---	---	---	
SMG7	9887	broad.mit.edu	37	1	183511825	183511826	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183511825_183511826insA	uc001gqg.2	+						SMG7_uc010pob.1_Intron|SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Intron	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						AATTGTGAGTGAAAAAAAAATC	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	200500148	200500149	+	IGR	INS	-	TG	TG	rs56229841	byFrequency	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200500148_200500149insTG								ZNF281 (120982 upstream) : KIF14 (20476 downstream)																							TTGTGCCTGCATGTGTGTGTGT	0.292													4	3	---	---	---	---	
FMOD	2331	broad.mit.edu	37	1	203210355	203210356	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203210355_203210356insA	uc010pqi.1	-						CHIT1_uc001gzm.1_Intron	NM_002023		Q06828	FMOD_HUMAN	fibromodulin precursor						transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)			gactccgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209558086	209558086	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209558086delG								None (None upstream) : LOC642587 (44082 downstream)																							GAAGAACCTTGGGAGATCACC	0.483													4	2	---	---	---	---	
HHAT	55733	broad.mit.edu	37	1	210500643	210500643	+	5'Flank	DEL	T	-	-	rs10558231		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210500643delT	uc009xcx.2	+						HHAT_uc010psq.1_5'Flank|HHAT_uc001hhz.3_5'Flank|HHAT_uc010psr.1_5'Flank|HHAT_uc010pss.1_5'Flank|HHAT_uc009xcy.2_5'Flank|HHAT_uc010pst.1_5'Flank	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)		AGATATACCATTTTTtttttt	0.119													4	2	---	---	---	---	
KCNH1	3756	broad.mit.edu	37	1	211080871	211080872	+	Intron	INS	-	A	A	rs72039470		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211080871_211080872insA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		GGACTGGGAAGAAAAAAAAAAA	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	211861930	211861931	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211861930_211861931insA								NEK2 (12963 upstream) : LPGAT1 (54869 downstream)																							gagaggaagagaaaaaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	212676130	212676131	+	IGR	INS	-	ATAC	ATAC	rs140499976	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212676130_212676131insATAC								NENF (56411 upstream) : ATF3 (62566 downstream)																							ACAGGGTCTAGATACATACATA	0.337													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214154652	214154653	+	IGR	INS	-	T	T	rs140673869		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214154652_214154653insT								RPS6KC1 (707845 upstream) : PROX1 (6633 downstream)																							GGAATGTTGTCTTTTTTTTTTT	0.351													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	221279163	221279163	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221279163delT								HLX (220765 upstream) : LOC400804 (224107 downstream)																							ATTCCTTCACTTTTAGATTTG	0.428													4	2	---	---	---	---	
TMEM63A	9725	broad.mit.edu	37	1	226049495	226049496	+	Intron	DEL	CA	-	-	rs71748929		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226049495_226049496delCA	uc001hpm.1	-							NM_014698	NP_055513	O94886	TM63A_HUMAN	transmembrane protein 63A							integral to membrane|lysosomal membrane	nucleotide binding			ovary(1)|breast(1)	2	Breast(184;0.197)					GGGTCTTCCCCACAGCTTTGCA	0.619													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228671692	228671693	+	IGR	INS	-	TCTTTTTC	TCTTTTTC	rs147838717	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228671692_228671693insTCTTTTTC								HIST3H2BB (25434 upstream) : RNF187 (3375 downstream)																							ctttccttccttctttttctcc	0.040													4	2	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231850476	231850477	+	Intron	DEL	GA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231850476_231850477delGA	uc001huz.2	+						TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_Intron|DISC1_uc010pwp.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron|DISC1_uc001hux.1_Intron|DISC1_uc001hvc.3_Intron|DISC1_uc010pwn.1_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				aagatatagggagagagagaga	0.089													4	2	---	---	---	---	
EDARADD	128178	broad.mit.edu	37	1	236629760	236629761	+	Intron	DEL	CT	-	-	rs34021141		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236629760_236629761delCT	uc001hxu.1	+						EDARADD_uc001hxv.1_Intron	NM_145861	NP_665860	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain isoform A						cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			cacacacacactcacactcaca	0.168													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	245104394	245104395	+	IGR	DEL	AC	-	-	rs112475238		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245104394_245104395delAC								HNRNPU (76567 upstream) : EFCAB2 (28776 downstream)																							ctgtctcaaaacacacacacac	0.000													4	2	---	---	---	---	
FAM150B	285016	broad.mit.edu	37	2	283231	283232	+	Intron	INS	-	T	T	rs151276612	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:283231_283232insT	uc002qwi.3	-						FAM150B_uc010ewf.1_Intron	NM_001002919	NP_001002919	Q6UX46	F150B_HUMAN	hypothetical protein LOC285016 precursor							extracellular region					0	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.00091)|Epithelial(75;0.00656)|OV - Ovarian serous cystadenocarcinoma(76;0.00954)|GBM - Glioblastoma multiforme(21;0.128)		AATAAATCGCATTTTTTTGCAA	0.381													7	4	---	---	---	---	
SNTG2	54221	broad.mit.edu	37	2	1108670	1108671	+	Intron	INS	-	T	T	rs147602280	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1108670_1108671insT	uc002qwq.2	+						SNTG2_uc002qwp.2_Intron|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		ACTAAGTGAGGTTAAACCTTGC	0.401													4	2	---	---	---	---	
SNTG2	54221	broad.mit.edu	37	2	1285097	1285098	+	Intron	DEL	GT	-	-	rs142654588		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1285097_1285098delGT	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		tgtttgtgtggtgtgtgtgtgt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2910744	2910744	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2910744delC	uc002qxh.1	-											Homo sapiens cDNA FLJ37991 fis, clone CTONG2011765.																		cagccactcacccctacacct	0.050													5	4	---	---	---	---	
TSSC1	7260	broad.mit.edu	37	2	3366527	3366527	+	Intron	DEL	T	-	-	rs78935576		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3366527delT	uc002qxj.2	-							NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		ACAGAGGGCATTGGCTGCTGA	0.478													3	4	---	---	---	---	
YWHAQ	10971	broad.mit.edu	37	2	9770589	9770590	+	5'UTR	INS	-	CGGGGC	CGGGGC			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9770589_9770590insCGGGGC	uc002qzw.2	-	1					YWHAQ_uc002qzx.2_5'UTR	NM_006826	NP_006817	P27348	1433T_HUMAN	tyrosine 3/tryptophan 5 -monooxygenase						negative regulation of transcription, DNA-dependent	centrosome|nucleus	protein N-terminus binding			breast(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.241)		CATggcgggcgcggggccgggg	0.599													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	11060846	11060847	+	IGR	INS	-	TG	TG	rs149638295	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11060846_11060847insTG								KCNF1 (6496 upstream) : C2orf50 (212332 downstream)																							gtgcgtgtgcctgtgtgtgtgt	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13557423	13557424	+	IGR	DEL	TG	-	-	rs150857632	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13557423_13557424delTG								TRIB2 (674567 upstream) : None (None downstream)																							actacacacatgtgcacacata	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17269683	17269684	+	IGR	INS	-	A	A	rs140544821	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17269683_17269684insA								FAM49A (422587 upstream) : RAD51AP2 (422302 downstream)																							cttcaatttgtaaaaaaaatgc	0.089													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17274874	17274875	+	IGR	INS	-	GGCTG	GGCTG	rs143496880	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17274874_17274875insGGCTG								FAM49A (427778 upstream) : RAD51AP2 (417111 downstream)																							TTTATCCCCCAGATTAAATCGG	0.302													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	17673408	17673408	+	IGR	DEL	A	-	-	rs74847661		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17673408delA								FAM49A (826312 upstream) : RAD51AP2 (18578 downstream)																							ATATTGAGAGAAAAAAAAACA	0.249													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20447189	20447189	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20447189delT								SDC1 (21995 upstream) : PUM2 (1264 downstream)																							AGCTAGGTACTTTTAAGTGAG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	25157382	25157382	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25157382delC								ADCY3 (15327 upstream) : DNAJC27 (9123 downstream)																							gatctcggctcactgcaacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	47090166	47090166	+	IGR	DEL	A	-	-	rs11367598		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47090166delA								LOC100134259 (4021 upstream) : MCFD2 (38851 downstream)																							GCTATAAGACAATGACACCTC	0.468													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53682544	53682544	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53682544delC								None (None upstream) : ASB3 (214574 downstream)																							ACGGAAGTGGCCCCAGGCACT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57449098	57449099	+	IGR	DEL	CT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57449098_57449099delCT								CCDC85A (835790 upstream) : VRK2 (685687 downstream)																							catcctctccctctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	59103171	59103182	+	Intron	DEL	TGTGTGTGTGTG	-	-	rs72298093		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59103171_59103182delTGTGTGTGTGTG	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																		GGCCTGATTTtgtgtgtgtgtgtgtgtgtgtg	0.316													4	2	---	---	---	---	
C2orf74	339804	broad.mit.edu	37	2	61387298	61387299	+	5'Flank	INS	-	T	T	rs140089960		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61387298_61387299insT	uc010ypm.1	+						C2orf74_uc002sba.2_Intron|C2orf74_uc010ypl.1_Intron	NM_001143959	NP_001137431	A8MZ97	CB074_HUMAN	hypothetical protein LOC339804 isoform 1							integral to membrane					0						aatgtcattccttttttttttt	0.000													3	3	---	---	---	---	
C2orf86	51057	broad.mit.edu	37	2	63397904	63397904	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63397904delT	uc002sch.2	-						C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_Intron	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						ttcctgcttatttttgtggta	0.025													4	2	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72725736	72725736	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72725736delT	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						TTTTTTTCGGTTTTTTTTTTT	0.299													6	4	---	---	---	---	
SFXN5	94097	broad.mit.edu	37	2	73260875	73260875	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73260875delT	uc002siq.2	-						SFXN5_uc002sio.2_Intron|SFXN5_uc010yrc.1_Intron|SFXN5_uc002sip.2_Intron|SFXN5_uc010fet.2_Intron	NM_144579	NP_653180	Q8TD22	SFXN5_HUMAN	sideroflexin 5						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity			ovary(1)	1						ggactatggcttttactctaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	78291451	78291452	+	Intron	DEL	TG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78291451_78291452delTG	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																		aaaagaagtatgtgtgtgtgtg	0.000													4	3	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87404479	87404479	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87404479delT	uc002srs.3	+						uc002ssh.2_5'Flank			Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						TTCAACTTAGTTATATTCCTG	0.333													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87591421	87591423	+	Intron	DEL	ATG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87591421_87591423delATG	uc002srs.3	+									Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						gagatgaaaaatgatgagatgaa	0.000													4	2	---	---	---	---	
LOC654342	654342	broad.mit.edu	37	2	91838015	91838015	+	Intron	DEL	T	-	-	rs71380653		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91838015delT	uc002sts.3	-						LOC654342_uc002stt.2_Intron|LOC654342_uc010yub.1_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0						actttatttattttttttttt	0.015													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96814661	96814664	+	IGR	DEL	GTGT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96814661_96814664delGTGT								DUSP2 (3482 upstream) : STARD7 (35941 downstream)																							GTCTTGTCACgtgtgtgtgtgtgt	0.559													4	2	---	---	---	---	
INPP4A	3631	broad.mit.edu	37	2	99087131	99087131	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99087131delT	uc002syy.2	+						INPP4A_uc010yvj.1_Intron|INPP4A_uc010yvk.1_Intron|INPP4A_uc002syx.2_Intron|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1						tctttttttcttttttttttt	0.244													4	2	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100657957	100657957	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100657957delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						CCACTTATCCTTGGAACTGGC	0.428													4	2	---	---	---	---	
C2orf40	84417	broad.mit.edu	37	2	106685576	106685577	+	Intron	DEL	TC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106685576_106685577delTC	uc010fjf.2	+							NM_032411	NP_115787	Q9H1Z8	AUGN_HUMAN	esophageal cancer related gene 4 protein							extracellular region|transport vesicle					0						tctttttctttcttcctttctc	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	107110928	107110929	+	IGR	INS	-	T	T	rs141535496		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107110928_107110929insT								RGPD3 (26127 upstream) : ST6GAL2 (307129 downstream)																							cttttcttttctttttttttTT	0.208													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	109713904	109713904	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109713904delA								EDAR (108076 upstream) : SH3RF3 (32093 downstream)																							AAAGAAGACCAAAAAaaaaaa	0.035													4	2	---	---	---	---	
ANAPC1	64682	broad.mit.edu	37	2	112610713	112610713	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112610713delT	uc002thi.2	-							NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						ttcctggtcatttttttttcc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119224070	119224071	+	IGR	DEL	CA	-	-	rs72473810		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119224070_119224071delCA								INSIG2 (356474 upstream) : EN1 (375677 downstream)																							CTCCCCCCACcacacacacaca	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121287187	121287188	+	IGR	INS	-	CA	CA			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121287187_121287188insCA								LOC84931 (63262 upstream) : GLI2 (206011 downstream)																							TCCTTCATGTGcacacacacac	0.248													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122814898	122814898	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122814898delT								TSN (289472 upstream) : None (None downstream)																							cattaatcggttaaatagaac	0.055													4	2	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	132974712	132974712	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132974712delG	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						tctttgtgatgtcagcattcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133025287	133025288	+	IGR	INS	-	AAC	AAC	rs148490362		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133025287_133025288insAAC								NCRNA00164 (9745 upstream) : GPR39 (148859 downstream)																							AAGCTCTAGTTAACAGGAGAAA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133066592	133066592	+	Intron	DEL	G	-	-	rs78544491		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133066592delG	uc002ttk.1	+											Homo sapiens cDNA FLJ37280 fis, clone BRAMY2012881.																		AAAAGGAAAAGAATGTGCAGG	0.433													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134885782	134885782	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134885782delA								NCKAP5 (559751 upstream) : MGAT5 (126048 downstream)																							ctctacaaagaaaaaaaaaaa	0.055													4	2	---	---	---	---	
GTDC1	79712	broad.mit.edu	37	2	144848961	144848961	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144848961delA	uc002tvp.2	-						GTDC1_uc002tvo.2_Intron|GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)		tgtgatgtataaaataaaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	147222891	147222892	+	IGR	DEL	TC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147222891_147222892delTC								None (None upstream) : PABPC1P2 (121733 downstream)																							ggctcatgtgtcctgctgtcct	0.000													4	2	---	---	---	---	
GALNT13	114805	broad.mit.edu	37	2	155082203	155082203	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155082203delT	uc002tyr.3	+						GALNT13_uc002tyt.3_Intron|GALNT13_uc010foc.1_Intron	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						tttatcatagttttacgtgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	162400184	162400185	+	IGR	INS	-	A	A	rs147443922	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162400184_162400185insA								TBR1 (118611 upstream) : SLC4A10 (80660 downstream)																							attcctcactgaaaaaaaagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	170944284	170944284	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170944284delT								UBR3 (3647 upstream) : MYO3B (90371 downstream)																							aggaattatgtttttttttta	0.000													4	2	---	---	---	---	
CCDC141	285025	broad.mit.edu	37	2	179828388	179828389	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179828388_179828389insT	uc002ung.2	-									Q6ZP82	CC141_HUMAN	SubName: Full=Putative uncharacterized protein CCDC141; SubName: Full=Putative uncharacterized protein FLJ39502;								protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TCAATTGACACTTTTTTTTTTT	0.342													4	2	---	---	---	---	
ZNF385B	151126	broad.mit.edu	37	2	180554511	180554516	+	Intron	DEL	TGTGTG	-	-	rs112957152		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180554511_180554516delTGTGTG	uc002unn.3	-						ZNF385B_uc002unm.2_Intron	NM_152520	NP_689733	Q569K4	Z385B_HUMAN	zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			ggcaggggcatgtgtgtgtgtgtgtg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187844447	187844448	+	IGR	INS	-	G	G	rs142024775	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187844447_187844448insG								ZSWIM2 (130550 upstream) : CALCRL (363403 downstream)																							TAAGTTGTCACGTGAAGAAAGA	0.520													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193379307	193379308	+	IGR	INS	-	TG	TG	rs147990571	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193379307_193379308insTG								TMEFF2 (319663 upstream) : PCGEM1 (235263 downstream)																							cacctgtactttgtgtgtgtgt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	195652514	195652514	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195652514delT								None (None upstream) : SLC39A10 (869018 downstream)																							tttttgacggtttttttttta	0.000													2	4	---	---	---	---	
TRAK2	66008	broad.mit.edu	37	2	202315411	202315412	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202315411_202315412insT	uc002uyb.3	-						TRAK2_uc002uyc.2_Intron|STRADB_uc002uyd.3_5'Flank	NM_015049	NP_055864	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2							early endosome|plasma membrane	GABA receptor binding				0						GTGAAGTTACCTTTTTTTTTTT	0.366													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	213844829	213844829	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213844829delC								ERBB4 (441477 upstream) : IKZF2 (19584 downstream)																							GGAGGGGTGTCGGGGCTGAAG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	216108481	216108481	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216108481delC								ABCA12 (105330 upstream) : ATIC (68211 downstream)																							tgctctgttgcccaggctgaa	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	218143571	218143572	+	IGR	DEL	TT	-	-	rs67111564		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218143571_218143572delTT								TNP1 (418789 upstream) : DIRC3 (5176 downstream)																							ttccatgctcttttaaacaaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	224926708	224926709	+	IGR	INS	-	GT	GT	rs143838659	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224926708_224926709insGT								SERPINE2 (22672 upstream) : FAM124B (316707 downstream)																							CCGAAATCtgcgtgtgtgtgtg	0.277													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	228311938	228311938	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228311938delT								TM4SF20 (67916 upstream) : AGFG1 (24950 downstream)																							GTGGTAGGCATTTTTTTTTTC	0.269													4	2	---	---	---	---	
DNER	92737	broad.mit.edu	37	2	230574196	230574197	+	Intron	DEL	TG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230574196_230574197delTG	uc002vpv.2	-							NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		tgtgtgtgtctgtgtgtgtgtg	0.168													4	2	---	---	---	---	
INPP5D	3635	broad.mit.edu	37	2	234108601	234108601	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234108601delT	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		AGTTCCCCTCTTTTTTCTCGA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	234985799	234985800	+	IGR	INS	-	GTT	GTT	rs147843745	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234985799_234985800insGTT								SPP2 (23 upstream) : ARL4C (415888 downstream)																							TTCGTTGCCTGgttgttgttgt	0.252													4	2	---	---	---	---	
CNTN6	27255	broad.mit.edu	37	3	1234383	1234384	+	Intron	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1234383_1234384delCA	uc003boz.2	+						CNTN6_uc010hbo.2_Intron|CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		CAATGACAACCACACACACACA	0.386													4	2	---	---	---	---	
ARL8B	55207	broad.mit.edu	37	3	5174786	5174787	+	Intron	INS	-	A	A	rs145603437	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5174786_5174787insA	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654	Q9NVJ2	ARL8B_HUMAN	ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)		atcatgtggggaaaaaagataT	0.178													6	3	---	---	---	---	
TBC1D5	9779	broad.mit.edu	37	3	17431159	17431159	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17431159delC	uc003cbf.2	-						TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_Intron	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						ccagccaacaccatgtgcaac	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23818984	23818984	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23818984delT								UBE2E2 (186688 upstream) : UBE2E1 (28455 downstream)																							TCCCCAGCTCTTTTTTTTTTT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	27047737	27047737	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27047737delT								LRRC3B (295474 upstream) : NEK10 (104658 downstream)																							ggggaacctgttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	30594126	30594126	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30594126delG								RBMS3 (547507 upstream) : TGFBR2 (53868 downstream)																							GAACTCATATGGAAGAATACT	0.373													4	2	---	---	---	---	
GLB1	2720	broad.mit.edu	37	3	33104923	33104925	+	Intron	DEL	GAG	-	-	rs71741399		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33104923_33104925delGAG	uc003cfi.1	-						GLB1_uc003cfh.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron	NM_000404	NP_000395	P16278	BGAL_HUMAN	galactosidase, beta 1 isoform a preproprotein						carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)				GGGAAGGGGAGAGGAGGAGGAGG	0.404													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	35501687	35501687	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35501687delG								None (None upstream) : ARPP21 (179394 downstream)																							gggaagaggtggaaataaaga	0.000													4	2	---	---	---	---	
EXOG	9941	broad.mit.edu	37	3	38540046	38540046	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38540046delA	uc003cih.2	+						EXOG_uc010hhg.2_Intron|EXOG_uc011ayq.1_Intron|EXOG_uc003cij.2_Intron|EXOG_uc010hhd.2_Intron|EXOG_uc010hhe.2_Intron|EXOG_uc003cik.2_Intron|EXOG_uc010hhf.2_Intron|EXOG_uc003cii.2_Intron	NM_005107	NP_005098	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like							mitochondrial inner membrane	endonuclease activity|metal ion binding|nucleic acid binding				0						aatgtgtctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41338410	41338412	+	Intron	DEL	GAA	-	-	rs34460419		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41338410_41338412delGAA	uc003ckv.3	-							NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		cagatggcaggaagaagagaggg	0.192													3	4	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41643837	41643841	+	Intron	DEL	GGAAA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41643837_41643841delGGAAA	uc003ckv.3	-							NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		aaggaggaagggaaaggaaaggaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	51702082	51702083	+	IGR	DEL	TG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51702082_51702083delTG								RAD54L2 (4472 upstream) : TEX264 (3139 downstream)																							TCAGCCCAGCtgtgtgtgtgtg	0.396													4	2	---	---	---	---	
SYNPR	132204	broad.mit.edu	37	3	63279460	63279461	+	Intron	DEL	TG	-	-	rs35599811		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63279460_63279461delTG	uc003dlp.2	+						SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron	NM_001130003	NP_001123475	Q8TBG9	SYNPR_HUMAN	synaptoporin isoform 1							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)		atggttatactgtgtgtgtgtg	0.000													3	3	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71154353	71154355	+	Intron	DEL	GCG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71154353_71154355delGCG	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doj.2_Intron|FOXP1_uc003dok.2_Intron	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)		AATATGGCTTGCGTTTTCTTTTT	0.438			T	PAX5	ALL								3	3	---	---	---	---	
EIF4E3	317649	broad.mit.edu	37	3	71739018	71739019	+	Intron	INS	-	C	C	rs1104557	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71739018_71739019insC	uc003dov.3	-						EIF4E3_uc011bgc.1_Intron|EIF4E3_uc003dox.2_Intron|EIF4E3_uc011bgd.1_Intron|EIF4E3_uc010hoc.2_Intron	NM_001134651	NP_001128123	Q8N5X7	IF4E3_HUMAN	eukaryotic translation initiation factor 4E						regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)		aaaaaaaaaaaaCTTAAATGTA	0.248													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	73906333	73906333	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73906333delT								PDZRN3 (232261 upstream) : CNTN3 (405389 downstream)																							ccttccttccttccttccttc	0.000													6	3	---	---	---	---	
CNTN3	5067	broad.mit.edu	37	3	74399980	74399980	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74399980delA	uc003dpm.1	-							NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor						cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		aacacaaaataaaaaaaaaag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	76845570	76845570	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76845570delA								None (None upstream) : ROBO2 (243724 downstream)																							cacaggaaggaaaaaaaaaag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	82539658	82539658	+	IGR	DEL	A	-	-	rs67014363		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82539658delA								GBE1 (728708 upstream) : None (None downstream)																							CCTGTAAAAGAAAAAAAAAAA	0.388													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	84314203	84314204	+	IGR	INS	-	CCTT	CCTT	rs148070793	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84314203_84314204insCCTT								None (None upstream) : CADM2 (693929 downstream)																							cccactcactcccttccttcct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	90478590	90478590	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90478590delT								EPHA3 (947308 upstream) : None (None downstream)																							ttctgtctactttttatgtga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	94333972	94333972	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94333972delT								NSUN3 (488342 upstream) : LOC255025 (323135 downstream)																							tctttcttccttttttttttt	0.209													3	3	---	---	---	---	
WDR52	55779	broad.mit.edu	37	3	113097674	113097674	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113097674delT	uc003eae.1	-							NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2											central_nervous_system(1)	1						CTAAAAACACTTATCTTCCTA	0.388													4	2	---	---	---	---	
GAP43	2596	broad.mit.edu	37	3	115423634	115423634	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115423634delA	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		GCTGAATTctaattagctgtg	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117732527	117732528	+	IGR	DEL	TT	-	-	rs71642587		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117732527_117732528delTT								None (None upstream) : IGSF11 (886953 downstream)																							CCCTTTAGTCTTTTTTTTTTTT	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	118496316	118496317	+	Intron	INS	-	GACA	GACA	rs146706899	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118496316_118496317insGACA	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																		aaagaaaatgtgacaaacacca	0.000													4	4	---	---	---	---	
SLC15A2	6565	broad.mit.edu	37	3	121643447	121643448	+	Intron	INS	-	T	T	rs145210388	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121643447_121643448insT	uc003eep.2	+						SLC15A2_uc011bjn.1_Intron	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a						protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)	TAAGCATTGGATTTTTTTCCAA	0.376													5	3	---	---	---	---	
KPNA1	3836	broad.mit.edu	37	3	122166767	122166768	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122166767_122166768insA	uc003efd.1	-						KPNA1_uc003efb.1_Intron|KPNA1_uc003efc.1_Intron|KPNA1_uc011bjr.1_Intron|KPNA1_uc010hrh.2_Intron|KPNA1_uc003efe.2_Intron	NM_002264	NP_002255	P52294	IMA1_HUMAN	karyopherin alpha 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|regulation of DNA recombination|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein binding|protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.0898)		taatttacaagaaaaaaaaacc	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	130230573	130230573	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130230573delT								COL29A1 (26885 upstream) : COL6A6 (48605 downstream)																							cacgctggtcttttttttgtt	0.000													4	2	---	---	---	---	
ACAD11	84129	broad.mit.edu	37	3	132332718	132332718	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132332718delG	uc003eov.3	-						ACAD11_uc011blr.1_Intron	NM_032169	NP_115545	Q709F0	ACD11_HUMAN	putative acyl-CoA dehydrogenase							peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|transferase activity, transferring phosphorus-containing groups			ovary(1)	1						tctccagcttgggcgagacga	0.000													4	2	---	---	---	---	
PPP2R3A	5523	broad.mit.edu	37	3	135704172	135704173	+	Intron	DEL	TC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135704172_135704173delTC	uc003eqv.1	+						PPP2R3A_uc011blz.1_Intron	NM_002718	NP_002709	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'',						protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7						cctttccctttctctctctctc	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139437173	139437174	+	IGR	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139437173_139437174delGT								NMNAT3 (40333 upstream) : CLSTN2 (216853 downstream)																							gtgtgtaggggtgtgtgtgtgt	0.401													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145142996	145142998	+	IGR	DEL	CAA	-	-	rs145399567		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145142996_145142998delCAA								None (None upstream) : PLOD2 (644230 downstream)																							CAGTTTTGTTCAACAACTTTCCC	0.305													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	146857217	146857218	+	IGR	INS	-	C	C	rs143438865	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146857217_146857218insC								PLSCR5 (533214 upstream) : ZIC4 (246619 downstream)																							ATTTATATGAACACATAAGCAA	0.272													3	3	---	---	---	---	
CLRN1OS	116933	broad.mit.edu	37	3	150598093	150598098	+	Intron	DEL	TGTGTG	-	-	rs72355159		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150598093_150598098delTGTGTG	uc011bny.1	+											Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0						GGTTCCCATCtgtgtgtgtgtgtgtg	0.282													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	153737759	153737762	+	IGR	DEL	ACAC	-	-	rs140488261		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153737759_153737762delACAC								C3orf79 (517276 upstream) : SGEF (101387 downstream)																							ATATCCAAAGacacacacacacac	0.250													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157691838	157691838	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157691838delT								C3orf55 (372819 upstream) : SHOX2 (121963 downstream)																							GAAAGTCAGCTTTACAGGCAC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162130740	162130740	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162130740delA								OTOL1 (909012 upstream) : None (None downstream)																							gtgatgaaagaaaaaaaaatc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162576491	162576492	+	Intron	INS	-	A	A	rs142766455	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162576491_162576492insA	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																		cagtcatggttaaaaaaaaact	0.000													3	3	---	---	---	---	
SLITRK3	22865	broad.mit.edu	37	3	164905000	164905003	+	3'UTR	DEL	GTGT	-	-	rs34462639		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164905000_164905003delGTGT	uc003fej.3	-	2					SLITRK3_uc003fek.2_3'UTR	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor							integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						ATGGTATGGAgtgtgtgtgtgtgt	0.363										HNSCC(40;0.11)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166060778	166060779	+	IGR	DEL	AG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166060778_166060779delAG								BCHE (505525 upstream) : ZBBX (897302 downstream)																							ggctcagagcagagagagagag	0.000													4	2	---	---	---	---	
SERPINI2	5276	broad.mit.edu	37	3	167179694	167179695	+	Intron	INS	-	ACT	ACT	rs111669544		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167179694_167179695insACT	uc003fer.1	-						SERPINI2_uc003fes.1_Intron|SERPINI2_uc003fet.1_Intron	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),						cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3						aggcataagccacATCTGGCAA	0.213													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	169592825	169592828	+	IGR	DEL	TTTG	-	-	rs68156089		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169592825_169592828delTTTG								LRRC31 (5165 upstream) : SAMD7 (36654 downstream)																							AGTGGGgttttttgtttgtttgtt	0.103													4	2	---	---	---	---	
LOC100128164	100128164	broad.mit.edu	37	3	169664945	169664946	+	RNA	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169664945_169664946delGT	uc011bpp.1	-	2		c.2857_2858delAC				NR_027622				Homo sapiens cDNA FLJ41016 fis, clone UTERU2018784.												0						AGGTATATTCgtgtgtgtgtgt	0.168													4	2	---	---	---	---	
PHC3	80012	broad.mit.edu	37	3	169846305	169846305	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169846305delT	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			AACAATGGCATTTTTTTTTTT	0.303													4	2	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	175192520	175192520	+	Intron	DEL	C	-	-	rs62285248		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175192520delC	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron|NAALADL2_uc010hwz.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		ttcaggactgcttttccctac	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	175905075	175905077	+	IGR	DEL	AAC	-	-	rs67157836		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175905075_175905077delAAC								NAALADL2 (381649 upstream) : TBL1XR1 (833466 downstream)																							TCATATAGATAACAACAACCACA	0.177													3	3	---	---	---	---	
USP13	8975	broad.mit.edu	37	3	179473533	179473533	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179473533delT	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TGCTCACCTGTTTACTGTTTA	0.388													4	2	---	---	---	---	
PARL	55486	broad.mit.edu	37	3	183598188	183598188	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183598188delT	uc003fmd.2	-						PARL_uc003fme.2_Intron	NM_018622	NP_061092	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like isoform 1						proteolysis	integral to membrane|mitochondrial inner membrane|nucleus	serine-type endopeptidase activity				0	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TATAGTTCAGttttttttttt	0.219													5	3	---	---	---	---	
EPHB3	2049	broad.mit.edu	37	3	184300042	184300047	+	3'UTR	DEL	GTGTGT	-	-	rs35514470		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184300042_184300047delGTGTGT	uc003foz.2	+	16						NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|breast(2)|upper_aerodigestive_tract(1)|stomach(1)|skin(1)|ovary(1)	11	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			GGAtgtgtgagtgtgtgtgtgtgtgt	0.447													1	5	---	---	---	---	
MAP3K13	9175	broad.mit.edu	37	3	185026311	185026313	+	Intron	DEL	AGT	-	-	rs146743989		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185026311_185026313delAGT	uc010hyf.2	+						MAP3K13_uc011brt.1_Intron	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			aaaggccatgagttgggcatttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186179391	186179392	+	Intron	INS	-	TTTCTTTTC	TTTCTTTTC	rs142057147	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186179391_186179392insTTTCTTTTC	uc003fqd.1	-											Homo sapiens cDNA FLJ32735 fis, clone TESTI2001229.																		tatgtatctcatttcttttctt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191615677	191615677	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191615677delG								PYDC2 (436434 upstream) : FGF12 (244007 downstream)																							atatgggtttggcactatggg	0.000													4	2	---	---	---	---	
FGF12	2257	broad.mit.edu	37	3	192177628	192177629	+	Intron	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192177628_192177629delGT	uc003fsy.2	-							NM_004113	NP_004104	P61328	FGF12_HUMAN	fibroblast growth factor 12 isoform 2						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		TGTATGTTTAgtgtgtgtgtgt	0.257													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194572738	194572738	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194572738delC								FAM43A (162974 upstream) : C3orf21 (216277 downstream)																							ATCCTTCCCTCCACAGCCTCC	0.378													4	2	---	---	---	---	
ACAP2	23527	broad.mit.edu	37	3	195056972	195056972	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195056972delA	uc003fun.3	-						ACAP2_uc003fuo.2_3'UTR	NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2						TCCCCACCGCAAAAAAAAAAA	0.274													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195429829	195429829	+	Intron	DEL	T	-	-	rs57681905		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195429829delT	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		aagaccagcctgggtaacatg	0.010													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3604323	3604325	+	IGR	DEL	CTG	-	-	rs10571400		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3604323_3604325delCTG								LRPAP1 (70099 upstream) : ADRA2C (163750 downstream)																							GGTAGTGAGACTGCTGCTGGGTC	0.542													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9528968	9528969	+	IGR	INS	-	TT	TT	rs144214705		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9528968_9528969insTT								DEFB131 (76729 upstream) : MIR548I2 (28820 downstream)																							attgaaaatgattttttttttt	0.015													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14038321	14038322	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14038321_14038322insA								BOD1L (408993 upstream) : CPEB2 (967200 downstream)																							ATCAAAGAAACAAAAAAGAAAC	0.342													4	2	---	---	---	---	
CC2D2A	57545	broad.mit.edu	37	4	15517757	15517757	+	Intron	DEL	T	-	-	rs142208236		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15517757delT	uc010idv.2	+						CC2D2A_uc003gnx.2_Intron|CC2D2A_uc003gnv.2_Intron|uc003gny.1_5'Flank	NM_001080522	NP_001073991	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A isoform						cell projection organization	cilium|microtubule basal body				pancreas(2)|ovary(1)	3						AAGTGGTTCATTTTTTTTTTT	0.383													2	4	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20421291	20421294	+	Intron	DEL	TGTG	-	-	rs55679047		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20421291_20421294delTGTG	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						agttttaagctgtgtgtgtgtgtg	0.015													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21521047	21521048	+	Intron	DEL	AC	-	-	rs35530796		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21521047_21521048delAC	uc003gqh.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				gtgtatatatacacatatgtgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25630591	25630591	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25630591delT								ANAPC4 (210472 upstream) : SLC34A2 (26844 downstream)																							CCAGGAAGCATTTTTTTTTTT	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26845525	26845525	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26845525delA								TBC1D19 (88610 upstream) : STIM2 (16839 downstream)																							gagagtgtggaagtgccacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	33848559	33848559	+	IGR	DEL	G	-	-	rs33978831		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33848559delG								None (None upstream) : None (None downstream)																							TGACCAGCATGGGGGTGCTTG	0.383													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49213885	49213886	+	IGR	INS	-	GCTGT	GCTGT	rs112371447		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49213885_49213886insGCTGT								CWH43 (149792 upstream) : None (None downstream)																							tttgtagtgtggctgtgctgtg	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49242061	49242061	+	IGR	DEL	C	-	-	rs61467355		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49242061delC								CWH43 (177968 upstream) : None (None downstream)																							AAACTTTTCTCtttttttttt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49553201	49553202	+	IGR	INS	-	AT	AT			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49553201_49553202insAT								CWH43 (489108 upstream) : None (None downstream)																							AACATACACTCAGAGAATGAAT	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49581656	49581657	+	IGR	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49581656_49581657insT								CWH43 (517563 upstream) : None (None downstream)																							GTAATGCAAAATTTTTTAAATC	0.376													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49652473	49652477	+	IGR	DEL	AGGAG	-	-	rs147056711		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49652473_49652477delAGGAG								CWH43 (588380 upstream) : None (None downstream)																							tggaatggaaaggagtgtaatggaa	0.000													4	2	---	---	---	---	
LPHN3	23284	broad.mit.edu	37	4	62279475	62279478	+	Intron	DEL	AACA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62279475_62279478delAACA	uc003hcq.3	+						LPHN3_uc010ihg.1_Intron			Q9HAR2	LPHN3_HUMAN	RecName: Full=Latrophilin-3; AltName: Full=Calcium-independent alpha-latrotoxin receptor 3; AltName: Full=Lectomedin-3; Flags: Precursor;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						aacaacaaacaacaaacaaacaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69721300	69721301	+	IGR	DEL	AC	-	-	rs114273623	byFrequency	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69721300_69721301delAC								UGT2B10 (23561 upstream) : UGT2A3 (72876 downstream)																							ATTTATATATacacacacacac	0.079													3	3	---	---	---	---	
AFM	173	broad.mit.edu	37	4	74350259	74350259	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74350259delT	uc003hhb.2	+							NM_001133	NP_001124	P43652	AFAM_HUMAN	afamin precursor						vitamin transport		vitamin E binding			ovary(2)|central_nervous_system(1)	3	Breast(15;0.00102)		Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			tctttccttcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	80446386	80446386	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80446386delT	uc003hlv.2	+											Homo sapiens cDNA FLJ41919 fis, clone PERIC2002272.																		tgacgtctggtgaggagcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	85447032	85447033	+	IGR	DEL	AG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85447032_85447033delAG								NKX6-1 (27645 upstream) : CDS1 (57024 downstream)																							aaaaaaaaaaagaaagaaagaa	0.000													4	2	---	---	---	---	
SNCA	6622	broad.mit.edu	37	4	90749803	90749804	+	Intron	DEL	AC	-	-	rs35798275		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90749803_90749804delAC	uc003hsq.2	-						SNCA_uc010ikt.2_Intron|SNCA_uc003hso.2_Intron|SNCA_uc003hsp.2_Intron|SNCA_uc003hsr.2_Intron	NM_001146054	NP_001139526	P37840	SYUA_HUMAN	alpha-synuclein isoform NACP140						activation of caspase activity|anti-apoptosis|negative regulation of dopamine uptake|negative regulation of exocytosis|negative regulation of histone acetylation|negative regulation of microtubule polymerization|negative regulation of monooxygenase activity|negative regulation of norepinephrine uptake|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of serotonin uptake|negative regulation of thrombin receptor signaling pathway|negative regulation of transporter activity|positive regulation of endocytosis|positive regulation of inositol phosphate biosynthetic process|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein serine/threonine kinase activity|positive regulation of receptor recycling|positive regulation of release of sequestered calcium ion into cytosol|receptor internalization|regulation of phospholipase activity|response to interferon-gamma|response to interleukin-1|response to iron(II) ion|response to lipopolysaccharide|response to magnesium ion|synaptic vesicle endocytosis	actin cytoskeleton|axon|cell cortex|cell junction|cytosol|fibril|growth cone|nucleus|synapse	alpha-tubulin binding|calcium ion binding|caspase inhibitor activity|dynein binding|ferrous iron binding|histone binding|Hsp70 protein binding|kinesin binding|magnesium ion binding|phosphoprotein binding|tau protein binding|zinc ion binding				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.42e-05)	Melatonin(DB01065)	tgtaaaaaaaacattttaggct	0.149													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104444929	104444929	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104444929delC								CENPE (325363 upstream) : TACR3 (65696 downstream)																							ttccttccttccctcccttcc	0.070													4	3	---	---	---	---	
NPNT	255743	broad.mit.edu	37	4	106850442	106850442	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106850442delT	uc003hya.2	+						NPNT_uc011cfc.1_Intron|NPNT_uc011cfd.1_Intron|NPNT_uc011cfe.1_Intron|NPNT_uc010ilt.1_Intron|NPNT_uc011cff.1_Intron|NPNT_uc010ilu.1_Intron	NM_001033047	NP_001028219	Q6UXI9	NPNT_HUMAN	nephronectin precursor						cell differentiation	membrane	calcium ion binding			skin(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		AAAATGGTGGTTCATGAACCA	0.284													4	2	---	---	---	---	
NDST3	9348	broad.mit.edu	37	4	118953905	118953905	+	5'Flank	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118953905delA	uc003ibx.2	+						NDST3_uc011cgf.1_5'Flank|NDST3_uc003ibw.2_5'Flank	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1						gagaggaaggaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	129691341	129691341	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129691341delC								PGRMC2 (482393 upstream) : PHF17 (39438 downstream)																							taaatcatctccacatttaag	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130680057	130680058	+	Intron	INS	-	C	C	rs148628605	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130680057_130680058insC	uc003igv.2	-											Homo sapiens cDNA clone IMAGE:5265890.																		ttcctctcctacttatcctcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	135068882	135068883	+	IGR	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135068882_135068883delGT								PCDH10 (956151 upstream) : PABPC4L (48608 downstream)																							AGAAATTACAgtgtgtgtgtgt	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	135874873	135874873	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135874873delT								PABPC4L (751970 upstream) : None (None downstream)																							gtctttggggttttttaggga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	136593597	136593597	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136593597delT								None (None upstream) : None (None downstream)																							AGTAAATGGATTACAAGTTAA	0.348													4	2	---	---	---	---	
MAML3	55534	broad.mit.edu	37	4	141005122	141005135	+	Intron	DEL	AGAGAGAGAGAGAG	-	-	rs72201205		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141005122_141005135delAGAGAGAGAGAGAG	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187	Q96JK9	MAML3_HUMAN	mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)					acacacacacagagagagagagagagagagagag	0.280													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	144877374	144877378	+	Intron	DEL	TTTTT	-	-	rs35298868		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144877374_144877378delTTTTT	uc003ijl.2	+											Homo sapiens cDNA clone IMAGE:5268630.																		TTTATTGAGGttttttttttttttt	0.293													3	3	---	---	---	---	
SLC10A7	84068	broad.mit.edu	37	4	147260791	147260792	+	Intron	INS	-	CTTT	CTTT			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147260791_147260792insCTTT	uc010ioz.2	-						SLC10A7_uc003ikr.2_Intron|SLC10A7_uc010ipa.2_Intron|SLC10A7_uc003iks.2_Intron	NM_001029998	NP_001025169	Q0GE19	NTCP7_HUMAN	solute carrier family 10 (sodium/bile acid							integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)					TTGCTTCCTTCCCTATCTACCT	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	149679496	149679496	+	IGR	DEL	A	-	-	rs33984009		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149679496delA								NR3C2 (315853 upstream) : None (None downstream)																							GCAGTGTGTTaaaaaaaaaaa	0.313													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	150477453	150477453	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150477453delT	uc003ill.2	-											Homo sapiens cDNA clone IMAGE:5295442.																		TGGTCATGTCTTTTTTTTTTT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153998474	153998475	+	IGR	DEL	TC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153998474_153998475delTC								FHDC1 (97626 upstream) : TRIM2 (75795 downstream)																							CTCCTCCCTGTCTCTCTCCctc	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	163932691	163932691	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163932691delT								FSTL5 (847505 upstream) : NAF1 (115169 downstream)																							gcctagcccattaaatcattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	167490563	167490564	+	IGR	DEL	CA	-	-	rs3923452		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167490563_167490564delCA								TLL1 (465570 upstream) : SPOCK3 (163972 downstream)																							ttactttttgcacacacacaca	0.000													5	3	---	---	---	---	
NEK1	4750	broad.mit.edu	37	4	170415252	170415252	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170415252delT	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		gatttctTTCttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174272641	174272642	+	IGR	DEL	AA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174272641_174272642delAA								HMGB2 (17046 upstream) : SAP30 (19451 downstream)																							attttgtctgaaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	174720290	174720291	+	IGR	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174720290_174720291insT								MORF4 (182496 upstream) : FBXO8 (437521 downstream)																							cttcccttcccttccttccttc	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	184394172	184394176	+	IGR	DEL	TTCTC	-	-	rs10611603		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184394172_184394176delTTCTC								CDKN2AIP (25123 upstream) : ING2 (32044 downstream)																							ctggcctcttttctcttcctcagac	0.137													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190576865	190576866	+	IGR	DEL	CA	-	-	rs10570549	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190576865_190576866delCA								None (None upstream) : FRG1 (285108 downstream)																							cacacacacgcacacacacaca	0.163													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190826152	190826152	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190826152delC	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		TAAATGACATCGGGACCAgca	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190917346	190917347	+	IGR	DEL	TT	-	-	rs76107322		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190917346_190917347delTT								TUBB4Q (11322 upstream) : LOC653545 (91219 downstream)																							tgtgcctgacttatttcactta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	1048204	1048205	+	IGR	INS	-	GTTA	GTTA	rs149059976	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1048204_1048205insGTTA								NKD2 (9279 upstream) : SLC12A7 (2286 downstream)																							tgaatgagggggtgtgtgaacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2549991	2549991	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2549991delT								IRX4 (667111 upstream) : IRX2 (196290 downstream)																							ggaccacttgtttttttttca	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6350619	6350620	+	IGR	INS	-	TGC	TGC			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6350619_6350620insTGC								FLJ33360 (13214 upstream) : MED10 (21420 downstream)																							AGGAAGCTCCTTGCTGCTGCTG	0.554													5	3	---	---	---	---	
LOC285692	285692	broad.mit.edu	37	5	9768582	9768582	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9768582delC	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0						GCGCTGCTTTCCCAtgaccac	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	14073169	14073170	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14073169_14073170insA								DNAH5 (128580 upstream) : TRIO (70659 downstream)																							gagtctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
FAM105B	90268	broad.mit.edu	37	5	14692788	14692789	+	Intron	INS	-	T	T	rs144619199		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14692788_14692789insT	uc003jfk.2	+							NM_138348	NP_612357	Q96BN8	F105B_HUMAN	hypothetical protein LOC90268											ovary(2)	2	Lung NSC(4;0.00696)					TGATTATCTGCttttttttttt	0.233													3	4	---	---	---	---	
FAM134B	54463	broad.mit.edu	37	5	16551410	16551410	+	Intron	DEL	A	-	-	rs11307693		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16551410delA	uc003jfs.2	-							NM_001034850	NP_001030022	Q9H6L5	F134B_HUMAN	hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3						ACATATAAACAAAAAAACATG	0.428													2	4	---	---	---	---	
MYO10	4651	broad.mit.edu	37	5	16797100	16797101	+	Intron	INS	-	AAC	AAC	rs138141956	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16797100_16797101insAAC	uc003jft.3	-						MYO10_uc003jfu.2_Intron	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3						GGGTAACAAAAAACAAGAAAAC	0.302													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	17366490	17366490	+	IGR	DEL	C	-	-	rs76737742		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17366490delC								BASP1 (89555 upstream) : None (None downstream)																							tagtaaggagccccgtggtag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23046438	23046439	+	IGR	DEL	CT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23046438_23046439delCT								CDH12 (192707 upstream) : PRDM9 (461285 downstream)																							tctcccctcactctctctctct	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24013637	24013637	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24013637delC	uc003jgq.1	+											Homo sapiens cDNA FLJ34836 fis, clone NT2NE2010400.																		ctggtggcagcagccagtttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27682716	27682716	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27682716delT								CDH9 (644027 upstream) : None (None downstream)																							tcccacgtccttgggcagctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29372384	29372384	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29372384delA								None (None upstream) : None (None downstream)																							atgttaaaagaaaaaaaaata	0.000													4	2	---	---	---	---	
PDZD2	23037	broad.mit.edu	37	5	31761559	31761559	+	Intron	DEL	A	-	-	rs11321702		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31761559delA	uc003jhl.2	+							NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9						CGACACTAAGAAATTTGAATA	0.264													0	9	---	---	---	---	
SPEF2	79925	broad.mit.edu	37	5	35664380	35664381	+	Intron	INS	-	A	A	rs34622548		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35664380_35664381insA	uc003jjo.2	+						SPEF2_uc003jjn.1_Intron|SPEF2_uc003jjq.3_Intron	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1						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)			aTGAAATAAAGAAAAAAAAAAA	0.015													5	3	---	---	---	---	
EGFLAM	133584	broad.mit.edu	37	5	38351212	38351212	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38351212delT	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)					GCAGCACttcttttttttttt	0.239													4	2	---	---	---	---	
OSMR	9180	broad.mit.edu	37	5	38847596	38847597	+	Intron	INS	-	T	T	rs147707298	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38847596_38847597insT	uc003jln.1	+						uc003jlk.1_5'Flank|OSMR_uc003jlm.1_Intron	NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor precursor						cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)					aGCTCAAACTCTAAGACTGGGT	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40059887	40059887	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40059887delT								DAB2 (634552 upstream) : PTGER4 (620145 downstream)																							gtttccttcctgaagtcagtg	0.000													4	2	---	---	---	---	
GHR	2690	broad.mit.edu	37	5	42610769	42610769	+	Intron	DEL	A	-	-	rs112288959		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42610769delA	uc003jmt.2	+						GHR_uc011cpq.1_Intron	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	atcccagtggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
HCN1	348980	broad.mit.edu	37	5	45484637	45484637	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45484637delC	uc003jok.2	-							NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CCCTTGCCCTCCCCCTCTCTT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	46089482	46089482	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46089482delC								HCN1 (393262 upstream) : None (None downstream)																							ttgaacctttcttttgattga	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51762632	51762633	+	IGR	DEL	TC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51762632_51762633delTC								None (None upstream) : ITGA1 (321141 downstream)																							TCTTTCTCTTTCTCTCTCTCTG	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55329671	55329672	+	IGR	INS	-	T	T	rs11323699		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55329671_55329672insT								IL6ST (38908 upstream) : ANKRD55 (65836 downstream)																							ttttctttgacttttttttttt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56045796	56045796	+	IGR	DEL	A	-	-	rs113417697		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56045796delA								ANKRD55 (516610 upstream) : MAP3K1 (65104 downstream)																							gcactacaggaaaaaaaaata	0.000													4	2	---	---	---	---	
PDE4D	5144	broad.mit.edu	37	5	59413653	59413654	+	Intron	DEL	AC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59413653_59413654delAC	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194	Q08499	PDE4D_HUMAN	phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)	acacacacatacacacacacac	0.054													4	2	---	---	---	---	
IPO11	51194	broad.mit.edu	37	5	61748470	61748470	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61748470delT	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtb.1_Intron	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		TTTTTGCACCTTTTTTTTGGT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63226676	63226676	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63226676delT								None (None upstream) : HTR1A (29603 downstream)																							AGAGAGAAGCttttttttttt	0.229													3	4	---	---	---	---	
LOC645323	645323	broad.mit.edu	37	5	87913008	87913009	+	Intron	INS	-	ACAC	ACAC	rs138437442	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87913008_87913009insACAC	uc011cua.1	-							NR_015436				Homo sapiens cDNA FLJ34037 fis, clone FCBBF2005439.												0						tacacacacatacacacacaca	0.000													3	3	---	---	---	---	
FAM172A	83989	broad.mit.edu	37	5	93039775	93039784	+	Intron	DEL	ATGACTCAAA	-	-	rs36046139		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93039775_93039784delATGACTCAAA	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0						ATACTGCATGATGACTCAAAATGGCTTCAA	0.424													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96565048	96565049	+	IGR	INS	-	GT	GT	rs138721583	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96565048_96565049insGT								RIOK2 (46043 upstream) : None (None downstream)																							caacactcctggtgtgtgtgtg	0.074													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97159280	97159281	+	IGR	DEL	CT	-	-	rs35569866		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97159280_97159281delCT								RIOK2 (640275 upstream) : RGMB (945718 downstream)																							tctcgctttcctcttttttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	110901268	110901268	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110901268delT								STARD4 (53035 upstream) : C5orf13 (97055 downstream)																							TTTCTTCTTCTTTTTTTTTAA	0.129													4	2	---	---	---	---	
TMED7-TICAM2	100302736	broad.mit.edu	37	5	114957308	114957308	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114957308delT	uc003krd.2	-						TMED7-TICAM2_uc003kre.2_Intron|TMED7_uc011cwd.1_Intron|TMED7_uc003krf.2_Intron	NM_021649	NP_067681	Q86XR7	TCAM2_HUMAN	toll-like receptor adaptor molecule 2						I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	Golgi apparatus|intrinsic to membrane|plasma membrane	protein binding|transmembrane receptor activity				0						ATTCCAGCCATTTGGGTTGTA	0.274													4	2	---	---	---	---	
SNX24	28966	broad.mit.edu	37	5	122268801	122268801	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122268801delG	uc011cwo.1	+						SNX24_uc003ktf.2_Intron|SNX24_uc010jcy.2_Intron	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)		taagttacctggaaacaattt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	128547631	128547632	+	IGR	DEL	AC	-	-	rs150930344		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128547631_128547632delAC								ISOC1 (97914 upstream) : ADAMTS19 (248471 downstream)																							aacctgataaacacaagcaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	131581827	131581828	+	IGR	DEL	AG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131581827_131581828delAG								P4HA2 (18271 upstream) : PDLIM4 (11523 downstream)																							ctgtctccaaagagagagagag	0.000													4	3	---	---	---	---	
PKD2L2	27039	broad.mit.edu	37	5	137272149	137272150	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137272149_137272150insT	uc003lby.2	+						PKD2L2_uc003lbw.1_Intron|PKD2L2_uc003lbx.2_Intron|PKD2L2_uc011cyi.1_Intron	NM_014386	NP_055201	Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2							integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTGAGCAtttcttttttttttt	0.178													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164572834	164572835	+	IGR	DEL	AC	-	-	rs71726989		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164572834_164572835delAC								None (None upstream) : None (None downstream)																							GATTGGAAATacacacacacac	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	165161976	165161981	+	IGR	DEL	TATAAG	-	-	rs71775110		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165161976_165161981delTATAAG								None (None upstream) : None (None downstream)																							ttttgtctgatataagtataactatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166492445	166492445	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166492445delA								None (None upstream) : ODZ2 (219398 downstream)																							CACAAACAGTAAATTCCTTTT	0.358													4	2	---	---	---	---	
STK10	6793	broad.mit.edu	37	5	171590549	171590549	+	Intron	DEL	G	-	-	rs7736797	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171590549delG	uc003mbo.1	-							NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CCTTGGTGCCGGTTTCCCAAG	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	171929307	171929308	+	IGR	INS	-	TGTG	TGTG	rs62385488	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171929307_171929308insTGTG								SH3PXD2B (47780 upstream) : NEURL1B (138968 downstream)																							CCAACTTATTTtgtgtgtgtgt	0.277													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173269930	173269930	+	IGR	DEL	A	-	-	rs149121300		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173269930delA								BOD1 (226264 upstream) : CPEB4 (45401 downstream)																							tctcagaaagaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	178165081	178165081	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178165081delT								ZNF354A (7378 upstream) : AACSL (26785 downstream)																							GCTCTCAGGGTTTTTTTTTTC	0.199													4	2	---	---	---	---	
MAML1	9794	broad.mit.edu	37	5	179213589	179213589	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179213589delT	uc003mkn.1	+							NM_014757	NP_055572	Q92585	MAML1_HUMAN	mastermind-like 1						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	peptide antigen binding|protein kinase binding|transcription coactivator activity			lung(4)|ovary(2)	6	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATAGGTGCCttttttttttt	0.184													4	2	---	---	---	---	
MGAT1	4245	broad.mit.edu	37	5	180229120	180229121	+	Intron	INS	-	GGAGAC	GGAGAC	rs148912044	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180229120_180229121insGGAGAC	uc003mmg.3	-						MGAT1_uc010jlf.2_Intron|MGAT1_uc010jlg.2_Intron|MGAT1_uc003mmh.3_Intron|MGAT1_uc010jlh.2_Intron|MGAT1_uc003mmi.3_Intron	NM_002406	NP_002397	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCAGCCTTCAGGGAGCCGGCCA	0.520													4	2	---	---	---	---	
MGAT1	4245	broad.mit.edu	37	5	180235390	180235390	+	Intron	DEL	T	-	-	rs3832332		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180235390delT	uc003mmh.3	-						MGAT1_uc010jlh.2_Intron|MGAT1_uc003mmi.3_Intron	NM_001114618	NP_001108090	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ttcAGAAGTCTTCAATTATTA	0.308													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	353069	353072	+	IGR	DEL	CATT	-	-	rs148332139		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:353069_353072delCATT								DUSP22 (1716 upstream) : IRF4 (38680 downstream)																							GCTGCCTCTCcattcattcattca	0.230													4	3	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	1653902	1653903	+	Intron	INS	-	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1653902_1653903insC	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		ccaattgattttcaacaagggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	4247015	4247016	+	IGR	INS	-	T	T	rs34375490		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4247015_4247016insT								PECI (111184 upstream) : CDYL (459377 downstream)																							cttttctcttattttttttttt	0.000													2	4	---	---	---	---	
FARS2	10667	broad.mit.edu	37	6	5336136	5336136	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5336136delC	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	GCTTTTAATTCCGTTCTTTTT	0.358													4	2	---	---	---	---	
CAP2	10486	broad.mit.edu	37	6	17393781	17393782	+	5'UTR	INS	-	C	C	rs151171629	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17393781_17393782insC	uc003ncb.2	+	1					CAP2_uc010jpk.1_RNA|CAP2_uc011dja.1_5'UTR|CAP2_uc011djb.1_5'UTR|CAP2_uc011djc.1_5'UTR|CAP2_uc011djd.1_5'UTR	NM_006366	NP_006357	P40123	CAP2_HUMAN	adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			gctctccctctcccccctcAGC	0.347													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	20246364	20246364	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20246364delA								MBOAT1 (33694 upstream) : E2F3 (155773 downstream)																							gaccttgcttaaatagtattt	0.000													4	2	---	---	---	---	
CDKAL1	54901	broad.mit.edu	37	6	20604231	20604232	+	Intron	INS	-	T	T	rs143771764	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20604231_20604232insT	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)			aacaaacaggatgtgaagactg	0.000													4	2	---	---	---	---	
PRSS16	10279	broad.mit.edu	37	6	27213194	27213194	+	5'Flank	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27213194delT	uc003nja.2	+						PRSS16_uc011dkt.1_5'Flank|PRSS16_uc003njb.2_5'Flank	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN	protease, serine, 16 precursor						protein catabolic process|proteolysis	cytoplasmic membrane-bounded vesicle	serine-type peptidase activity			ovary(2)|central_nervous_system(2)|skin(1)	5						ATATCAGTCCttttttttttt	0.095													4	2	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29932914	29932915	+	Intron	INS	-	AC	AC	rs144845647	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29932914_29932915insAC	uc011dmb.1	+							NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						ACAGAAAGGAAATGGGATGGCA	0.238													4	2	---	---	---	---	
HLA-DQB2	3120	broad.mit.edu	37	6	32729382	32729382	+	Intron	DEL	A	-	-	rs34694311		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32729382delA	uc003oby.3	-						HLA-DQB2_uc003obz.2_Intron	NR_003937		Q5SR06	Q5SR06_HUMAN	SubName: Full=Major histocompatibility complex, class II, DQ beta 2; SubName: Full=Putative uncharacterized protein ENSP00000372579;						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	integral to membrane|MHC class II protein complex					0						CTCTGTGCGCAAGAGACTCGG	0.672													3	3	---	---	---	---	
HLA-DPA1	3113	broad.mit.edu	37	6	33039589	33039590	+	Intron	INS	-	GG	GG	rs142692154	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33039589_33039590insGG	uc003ocs.1	-						HLA-DPA1_uc010juk.2_Intron|HLA-DPA1_uc003oct.1_Intron	NM_033554	NP_291032	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity			skin(1)	1						CACTTCTCTCAGGGAAGACAGC	0.297													3	3	---	---	---	---	
FKBP5	2289	broad.mit.edu	37	6	35582932	35582932	+	Intron	DEL	T	-	-	rs148530740	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35582932delT	uc011dte.1	-						FKBP5_uc003okx.2_Intron|FKBP5_uc011dtf.1_Intron|FKBP5_uc003oky.2_Intron|FKBP5_uc003okz.2_Intron	NM_001145776	NP_001139248	Q13451	FKBP5_HUMAN	FK506 binding protein 5 isoform 1						protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1						caacaacaactacacacacac	0.000													4	3	---	---	---	---	
FKBP5	2289	broad.mit.edu	37	6	35690410	35690410	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35690410delC	uc003oky.2	-							NM_001145775	NP_001139247	Q13451	FKBP5_HUMAN	FK506 binding protein 5 isoform 1						protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1						ccaaacaactcccagtgccca	0.000													4	2	---	---	---	---	
ABCC10	89845	broad.mit.edu	37	6	43414592	43414593	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43414592_43414593insT	uc003ouy.1	+						ABCC10_uc003ouz.1_Intron|ABCC10_uc010jyo.1_Intron	NM_033450	NP_258261	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C, member 10							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			tttttgttttgttttttttttt	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50842339	50842339	+	IGR	DEL	T	-	-	rs145806945		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50842339delT								TFAP2B (27014 upstream) : PKHD1 (637806 downstream)																							ATCTCCAGTCTTTTTTTTTTT	0.423													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57217632	57217633	+	Intron	INS	-	A	A	rs146771562	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57217632_57217633insA	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TGTAGAAGGGGAAAAAAAATAG	0.356													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57274860	57274860	+	Intron	DEL	T	-	-	rs149902800		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57274860delT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ctcacgcctgtaatcccagca	0.000													5	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57292260	57292261	+	Intron	INS	-	T	T	rs148719437	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57292260_57292261insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		gggattccaggcatgcgccacc	0.000													2	9	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57301956	57301963	+	Intron	DEL	ACACTTAA	-	-	rs146504937		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57301956_57301963delACACTTAA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		caggcactggacacttaaacaactagat	0.000													6	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57306229	57306230	+	Intron	INS	-	C	C	rs144543706	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57306229_57306230insC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ATGGTCTTTTTCTAAGGGAGGC	0.287													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57352202	57352202	+	Intron	DEL	C	-	-	rs67188531		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57352202delC	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		tattctcctgcctcaggctcc	0.045													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57371498	57371502	+	Intron	DEL	TTTTA	-	-	rs72491590		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57371498_57371502delTTTTA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TGTTTTGATGTTTTATTAAGTTTAC	0.259													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57378507	57378508	+	Intron	INS	-	AAGTCACATATTATA	AAGTCACATATTATA	rs147279041		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57378507_57378508insAAGTCACATATTATA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		GTCACTGTAATAGTTGCTATTA	0.198													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57404193	57404193	+	Intron	DEL	T	-	-	rs11331163		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57404193delT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		ATTGTGTCTCTAGATACCTTT	0.299													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57404370	57404371	+	Intron	INS	-	A	A	rs139203387		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57404370_57404371insA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		aaagaaacacgaaaagcagctc	0.104													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57466685	57466686	+	Intron	INS	-	T	T	rs150786912		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57466685_57466686insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		AGTAGAATGGGTAGATATGGGA	0.252													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57538130	57538131	+	IGR	DEL	TG	-	-	rs67422833		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57538130_57538131delTG								PRIM2 (24755 upstream) : GUSBL2 (708028 downstream)																							CGAGTTTGACTGTTTTGGTTAG	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57566096	57566096	+	IGR	DEL	C	-	-	rs112517932		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57566096delC								PRIM2 (52721 upstream) : GUSBL2 (680063 downstream)																							gttccgcccacctcagcctcc	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	72341114	72341115	+	IGR	DEL	TT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72341114_72341115delTT								C6orf155 (210666 upstream) : RIMS1 (255535 downstream)																							tttttgaggcttttttttttta	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	96922583	96922584	+	IGR	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96922583_96922584delGT								FUT9 (259096 upstream) : KIAA0776 (47118 downstream)																							ctggtcctgggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	109078041	109078041	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109078041delT	uc003pso.1	+						uc003psp.1_Intron|uc003psq.2_5'Flank|uc003psr.1_5'Flank					Homo sapiens mRNA sequence.																		TTAAAGCTGAttttttttttt	0.214													4	2	---	---	---	---	
SLC35F1	222553	broad.mit.edu	37	6	118239134	118239135	+	Intron	INS	-	A	A	rs72549806		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118239134_118239135insA	uc003pxx.3	+							NM_001029858	NP_001025029	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)		gaagccaagagagaagatgttt	0.000													3	4	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124386358	124386359	+	Intron	INS	-	AC	AC	rs144681461	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124386358_124386359insAC	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		ATCAGAAAATTacacacacaca	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	128285672	128285672	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128285672delT								THEMIS (45930 upstream) : PTPRK (4253 downstream)																							atcactcacatttttttgtgt	0.000													4	2	---	---	---	---	
ENPP1	5167	broad.mit.edu	37	6	132197245	132197245	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132197245delC	uc011ecf.1	+						ENPP1_uc003qcy.2_Intron	NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase						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)	GGGTGGTCTGCACACCCCCAC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	133870115	133870116	+	Intron	DEL	AT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133870115_133870116delAT	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																		ATATGTATGCATATATATATAT	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134052816	134052817	+	Intron	DEL	AC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134052816_134052817delAC	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																		ACCTCCTTATacacacacacac	0.139													4	2	---	---	---	---	
C6orf217	100131814	broad.mit.edu	37	6	135995599	135995599	+	Intron	DEL	A	-	-	rs148256273	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135995599delA	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron|C6orf217_uc010kgo.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0						cctcagccataAACAACAACT	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	138356089	138356092	+	IGR	DEL	ACAC	-	-	rs72294831		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138356089_138356092delACAC								TNFAIP3 (151644 upstream) : PERP (53550 downstream)																							tccatctcaaacacacacacacac	0.142													4	2	---	---	---	---	
CCDC28A	25901	broad.mit.edu	37	6	139103672	139103674	+	Intron	DEL	CGT	-	-	rs142899561		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139103672_139103674delCGT	uc003qie.2	+							NM_015439	NP_056254	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A												0				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		cacctagatccgtcctctgactc	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	142790745	142790746	+	IGR	DEL	AC	-	-	rs150002640		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142790745_142790746delAC								GPR126 (23344 upstream) : LOC153910 (56846 downstream)																							gCTTCTTGATacacacacacac	0.045													6	4	---	---	---	---	
STX11	8676	broad.mit.edu	37	6	144468949	144468950	+	5'Flank	DEL	GG	-	-	rs77020557	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144468949_144468950delGG	uc003qks.3	+							NM_003764	NP_003755	O75558	STX11_HUMAN	syntaxin 11						cellular membrane fusion|intracellular protein transport|vesicle-mediated transport	Golgi apparatus|membrane	SNAP receptor activity			ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		aggccaaggtgggaggatcact	0.084									Familial_Hemophagocytic_Lymphohistiocytosis				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	145587843	145587846	+	IGR	DEL	CTCT	-	-	rs71818429		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145587843_145587846delCTCT								UTRN (413675 upstream) : EPM2A (358600 downstream)																							ATGCACTTTACTCTCTCTCTGTCA	0.270													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	147212673	147212676	+	Intron	DEL	TAAG	-	-	rs146116357		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147212673_147212676delTAAG	uc003qls.1	-						uc003qlt.1_Intron|uc003qlu.1_Intron|uc003qlv.2_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																		CCTTGTTGATTAAGTAAGAACTAC	0.451													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164459260	164459261	+	IGR	DEL	AG	-	-	rs137858446		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164459260_164459261delAG								QKI (464368 upstream) : None (None downstream)																							ATGGGCAGGCAGAGATCAGTGG	0.540													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168052216	168052217	+	IGR	INS	-	TG	TG	rs149093424		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168052216_168052217insTG								TCP10 (254218 upstream) : C6orf123 (133004 downstream)																							acgtgtgtgaatgtgtggtgca	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168783874	168783875	+	IGR	DEL	TG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168783874_168783875delTG								DACT2 (63472 upstream) : SMOC2 (58156 downstream)																							tgtgtttgtatgtgcatgtgcg	0.094													4	3	---	---	---	---	
FAM120B	84498	broad.mit.edu	37	6	170664653	170664653	+	Intron	DEL	A	-	-	rs113064044		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170664653delA	uc003qxp.2	+						FAM120B_uc003qxo.1_Intron|FAM120B_uc011ehd.1_Intron|FAM120B_uc010kla.1_Intron	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B						cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		ggggactgtgagggggtcggg	0.000													3	3	---	---	---	---	
FAM20C	56975	broad.mit.edu	37	7	227124	227124	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:227124delT	uc003sip.2	+							NM_020223	NP_064608	Q8IXL6	DMP4_HUMAN	family with sequence similarity 20, member C							extracellular region					0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)		AGGAAAGTCATTTTTTTTTTC	0.512													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2667209	2667210	+	IGR	INS	-	A	A	rs148018760	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2667209_2667210insA								IQCE (12842 upstream) : TTYH3 (4393 downstream)																							aggaaggtggggggagggagaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	3337370	3337371	+	IGR	INS	-	AGA	AGA	rs79393726		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3337370_3337371insAGA								CARD11 (253791 upstream) : SDK1 (3709 downstream)																							ggaggaggaggagaagaagaag	0.144													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4646479	4646479	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4646479delA								SDK1 (337850 upstream) : FOXK1 (36909 downstream)																							ATGGTTGTTTAATGAGGAAAT	0.398													4	2	---	---	---	---	
ICA1	3382	broad.mit.edu	37	7	8192525	8192530	+	Intron	DEL	ACCATT	-	-	rs142994583	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8192525_8192530delACCATT	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)		caccactaccaccattatctccttca	0.024													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17770394	17770394	+	IGR	DEL	A	-	-	rs79124471		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17770394delA								AHR (384619 upstream) : SNX13 (59992 downstream)																							aaatcaaaagaaaaaaaatag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24058969	24058970	+	IGR	INS	-	A	A	rs10640588		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24058969_24058970insA								STK31 (114604 upstream) : NPY (264839 downstream)																							gactctgtcggaaaaaaaaaaa	0.183													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30412639	30412640	+	IGR	INS	-	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30412639_30412640insC								DKFZP586I1420 (231 upstream) : NOD1 (51504 downstream)																							cctccacccctcccccccccac	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	35450373	35450373	+	IGR	DEL	A	-	-	rs34023035		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35450373delA								TBX20 (157131 upstream) : HERPUD2 (221899 downstream)																							AGGGAATTTGAAAAAAAAAAA	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	47104466	47104468	+	IGR	DEL	CTC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47104466_47104468delCTC								None (None upstream) : TNS3 (210285 downstream)																							AGTTTtccttctcctcctcctcc	0.118													5	4	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48263556	48263556	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48263556delA	uc003toq.2	+						ABCA13_uc003top.2_Intron|ABCA13_uc010kyr.2_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						actcggtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ABCA13	154664	broad.mit.edu	37	7	48369482	48369482	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48369482delC	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc003tos.1_Intron	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						attcatctatccatccatcca	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	48748996	48748997	+	IGR	INS	-	TT	TT			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48748996_48748997insTT								ABCA13 (61905 upstream) : CDC14C (215160 downstream)																							gtgtgtgtgtgtgtgtgtgtgt	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56439441	56439442	+	IGR	INS	-	G	G	rs140774664		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56439441_56439442insG								PSPH (255351 upstream) : DKFZp434L192 (124474 downstream)																							GTGTGAGGCAAGGGGCTCACGC	0.708													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56557369	56557370	+	IGR	INS	-	GTTTCCAT	GTTTCCAT	rs139632643	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56557369_56557370insGTTTCCAT								PSPH (373279 upstream) : DKFZp434L192 (6546 downstream)																							CTTTACCCTGAGTTTCCATCCT	0.347													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57608535	57608536	+	IGR	INS	-	T	T	rs147153132	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57608535_57608536insT								ZNF716 (75270 upstream) : None (None downstream)																							CGTTATTTGAgtaaactttgtg	0.178													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61749684	61749684	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61749684delG								None (None upstream) : None (None downstream)																							tgaatcaaatggaatcatcaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61755271	61755272	+	IGR	INS	-	G	G	rs150943146		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61755271_61755272insG								None (None upstream) : LOC643955 (996400 downstream)																							aatcatcaaatgacttgagtgg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61755510	61755511	+	IGR	INS	-	CAA	CAA			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61755510_61755511insCAA								None (None upstream) : LOC643955 (996161 downstream)																							tcgaacggagtcattgaatgga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61823994	61823995	+	IGR	INS	-	A	A	rs138154535		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61823994_61823995insA								None (None upstream) : LOC643955 (927677 downstream)																							aattaaaaattaaaaaaaGGAG	0.173													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64179885	64179885	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64179885delA								ZNF107 (8486 upstream) : ZNF138 (74886 downstream)																							cctttgtcttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68282516	68282517	+	IGR	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68282516_68282517delCA								None (None upstream) : AUTS2 (781388 downstream)																							GCAAGCCTCTCACAGAGTCTAC	0.406													0	6	---	---	---	---	
SEMA3E	9723	broad.mit.edu	37	7	83266340	83266341	+	Intron	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83266340_83266341delGT	uc003uhy.1	-							NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				Atgtgtgagagtgtgtgtgtgt	0.158													4	2	---	---	---	---	
SEMA3A	10371	broad.mit.edu	37	7	83648703	83648704	+	Intron	INS	-	A	A	rs36003945		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83648703_83648704insA	uc003uhz.2	-							NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor						axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4						AGAGTAAAAAGAAAAAAAAAAA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84357497	84357498	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84357497_84357498insA								SEMA3A (533280 upstream) : SEMA3D (267376 downstream)																							caaattacaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	89049511	89049512	+	IGR	DEL	TC	-	-	rs142287013		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89049511_89049512delTC								ZNF804B (83167 upstream) : DPY19L2P4 (699202 downstream)																							ATCATCCTTGTCTCTGTTTTCC	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	91544559	91544560	+	IGR	INS	-	A	A	rs113590839		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91544559_91544560insA								MTERF (34543 upstream) : AKAP9 (25629 downstream)																							gactctgtctcaaaaaaaaaaa	0.188													4	2	---	---	---	---	
PON1	5444	broad.mit.edu	37	7	94944184	94944184	+	Intron	DEL	A	-	-	rs3917506		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94944184delA	uc003uns.2	-						PON1_uc011kih.1_Intron	NM_000446	NP_000437	P27169	PON1_HUMAN	paraoxonase 1 precursor						aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity			pancreas(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Atorvastatin(DB01076)|Cefazolin(DB01327)	AGAACAGAGGAACCAGCGGAC	0.463													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	95269476	95269480	+	IGR	DEL	TTCTT	-	-	rs77176691		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95269476_95269480delTTCTT								PDK4 (43551 upstream) : DYNC1I1 (132338 downstream)																							ATTTGAGCACttctttttttttttt	0.161													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	96555112	96555112	+	IGR	DEL	T	-	-	rs112255211		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96555112delT								SHFM1 (215909 upstream) : DLX6AS (42716 downstream)																							tgtgtGTGGGTTTTTTTTTTA	0.229													4	2	---	---	---	---	
ZAN	7455	broad.mit.edu	37	7	100345610	100345611	+	Intron	INS	-	A	A	rs3884114		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100345610_100345611insA	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			gcaagactctgaaaaaaaaaaa	0.208													4	2	---	---	---	---	
LRWD1	222229	broad.mit.edu	37	7	102106858	102106861	+	Intron	DEL	TTTA	-	-	rs66463732		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102106858_102106861delTTTA	uc003uzn.2	+						ALKBH4_uc003uzl.2_5'Flank|ALKBH4_uc003uzm.2_5'Flank|LRWD1_uc003uzo.2_Intron	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain						chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding			skin(1)	1						GATGTGCTACtttatttatttatt	0.260													3	4	---	---	---	---	
LHFPL3	375612	broad.mit.edu	37	7	104531625	104531626	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104531625_104531626insA	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3							integral to membrane					0						cagaataccataaaAAAAAAAT	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109222417	109222417	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109222417delG								C7orf66 (697780 upstream) : EIF3IP1 (376867 downstream)																							GTGAAAATGTGGGAAAGGTCT	0.443													4	2	---	---	---	---	
KCND2	3751	broad.mit.edu	37	7	120095708	120095708	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120095708delA	uc003vjj.1	+							NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)					acacagacataaaaaatgaat	0.000													4	2	---	---	---	---	
AASS	10157	broad.mit.edu	37	7	121735636	121735636	+	Intron	DEL	A	-	-	rs5887069		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121735636delA	uc003vka.2	-						AASS_uc011knu.1_Intron|AASS_uc011knv.1_Intron|AASS_uc003vkb.2_Intron|AASS_uc011knw.1_Intron	NM_005763	NP_005754	Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase precursor						protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)	TCTACTTCATAAAAAAAAAAA	0.259													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124729293	124729294	+	Intron	DEL	AC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124729293_124729294delAC	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																		aatgatgagaacacacacacac	0.005													4	2	---	---	---	---	
GRM8	2918	broad.mit.edu	37	7	126547155	126547157	+	Intron	DEL	AGA	-	-	rs35917511		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126547155_126547157delAGA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	gaagagcaggagaaggaggagga	0.079										HNSCC(24;0.065)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128210235	128210236	+	IGR	DEL	TT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128210235_128210236delTT								METTL2B (67258 upstream) : FLJ45340 (71059 downstream)																							gttttagttcttTTTTTTTTTT	0.193													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131685719	131685720	+	IGR	DEL	GT	-	-	rs35463830		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131685719_131685720delGT								PODXL (444343 upstream) : PLXNA4 (122372 downstream)																							TGCCATGGGAgtgtgtgtgtgt	0.317													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	135767819	135767820	+	IGR	DEL	TC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135767819_135767820delTC								LUZP6 (105615 upstream) : CHRM2 (785579 downstream)																							CCCCCCACCATCTCTCTCTCTC	0.153													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140871641	140871648	+	IGR	DEL	TGAATGAA	-	-	rs72192328		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140871641_140871648delTGAATGAA								MRPS33 (156860 upstream) : AGK (379430 downstream)																							tacacatttgtgaatgaatgaatgaatg	0.255													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142128679	142128680	+	Intron	INS	-	A	A	rs35100255	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142128679_142128680insA	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		AGGAAGGCGATGGGCAGATAGG	0.490													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145651774	145651774	+	IGR	DEL	T	-	-	rs71525914		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145651774delT								None (None upstream) : CNTNAP2 (161679 downstream)																							gaaaaacctatttttttttca	0.000													2	4	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152103531	152103534	+	Intron	DEL	AAAA	-	-	rs10544115		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152103531_152103534delAAAA	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)		aacctgtctcaaaaaaaaaaaaGG	0.093			N		medulloblastoma								7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155739562	155739565	+	IGR	DEL	CTCT	-	-	rs5000070	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155739562_155739565delCTCT								SHH (134595 upstream) : C7orf4 (593620 downstream)																							ccctccctccctctctctctctct	0.000													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157940546	157940547	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157940546_157940547insA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CGCCACGTGTCTTTCCCCTTCA	0.579													4	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158130122	158130123	+	Intron	DEL	AA	-	-	rs112630062		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158130122_158130123delAA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CTCTCACCATAAGAGGTGACAC	0.550													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2427833	2427836	+	IGR	DEL	AAAG	-	-	rs116771344	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2427833_2427836delAAAG								MYOM2 (334454 upstream) : CSMD1 (365040 downstream)																							gaaggaaagaaaagaaagaaagaa	0.059													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3116948	3116949	+	Intron	INS	-	TGAA	TGAA	rs142067674	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3116948_3116949insTGAA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		gaatgaatgagtgaatgaatga	0.356													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	8001936	8001936	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8001936delC								MIR548I3 (55325 upstream) : FLJ10661 (84156 downstream)																							aagactcagacactccaagag	0.000													7	7	---	---	---	---	
MSRA	4482	broad.mit.edu	37	8	10263346	10263347	+	Intron	DEL	CA	-	-	rs147521797		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10263346_10263347delCA	uc003wsx.2	+						MSRA_uc011kwx.1_Intron|MSRA_uc003wsz.2_Intron|MSRA_uc003wsy.2_Intron	NM_012331	NP_036463	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	cacacgtaatcacagacatgct	0.104													4	2	---	---	---	---	
FAM66D	100132923	broad.mit.edu	37	8	12018138	12018138	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12018138delT	uc011kxp.1	+											Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						catcacatgcttttttttttc	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12433317	12433320	+	Intron	DEL	CTTG	-	-	rs2946710		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12433317_12433320delCTTG	uc003wvy.3	-						uc003wwb.1_5'Flank					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		AAATTATGTTCTTGCTGACAGTTT	0.358													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	13639980	13639981	+	IGR	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13639980_13639981insT								C8orf48 (214184 upstream) : SGCZ (307393 downstream)																							TCTTAGTTCACTTTTTTTTTAT	0.351													4	2	---	---	---	---	
ZDHHC2	51201	broad.mit.edu	37	8	17045880	17045881	+	Intron	INS	-	AAT	AAT	rs140602273	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17045880_17045881insAAT	uc003wxe.2	+							NM_016353	NP_057437	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2							integral to membrane	acyltransferase activity|zinc ion binding				0				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		TTCTGCCTAGCAATAGCAGCTC	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	18147195	18147196	+	IGR	INS	-	AC	AC	rs150659849	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18147195_18147196insAC								NAT1 (65998 upstream) : NAT2 (101559 downstream)																							AATACAGCCTTacacacacaca	0.307													4	2	---	---	---	---	
CSGALNACT1	55790	broad.mit.edu	37	8	19551366	19551366	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19551366delT	uc011kyp.1	-							NM_018371	NP_060841	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)		gtaattacggtttttgccata	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	27424885	27424887	+	IGR	DEL	CTC	-	-	rs35969949		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27424885_27424887delCTC								EPHX2 (22401 upstream) : CLU (29564 downstream)																							CCTTGCCCTTCTCCTCCTCCCTC	0.507													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	28112477	28112478	+	IGR	INS	-	AA	AA			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28112477_28112478insAA								ELP3 (63810 upstream) : PNOC (62171 downstream)																							TCTGTGCCAGGAAAAAAAAAAA	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37207230	37207230	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37207230delT								KCNU1 (413589 upstream) : ZNF703 (346071 downstream)																							TCATCTCATCttttttttttt	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37588922	37588923	+	Intron	INS	-	A	A	rs77124769		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37588922_37588923insA	uc003xka.1	+											Homo sapiens cDNA clone IMAGE:4827062.																		aattccgtcacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40735205	40735206	+	Intron	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40735205_40735206delGT	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			AAACATATGCGTGTGTGTGTGT	0.238													4	2	---	---	---	---	
SFRP1	6422	broad.mit.edu	37	8	41161962	41161962	+	Intron	DEL	C	-	-	rs66846282		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41161962delC	uc003xnt.2	-							NM_003012	NP_003003	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1 precursor						brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|regulation of angiogenesis|regulation of cell cycle process|response to drug|response to organic cyclic compound|vasculature development	cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix	cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			TATCAAGCAGCCTGGAGCTTA	0.572													1	6	---	---	---	---	
CHRNA6	8973	broad.mit.edu	37	8	42615478	42615479	+	Intron	INS	-	GC	GC	rs142903727	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42615478_42615479insGC	uc003xpj.2	-						CHRNA6_uc011lcw.1_Intron	NM_004198	NP_004189	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6							cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ctcacactcatgcgcacacaca	0.000													4	2	---	---	---	---	
RNF170	81790	broad.mit.edu	37	8	42738210	42738210	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42738210delA	uc003xpo.2	-						RNF170_uc011lcx.1_Intron|RNF170_uc010lxp.2_Intron|RNF170_uc003xpm.2_Intron|RNF170_uc003xpp.2_Intron|RNF170_uc003xpn.2_Intron|RNF170_uc003xpq.3_Intron	NM_001160223	NP_001153695	Q96K19	RN170_HUMAN	ring finger protein 170 isoform a							integral to membrane	zinc ion binding				0	all_lung(13;1.25e-11)|Lung NSC(13;3.55e-10)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00645)|Lung NSC(58;0.0176)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			gtctcaagagaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49614297	49614297	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49614297delA								UBE2V2 (639845 upstream) : EFCAB1 (9054 downstream)																							TATGACATGGAAGACAAAGTG	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55763611	55763612	+	IGR	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55763611_55763612delGT								RP1 (81080 upstream) : XKR4 (251405 downstream)																							GTACACGTACgtgtgtgtgtgt	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58241862	58241862	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58241862delG								C8orf71 (44574 upstream) : FAM110B (665251 downstream)																							CATAGTGTGTGTGTCAGTGTC	0.547													4	2	---	---	---	---	
TOX	9760	broad.mit.edu	37	8	59843070	59843071	+	Intron	DEL	GG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59843070_59843071delGG	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)				AATGCTGAATGGGGAAGGAAGG	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61049958	61049958	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61049958delT								None (None upstream) : CA8 (51465 downstream)																							TAATGTAAAGTTTAAAAGATG	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61236760	61236760	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61236760delT								CA8 (42806 upstream) : RAB2A (192799 downstream)																							TTAAGGAAACTACATTCACGA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62726268	62726269	+	IGR	DEL	CC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62726268_62726269delCC								ASPH (99069 upstream) : NKAIN3 (435232 downstream)																							ttccttccttccttccttcctt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	69223298	69223298	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69223298delC	uc003xxx.2	-											Homo sapiens hypothetical protein LOC286189, mRNA (cDNA clone IMAGE:5249083), partial cds.																		cttcttctttccttccttcct	0.055													4	2	---	---	---	---	
SULF1	23213	broad.mit.edu	37	8	70387650	70387651	+	Intron	INS	-	A	A	rs140522484	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70387650_70387651insA	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor						apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			TCAAATAAATTAAAAAAAAAAT	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98768102	98768102	+	IGR	DEL	T	-	-	rs114430156	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98768102delT								MTDH (25615 upstream) : LAPTM4B (19707 downstream)																							CCCTCTCCCCttttttttttt	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103649953	103649953	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103649953delG								ODF1 (76708 upstream) : KLF10 (11052 downstream)																							TTGAAATACAGGCATCGTCAT	0.463													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	109436577	109436577	+	IGR	DEL	G	-	-	rs66511577		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109436577delG								EIF3E (175618 upstream) : TTC35 (19276 downstream)																							GTGTGTGTGTGTTTTTTTTTT	0.219													2	4	---	---	---	---	
PKHD1L1	93035	broad.mit.edu	37	8	110535739	110535740	+	Intron	INS	-	T	T	rs151092381	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110535739_110535740insT	uc003yne.2	+							NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor						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)			AGAATGCTATATTTTGCCTTGT	0.233										HNSCC(38;0.096)			6	6	---	---	---	---	
CSMD3	114788	broad.mit.edu	37	8	114390991	114390992	+	Intron	INS	-	GT	GT	rs143016847	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114390991_114390992insGT	uc003ynu.2	-						CSMD3_uc003ynt.2_5'Flank|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron|CSMD3_uc003ynx.3_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						gtcacactgaagtgtgtgtgtg	0.025										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	115036744	115036745	+	IGR	DEL	AC	-	-	rs5894186		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115036744_115036745delAC								CSMD3 (587502 upstream) : None (None downstream)																							ACACAGACAAACACacacacac	0.238													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116235480	116235480	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116235480delT								None (None upstream) : TRPS1 (185245 downstream)																							catgctcctctttctccatgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	118344480	118344481	+	IGR	INS	-	AC	AC	rs148373075	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118344480_118344481insAC								SLC30A8 (155528 upstream) : MED30 (188484 downstream)																							tcaatctccaaacacacacaca	0.030													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125176813	125176813	+	Intron	DEL	C	-	-	rs10717191		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125176813delC	uc003yqy.1	-											Homo sapiens cDNA FLJ32770 fis, clone TESTI2001898.																		TACTCCCATTCCCCAGTGGTA	0.493													1	6	---	---	---	---	
TG	7038	broad.mit.edu	37	8	134093969	134093969	+	Intron	DEL	A	-	-	rs33935978		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134093969delA	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc003ytz.2_Intron|SLA_uc011lje.1_Intron|SLA_uc011ljf.1_Intron|SLA_uc011ljg.1_Intron|SLA_uc010mea.2_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGGAGATCTTACTGTTCTCAG	0.493													5	3	---	---	---	---	
ZFAT	57623	broad.mit.edu	37	8	135646313	135646314	+	Intron	INS	-	AAC	AAC	rs146678141	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135646313_135646314insAAC	uc003yup.2	-						ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron|ZFAT_uc003yur.2_Intron	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			aaaacaaaacaaacaacaacaa	0.000													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	139594195	139594196	+	IGR	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139594195_139594196insT								FAM135B (85130 upstream) : COL22A1 (6283 downstream)																							TGCCTTCTGCAGGCCTGCTGCA	0.475													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141199081	141199081	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141199081delA	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						tttctaacccaggggatggct	0.144													2	4	---	---	---	---	
DGAT1	8694	broad.mit.edu	37	8	145547172	145547172	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145547172delG	uc003zbv.3	-						DGAT1_uc010mfv.2_Intron	NM_012079	NP_036211	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1						triglyceride biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane	diacylglycerol O-acyltransferase activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			AGCAGCATGTGGGCTACAGGG	0.632													4	2	---	---	---	---	
VLDLR	7436	broad.mit.edu	37	9	2627065	2627066	+	Intron	INS	-	TGG	TGG	rs149908156	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2627065_2627066insTGG	uc003zhk.1	+						VLDLR_uc003zhl.1_Intron|VLDLR_uc003zhm.1_Intron|VLDLR_uc003zhn.1_Intron	NM_003383	NP_003374	P98155	VLDLR_HUMAN	very low density lipoprotein receptor isoform a						cholesterol metabolic process|endocytosis|lipid transport|memory|very-low-density lipoprotein particle clearance	coated pit|integral to membrane|membrane fraction|plasma membrane|very-low-density lipoprotein particle	apolipoprotein binding|calcium ion binding|low-density lipoprotein receptor activity|very-low-density lipoprotein particle receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		gaccatagcactggttccttcc	0.069													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	3673765	3673765	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3673765delC								RFX3 (147782 upstream) : GLIS3 (150363 downstream)																							ggtatgggttccagacattgt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	15126843	15126845	+	Intron	DEL	CGG	-	-	rs148267677		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15126843_15126845delCGG	uc003zln.1	-											Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																		gaggaggagacggaggaggagaa	0.034													6	3	---	---	---	---	
KIAA1797	54914	broad.mit.edu	37	9	20698021	20698021	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20698021delT	uc003zog.1	+							NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)		CAAGTGAGACTTTTTTTGCCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25565419	25565420	+	IGR	INS	-	CTT	CTT	rs148384604	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25565419_25565420insCTT								None (None upstream) : TUSC1 (110974 downstream)																							CCTCTACTCTCCTTCTTCCTTT	0.366													6	4	---	---	---	---	
C9orf82	79886	broad.mit.edu	37	9	26845978	26845979	+	Intron	INS	-	T	T	rs145004611	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26845978_26845979insT	uc003zqc.2	-						C9orf82_uc003zqb.2_Intron	NM_024828	NP_079104	Q9H8G2	CI082_HUMAN	hypothetical protein LOC79886												0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(42;1.39e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		GCCTCTCAGAGTAGAGTGCTTG	0.322													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	30835781	30835781	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30835781delT								None (None upstream) : None (None downstream)																							cttttaagaatttttttgtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	34146728	34146729	+	IGR	DEL	AC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34146728_34146729delAC								DCAF12 (19957 upstream) : UBAP1 (32282 downstream)																							ACATAAAGGGACACACACACAC	0.391													3	5	---	---	---	---	
C9orf100	84904	broad.mit.edu	37	9	35660258	35660258	+	3'UTR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35660258delT	uc003zxm.1	-	9					RMRP_uc003zxh.1_5'Flank|CCDC107_uc011lox.1_Intron|CCDC107_uc011loy.1_Intron|CCDC107_uc003zxj.2_Intron|CCDC107_uc003zxk.2_Intron|C9orf100_uc003zxl.2_RNA	NM_032818	NP_116207	Q8N4T4	CI100_HUMAN	hypothetical protein LOC84904						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ctagatagactaggattgtga	0.194													4	2	---	---	---	---	
TMEM8B	51754	broad.mit.edu	37	9	35848673	35848673	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35848673delT	uc003zym.2	+						TMEM8B_uc003zyo.2_Intron	NM_001042589	NP_001036054	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B isoform a						cell-matrix adhesion|regulation of growth|regulation of mitotic cell cycle	cell surface|endoplasmic reticulum|integral to membrane|mitochondrion|nucleus|plasma membrane	protein binding			ovary(1)	1						gttttttttcttttttttttt	0.219													4	3	---	---	---	---	
IGFBPL1	347252	broad.mit.edu	37	9	38419861	38419863	+	Intron	DEL	CCT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38419861_38419863delCCT	uc004aba.2	-							NM_001007563	NP_001007564	Q8WX77	IBPL1_HUMAN	insulin-like growth factor binding protein-like						regulation of cell growth	extracellular region	insulin-like growth factor binding				0				GBM - Glioblastoma multiforme(29;0.0437)|Lung(182;0.116)		tcctcctccccctcctcctcctc	0.138													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66849014	66849014	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66849014delT								LOC442421 (345987 upstream) : AQP7P1 (405253 downstream)																							ggaaacactcttttttgtaga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68359063	68359064	+	IGR	INS	-	AT	AT	rs2772795	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68359063_68359064insAT								FAM27B (564874 upstream) : MIR1299 (643175 downstream)																							agatatgactgatatatatatc	0.124													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68386957	68386958	+	IGR	INS	-	ATTC	ATTC	rs140000674	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68386957_68386958insATTC								FAM27B (592768 upstream) : MIR1299 (615281 downstream)																							gaaacaaaggtattcaattagg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68406251	68406251	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68406251delA								FAM27B (612062 upstream) : MIR1299 (595988 downstream)																							atcaatggggaaaagattccc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68406889	68406889	+	IGR	DEL	G	-	-	rs113316891		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68406889delG								FAM27B (612700 upstream) : MIR1299 (595350 downstream)																							atccagggcagtcatagtggt	0.000													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68713376	68713376	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68713376delT								FAM27B (919187 upstream) : MIR1299 (288863 downstream)																							caaatagctgtttttttaaaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	72653444	72653453	+	IGR	DEL	AAGTGGCCTT	-	-	rs79327897		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72653444_72653453delAAGTGGCCTT								C9orf135 (132297 upstream) : MAMDC2 (5044 downstream)																							gaatggaatgaagtggccttgaatgcaata	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	78808345	78808345	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78808345delA								PCSK5 (7 upstream) : RFK (192088 downstream)																							agccaaaaagaaaaaaaaaaa	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82781577	82781577	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82781577delC								TLE4 (439920 upstream) : None (None downstream)																							aagaggaaaaccccacattta	0.144													4	2	---	---	---	---	
LOC440173	440173	broad.mit.edu	37	9	89628125	89628125	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89628125delA	uc010mqg.2	-							NR_027471				Homo sapiens cDNA FLJ60829 complete cds.												0						GTCTCCCTTCAAAAAAAAAAA	0.363													4	4	---	---	---	---	
KIAA1529	57653	broad.mit.edu	37	9	100049117	100049118	+	Intron	INS	-	T	T	rs80068054		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100049117_100049118insT	uc011lut.1	+						KIAA1529_uc011lur.1_Intron|KIAA1529_uc004axe.1_Intron|KIAA1529_uc011lus.1_Intron|KIAA1529_uc011luu.1_Intron	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)				TTCTACACAAGttttttttttt	0.025													2	4	---	---	---	---	
GABBR2	9568	broad.mit.edu	37	9	101200455	101200458	+	Intron	DEL	ATCC	-	-	rs34647195		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101200455_101200458delATCC	uc004ays.2	-							NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	ccatctacctatccatccatccat	0.000													6	3	---	---	---	---	
ABCA1	19	broad.mit.edu	37	9	107624331	107624332	+	Intron	DEL	AC	-	-	rs72333800		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107624331_107624332delAC	uc004bcl.2	-						ABCA1_uc004bcm.2_Intron	NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)	TGGTGCTGTTacacacacacac	0.238													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	108778786	108778787	+	IGR	INS	-	GTGTGTGT	GTGTGTGT	rs151018670	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108778786_108778787insGTGTGTGT								TMEM38B (241342 upstream) : ZNF462 (846591 downstream)																							tgtgtatgtgagtgtgtgtgtg	0.312													3	4	---	---	---	---	
CTNNAL1	8727	broad.mit.edu	37	9	111723352	111723355	+	Intron	DEL	TACT	-	-	rs138257205		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111723352_111723355delTACT	uc004bdo.1	-						CTNNAL1_uc010mts.1_Intron|CTNNAL1_uc010mtt.1_Intron|CTNNAL1_uc004bdp.1_Intron|CTNNAL1_uc004bdq.1_Intron	NM_003798	NP_003789	Q9UBT7	CTNL1_HUMAN	catenin, alpha-like 1						cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)		GGTTGAATGATACTTACAAGTATG	0.417													4	4	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111864294	111864295	+	Intron	INS	-	A	A	rs142186069	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111864294_111864295insA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		GTCAAAAGGGGAAACCATTCTG	0.386													4	2	---	---	---	---	
DFNB31	25861	broad.mit.edu	37	9	117220195	117220195	+	Intron	DEL	A	-	-	rs139180274		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117220195delA	uc004biz.3	-						DFNB31_uc004biy.3_Intron|DFNB31_uc004bja.3_Intron	NM_015404	NP_056219	Q9P202	WHRN_HUMAN	CASK-interacting protein CIP98 isoform 1						inner ear receptor stereocilium organization|retina homeostasis|sensory perception of light stimulus|sensory perception of sound	cytoplasm|growth cone|stereocilium				ovary(4)|central_nervous_system(1)|pancreas(1)	6						gactctgttcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
LRSAM1	90678	broad.mit.edu	37	9	130252526	130252529	+	Intron	DEL	TTTC	-	-	rs34960873		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130252526_130252529delTTTC	uc004brb.1	+						LRSAM1_uc010mxk.1_Intron|LRSAM1_uc004brc.1_Intron|LRSAM1_uc004brd.1_Intron|LRSAM1_uc004bre.1_Intron	NM_001005373	NP_001005373	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif						negative regulation of endocytosis|non-lytic virus budding|protein autoubiquitination|protein catabolic process|protein polyubiquitination|protein transport|ubiquitin-dependent endocytosis	cytoplasm|extracellular region|membrane part	hormone activity|ubiquitin-protein ligase activity|zinc ion binding				0						tttctctatttttctttctttctt	0.284													4	2	---	---	---	---	
WDR34	89891	broad.mit.edu	37	9	131406554	131406555	+	Intron	INS	-	TT	TT	rs10660438		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131406554_131406555insTT	uc004bvq.1	-						WDR34_uc004bvs.1_Intron|WDR34_uc004bvr.1_Intron	NM_052844	NP_443076	Q96EX3	WDR34_HUMAN	WD repeat domain 34							cytoplasm				central_nervous_system(2)|skin(1)	3						cccaggcggccttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132338778	132338779	+	Intron	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132338778_132338779delCA	uc004bya.1	+											Homo sapiens cDNA clone IMAGE:4812570.																		ACGTACTCCTCACACACACACT	0.317													4	2	---	---	---	---	
EXOSC2	23404	broad.mit.edu	37	9	133577856	133577857	+	Intron	INS	-	TC	TC	rs141015079	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133577856_133577857insTC	uc004bzu.2	+						EXOSC2_uc011mbz.1_Intron|EXOSC2_uc011mca.1_Intron	NM_014285	NP_055100	Q13868	EXOS2_HUMAN	exosome component 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|positive regulation of cell growth|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|7S RNA binding|protein binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		CCATATTATCTTCTCTTCTAAG	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137415518	137415519	+	IGR	INS	-	T	T	rs141862754	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137415518_137415519insT								RXRA (83087 upstream) : COL5A1 (118133 downstream)																							atcccctcccatcccctcccat	0.228													2	4	---	---	---	---	
CACNA1B	774	broad.mit.edu	37	9	140781064	140781064	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140781064delC	uc004cog.2	+						uc004cof.1_Intron	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)	caagacaCCTCCCGGGCCTGG	0.353													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	118792	118792	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118792delA								TUBB8 (23288 upstream) : ZMYND11 (61632 downstream)																							actccatctcaaaaaaaaaaa	0.134													4	2	---	---	---	---	
DIP2C	22982	broad.mit.edu	37	10	516158	516158	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:516158delA	uc001ifp.2	-						DIP2C_uc009xhk.1_Intron	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		ATGTGGTTATAATGGCGATGG	0.254													4	2	---	---	---	---	
IDI1	3422	broad.mit.edu	37	10	1091807	1091808	+	Intron	DEL	GT	-	-	rs71676367		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1091807_1091808delGT	uc001iga.2	-						IDI1_uc001ifz.2_5'Flank|IDI1_uc001igb.2_Intron|IDI1_uc001igc.2_Intron	NM_004508	NP_004499	Q13907	IDI1_HUMAN	isopentenyl-diphosphate delta isomerase						carotenoid biosynthetic process|cholesterol biosynthetic process	cytosol|peroxisome	hydrolase activity|isopentenyl-diphosphate delta-isomerase activity|metal ion binding				0		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.221)	Epithelial(11;0.0972)		TAGGGTCTGGgtgtgtgtgtgt	0.282													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	7715473	7715475	+	IGR	DEL	GAG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7715473_7715475delGAG								ITIH5 (6539 upstream) : ITIH2 (29761 downstream)																							GCCAAAAgaagaggaggaggagg	0.266													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10548232	10548233	+	IGR	INS	-	GT	GT	rs141549916	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10548232_10548233insGT								None (None upstream) : SFTA1P (278169 downstream)																							AGATGCACTTCgtgtgtgtgtg	0.277													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	11748225	11748226	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11748225_11748226insA								USP6NL (94546 upstream) : ECHDC3 (36130 downstream)																							gaccctgtctcaaaaaaaaaat	0.114													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12389255	12389256	+	5'Flank	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12389255_12389256insT	uc001ilo.2	+						CAMK1D_uc001iln.2_5'Flank	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		acttcttctccttttttttttt	0.000													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14351417	14351417	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14351417delC	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imv.2_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						ccactgcactccagcctgggc	0.025													4	2	---	---	---	---	
RSU1	6251	broad.mit.edu	37	10	16708123	16708123	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16708123delT	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron	NM_152724	NP_689937	Q15404	RSU1_HUMAN	ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)		TCTGTGACTATTTTACAGGTT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	19728467	19728467	+	IGR	DEL	A	-	-	rs11353528		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19728467delA								ARL5B (761527 upstream) : PLXDC2 (376905 downstream)																							accctgtctcaaaaaaaaaGT	0.154													3	3	---	---	---	---	
PLXDC2	84898	broad.mit.edu	37	10	20361353	20361354	+	Intron	INS	-	AGAA	AGAA	rs145747912	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20361353_20361354insAGAA	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4						gaaagaaagagagaaagaaaga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	37343745	37343746	+	IGR	INS	-	AGAA	AGAA	rs140768517	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37343745_37343746insAGAA								None (None upstream) : ANKRD30A (71039 downstream)																							aagaaagagagagaaagaaaga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38872334	38872335	+	IGR	INS	-	GA	GA			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38872334_38872335insGA								LOC399744 (131254 upstream) : None (None downstream)																							ggaatggattgaaggaatggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38878064	38878064	+	IGR	DEL	T	-	-	rs113921581		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38878064delT								LOC399744 (136984 upstream) : None (None downstream)																							ggaatcatcgtatggactcga	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38989178	38989178	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38989178delT								LOC399744 (248098 upstream) : None (None downstream)																							ATTTGTCTCCTTTTCTTGTAT	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42527764	42527765	+	IGR	INS	-	CC	CC	rs147441291		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42527764_42527765insCC								None (None upstream) : LOC441666 (299550 downstream)																							acagagtgtttaaactgctcta	0.000													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44244033	44244033	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44244033delT								ZNF32 (99707 upstream) : HNRNPA3P1 (38827 downstream)																							gtggttatggtttattacagt	0.025													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44295815	44295815	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44295815delA								HNRNPA3P1 (9950 upstream) : CXCL12 (569792 downstream)																							GCAAATGCAGAAAAAAAAAAA	0.463													3	3	---	---	---	---	
MARCH8	220972	broad.mit.edu	37	10	46049281	46049282	+	Intron	INS	-	CA	CA	rs147078452	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46049281_46049282insCA	uc001jcj.1	-						MARCH8_uc001jck.1_Intron	NM_001002265	NP_001002265	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0						gcatggacatgcacacacacac	0.233													2	4	---	---	---	---	
SYT15	83849	broad.mit.edu	37	10	46957467	46957468	+	Intron	INS	-	G	G	rs150404308	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46957467_46957468insG	uc001jdz.2	-							NM_181519	NP_852660	Q9BQS2	SYT15_HUMAN	synaptotagmin XV isoform b							integral to membrane|plasma membrane					0						aaccaatggtagggggggaaac	0.000													5	3	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51488699	51488700	+	Intron	INS	-	GAGGGGGA	GAGGGGGA	rs146788498	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51488699_51488700insGAGGGGGA	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|AGAP7_uc001jio.2_5'Flank	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		aaaaagacagtgagagagggaa	0.168													6	3	---	---	---	---	
SLC16A9	220963	broad.mit.edu	37	10	61433048	61433048	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61433048delA	uc010qig.1	-							NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						tgggaattataatagtaccca	0.169													4	2	---	---	---	---	
RTKN2	219790	broad.mit.edu	37	10	64005582	64005583	+	Intron	INS	-	A	A	rs145698745	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64005582_64005583insA	uc001jlw.2	-						RTKN2_uc001jlx.2_Intron	NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2						signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)					tcttaaactctaaagttctata	0.129													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65645617	65645617	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65645617delC	uc001jmu.1	-											full-length cDNA clone CS0DI034YJ20 of Placenta Cot 25-normalized of Homo sapiens (human).																		GGACTTCATGCCAAGGGAAAA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	70794817	70794818	+	IGR	INS	-	A	A	rs112373909		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70794817_70794818insA								KIAA1279 (18083 upstream) : SRGN (53010 downstream)																							actctgtctcgaaaaaaaaaaa	0.243													3	3	---	---	---	---	
AIFM2	84883	broad.mit.edu	37	10	71886678	71886679	+	5'Flank	INS	-	G	G	rs139245302	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71886678_71886679insG	uc010qjg.1	-						AIFM2_uc001jqp.1_Intron	NM_032797	NP_116186	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor (AIF)-like						apoptotic mitochondrial changes|chromosome condensation|induction of apoptosis	cytosol|integral to membrane|mitochondrial outer membrane	DNA binding|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding			central_nervous_system(1)	1						acccaagacaaccccccggcag	0.337													3	3	---	---	---	---	
MBL1P	8512	broad.mit.edu	37	10	81684988	81684988	+	Intron	DEL	T	-	-	rs66593745		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81684988delT	uc001kbf.2	+											Homo sapiens mannose-binding protein-A pseudogene (MBL1P1) mRNA sequence.												0						ATAAGCCTCCTTTCCCTGCCC	0.483													3	3	---	---	---	---	
SH2D4B	387694	broad.mit.edu	37	10	82340104	82340104	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82340104delA	uc001kck.1	+						SH2D4B_uc001kcl.1_Intron	NM_207372	NP_997255	Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B isoform 1												0			Colorectal(32;0.229)			cctatacatcaaaaggcaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	94543891	94543891	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94543891delT								HHEX (88485 upstream) : EXOC6 (47044 downstream)																							tgtggttctcttacttcagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	97939598	97939599	+	IGR	INS	-	CTT	CTT	rs139762736	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97939598_97939599insCTT								ZNF518A (16088 upstream) : BLNK (11864 downstream)																							tcctcctcatccttcttctttt	0.010													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	98561452	98561453	+	IGR	INS	-	AGACAGAG	AGACAGAG			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98561452_98561453insAGACAGAG								PIK3AP1 (81173 upstream) : MIR607 (26973 downstream)																							aagagacagacagagaaagaga	0.054													4	2	---	---	---	---	
C10orf75	90271	broad.mit.edu	37	10	102137846	102137846	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102137846delA	uc001kqz.3	+						C10orf75_uc001kra.3_Intron	NR_026762				Homo sapiens cDNA FLJ12974 fis, clone NT2RP2006103.												0						agactgtctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
FAM178A	55719	broad.mit.edu	37	10	102691749	102691749	+	Intron	DEL	A	-	-	rs142482241		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102691749delA	uc001krt.3	+						FAM178A_uc001krs.2_Intron	NM_018121	NP_060591	Q8IX21	F178A_HUMAN	hypothetical protein LOC55719 isoform 1												0						actctgtctcaaaaaaaaaaa	0.164													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109121527	109121530	+	IGR	DEL	AGAT	-	-	rs149075854		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109121527_109121530delAGAT								SORCS1 (197235 upstream) : None (None downstream)																							gctctatgccagatagatagatag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	118272314	118272315	+	IGR	INS	-	AT	AT	rs56861958		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118272314_118272315insAT								PNLIPRP3 (34848 upstream) : PNLIP (33113 downstream)																							gcaagagagagtaatgctagag	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122496301	122496302	+	IGR	INS	-	TTCT	TTCT	rs139546701	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122496301_122496302insTTCT								PPAPDC1A (146934 upstream) : WDR11 (114393 downstream)																							tcattccttccttctttctttc	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	123692389	123692389	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123692389delA								ATE1 (4172 upstream) : NSMCE4A (24220 downstream)																							AAGGCAGAGCAAAAAGGGTAA	0.433													4	2	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127585359	127585359	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127585359delT	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)				TTGCGTCTCCTCGCGCTTTTC	0.602													4	2	---	---	---	---	
DOCK1	1793	broad.mit.edu	37	10	128925008	128925008	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128925008delG	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CCCTAGCCCTGGACAGAGTGG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	129481902	129481903	+	IGR	INS	-	T	T	rs146340380	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129481902_129481903insT								NPS (130967 upstream) : FOXI2 (53635 downstream)																							CTTCTGCTCCCTTTTTTTTTGA	0.520													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132595679	132595679	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132595679delA								GLRX3 (612895 upstream) : TCERG1L (294977 downstream)																							AGGAGGTGACAAAAGGATGGC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133184596	133184607	+	IGR	DEL	GGAGGGAGGAAT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133184596_133184607delGGAGGGAGGAAT								TCERG1L (74612 upstream) : PPP2R2D (563353 downstream)																							agggaggagcggagggaggaatggagggagaa	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133733499	133733500	+	IGR	DEL	AC	-	-	rs111597604		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133733499_133733500delAC								TCERG1L (623515 upstream) : PPP2R2D (14460 downstream)																							GGGTGGAATGACACAGTGTTTG	0.554													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133862095	133862096	+	IGR	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133862095_133862096delGT								BNIP3 (66660 upstream) : JAKMIP3 (56217 downstream)																							tggttttgcggtgtgtgtgtgt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	189702	189702	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:189702delC								LOC100133161 (50550 upstream) : SCGB1C1 (3378 downstream)																							ggctcgggcgccccctgcttg	0.000													5	3	---	---	---	---	
RHOG	391	broad.mit.edu	37	11	3859884	3859885	+	Intron	INS	-	A	A	rs138368515	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3859884_3859885insA	uc001lyu.2	-							NM_001665	NP_001656	P84095	RHOG_HUMAN	ras homolog gene family, member G precursor						actin cytoskeleton organization|activation of Rac GTPase activity|axon guidance|cell chemotaxis|platelet activation|positive regulation of cell proliferation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of transcription, DNA-dependent|Rac protein signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|protein binding				0		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0349)|LUSC - Lung squamous cell carcinoma(625;0.194)		TGTGACATGGGAAGATGACAGA	0.450													3	4	---	---	---	---	
SPON1	10418	broad.mit.edu	37	11	14133656	14133657	+	Intron	DEL	AA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14133656_14133657delAA	uc001mle.2	+							NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)		TTTGCAGGGGaaaaaaaaaaaa	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	17581455	17581456	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17581455_17581456insA								USH1C (15492 upstream) : MYOD1 (159654 downstream)																							gagggaggaaggaaggaaagaa	0.124													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	32497726	32497727	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32497726_32497727insA								WIT1 (29465 upstream) : EIF3M (107664 downstream)																							aattccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	32551671	32551672	+	IGR	INS	-	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32551671_32551672insG								WIT1 (83410 upstream) : EIF3M (53719 downstream)																							gaaggaaagaaagaaggaaaga	0.084													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	41556012	41556012	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41556012delA								LRRC4C (74689 upstream) : None (None downstream)																							GAAGAAAATTAAAAAAAAAAA	0.368													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	46224038	46224039	+	IGR	DEL	CT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46224038_46224039delCT								PHF21A (81053 upstream) : CREB3L1 (75189 downstream)																							ctctcattccctctcctccatg	0.000													4	2	---	---	---	---	
CREB3L1	90993	broad.mit.edu	37	11	46307770	46307770	+	Intron	DEL	G	-	-	rs143154984		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46307770delG	uc001ncf.2	+							NM_052854	NP_443086	Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like						response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L1(6)	soft_tissue(6)|ovary(2)	8				GBM - Glioblastoma multiforme(35;0.0285)		GGAGTAGGGTGGGGACGATAG	0.284			T	FUS	myxofibrosarcoma								4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	55413170	55413170	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55413170delA								OR4P4 (6399 upstream) : OR4S2 (5210 downstream)																							ttggaaaactaaaattgaatc	0.000													4	2	---	---	---	---	
OR9Q1	219956	broad.mit.edu	37	11	57796168	57796168	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57796168delC	uc001nmj.2	+						OR6Q1_uc010rjz.1_5'Flank	NM_001005212	NP_001005212	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.222)				TTTCCTTGAGCCAACAGAAGC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	58169869	58169869	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58169869delT								OR5B17 (43327 upstream) : OR5B3 (71 downstream)																							ATTGTGGACCTTAAATGTGAT	0.353													11	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64280426	64280426	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64280426delA								RPS6KA4 (140740 upstream) : SLC22A11 (42672 downstream)																							CCTCATTTGGAACATCcatcc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	82829023	82829023	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82829023delC								RAB30 (46139 upstream) : PCF11 (39114 downstream)																							ttattatcatcatctcattaa	0.025													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83585319	83585322	+	Intron	DEL	GGGA	-	-	rs112557348		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83585319_83585322delGGGA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				aggaaggaaggggagaaggaagga	0.020													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83702584	83702585	+	Intron	DEL	TC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83702584_83702585delTC	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				tttctttttttctctctctctc	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	103708643	103708644	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103708643_103708644insA								DYNC2H1 (358052 upstream) : PDGFD (69271 downstream)																							attaaaaagtcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	104130046	104130047	+	IGR	INS	-	G	G	rs7108189		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104130046_104130047insG								PDGFD (95019 upstream) : CASP12 (626395 downstream)																							ACTGTTTTTTTTTTTGTTTTGT	0.391													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112618608	112618609	+	IGR	DEL	TG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112618608_112618609delTG								PTS (477931 upstream) : NCAM1 (213386 downstream)																							gggaggtgtatgtgtgtgtgtg	0.381													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	114743667	114743667	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114743667delA								FAM55B (166015 upstream) : CADM1 (296286 downstream)																							agagttaggtaaagagagcta	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124635823	124635823	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124635823delA								ESAM (3600 upstream) : C11orf61 (571 downstream)																							ccaaaaaaagaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128501281	128501281	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128501281delG								ETS1 (43828 upstream) : FLI1 (55149 downstream)																							tgtcacatatggcacgatttt	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128698604	128698605	+	IGR	INS	-	G	G	rs150043498	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128698604_128698605insG								FLI1 (15443 upstream) : KCNJ1 (9310 downstream)																							gcagactcaaaggttgaggaat	0.040													3	5	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	133262455	133262455	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133262455delG	uc001qgu.2	-							NM_001012393	NP_001012393	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GTGTGCTTCAGGGGGACCTGA	0.567													4	2	---	---	---	---	
FKBP4	2288	broad.mit.edu	37	12	2903958	2903959	+	5'Flank	DEL	AA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2903958_2903959delAA	uc001qkz.2	+							NM_002014	NP_002005	Q02790	FKBP4_HUMAN	FK506 binding protein 52						negative regulation of microtubule polymerization or depolymerization|negative regulation of neuron projection development|protein folding	axonal growth cone|cytosol|membrane|microtubule|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity|protein binding, bridging				0			OV - Ovarian serous cystadenocarcinoma(31;0.00105)		Dimethyl sulfoxide(DB01093)	GGCAAGAACCaaaaaaaaaaaa	0.614													4	2	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5921538	5921541	+	Intron	DEL	AAAG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5921538_5921541delAAAG	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						agagaaagaaaaagaaagaaagaa	0.000													5	3	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5922220	5922223	+	Intron	DEL	AGGA	-	-	rs147780677		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5922220_5922223delAGGA	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						agaaagaaagaggaaggaaggaag	0.137													4	3	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6137016	6137019	+	Intron	DEL	ACAC	-	-	rs146692381		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6137016_6137019delACAC	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	GAAGacacatacacacacacacac	0.039													4	2	---	---	---	---	
IFFO1	25900	broad.mit.edu	37	12	6658357	6658357	+	Intron	DEL	A	-	-	rs72489368		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6658357delA	uc001qpd.1	-						IFFO1_uc001qoy.2_Intron|IFFO1_uc001qpa.1_5'Flank|IFFO1_uc001qpb.1_Intron|IFFO1_uc001qpe.1_Intron|IFFO1_uc010sfe.1_Intron|IFFO1_uc001qpf.1_Intron|IFFO1_uc001qoz.1_5'Flank|IFFO1_uc001qpc.1_Intron|IFFO1_uc001qpg.2_5'Flank	NM_080730	NP_542768	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan isoform 2							intermediate filament					0						TGACTCAACTAAAAAAAAAAA	0.428													7	4	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11171563	11171563	+	Intron	DEL	G	-	-	rs112482285		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11171563delG	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						agtagaaagcggggaaacata	0.000										HNSCC(22;0.051)			3	3	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	14102075	14102076	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14102075_14102076insA	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	CCCAGAGATCCAAATCAGGGCT	0.515													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	15151241	15151242	+	IGR	INS	-	T	T	rs150376247	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15151241_15151242insT								PDE6H (16444 upstream) : RERG (109476 downstream)																							aattttttctgtttttttttct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17072334	17072335	+	IGR	INS	-	TG	TG	rs140191552	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17072334_17072335insTG								LMO3 (309576 upstream) : None (None downstream)																							tttacccagaatgtgtgtgtgt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	18809689	18809691	+	IGR	DEL	ACA	-	-	rs148699097		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18809689_18809691delACA								PIK3C2G (8338 upstream) : PLCZ1 (26425 downstream)																							aacaacaacgacaacaacaacaa	0.000													2	4	---	---	---	---	
IFLTD1	160492	broad.mit.edu	37	12	25634799	25634800	+	Intron	INS	-	CACA	CACA	rs138084240	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25634799_25634800insCACA	uc001rgs.2	-						IFLTD1_uc001rgt.1_Intron|IFLTD1_uc010sji.1_Intron	NM_152590	NP_689803	Q8N9Z9	ILFT1_HUMAN	intermediate filament tail domain containing 1							intermediate filament	structural molecule activity			ovary(2)|central_nervous_system(1)	3	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					TATTGCCTCTTcacacacacac	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	27250061	27250064	+	IGR	DEL	TGTT	-	-	rs35577987		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27250061_27250064delTGTT								C12orf71 (14606 upstream) : STK38L (147014 downstream)																							tttgtttgtctgtttgtttgtttg	0.221													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29946795	29946796	+	IGR	INS	-	AC	AC	rs145392899	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29946795_29946796insAC								TMTC1 (9103 upstream) : IPO8 (835127 downstream)																							ACATGCTTACTATAGTTGCAAC	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30605173	30605176	+	IGR	DEL	AAAC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30605173_30605176delAAAC								TMTC1 (667481 upstream) : IPO8 (176747 downstream)																							caaaacaaagaaacaaacaaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31921000	31921001	+	IGR	DEL	GA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31921000_31921001delGA								AMN1 (38892 upstream) : H3F3C (23120 downstream)																							agtcctagatgagagagagaga	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	32602360	32602360	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32602360delT								BICD1 (71220 upstream) : FGD4 (36546 downstream)																							atccttagtctttccttgact	0.000													4	2	---	---	---	---	
FGD4	121512	broad.mit.edu	37	12	32637017	32637017	+	5'Flank	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32637017delA	uc001rlc.2	+							NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AAATTACACCAAAAAAAATCC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	38048613	38048613	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38048613delA								None (None upstream) : ALG10B (661944 downstream)																							cacagagttgaaactatcttt	0.000													4	2	---	---	---	---	
CPNE8	144402	broad.mit.edu	37	12	39114720	39114721	+	Intron	DEL	CC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39114720_39114721delCC	uc001rls.1	-						CPNE8_uc001rlr.1_5'UTR	NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN	copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				cctcgcatttccccacacagct	0.000													4	2	---	---	---	---	
CPNE8	144402	broad.mit.edu	37	12	39216808	39216811	+	Intron	DEL	GTGA	-	-	rs10608225		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39216808_39216811delGTGA	uc001rls.1	-							NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN	copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				CTGTTTTATGGTGAGTTTGTATGT	0.363													4	2	---	---	---	---	
TMEM117	84216	broad.mit.edu	37	12	44378168	44378170	+	Intron	DEL	AAC	-	-	rs35647701		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44378168_44378170delAAC	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632	Q9H0C3	TM117_HUMAN	transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)		gagactccgtaacaacaacaaca	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	44814257	44814258	+	IGR	DEL	TG	-	-	rs67300422		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44814257_44814258delTG								TMEM117 (30717 upstream) : NELL2 (87800 downstream)																							GGTGTTGTATtgtgtgtgtgtg	0.134													4	2	---	---	---	---	
LOC283404	283404	broad.mit.edu	37	12	52607167	52607167	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52607167delC	uc010snp.1	+						uc001rzz.2_5'Flank	NR_027358				Homo sapiens hypothetical protein LOC283404, mRNA (cDNA clone IMAGE:4828118).												0						ccttccatttcccatctcctc	0.224											OREG0021843	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
BLOC1S1	2647	broad.mit.edu	37	12	56112277	56112278	+	Intron	DEL	TG	-	-	rs68039115		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56112277_56112278delTG	uc009zny.1	+						BLOC1S1_uc001shi.2_Intron|BLOC1S1_uc001shj.3_Intron|RDH5_uc010spt.1_5'Flank|RDH5_uc010spu.1_5'Flank|RDH5_uc001shk.2_5'Flank|RDH5_uc001shl.2_5'Flank			P78537	BL1S1_HUMAN	RecName: Full=Biogenesis of lysosome-related organelles complex 1 subunit 1;          Short=BLOC-1 subunit 1; AltName: Full=GCN5-like protein 1; AltName: Full=Protein RT14;						cellular membrane organization|melanosome organization|platelet dense granule organization|post-Golgi vesicle-mediated transport	BLOC-1 complex|lysosomal membrane	protein binding				0						AGGGAGAGCAtgtgtgtgtgtg	0.426													5	3	---	---	---	---	
RPSAP52	204010	broad.mit.edu	37	12	66200103	66200104	+	Intron	INS	-	T	T	rs111298673		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66200103_66200104insT	uc001sso.2	-							NR_026825				SubName: Full=Putative uncharacterized protein RPSAP52;												0						ATGTGCTAGTCttttttttttt	0.064													4	2	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	66851996	66851997	+	Intron	DEL	CT	-	-	rs140154256		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66851996_66851997delCT	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stj.2_Intron|GRIP1_uc001stl.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TGGATTccccctctctctccac	0.198													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	68579675	68579677	+	IGR	DEL	GAG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68579675_68579677delGAG								IFNG (26154 upstream) : IL26 (15452 downstream)																							gaagaagaacgaggaggaggagg	0.113													4	2	---	---	---	---	
MGAT4C	25834	broad.mit.edu	37	12	87191124	87191125	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87191124_87191125insT	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						tttctttcaagttttttttttt	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93477741	93477741	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93477741delG								EEA1 (154634 upstream) : NUDT4 (293960 downstream)																							ctcctcccttggcatccacaa	0.080													4	2	---	---	---	---	
TMCC3	57458	broad.mit.edu	37	12	95029767	95029768	+	Intron	DEL	CT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95029767_95029768delCT	uc001tdj.2	-							NM_020698	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3							integral to membrane				ovary(1)|skin(1)	2						TTTCAAATCCCTGAGGGGAGAG	0.257													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96514457	96514458	+	IGR	INS	-	GGGGAGGAGA	GGGGAGGAGA	rs148372803	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96514457_96514458insGGGGAGGAGA								LTA4H (77159 upstream) : ELK3 (73749 downstream)																							AGAGGAGGGGTGGGGAGGAgag	0.109													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	98905440	98905441	+	IGR	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98905440_98905441insT								RMST (946647 upstream) : LOC100128191 (1312 downstream)																							CCTCCAGATGATTTTTTTTTAA	0.079													2	5	---	---	---	---	
APPL2	55198	broad.mit.edu	37	12	105603745	105603745	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105603745delT	uc001tlf.1	-						APPL2_uc010swt.1_Intron|APPL2_uc001tlg.1_Intron|APPL2_uc010swu.1_Intron|APPL2_uc009zuq.2_Intron	NM_018171	NP_060641	Q8NEU8	DP13B_HUMAN	adaptor protein, phosphotyrosine interaction, PH						cell cycle|cell proliferation|signal transduction	early endosome membrane|nucleus	protein binding			upper_aerodigestive_tract(1)	1						ATCTTCACCCttttttttttt	0.239													4	2	---	---	---	---	
POLR3B	55703	broad.mit.edu	37	12	106768297	106768297	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106768297delT	uc001tlp.2	+						POLR3B_uc001tlq.2_Intron	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2						ttgtggcatgttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112853054	112853055	+	IGR	INS	-	AG	AG	rs140889150	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112853054_112853055insAG								RPL6 (5611 upstream) : PTPN11 (3481 downstream)																							agtggggagacggggtggtgaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112948167	112948168	+	IGR	INS	-	AC	AC	rs144350499	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112948167_112948168insAC								PTPN11 (451 upstream) : RPH3A (64733 downstream)																							cacacacacatacacacacaca	0.228													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	113483665	113483666	+	IGR	INS	-	TG	TG	rs138914387	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113483665_113483666insTG								OAS2 (34138 upstream) : DTX1 (11996 downstream)																							tgtattgtgtttgtgtgtgtgt	0.015													4	2	---	---	---	---	
SDSL	113675	broad.mit.edu	37	12	113875213	113875213	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113875213delA	uc001tvi.2	+						SDSL_uc009zwh.2_Intron	NM_138432	NP_612441	Q96GA7	SDSL_HUMAN	serine dehydratase-like						cellular amino acid metabolic process		L-serine ammonia-lyase activity|L-threonine ammonia-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)	GAGTGAGTGGAAAGGTGGGTA	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114038886	114038887	+	IGR	INS	-	AAG	AAG	rs137987398	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114038886_114038887insAAG								LHX5 (129009 upstream) : RBM19 (215656 downstream)																							GAGTGTTTGTAAAGGAGTATAA	0.446													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115786074	115786075	+	IGR	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115786074_115786075delCA								TBX3 (664105 upstream) : MED13L (610308 downstream)																							CTCTCTCTCTcacacacacacg	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	117120902	117120902	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117120902delG								MAP1LC3B2 (106477 upstream) : C12orf49 (32694 downstream)																							TCTGGGTTCTGGTAGCTTCTG	0.592													4	2	---	---	---	---	
CCDC60	160777	broad.mit.edu	37	12	119824840	119824841	+	Intron	DEL	CA	-	-	rs67941826	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119824840_119824841delCA	uc001txe.2	+							NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		ctgtctctctcacacacacaca	0.267													3	3	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124818500	124818501	+	Intron	DEL	GT	-	-	rs72350510		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124818500_124818501delGT	uc010tay.1	-						NCOR2_uc010taz.1_Intron|NCOR2_uc010tax.1_Intron	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		gggtgtgcacgtgtgtgtgtgc	0.010													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132641909	132641909	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132641909delA								NOC4L (4923 upstream) : GALNT9 (39009 downstream)																							cactacacacacactacacac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22614540	22614541	+	5'Flank	DEL	TT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22614540_22614541delTT	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																		aatcatattctttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22885231	22885231	+	IGR	DEL	A	-	-	rs67996361		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22885231delA								FGF9 (606591 upstream) : SGCG (869829 downstream)																							CCCTCCCCTGAAAAAAAAAAA	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	24279067	24279067	+	IGR	DEL	T	-	-	rs75929601		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24279067delT								TNFRSF19 (28836 upstream) : MIPEP (25262 downstream)																							TGGTGACCCCTGGGTGGGCCT	0.527													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	24989197	24989198	+	IGR	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24989197_24989198insT								C1QTNF9 (92532 upstream) : PARP4 (5877 downstream)																							tcctaaactcattttttttttt	0.000													3	3	---	---	---	---	
USP12	219333	broad.mit.edu	37	13	27718337	27718338	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27718337_27718338insA	uc001uqy.2	-							NM_182488	NP_872294	O75317	UBP12_HUMAN	ubiquitin thiolesterase 12						protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)	1		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		ctctgactcccaaaaaaaaaaa	0.040													4	3	---	---	---	---	
HMGB1	3146	broad.mit.edu	37	13	31071374	31071375	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31071374_31071375insT	uc001usz.2	-							NM_002128	NP_002119	P09429	HMGB1_HUMAN	high-mobility group box 1						base-excision repair, DNA ligation|dendritic cell chemotaxis|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|inflammatory response to antigenic stimulus|innate immune response|myeloid dendritic cell activation|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|neuron projection development|positive regulation of apoptosis|positive regulation of caspase activity|positive regulation of DNA binding|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	cell surface|condensed chromosome|extracellular space|nucleolus|nucleoplasm	chemoattractant activity|cytokine activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|repressing transcription factor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CACTCATTCCATTTTTGGATCT	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	35061314	35061315	+	IGR	DEL	AC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35061314_35061315delAC								RFC3 (520620 upstream) : NBEA (455141 downstream)																							GCACCGCTAAacacacacacac	0.366													4	2	---	---	---	---	
FOXO1	2308	broad.mit.edu	37	13	41235086	41235094	+	Intron	DEL	AACAACAAC	-	-	rs111337241		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41235086_41235094delAACAACAAC	uc001uxl.3	-							NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1						anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase 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 factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		ggctcagaaaaacaacaacaacaacaaca	0.148													3	3	---	---	---	---	
DLEU2	8847	broad.mit.edu	37	13	50657077	50657077	+	Intron	DEL	T	-	-	rs35701240		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50657077delT	uc001vdn.1	-						DLEU2_uc001vdo.1_Intron|DLEU1_uc010adl.1_Intron|DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|DLEU2_uc001vdx.2_5'Flank|DLEU2_uc001vdy.2_5'Flank|DLEU2_uc001vdz.2_5'Flank|DLEU2_uc001veb.1_5'Flank|DLEU1_uc001vec.2_Intron|DLEU1_uc001ved.2_Intron	NR_002612				Homo sapiens BCMS-upstream neighbor (BCMSUN) mRNA, partial sequence.												0						CTTAGGATGATTTTTTTTTTT	0.338													4	2	---	---	---	---	
DLEU1	10301	broad.mit.edu	37	13	51086349	51086349	+	Intron	DEL	A	-	-	rs36064696		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51086349delA	uc010adm.1	+						DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|uc001vem.1_Intron|uc001veq.1_Intron|uc001ver.2_Intron|uc001ves.1_Intron|uc001vet.1_Intron|uc001veu.2_Intron|uc001vev.2_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0						CAGAATTTGGAAAAAAAAAAA	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63634789	63634789	+	IGR	DEL	T	-	-	rs63096761		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63634789delT								None (None upstream) : OR7E156P (676779 downstream)																							GTTTATTCACTTTTTACATAA	0.214													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71790736	71790737	+	IGR	DEL	CT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71790736_71790737delCT								None (None upstream) : DACH1 (221361 downstream)																							gggaccagagctctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82800342	82800343	+	IGR	DEL	AC	-	-	rs149762906		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82800342_82800343delAC								None (None upstream) : None (None downstream)																							CCCACATAAAACACACACACAC	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90512950	90512951	+	IGR	INS	-	A	A	rs150372086	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90512950_90512951insA								None (None upstream) : MIR622 (370485 downstream)																							TACATACAAACACTGCTTCTTC	0.421													2	4	---	---	---	---	
HS6ST3	266722	broad.mit.edu	37	13	97198568	97198569	+	Intron	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97198568_97198569delGT	uc001vmw.2	+							NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					TTACAGGGGCGTGTGTGTGTGT	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	105177429	105177430	+	IGR	DEL	CA	-	-	rs66770073		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105177429_105177430delCA								None (None upstream) : DAOA (940786 downstream)																							cacacgcgcgcacacacacaca	0.015													9	4	---	---	---	---	
COL4A2	1284	broad.mit.edu	37	13	111061159	111061160	+	Intron	INS	-	AC	AC	rs61963207		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111061159_111061160insAC	uc001vqx.2	+							NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein						angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			cacatatatatacacacacaca	0.183													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	112293635	112293636	+	IGR	INS	-	AGAG	AGAG	rs5806913		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112293635_112293636insAGAG								C13orf16 (297042 upstream) : SOX1 (428277 downstream)																							CTTCTGCACATAGAAATGGAGT	0.426													5	3	---	---	---	---	
LAMP1	3916	broad.mit.edu	37	13	113953589	113953590	+	Intron	INS	-	T	T	rs75937787		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113953589_113953590insT	uc001vtm.1	+						LAMP1_uc010tka.1_Intron	NM_005561	NP_005552	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1							endosome membrane|integral to plasma membrane|lysosomal membrane|membrane fraction				central_nervous_system(2)	2	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			ACAATCTTAACttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19030772	19030772	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19030772delA								None (None upstream) : OR11H12 (346822 downstream)																							aggcctcaagacgctctaaat	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20315828	20315829	+	IGR	INS	-	T	T	rs150158951	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20315828_20315829insT								OR4N2 (19298 upstream) : OR4K2 (28598 downstream)																							TTTCTCAGATCTTTTTTTGCAC	0.416													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21576226	21576226	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21576226delT								ZNF219 (3363 upstream) : OR5AU1 (46871 downstream)																							TGGTGTTTGCTTTAACCTGAT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22051170	22051171	+	IGR	DEL	TT	-	-	rs34204489		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22051170_22051171delTT								OR10G3 (12295 upstream) : OR10G2 (50896 downstream)																							GACAGACCAAtttttttttttt	0.213													4	2	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35037841	35037841	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35037841delT	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419	Q9UNH7	SNX6_HUMAN	sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)		actcagccTGTTTTTTTTTTT	0.194													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49375596	49375596	+	IGR	DEL	G	-	-	rs5808468		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49375596delG								None (None upstream) : SDCCAG1 (657431 downstream)																							GAATCATGTTGGGGTATGGAT	0.333													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	50501210	50501211	+	IGR	DEL	AC	-	-	rs113147541		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50501210_50501211delAC								C14orf182 (26972 upstream) : C14orf183 (49159 downstream)																							AGAGGTTAAAacacacacacac	0.406													4	2	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58578404	58578404	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58578404delT	uc001xdc.2	-						C14orf37_uc010tro.1_Intron|C14orf37_uc001xdd.2_Intron	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						ttccttcttcttttttttttt	0.000													4	2	---	---	---	---	
RBM25	58517	broad.mit.edu	37	14	73525949	73525949	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73525949delG	uc001xno.2	+						RBM25_uc001xnn.3_Intron|RBM25_uc010ttu.1_Intron	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		CAAGTGAACTGGGCCCCACCC	0.507													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	78917256	78917257	+	Intron	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78917256_78917257delGT	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						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)		GGTGTTTGGGgtgtgtgtgtgt	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	84676589	84676590	+	IGR	DEL	TG	-	-	rs149902662		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84676589_84676590delTG								None (None upstream) : None (None downstream)																							TTTGTGATTTtgtgtgtgtgtg	0.282													3	5	---	---	---	---	
RPS6KA5	9252	broad.mit.edu	37	14	91502442	91502443	+	Intron	INS	-	G	G	rs150384480	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91502442_91502443insG	uc001xys.2	-						RPS6KA5_uc010twi.1_Intron|RPS6KA5_uc001xyt.2_Intron|RPS6KA5_uc010att.1_Intron	NM_004755	NP_004746	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, polypeptide 5						axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|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	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		AAATAGACTGTGGGGGGTGCAA	0.277													3	3	---	---	---	---	
CLMN	79789	broad.mit.edu	37	14	95657758	95657759	+	3'UTR	INS	-	C	C	rs60112171		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95657758_95657759insC	uc001yef.2	-	13						NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)		AAAAAAAAAAACCACAATAGCG	0.446													4	4	---	---	---	---	
PAPOLA	10914	broad.mit.edu	37	14	97003546	97003547	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97003546_97003547insT	uc001yfq.2	+						PAPOLA_uc001yfr.2_Intron|PAPOLA_uc010twv.1_Intron|PAPOLA_uc010avp.2_Intron	NM_032632	NP_116021	P51003	PAPOA_HUMAN	poly(A) polymerase alpha						mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding				0		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		GAACTCCTTAGTTTTTTTTGGT	0.366													4	2	---	---	---	---	
DYNC1H1	1778	broad.mit.edu	37	14	102442247	102442248	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102442247_102442248insT	uc001yks.2	+							NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						TAATATAAATCttttttttttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	102539233	102539233	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102539233delT								DYNC1H1 (22098 upstream) : HSP90AA1 (7843 downstream)																							GAGACGTCAGTTttttttttc	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	102544648	102544648	+	IGR	DEL	A	-	-	rs79844146		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102544648delA								DYNC1H1 (27513 upstream) : HSP90AA1 (2428 downstream)																							aaaagaaaggaaaaaaaaaaa	0.189													4	2	---	---	---	---	
KLC1	3831	broad.mit.edu	37	14	104105238	104105239	+	Intron	DEL	GT	-	-	rs35770236		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104105238_104105239delGT	uc001yno.2	+						KLC1_uc010tyd.1_Intron|KLC1_uc010tye.1_Intron|KLC1_uc001ynm.1_Intron|KLC1_uc001ynn.1_Intron|KLC1_uc010tyf.1_Intron	NM_182923	NP_891553	Q07866	KLC1_HUMAN	kinesin light chain 1 isoform 2						blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)				gagcacaagggtgtgtgtgtgt	0.025													4	2	---	---	---	---	
INF2	64423	broad.mit.edu	37	14	105174594	105174595	+	Intron	DEL	GG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105174594_105174595delGG	uc001ypb.2	+						INF2_uc010tyi.1_Intron|INF2_uc001ypc.2_Intron|INF2_uc010awz.1_Intron	NM_022489	NP_071934	Q27J81	INF2_HUMAN	inverted formin 2 isoform 1						actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		ATGGTGCCCTGGGGCCCTGCTA	0.663													4	2	---	---	---	---	
AHNAK2	113146	broad.mit.edu	37	14	105446384	105446385	+	5'Flank	DEL	AC	-	-	rs144898236		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105446384_105446385delAC	uc010axc.1	-							NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2							nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			gctctgtcatacacacacacac	0.218													5	3	---	---	---	---	
MTA1	9112	broad.mit.edu	37	14	105905575	105905576	+	Intron	INS	-	C	C	rs58389555		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105905575_105905576insC	uc001yqx.2	+						MTA1_uc001yqy.2_Intron|MTA1_uc001yqz.1_Intron|MTA1_uc001yra.1_Intron	NM_004689	NP_004680	Q13330	MTA1_HUMAN	metastasis associated protein						signal transduction	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		TCTGCCCCCAACCCTGAGGTGT	0.649													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20061722	20061722	+	IGR	DEL	T	-	-	rs76211936		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20061722delT								None (None upstream) : GOLGA6L6 (675372 downstream)																							TTAGAAGACCTGTAATAGACA	0.254													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20856321	20856321	+	IGR	DEL	A	-	-	rs74770895		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20856321delA								GOLGA8C (75295 upstream) : BCL8 (13735 downstream)																							agggagtcccatatgtcccta	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22448192	22448192	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22448192delA								OR4N3P (33807 upstream) : MIR1268 (65037 downstream)																							aaaaaaaaaCACCAAAAAACT	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22512144	22512145	+	IGR	DEL	CA	-	-	rs111284212		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22512144_22512145delCA								OR4N3P (97759 upstream) : MIR1268 (1084 downstream)																							GATTGGTGGCcacacacacaca	0.455													4	4	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33736035	33736035	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33736035delC	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CTGCCATCATCCTTAGCTCCT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	43003089	43003090	+	Intron	DEL	CT	-	-	rs34768575		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43003089_43003090delCT	uc010udj.1	+						uc010bcw.2_Intron					Homo sapiens mRNA for KIAA1300 protein, partial cds.																		cacttgtgcgctctctctctct	0.079													4	2	---	---	---	---	
CYP19A1	1588	broad.mit.edu	37	15	51513173	51513173	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51513173delT	uc001zyz.3	-						CYP19A1_uc001zza.3_Intron|CYP19A1_uc001zzb.2_Intron	NM_031226	NP_112503	P11511	CP19A_HUMAN	cytochrome P450, family 19						estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)	CATGCACATGTTTTTTTTTTT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	62538522	62538523	+	RNA	INS	-	GA	GA	rs3055695		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62538522_62538523insGA	uc002ain.1	-	5		c.694_695insTC			uc002ajj.1_3'UTR|uc002ajn.2_5'Flank|uc002ajo.2_5'Flank|uc002ajq.2_5'Flank|uc002ajr.1_5'Flank|uc010uhp.1_5'Flank|uc002ajt.2_5'Flank|uc002ajw.2_5'Flank|uc010uhq.1_5'Flank|uc002ajx.2_5'Flank|uc002ajy.2_5'Flank					Homo sapiens cDNA FLJ38723 fis, clone KIDNE2010137, weakly similar to GOLGIN-95.																		GGGGGCTCCGGGTAGGGGTTCA	0.609													4	3	---	---	---	---	
EFTUD1	79631	broad.mit.edu	37	15	82497880	82497881	+	Intron	INS	-	AC	AC	rs144966014	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82497880_82497881insAC	uc002bgt.1	-						EFTUD1_uc002bgu.1_Intron	NM_024580	NP_078856	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain						mature ribosome assembly		GTP binding|GTPase activity|ribosome binding|translation elongation factor activity			ovary(1)	1						CTCCAGTAAATacacacacaca	0.262													4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	87137153	87137153	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87137153delT	uc002blz.1	+							NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						cactgattgattttttttttt	0.010													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88275372	88275372	+	IGR	DEL	T	-	-	rs35550412		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88275372delT								NCRNA00052 (152455 upstream) : NTRK3 (144616 downstream)																							TTTCACTATGTTTTTTTTCCA	0.333													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92152527	92152530	+	IGR	DEL	AAAG	-	-	rs71959520		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92152527_92152530delAAAG								SV2B (313879 upstream) : SLCO3A1 (244408 downstream)																							ccatgaagataaagaaagaaaccc	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92205323	92205323	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92205323delT								SV2B (366675 upstream) : SLCO3A1 (191615 downstream)																							ATCCTGCTGGTTTTTTTTTTT	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94574301	94574303	+	IGR	DEL	AGA	-	-	rs150272572		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94574301_94574303delAGA								RGMA (941868 upstream) : MCTP2 (200498 downstream)																							TGAAAATCACAGAAGGAGAGCTG	0.399													1	6	---	---	---	---	
LOC91948	91948	broad.mit.edu	37	15	98381087	98381087	+	Intron	DEL	A	-	-	rs34048376		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98381087delA	uc002buh.1	-						LOC91948_uc002bug.1_Intron	NR_024173				SubName: Full=Putative uncharacterized protein ENSP00000381347;												0						TGGAGATATGAAAAAAAAAAA	0.289													3	4	---	---	---	---	
IGF1R	3480	broad.mit.edu	37	15	99209153	99209154	+	Intron	INS	-	T	T	rs140489556	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99209153_99209154insT	uc002bul.2	+						IGF1R_uc010urq.1_Intron|IGF1R_uc010bon.2_Intron	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)	CTTGAATGGTCTTGCTAAGCGA	0.436													3	4	---	---	---	---	
PCSK6	5046	broad.mit.edu	37	15	101930559	101930560	+	Intron	INS	-	C	C	rs148739434	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101930559_101930560insC	uc002bwy.2	-						PCSK6_uc010bpd.2_Intron|PCSK6_uc010bpe.2_Intron|PCSK6_uc002bxa.2_Intron|PCSK6_uc002bxb.2_Intron|PCSK6_uc002bxc.1_Intron|PCSK6_uc002bxd.1_Intron|PCSK6_uc002bxe.2_Intron|PCSK6_uc002bxg.1_Intron	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4						glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGGGATTGTCGCCCCATCATCT	0.371													4	2	---	---	---	---	
NARFL	64428	broad.mit.edu	37	16	793045	793046	+	5'Flank	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:793045_793046insA	uc002cjr.2	-						NARFL_uc002cjq.2_5'Flank|NARFL_uc002cjs.2_5'Flank|NARFL_uc010brc.1_5'Flank|NARFL_uc010uur.1_5'Flank	NM_022493	NP_071938	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like						iron-sulfur cluster assembly|oxygen homeostasis|regulation of transcription, DNA-dependent|response to hypoxia		4 iron, 4 sulfur cluster binding|metal ion binding				0		Hepatocellular(780;0.0218)				gacactgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PRR25	388199	broad.mit.edu	37	16	863772	863772	+	Frame_Shift_Del	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:863772delG	uc010uut.1	+	3	1120	c.1120delG	c.(1120-1122)GGGfs	p.G374fs		NM_001013638	NP_001013660	Q96S07	PRR25_HUMAN	proline rich 25	374										large_intestine(1)	1						GCGGATCCCCGGGGCCGCGCG	0.796													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	1321804	1321804	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1321804delC								TPSD1 (13310 upstream) : UBE2I (37376 downstream)																							GGGTGAAGGGCCTGGGGATGG	0.667													4	2	---	---	---	---	
LOC652276	652276	broad.mit.edu	37	16	2660756	2660756	+	RNA	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2660756delA	uc002cqx.2	+	2		c.638delA			LOC652276_uc002cqy.3_RNA					Homo sapiens cDNA FLJ39075 fis, clone NT2RP7016911.												0						GCTGTCTTACAAAAAAAAAAA	0.294													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5700327	5700328	+	IGR	INS	-	GGT	GGT			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5700327_5700328insGGT								FAM86A (552538 upstream) : A2BP1 (368804 downstream)																							GCAGCCACggcggtggtggtgg	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8517000	8517003	+	IGR	DEL	AGGA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8517000_8517003delAGGA								A2BP1 (753660 upstream) : TMEM114 (102500 downstream)																							ggtgggagggaggaaggaaggaag	0.000													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	10612763	10612766	+	IGR	DEL	TCCC	-	-	rs36095074		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10612763_10612766delTCCC								ATF7IP2 (35269 upstream) : EMP2 (9514 downstream)																							catccctccttccctccctccctc	0.000													5	3	---	---	---	---	
MYH11	4629	broad.mit.edu	37	16	15934157	15934157	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15934157delA	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002deb.3_Intron	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						aaggacattgaatgttcccaa	0.035			T	CBFB	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	23745612	23745612	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23745612delT								ERN2 (20791 upstream) : CHP2 (20336 downstream)																							GGTCTGCCCGTGGGTTTTGTC	0.363													4	2	---	---	---	---	
PRKCB	5579	broad.mit.edu	37	16	24052848	24052848	+	Intron	DEL	T	-	-	rs111804466		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24052848delT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)	AGAAAGAACCTTTTTTTTTTT	0.358													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	24250006	24250007	+	IGR	INS	-	CA	CA	rs61536401		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24250006_24250007insCA								PRKCB (18076 upstream) : CACNG3 (16869 downstream)																							aacagcacgtgcacacacacac	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25078519	25078519	+	RNA	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25078519delC	uc002dnh.1	+	1		c.161delC			uc002dni.1_5'Flank|uc010vch.1_5'Flank|uc002dnj.2_5'Flank					Homo sapiens cDNA FLJ36063 fis, clone TESTI2018975.																		TCCTCTCTTGCCGCGCGCCGA	0.652													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	29166379	29166380	+	Intron	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29166379_29166380delCA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		cacgcgcgcgcacacacacaca	0.104													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	31525354	31525361	+	IGR	DEL	CCTCCCTT	-	-	rs72015335		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31525354_31525361delCCTCCCTT								C16orf58 (5648 upstream) : AHSP (13842 downstream)																							ttccttcctccctcccttcctcccttcc	0.034													1	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32212321	32212321	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32212321delC								HERC2P4 (48447 upstream) : TP53TG3B (472520 downstream)																							GCTTCCTGGGCCCCCTCCTGT	0.672													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32312207	32312207	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32312207delT	uc002edb.2	-											Homo sapiens similar to protein phosphatase 2A 48 kDa regulatory subunit isoform 1; serine/threonine protein phosphatase 2A, 48kDa regulatory subunit; PP2A, subunit B, PR48 isoform; PP2A B subunit PR48; NY-REN-8 antigen, mRNA (cDNA clone IMAGE:5272051).																		CTTCTTTTCCTTTTTTTTTGT	0.269													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32440982	32440982	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32440982delA								HERC2P4 (277108 upstream) : TP53TG3B (243859 downstream)																							CCAGACTGAGACTGAAATCTC	0.373													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32550598	32550599	+	IGR	DEL	CT	-	-	rs146554747		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32550598_32550599delCT								HERC2P4 (386724 upstream) : TP53TG3B (134242 downstream)																							tttggaaacactgtttttgtaa	0.000													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33494238	33494238	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33494238delC								SLC6A10P (597775 upstream) : MIR1826 (471270 downstream)																							caaatgatgtccacatcacag	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	49370842	49370843	+	IGR	INS	-	ATTC	ATTC	rs140206776	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49370842_49370843insATTC								CBLN1 (55127 upstream) : C16orf78 (36965 downstream)																							TGCACACGTTGattcattcatt	0.292													4	2	---	---	---	---	
ZNF423	23090	broad.mit.edu	37	16	49536701	49536702	+	Intron	INS	-	AC	AC	rs147325861	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49536701_49536702insAC	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)				aaatactctagacacacacaca	0.455													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	52906214	52906214	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52906214delA								TOX3 (324500 upstream) : CHD9 (182731 downstream)																							ATGATGAGGCAGGAAAACTAA	0.353													4	2	---	---	---	---	
CES7	221223	broad.mit.edu	37	16	55937042	55937042	+	Intron	DEL	A	-	-	rs112904387		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55937042delA	uc002eir.2	-						CES7_uc002eiq.2_Intron			Q6NT32	EST5A_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000383269; Flags: Fragment;							extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)		GGATGCAGAGAAAAAAAAAAA	0.453													4	3	---	---	---	---	
SLC12A3	6559	broad.mit.edu	37	16	56936679	56936681	+	Intron	DEL	TCC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56936679_56936681delTCC	uc010ccm.2	+						SLC12A3_uc002ekd.3_Intron|SLC12A3_uc010ccn.2_Intron	NM_001126108	NP_001119580	P55017	S12A3_HUMAN	solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	CTGCCCGGAGtcctcctcctcct	0.468													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	62884154	62884177	+	IGR	DEL	GGAGGGAAAGAGGGAGGGAAGGAA	-	-	rs11272791		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62884154_62884177delGGAGGGAAAGAGGGAGGGAAGGAA								CDH8 (814118 upstream) : None (None downstream)																							gacaaggaggggagggaaagagggagggaaggaaggagggaaag	0.138													4	2	---	---	---	---	
LOC283867	283867	broad.mit.edu	37	16	65474356	65474357	+	Intron	INS	-	TTTG	TTTG	rs139441863	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65474356_65474357insTTTG	uc010cdp.1	-						LOC283867_uc002eol.1_Intron					Homo sapiens cDNA clone IMAGE:5276218.												0				OV - Ovarian serous cystadenocarcinoma(108;0.17)		GTATGTCATCATTTAACTTATC	0.312													3	4	---	---	---	---	
KCTD19	146212	broad.mit.edu	37	16	67342074	67342074	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67342074delT	uc002esu.2	-						KCTD19_uc002est.2_Intron|KCTD19_uc010vjj.1_Intron	NM_001100915	NP_001094385	Q17RG1	KCD19_HUMAN	potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		ctttcttttcttttttttttt	0.055													6	3	---	---	---	---	
CLEC18C	283971	broad.mit.edu	37	16	70024114	70024119	+	Intron	DEL	GGAGGA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70024114_70024119delGGAGGA	uc002exy.2	+						PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron|PDXDC2_uc010vlq.1_5'Flank	NM_182619	NP_872425	Q8NCF0	CL18C_HUMAN	secretory protein LOC348174 precursor							extracellular region	sugar binding				0						TTGGGCACCTggaggaggaggaggag	0.291													4	3	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	71018828	71018829	+	Intron	INS	-	A	A	rs112227827		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71018828_71018829insA	uc002ezr.2	-							NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				CATTATCATGGAAAAAAAATCc	0.238													5	4	---	---	---	---	
CLEC18B	497190	broad.mit.edu	37	16	74444233	74444234	+	Intron	INS	-	G	G	rs143495339	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74444233_74444234insG	uc002fct.2	-						CLEC18B_uc002fcu.2_Intron	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						CTCTCCCCCACGTGACGTGCCT	0.634													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78218467	78218473	+	Intron	DEL	TATACTA	-	-	rs72565124	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78218467_78218473delTATACTA	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron|WWOX_uc002ffj.1_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		TTTCCCCGTTTATACTATAAACATATG	0.333													3	3	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78690172	78690172	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78690172delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		TGATGAGGCCTTTTTTGGGAT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	82476511	82476512	+	IGR	DEL	TC	-	-	rs67282940		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82476511_82476512delTC								MPHOSPH6 (272682 upstream) : CDH13 (184066 downstream)																							TTTTTTtctgtctctctctctc	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	86254217	86254218	+	IGR	INS	-	TTTC	TTTC	rs146554203	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86254217_86254218insTTTC								IRF8 (298008 upstream) : LOC732275 (111238 downstream)																							GTGTTGTATTTTTTCTTTCTTT	0.282													3	4	---	---	---	---	
ZCCHC14	23174	broad.mit.edu	37	16	87449490	87449493	+	Intron	DEL	TTTT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87449490_87449493delTTTT	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron|ZCCHC14_uc002fkb.2_Intron	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		TTTTTCTTCCTTTTTTTGAGACAA	0.333													4	3	---	---	---	---	
NXN	64359	broad.mit.edu	37	17	747701	747701	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:747701delC	uc002fsa.2	-						NXN_uc002fsb.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		CTAACCCCAGCCCATCCACTC	0.532													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	1816893	1816893	+	IGR	DEL	A	-	-	rs66496131		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1816893delA								RPA1 (14045 upstream) : RTN4RL1 (21080 downstream)																							cccagctctgaaaaaaaaaaa	0.000													4	4	---	---	---	---	
P2RX1	5023	broad.mit.edu	37	17	3821725	3821727	+	5'Flank	DEL	TCC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3821725_3821727delTCC	uc002fww.2	-						P2RX1_uc010ckm.1_5'Flank	NM_002558	NP_002549	P51575	P2RX1_HUMAN	purinergic receptor P2X1						platelet activation	integral to plasma membrane	calcium channel activity|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity			ovary(1)|skin(1)	2				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		CATGtcttcttcctcctcctcct	0.232													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	5842551	5842552	+	IGR	DEL	TG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5842551_5842552delTG								NLRP1 (354719 upstream) : WSCD1 (129885 downstream)																							TAAAAATTGCTGTGTGTGTGTG	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7996427	7996428	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7996427_7996428insA								ALOX12B (5406 upstream) : ALOXE3 (2791 downstream)																							TTAGACTGACCAAAAAACAGTG	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13147206	13147206	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13147206delA								ELAC2 (225847 upstream) : HS3ST3A1 (251800 downstream)																							gtttcaggtgaaaaagtcaag	0.000													4	2	---	---	---	---	
CDRT4	284040	broad.mit.edu	37	17	15396979	15396980	+	Intron	DEL	CT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15396979_15396980delCT	uc010vvw.1	-						FAM18B2_uc010vvx.1_Intron			Q8N9R6	CDRT4_HUMAN	SubName: Full=cDNA FLJ53614, highly similar to Protein FAM18B;												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)		cttttccttcctctctccctcc	0.050													3	3	---	---	---	---	
AKAP10	11216	broad.mit.edu	37	17	19841551	19841552	+	Intron	DEL	TT	-	-	rs112182588		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19841551_19841552delTT	uc002gwo.2	-						AKAP10_uc002gwp.1_Intron|AKAP10_uc010cqw.1_Intron	NM_007202	NP_009133	O43572	AKA10_HUMAN	A-kinase anchor protein 10 precursor						blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					TGAAAACCTAtttttttttttt	0.045													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20978234	20978237	+	IGR	DEL	CCTC	-	-	rs75278704		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20978234_20978237delCCTC								USP22 (31161 upstream) : DHRS7B (52021 downstream)																							ttccttctttcctccctccctccc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21218954	21218954	+	IGR	DEL	C	-	-	rs5819751		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21218954delC								MAP2K3 (405 upstream) : KCNJ12 (60745 downstream)																							cagatgggaacaacagaccca	0.030													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21221283	21221291	+	IGR	DEL	CCACCCCTG	-	-	rs11278363		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21221283_21221291delCCACCCCTG								MAP2K3 (2734 upstream) : KCNJ12 (58408 downstream)																							CCCCGGGCGCCCACCCCTGCCTCCCCTGT	0.679													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21233367	21233368	+	IGR	INS	-	C	C	rs149851313		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21233367_21233368insC								MAP2K3 (14818 upstream) : KCNJ12 (46331 downstream)																							GTGTAGCAAGACCTCCCAGTCT	0.495													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21552489	21552490	+	IGR	INS	-	GAGGGG	GAGGGG	rs141238951		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21552489_21552490insGAGGGG								C17orf51 (74758 upstream) : FAM27L (272880 downstream)																							CAATGCTACTAGAGGGGAACAA	0.307													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21553811	21553813	+	IGR	DEL	TAA	-	-	rs75768971		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21553811_21553813delTAA								C17orf51 (76080 upstream) : FAM27L (271557 downstream)																							atggtggtggtaatgaagatgat	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21965881	21965881	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21965881delT								FLJ36000 (52811 upstream) : None (None downstream)																							ttttcaaatgtttttgaatcg	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25278196	25278197	+	IGR	INS	-	AT	AT	rs62050990		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25278196_25278197insAT								None (None upstream) : WSB1 (342909 downstream)																							CCCTCATACACAGAGATCATTT	0.302													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25279303	25279304	+	IGR	INS	-	GAAG	GAAG	rs138846612	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25279303_25279304insGAAG								None (None upstream) : WSB1 (341802 downstream)																							aggaaatgagagaaggaaggga	0.000													6	3	---	---	---	---	
NF1	4763	broad.mit.edu	37	17	29598924	29598925	+	Intron	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29598924_29598925delCA	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(3)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCACATACACCACACACACACA	0.431			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			4	2	---	---	---	---	
RHOT1	55288	broad.mit.edu	37	17	30477375	30477376	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30477375_30477376insT	uc002hgz.2	+						RHOT1_uc002hgw.2_Intron|RHOT1_uc002hgy.2_Intron|RHOT1_uc002hha.2_Intron|RHOT1_uc010csv.2_Intron|RHOT1_uc002hgx.2_Intron|RHOT1_uc010wby.1_Intron|RHOT1_uc002hhb.2_Intron|RHOT1_uc002hgv.2_Intron	NM_018307	NP_060777	Q8IXI2	MIRO1_HUMAN	ras homolog gene family, member T1 isoform 3						apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)				TGCTAATGAACTTTTTTTTTTT	0.312													4	3	---	---	---	---	
ITGA2B	3674	broad.mit.edu	37	17	42463236	42463236	+	Frame_Shift_Del	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42463236delG	uc002igt.1	-	3	396	c.364delC	c.(364-366)CAAfs	p.Q122fs		NM_000419	NP_000410	P08514	ITA2B_HUMAN	integrin alpha 2b preproprotein	122	Extracellular (Potential).|FG-GAP 2.				axon guidance|integrin-mediated signaling pathway|platelet activation|platelet degranulation	integrin complex|platelet alpha granule membrane	identical protein binding|receptor activity			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Tirofiban(DB00775)	CCCAGTCCTTGGCGGGCCTTG	0.642													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	42679703	42679703	+	IGR	DEL	G	-	-	rs11349584		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42679703delG								FZD2 (42796 upstream) : C17orf104 (54279 downstream)																							GACGGGTGGCGGGGGTCACAG	0.617													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43672370	43672387	+	IGR	DEL	GAGGAAGGAGAGGAAGAG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43672370_43672387delGAGGAAGGAGAGGAAGAG								LRRC37A4 (76854 upstream) : LOC644172 (5104 downstream)																							agaagaggaagaggaaggagaggaagaggaggaagagg	0.000													3	3	---	---	---	---	
CRHR1	1394	broad.mit.edu	37	17	43746188	43746188	+	Intron	DEL	C	-	-	rs66750197		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43746188delC	uc002ijp.2	+						CRHR1_uc010wjx.1_Intron			P34998	CRFR1_HUMAN	SubName: Full=cDNA FLJ60308, highly similar to Corticotropin-releasing factor receptor 1;						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		atgactgcctccttactttgc	0.209													2	4	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44229709	44229712	+	Intron	DEL	ACAA	-	-	rs142694544		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44229709_44229712delACAA	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				CGTATTTCAGACAAACATTCACTT	0.319													4	3	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44259313	44259314	+	Intron	INS	-	A	A	rs141371634	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44259313_44259314insA	uc002ikc.2	-						KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				aaaaacttcttagactcttcca	0.134													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46773947	46773947	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46773947delC								MIR196A1 (64026 upstream) : PRAC (25145 downstream)																							cagtgactcacacctgtaata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47643580	47643580	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47643580delA								NGFR (51215 upstream) : NXPH3 (9718 downstream)																							gccaagaaggaaagggggggt	0.000													4	2	---	---	---	---	
LRRC37A3	374819	broad.mit.edu	37	17	62864850	62864851	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62864850_62864851insT	uc002jey.2	-						LRRC37A3_uc010wqg.1_Intron|LRRC37A3_uc010wqf.1_Intron|LRRC37A3_uc010dek.1_Intron	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3							integral to membrane					0						AGAACTTACACTTTTTTTTTTT	0.292													4	2	---	---	---	---	
LRRC37A3	374819	broad.mit.edu	37	17	62917127	62917128	+	5'Flank	INS	-	AGGG	AGGG	rs140057763		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62917127_62917128insAGGG	uc002jey.2	-						LRRC37A3_uc010wqg.1_5'Flank	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3							integral to membrane					0						tgccaggaaccaggaagatcaa	0.163													2	5	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64645216	64645216	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64645216delA	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	agtccatctcaaaaaaaaaaa	0.119													4	3	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64678824	64678825	+	Intron	INS	-	TTG	TTG	rs146747870	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64678824_64678825insTTG	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	GTAGTGTGATTttgttgttgtt	0.312													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69912674	69912676	+	IGR	DEL	TTC	-	-	rs35202043		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69912674_69912676delTTC								None (None upstream) : SOX9 (204485 downstream)																							atcaatgtgtttcttaagtgtat	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	72150529	72150529	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72150529delA								C17orf54 (325853 upstream) : RPL38 (49266 downstream)																							CTTTCCATACAAAGATCGGGC	0.522													4	2	---	---	---	---	
EXOC7	23265	broad.mit.edu	37	17	74090829	74090829	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74090829delC	uc002jqs.2	-						EXOC7_uc010dgv.1_Intron|EXOC7_uc002jqq.2_Intron|EXOC7_uc010wsw.1_Intron|EXOC7_uc010wsx.1_Intron|EXOC7_uc002jqr.2_Intron|EXOC7_uc010wsv.1_Intron|EXOC7_uc002jqu.2_Intron	NM_001145297	NP_001138769	Q9UPT5	EXOC7_HUMAN	exocyst complex component 7 isoform 4						exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)			CTTTCAAAGtctttttttttt	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	74999051	74999052	+	IGR	DEL	TG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74999051_74999052delTG								MGAT5B (52581 upstream) : C17orf86 (85673 downstream)																							tctctctctttgtgtgtgtgtg	0.000													2	4	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78607919	78607920	+	Intron	DEL	TG	-	-	rs67908395		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78607919_78607920delTG	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						GTGTGCATACtgtgtgtgtgtg	0.084													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3846044	3846047	+	Intron	DEL	GTGT	-	-	rs144382339		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3846044_3846047delGTGT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_5'Flank|DLGAP1_uc010dkn.2_5'Flank|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_5'Flank|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TGAAAgtgtggtgtgtgtgtgtgt	0.279													4	2	---	---	---	---	
GNAL	2774	broad.mit.edu	37	18	11810623	11810624	+	Intron	DEL	AG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11810623_11810624delAG	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron	NM_001142339	NP_001135811	P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1						GTGGGTCACTAGCATCCCCTTA	0.569													4	2	---	---	---	---	
CEP192	55125	broad.mit.edu	37	18	13003450	13003451	+	Intron	INS	-	A	A	rs72572593		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13003450_13003451insA	uc010xac.1	+						CEP192_uc002krs.1_Intron	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa											ovary(4)|pancreas(1)	5						tctgtctcaagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15299281	15299282	+	IGR	DEL	CA	-	-	rs113248324		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15299281_15299282delCA								ANKRD30B (446544 upstream) : LOC644669 (14273 downstream)																							gcttgagccccagagtttgagg	0.015													4	3	---	---	---	---	
ASXL3	80816	broad.mit.edu	37	18	31233097	31233097	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31233097delT	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						TTGCTGGAGGTTTTACAGTAA	0.463													4	2	---	---	---	---	
NOL4	8715	broad.mit.edu	37	18	31651402	31651403	+	Intron	INS	-	AC	AC	rs150543573	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31651402_31651403insAC	uc010dmi.2	-						NOL4_uc002kxr.3_Intron|NOL4_uc010xbt.1_Intron|NOL4_uc010dmh.2_Intron|NOL4_uc010xbu.1_Intron|NOL4_uc002kxt.3_Intron|NOL4_uc010xbw.1_Intron	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3						cagacagacagacacacacaca	0.050													4	2	---	---	---	---	
DTNA	1837	broad.mit.edu	37	18	32234818	32234819	+	Intron	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32234818_32234819delGT	uc010dmj.2	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron	NM_032975	NP_116757	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 2						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						agcctcccaagtagctgggatt	0.000													4	2	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34069486	34069486	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34069486delT	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				aatttaaaaattagccaggca	0.000													4	2	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	36811114	36811115	+	Intron	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36811114_36811115delCA	uc002lak.1	-						LOC647946_uc010xcj.1_Intron|LOC647946_uc002lal.1_Intron					Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						ACCTATTCTCcacacacacaca	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37906081	37906083	+	IGR	DEL	AGA	-	-	rs35468818		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37906081_37906083delAGA								LOC647946 (525799 upstream) : None (None downstream)																							gagaaggaggagaagaagaagaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	39201280	39201281	+	IGR	DEL	GA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39201280_39201281delGA								KC6 (100719 upstream) : PIK3C3 (333918 downstream)																							agagaaagaggagagagagaga	0.337													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41395978	41395979	+	IGR	INS	-	AAC	AAC	rs148150840	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41395978_41395979insAAC								SYT4 (538363 upstream) : SETBP1 (864159 downstream)																							tcaaacagacaaacaacaacaa	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	44910158	44910158	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44910158delG	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																		actgaggattgggaaggtgga	0.204													4	2	---	---	---	---	
ZBTB7C	201501	broad.mit.edu	37	18	45633673	45633684	+	Intron	DEL	GAGGAGGGATGG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45633673_45633684delGAGGAGGGATGG	uc010dnv.2	-						ZBTB7C_uc002ldb.2_Intron|ZBTB7C_uc010dnu.2_Intron|ZBTB7C_uc010dnw.2_Intron|ZBTB7C_uc010dnx.1_Intron|ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449	A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1						gaggaggagtgaggagggatgggaggagggtg	0.000													4	3	---	---	---	---	
KIAA0427	9811	broad.mit.edu	37	18	46342288	46342288	+	Intron	DEL	C	-	-	rs74174723		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46342288delC	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron|KIAA0427_uc002lde.3_Intron	NM_014772	NP_055587	O43310	CTIF_HUMAN	hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0						cttggagtctcccctttccat	0.214													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	47823549	47823556	+	IGR	DEL	AGAAAGAA	-	-	rs146241751		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47823549_47823556delAGAAAGAA								CXXC1 (8857 upstream) : SKA1 (77836 downstream)																							aagaaaagagagaaagaaagaaagaaag	0.000													3	3	---	---	---	---	
DCC	1630	broad.mit.edu	37	18	50720847	50720847	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50720847delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		ttgttgttTGtttttttttta	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53661017	53661018	+	IGR	DEL	GA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53661017_53661018delGA								TCF4 (357832 upstream) : TXNL1 (609037 downstream)																							AGTCTAGGCTGAGATAATTTGC	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53762225	53762227	+	Intron	DEL	GGA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53762225_53762227delGGA	uc002lgf.1	-						uc010dpj.1_Intron					Homo sapiens cDNA FLJ32774 fis, clone TESTI2002002.																		acatttaaagggaggaggaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	66880974	66880975	+	IGR	INS	-	TG	TG	rs146753365	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66880974_66880975insTG								CCDC102B (158548 upstream) : DOK6 (187316 downstream)																							atgtgtgtgcctgtgtgtgtgt	0.267													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	70751005	70751005	+	IGR	DEL	T	-	-	rs67538251		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70751005delT								NETO1 (216195 upstream) : FBXO15 (989583 downstream)																							GCTTTTCAACttttttttttt	0.139													4	2	---	---	---	---	
TSHZ1	10194	broad.mit.edu	37	18	72986690	72986691	+	Intron	DEL	TT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72986690_72986691delTT	uc002lly.2	+							NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GCCAAAGTAATTTTTTTTAAAA	0.267													4	2	---	---	---	---	
ZNF516	9658	broad.mit.edu	37	18	74116232	74116232	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74116232delG	uc010dqx.1	-						ZNF516_uc002lme.2_Intron	NM_014643	NP_055458	Q92618	ZN516_HUMAN	zinc finger protein 516						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		ACACACGCCTGGGGGAGACGA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75629416	75629416	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75629416delT								GALR1 (647322 upstream) : None (None downstream)																							tctgaagtcctacatgttgag	0.000													4	2	---	---	---	---	
NFIC	4782	broad.mit.edu	37	19	3446865	3446865	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3446865delA	uc010xhi.1	+						NFIC_uc002lxo.2_Intron|NFIC_uc010xhh.1_Intron|NFIC_uc002lxp.2_Intron|NFIC_uc010xhj.1_Intron	NM_205843	NP_995315	P08651	NFIC_HUMAN	nuclear factor I/C isoform 2						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		ccccatctctaaaaaaaaaat	0.000													4	2	---	---	---	---	
ATCAY	85300	broad.mit.edu	37	19	3898174	3898175	+	Intron	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3898174_3898175insT	uc002lyy.3	+						ATCAY_uc010xhz.1_Intron	NM_033064	NP_149053	Q86WG3	ATCAY_HUMAN	caytaxin						transport		protein binding			breast(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		ctaaacatctcttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	5514868	5514878	+	IGR	DEL	AAAAAAAAAAA	-	-	rs10420941		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5514868_5514878delAAAAAAAAAAA								ZNRF4 (58002 upstream) : PLAC2 (43302 downstream)																							actccatctcaaaaaaaaaaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ZNF562	54811	broad.mit.edu	37	19	9764669	9764669	+	Intron	DEL	T	-	-	rs145922849		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9764669delT	uc010xks.1	-						ZNF562_uc002mly.2_Intron|ZNF562_uc002mlx.2_Intron|ZNF562_uc010xkt.1_Intron|ZNF562_uc010xku.1_Intron|ZNF562_uc010xkv.1_Intron|ZNF562_uc010xkw.1_Intron	NM_001130032	NP_001123504	Q6V9R5	ZN562_HUMAN	zinc finger protein 562 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TAATGTTTAAttttttttttt	0.114													4	3	---	---	---	---	
CACNA1A	773	broad.mit.edu	37	19	13552267	13552267	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13552267delG	uc010dze.2	-						CACNA1A_uc002mwy.3_Intron	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	gatcacctgaggggagaagtt	0.045													4	2	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17714737	17714738	+	3'UTR	INS	-	A	A	rs142003261	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17714737_17714738insA	uc002nhd.2	-	43						NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						tctcccgcctcagtctcctgag	0.000													3	3	---	---	---	---	
ZNF626	199777	broad.mit.edu	37	19	20830982	20830982	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20830982delA	uc002npb.1	-						ZNF626_uc002npc.1_Intron|ZNF626_uc002npd.1_Intron	NM_001076675	NP_001070143	Q68DY1	ZN626_HUMAN	zinc finger protein 626 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						actccgtgtcaaaaaaaaaaa	0.104													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	24362994	24362995	+	IGR	INS	-	AG	AG	rs148884296	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24362994_24362995insAG								LOC100101266 (16745 upstream) : None (None downstream)																							caggaggaaaaagaaggaaagg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27843421	27843421	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27843421delT								None (None upstream) : LOC148189 (437981 downstream)																							taatagtttctttttcaccac	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27858357	27858357	+	IGR	DEL	C	-	-	rs143331608		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27858357delC								None (None upstream) : LOC148189 (423045 downstream)																							tcctttttcaccataggactc	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27904220	27904220	+	IGR	DEL	A	-	-	rs151018171		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27904220delA								None (None upstream) : LOC148189 (377182 downstream)																							tctagtttttatgtgaagata	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31758554	31758554	+	IGR	DEL	T	-	-	rs71335124		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31758554delT								DKFZp566F0947 (117245 upstream) : TSHZ3 (7299 downstream)																							AATAAGCCCATTTTTTTTTTC	0.512													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32624083	32624083	+	IGR	DEL	A	-	-	rs71335170		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32624083delA								TSHZ3 (783893 upstream) : ZNF507 (212431 downstream)																							aacatttctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
CHST8	64377	broad.mit.edu	37	19	34133719	34133719	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34133719delA	uc002nus.3	+						CHST8_uc002nut.3_Intron	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)						carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)					TTATATACGTAAACTCGTAAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36668045	36668046	+	IGR	INS	-	G	G	rs147682483	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36668045_36668046insG								COX7A1 (24274 upstream) : ZNF565 (5142 downstream)																							tgcaaaaaaaaagccagtaaag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	39550383	39550383	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39550383delT								FBXO27 (27185 upstream) : PAPL (24562 downstream)																							aggtgttttgttttttttttt	0.000													4	2	---	---	---	---	
PRX	57716	broad.mit.edu	37	19	40905483	40905483	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40905483delA	uc002onr.2	-						PRX_uc002onq.2_Intron|PRX_uc002ons.2_Intron	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2						axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			tcatctgcttaaaccactcag	0.000													4	2	---	---	---	---	
SNAR-C3	100170226	broad.mit.edu	37	19	48451031	48451031	+	5'Flank	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48451031delC	uc010xzb.1	+							NR_024221				Homo sapiens small ILF3/NF90-associated RNA C3 (SNAR-C3), non-coding RNA.												0						aaaaaaaaaacaaaatcagag	0.000													3	3	---	---	---	---	
CD33	945	broad.mit.edu	37	19	51746477	51746477	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51746477delT	uc010eou.1	+									P20138	CD33_HUMAN	Homo sapiens mRNA for FLJ00391 protein.						cell adhesion|cell-cell signaling|negative regulation of cell proliferation	external side of plasma membrane|integral to plasma membrane	receptor activity|sugar binding				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	GTACAAGGTCTTCTCCAGCAT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	55960323	55960324	+	IGR	DEL	CA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55960323_55960324delCA								SHISA7 (6093 upstream) : ISOC2 (4024 downstream)																							ccacacagaccacacacacaca	0.000													4	2	---	---	---	---	
ZSCAN5A	79149	broad.mit.edu	37	19	56813684	56813685	+	Intron	INS	-	C	C			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56813684_56813685insC	uc002qmr.2	-						ZSCAN5A_uc010ygi.1_Intron	NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3						cttttctccctccctccctccc	0.158													4	3	---	---	---	---	
ZNF542	147947	broad.mit.edu	37	19	56889273	56889274	+	3'UTR	INS	-	AGTCCTTT	AGTCCTTT	rs143807509	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56889273_56889274insAGTCCTTT	uc002qmu.3	+	7					ZNF542_uc010ygj.1_3'UTR|ZNF542_uc010ygk.1_3'UTR|ZNF542_uc002qmv.3_3'UTR|ZNF542_uc010etk.2_3'UTR|ZNF542_uc010etj.2_RNA	NR_003127				SubName: Full=cDNA FLJ58906;												0						TCAATGCGGGAAGTCCTTTAGC	0.371													5	3	---	---	---	---	
RBCK1	10616	broad.mit.edu	37	20	401109	401110	+	Intron	INS	-	G	G	rs142244126	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:401109_401110insG	uc002wdp.3	+						RBCK1_uc010zpm.1_Intron|RBCK1_uc002wdq.3_Intron|RBCK1_uc010fzy.2_Intron|RBCK1_uc002wdr.3_Intron	NM_031229	NP_112506	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing						interspecies interaction between organisms|negative regulation of NF-kappaB transcription factor activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|proteasomal ubiquitin-dependent protein catabolic process|protein linear polyubiquitination|T cell receptor signaling pathway	LUBAC complex	protein binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				CCTGACGTTGAGTGGCTCCACC	0.668													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2662691	2662692	+	IGR	INS	-	A	A	rs143446248		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2662691_2662692insA								IDH3B (17848 upstream) : EBF4 (10832 downstream)																							ctctgcatttgaaaaaaaaaaa	0.015													4	2	---	---	---	---	
CDS2	8760	broad.mit.edu	37	20	5165755	5165756	+	Intron	INS	-	AA	AA			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5165755_5165756insAA	uc002wls.2	+						CDS2_uc002wlr.1_Intron|CDS2_uc010zqt.1_Intron|CDS2_uc002wlu.2_Intron|CDS2_uc010zqu.1_Intron|CDS2_uc002wlv.2_Intron|CDS2_uc010zqv.1_Intron	NM_003818	NP_003809	O95674	CDS2_HUMAN	phosphatidate cytidylyltransferase 2						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphatidate cytidylyltransferase activity				0						GACAACTGATTAAAAAAAAAAA	0.233													4	2	---	---	---	---	
C20orf94	128710	broad.mit.edu	37	20	10466128	10466128	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10466128delG	uc010zre.1	+							NM_001009608	NP_001009608	Q5VYV7	CT094_HUMAN	hypothetical protein LOC128710								protein binding				0						agccgggcatggtagtgcaca	0.000													4	2	---	---	---	---	
C20orf94	128710	broad.mit.edu	37	20	10538990	10538993	+	Intron	DEL	AAAA	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10538990_10538993delAAAA	uc010zre.1	+							NM_001009608	NP_001009608	Q5VYV7	CT094_HUMAN	hypothetical protein LOC128710								protein binding				0						accctgtctcaaaaaaaaaaaaaa	0.162													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	14501604	14501605	+	Intron	DEL	CA	-	-	rs61020839	byFrequency	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14501604_14501605delCA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002wox.2_5'Flank	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)				tgcgtgcgcgcacacacacaca	0.252													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16963235	16963246	+	IGR	DEL	CCTTCCTTCCTC	-	-	rs147489462	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16963235_16963246delCCTTCCTTCCTC								OTOR (230427 upstream) : PCSK2 (243506 downstream)																							ccccccttttccttccttcctcccttccttcc	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	18183076	18183077	+	IGR	INS	-	TGTG	TGTG	rs113929290		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18183076_18183077insTGTG								CSRP2BP (14061 upstream) : ZNF133 (86044 downstream)																							agagaattatttgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25937358	25937358	+	Intron	DEL	C	-	-	rs111987729		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25937358delC	uc002wvf.2	+											Homo sapiens cDNA clone IMAGE:5298175.																		ttggctgagacagaaagaaaa	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26074255	26074256	+	IGR	INS	-	TT	TT	rs79274024	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26074255_26074256insTT								FAM182A (6703 upstream) : C20orf191 (9797 downstream)																							TGCACATGTGGTCCCCCAAAGA	0.243													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26208693	26208694	+	IGR	INS	-	T	T	rs144075905		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26208693_26208694insT								MIR663 (19779 upstream) : None (None downstream)																							TTCTTATACCATTTTTATAAGT	0.342													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29451481	29451481	+	IGR	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29451481delA								None (None upstream) : FRG1B (160398 downstream)																							AAATTCCCCCAAAAGGTAAAC	0.219													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29489529	29489530	+	IGR	DEL	CA	-	-	rs80104086	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29489529_29489530delCA								None (None upstream) : FRG1B (122349 downstream)																							tatgtgtgtgcatgtctgtgtg	0.015													4	2	---	---	---	---	
C20orf117	140710	broad.mit.edu	37	20	35445670	35445670	+	Intron	DEL	A	-	-	rs72284834		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35445670delA	uc002xgd.1	-						C20orf117_uc002xge.1_5'Flank	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)				actccgtctcaaaaaaaaaaa	0.199													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	40770343	40770344	+	Intron	INS	-	CTG	CTG	rs144104706	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40770343_40770344insCTG	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)				CATCTCCCTGCCTGCTCCCTCT	0.530													4	4	---	---	---	---	
MYBL2	4605	broad.mit.edu	37	20	42308492	42308493	+	Intron	DEL	GG	-	-	rs67342750		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42308492_42308493delGG	uc002xlb.1	+						MYBL2_uc010zwj.1_Intron|MYBL2_uc002xla.1_Intron	NM_002466	NP_002457	P10244	MYBB_HUMAN	MYB-related protein B							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(3)|kidney(2)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			ttgaggatgcggggtgggctgt	0.000													3	3	---	---	---	---	
ARFGEF2	10564	broad.mit.edu	37	20	47565392	47565392	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47565392delG	uc002xtx.3	+							NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine						exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			GGAACAAGGTGGGGACATCTA	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	47977586	47977595	+	IGR	DEL	TGTGTGTGTG	-	-	rs137914429		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47977586_47977595delTGTGTGTGTG								C20orf199 (71793 upstream) : KCNB1 (10910 downstream)																							gttatatgtatgtgtgtgtgtgtgtgtgtg	0.114													3	3	---	---	---	---	
SALL4	57167	broad.mit.edu	37	20	50414069	50414069	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50414069delA	uc002xwh.3	-						SALL4_uc010gii.2_Intron|SALL4_uc002xwi.3_Intron	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						CTTGTGCAGTAAAAAGTGCTT	0.448													4	2	---	---	---	---	
STX16	8675	broad.mit.edu	37	20	57242132	57242132	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57242132delT	uc002xzi.2	+						STX16_uc010zzq.1_Intron|STX16_uc002xzk.2_Intron|STX16_uc002xzm.2_Intron|STX16_uc002xzj.2_Intron|STX16_uc002xzl.2_Intron	NM_001001433	NP_001001433	O14662	STX16_HUMAN	syntaxin 16 isoform a						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|microsome|SNARE complex	SNAP receptor activity			ovary(1)	1	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			TACTGCCTAGTTTTTTTTTTC	0.333													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60155696	60155696	+	Intron	DEL	A	-	-	rs5842357		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60155696delA	uc002ybn.1	+						CDH4_uc002ybo.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			TTGACGCTCTAGGGGGGGAAA	0.547													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61189085	61189086	+	IGR	DEL	TG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61189085_61189086delTG								C20orf166 (21115 upstream) : SLCO4A1 (84711 downstream)																							tgttcacggttgtgtgtgtgtg	0.163													4	2	---	---	---	---	
DNAJC5	80331	broad.mit.edu	37	20	62534338	62534338	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62534338delT	uc002yhf.2	+						DNAJC5_uc002yhg.1_Intron	NM_025219	NP_079495	Q9H3Z4	DNJC5_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5						neurotransmitter secretion|protein folding	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|melanosome|plasma membrane	heat shock protein binding|unfolded protein binding			pancreas(1)	1	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					ccACATCCTGttttttttaca	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9655453	9655456	+	IGR	DEL	ATAG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9655453_9655456delATAG								None (None upstream) : None (None downstream)																							ttaaatagttatagataaagacaa	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9829834	9829835	+	IGR	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9829834_9829835insA								None (None upstream) : None (None downstream)																							ccacatccaggatcacctacaa	0.030													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10732129	10732129	+	IGR	DEL	C	-	-	rs142467132		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10732129delC								None (None upstream) : TPTE (174614 downstream)																							tcttctgtctcattttttatg	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10751020	10751021	+	IGR	INS	-	T	T	rs148965273		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10751020_10751021insT								None (None upstream) : TPTE (155722 downstream)																							aagcttgcttggatgtgtgcat	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10753373	10753373	+	IGR	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10753373delC								None (None upstream) : TPTE (153370 downstream)																							tgtcttcacactaaaaactag	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10778109	10778118	+	IGR	DEL	GGAATGGAAG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10778109_10778118delGGAATGGAAG								None (None upstream) : TPTE (128625 downstream)																							tgagtggagtggaatggaagggaatggaag	0.000													4	2	---	---	---	---	
TPTE	7179	broad.mit.edu	37	21	10993858	10993861	+	5'Flank	DEL	TTTG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10993858_10993861delTTTG	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_5'Flank|TPTE_uc002yir.1_5'Flank|TPTE_uc010gkv.1_5'Flank	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			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)		TCCTTGGGTTtttgtttgtttgtt	0.225													5	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11050605	11050606	+	Intron	INS	-	A	A	rs150695624		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11050605_11050606insA	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)		CCTTTGATAATATATATAAATA	0.213													8	4	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11059001	11059003	+	Intron	DEL	AAG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11059001_11059003delAAG	uc002yit.1	-						BAGE_uc002yiw.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)		GTGAACACATAAGAAGTCAGAAG	0.384													3	3	---	---	---	---	
CHODL	140578	broad.mit.edu	37	21	19515928	19515928	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19515928delT	uc002ykt.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002yku.2_Intron			Q9H9P2	CHODL_HUMAN	RecName: Full=Chondrolectin; AltName: Full=Transmembrane protein MT75; Flags: Precursor;						muscle organ development	integral to membrane|perinuclear region of cytoplasm	sugar binding			upper_aerodigestive_tract(1)	1		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)		tgagtctcacttttctcatct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26514445	26514445	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26514445delT								None (None upstream) : NCRNA00158 (243689 downstream)																							CCAGTACACCTTTTACTTTGT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29514557	29514557	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29514557delT	uc002yml.2	-											Homo sapiens cDNA clone IMAGE:5541115, partial cds.																		gtgttaccacttttttttttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	32462049	32462049	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32462049delT								KRTAP19-8 (51254 upstream) : TIAM1 (28687 downstream)																							ttcaatctactttgtttctat	0.000													4	2	---	---	---	---	
HLCS	3141	broad.mit.edu	37	21	38127382	38127382	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38127382delT	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)	caagcacacatttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	41111179	41111180	+	IGR	INS	-	T	T			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41111179_41111180insT								B3GALT5 (76364 upstream) : IGSF5 (6154 downstream)																							TTTTCTTCTGCTTTTTTTTTTT	0.035													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41910895	41910895	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41910895delA	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)				AAATGAAGAGAAAAACGTGTC	0.433													4	2	---	---	---	---	
PDXK	8566	broad.mit.edu	37	21	45170664	45170665	+	Intron	INS	-	GT	GT	rs142693057	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45170664_45170665insGT	uc002zdm.3	+						PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Intron|PDXK_uc002zdq.3_Intron	NM_003681	NP_003672	O00764	PDXK_HUMAN	pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	attgtgtgtgggtgtgtgtgtg	0.035													4	5	---	---	---	---	
TRAPPC10	7109	broad.mit.edu	37	21	45467413	45467414	+	Intron	INS	-	TG	TG	rs60653631		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45467413_45467414insTG	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc002zdz.2_Intron	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2						ctgggggagtatgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16863379	16863380	+	IGR	DEL	CT	-	-	rs146053927		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16863379_16863380delCT								OR11H1 (413575 upstream) : CCT8L2 (208268 downstream)																							tttaaaacaactctcttaatta	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16954499	16954500	+	IGR	INS	-	T	T	rs141581068		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16954499_16954500insT								OR11H1 (504695 upstream) : CCT8L2 (117148 downstream)																							gttttgttttgttttttgagac	0.109													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17239409	17239410	+	IGR	INS	-	T	T	rs142595120	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17239409_17239410insT								psiTPTE22 (59888 upstream) : XKR3 (24903 downstream)																							gccaccgcaccggccagattgc	0.000													6	3	---	---	---	---	
CECR5	27440	broad.mit.edu	37	22	17646540	17646540	+	5'Flank	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17646540delT	uc002zmh.2	-							NM_017829	NP_060299	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5								hydrolase activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				gcccagcgaattttttttttc	0.000													4	2	---	---	---	---	
TUBA8	51807	broad.mit.edu	37	22	18593887	18593887	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18593887delA	uc002znv.1	+						TUBA8_uc002znr.2_Intron|TUBA8_uc002znu.1_Intron	NM_018943	NP_061816	Q9NY65	TBA8_HUMAN	tubulin, alpha 8						microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0						CGTGCAGACGAGGGGGAGGGA	0.637													6	3	---	---	---	---	
PPM1F	9647	broad.mit.edu	37	22	22283231	22283232	+	Intron	INS	-	C	C	rs146075500	by1000genomes	TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22283231_22283232insC	uc002zvp.1	-						PPM1F_uc011aik.1_Intron|PPM1F_uc002zvq.2_Intron	NM_014634	NP_055449	P49593	PPM1F_HUMAN	protein phosphatase 1F						apoptosis|protein dephosphorylation	protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			ovary(2)|large_intestine(1)|breast(1)|kidney(1)	5	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		GCCTCATCCTGCCAGGTCCTTG	0.342													3	3	---	---	---	---	
LOC91316	91316	broad.mit.edu	37	22	24043417	24043418	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24043417_24043418insA	uc002zxk.3	-						LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0						tatgcatgatcaaaatgtccca	0.050													4	2	---	---	---	---	
SGSM1	129049	broad.mit.edu	37	22	25319112	25319112	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25319112delA	uc003abg.2	+						SGSM1_uc003abh.2_Intron|SGSM1_uc010guu.1_Intron|SGSM1_uc003abj.2_Intron|SGSM1_uc003abi.1_Intron	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1							Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5						gtctcaaaagaaaaaaaaaga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25905739	25905739	+	Intron	DEL	C	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25905739delC	uc003abv.2	+											Homo sapiens cDNA clone IMAGE:3542716, partial cds.																		GCTGCTTCTACCATGGGGCCT	0.468													4	2	---	---	---	---	
SRRD	402055	broad.mit.edu	37	22	26883856	26883857	+	Intron	DEL	TC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26883856_26883857delTC	uc010gve.2	+						SRRD_uc003acp.3_Intron	NM_001013694	NP_001013716	Q9UH36	SRR1L_HUMAN	SRR1 domain containing						rhythmic process						0						GCTGGCAGCTTCTCTCTCTCTC	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27298635	27298638	+	IGR	DEL	CTCC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27298635_27298638delCTCC								MIAT (183686 upstream) : MN1 (845628 downstream)																							cctcctttctctccctccctccct	0.000													4	3	---	---	---	---	
INPP5J	27124	broad.mit.edu	37	22	31511662	31511662	+	Intron	DEL	A	-	-	rs71766797		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31511662delA	uc010gwf.2	+						SELM_uc011alj.1_Intron			Q15735	PI5PA_HUMAN	RecName: Full=Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A;          EC=3.1.3.56; AltName: Full=Inositol polyphosphate 5-phosphatase J;							cytoplasm|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|SH3 domain binding			skin(1)	1						actctatctcaaaaaaaaaaa	0.025													3	3	---	---	---	---	
C22orf30	253143	broad.mit.edu	37	22	32084014	32084014	+	Intron	DEL	A	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32084014delA	uc003alp.3	-						C22orf30_uc003alo.1_Intron|C22orf30_uc010gwj.1_Intron	NM_173566	NP_775837	Q5THK1	PR14L_HUMAN	hypothetical protein LOC253143												0						actctgtctcaaaaaaaaaaa	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	34896095	34896104	+	IGR	DEL	TGTGTGTGTA	-	-	rs56382837		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34896095_34896104delTGTGTGTGTA								LARGE (577511 upstream) : ISX (566025 downstream)																							tgtgtgtgtgtgtgtgtgtAtatgtgtata	0.019													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	42515200	42515203	+	Intron	DEL	AGAC	-	-	rs77200919		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42515200_42515203delAGAC	uc003bcc.1	+						uc003bcd.1_Intron					Homo sapiens cDNA FLJ41636 fis, clone FEBRA1000022.																		acagagagatagacagagacagag	0.049													3	3	---	---	---	---	
TTLL1	25809	broad.mit.edu	37	22	43440762	43440763	+	Intron	DEL	AG	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43440762_43440763delAG	uc003bdi.2	-						TTLL1_uc010gzh.2_Intron|TTLL1_uc003bdj.2_Intron|TTLL1_uc003bdh.2_Intron	NM_012263	NP_036395	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1						protein polyglutamylation	cytoplasm|microtubule	ATP binding|tubulin-glutamic acid ligase activity|tubulin-tyrosine ligase activity			skin(1)	1		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		ATGTACACACAGGGGATTCTGA	0.490													1	5	---	---	---	---	
PNPLA5	150379	broad.mit.edu	37	22	44282951	44282952	+	Intron	DEL	AC	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44282951_44282952delAC	uc003beg.2	-						PNPLA5_uc011aqc.1_Intron|PNPLA5_uc003beh.2_Intron	NM_138814	NP_620169	Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5						lipid catabolic process		hydrolase activity				0		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				tgccccatgaacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	44830056	44830056	+	IGR	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44830056delT								KIAA1644 (121325 upstream) : LDOC1L (58394 downstream)																							ttcctccatctccaaagctca	0.000													4	2	---	---	---	---	
CELSR1	9620	broad.mit.edu	37	22	46828093	46828093	+	Intron	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46828093delG	uc003bhw.1	-							NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCAGATGGGAGGGGCGGGCCA	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47850727	47850728	+	IGR	DEL	TG	-	-	rs138083550		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47850727_47850728delTG								TBC1D22A (281005 upstream) : None (None downstream)																							aaaaagagtttgtgtgtgtgtg	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49414334	49414334	+	IGR	DEL	G	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49414334delG								FAM19A5 (266592 upstream) : C22orf34 (393842 downstream)																							GGGCAGCAGAGGGACACACTG	0.582													4	2	---	---	---	---	
SAPS2	9701	broad.mit.edu	37	22	50854764	50854764	+	Intron	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50854764delT	uc003blb.1	+						SAPS2_uc003bky.1_Intron|SAPS2_uc003bkz.1_Intron|SAPS2_uc003blc.2_Intron|SAPS2_uc003bla.1_Intron	NM_014678	NP_055493	O75170	PP6R2_HUMAN	SAPS domain family, member 2							cytoplasm|intracellular membrane-bounded organelle	protein binding				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.222)		tttttttttcttttttttttt	0.209													4	2	---	---	---	---	
CSF2RA	1438	broad.mit.edu	37	X	1399746	1399747	+	Intron	INS	-	CTC	CTC			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1399746_1399747insCTC	uc010nct.2	+						CSF2RA_uc011mhb.1_Intron|CSF2RA_uc004cpq.2_Intron|CSF2RA_uc004cpn.2_Intron|CSF2RA_uc004cpo.2_Intron|CSF2RA_uc010ncu.2_Intron|CSF2RA_uc011mhc.1_Intron|CSF2RA_uc004cpp.2_Intron|CSF2RA_uc010ncv.2_5'Flank|CSF2RA_uc004cpr.2_5'Flank	NM_001161529	NP_001155001	P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor alpha chain							extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	ttcctctccttctcctcctcct	0.005													5	4	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1572039	1572039	+	5'Flank	DEL	T	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1572039delT	uc004cpx.1	-						ASMTL_uc011mhe.1_5'Flank|ASMTL_uc004cpy.1_5'Flank|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGACCACGCCTCCATTGCCCT	0.378													1	5	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2212705	2212706	+	Intron	INS	-	A	A			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2212705_2212706insA	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				gactctgtctcaaaaaaaaaaa	0.074													3	3	---	---	---	---	
CD99	4267	broad.mit.edu	37	X	2650612	2650613	+	Intron	INS	-	TT	TT			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2650612_2650613insTT	uc004cqm.2	+						CD99_uc010nda.2_Intron|CD99_uc004cqn.2_Intron|CD99_uc004cqo.2_Intron	NM_002414	NP_002405	P14209	CD99_HUMAN	CD99 antigen isoform a precursor						cell adhesion	cytoplasm|integral to plasma membrane				skin(1)	1						ccctctctctctcttttcattc	0.030													3	7	---	---	---	---	
ITM2A	9452	broad.mit.edu	37	X	78623641	78623642	+	5'Flank	DEL	GT	-	-			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78623641_78623642delGT	uc004edh.2	-						ITM2A_uc011mqr.1_5'Flank	NM_004867	NP_004858	O43736	ITM2A_HUMAN	integral membrane protein 2A							integral to membrane	protein binding			lung(2)	2						AAAAAAAAACgtgtgtgtgtgt	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	155259821	155259822	+	5'Flank	INS	-	G	G			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155259821_155259822insG	uc011nad.1	-											Homo sapiens partial mRNA for DEAD/H box polypeptide 11 like (DDX11L1 gene).																		ggggttagggtagggttagggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9368329	9368330	+	IGR	INS	-	TG	TG			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9368329_9368330insTG								TSPY1 (20940 upstream) : RBMY3AP (80000 downstream)																							gtctttgtgtttgtgtgtgtgt	0.272													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13273657	13273657	+	IGR	DEL	G	-	-	rs112787450		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13273657delG								None (None upstream) : None (None downstream)																							atacgtaggtgggagccaccT	0.035													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13446350	13446351	+	IGR	INS	-	AT	AT			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13446350_13446351insAT								None (None upstream) : None (None downstream)																							ttgagataatcgtggtttttga	0.000													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13452218	13452222	+	IGR	DEL	CACTC	-	-	rs112859967		TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13452218_13452222delCACTC								None (None upstream) : None (None downstream)																							cactccatttcactccactccactc	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59007961	59007962	+	IGR	INS	-	AAC	AAC			TCGA-46-3767-01A-01D-0983-08	TCGA-46-3767-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59007961_59007962insAAC								None (None upstream) : None (None downstream)																							ctacgtctcaaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
