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
ACTRT2	140625	broad.mit.edu	37	1	2938247	2938247	+	5'UTR	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2938247G>A	uc001ajz.2	+	1						NM_080431	NP_536356	Q8TDY3	ACTT2_HUMAN	actin-related protein M2							cytoplasm|cytoskeleton					0	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		GGAAGGCTGCGGGCATGTTTA	0.577													22	16	---	---	---	---	PASS
SPEN	23013	broad.mit.edu	37	1	16257904	16257904	+	Silent	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16257904A>T	uc001axk.1	+	11	5373	c.5169A>T	c.(5167-5169)TCA>TCT	p.S1723S	SPEN_uc010obp.1_Silent_p.S1682S	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1723					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		AGGAAGGTTCATCAGGTGACC	0.592													62	59	---	---	---	---	PASS
KLHDC7A	127707	broad.mit.edu	37	1	18808281	18808281	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18808281G>A	uc001bax.2	+	1	858	c.806G>A	c.(805-807)CGA>CAA	p.R269Q	KLHDC7A_uc009vpg.2_Missense_Mutation_p.R51Q	NM_152375	NP_689588	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	269						integral to membrane				ovary(2)|upper_aerodigestive_tract(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCCCGCGTCCGAATGGAGGAG	0.592													17	32	---	---	---	---	PASS
GRIK3	2899	broad.mit.edu	37	1	37337887	37337887	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37337887C>G	uc001caz.2	-	4	769	c.634G>C	c.(634-636)GAC>CAC	p.D212H	GRIK3_uc001cba.1_Missense_Mutation_p.D212H	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	212	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)	CGCGAGTCGTCAGAGTCGATG	0.592													5	16	---	---	---	---	PASS
LRRIQ3	127255	broad.mit.edu	37	1	74507460	74507460	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74507460G>T	uc001dfy.3	-	7	1347	c.1155C>A	c.(1153-1155)ATC>ATA	p.I385I	LRRIQ3_uc001dfz.3_RNA	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	385										ovary(2)	2						GAGTAGTATAGATTGGCTGAG	0.363													17	16	---	---	---	---	PASS
USP33	23032	broad.mit.edu	37	1	78207351	78207351	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78207351A>C	uc001dht.2	-	3	472	c.125T>G	c.(124-126)TTG>TGG	p.L42W	USP33_uc001dhu.2_Missense_Mutation_p.L11W|USP33_uc001dhv.2_5'Flank|USP33_uc001dhw.2_Missense_Mutation_p.L42W	NM_015017	NP_055832	Q8TEY7	UBP33_HUMAN	ubiquitin specific protease 33 isoform 1	42					axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3						AACTGAATCCAAATGTGGACA	0.313													10	10	---	---	---	---	PASS
WDR63	126820	broad.mit.edu	37	1	85592285	85592285	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85592285G>T	uc001dkt.2	+	20	2395	c.2204G>T	c.(2203-2205)CGA>CTA	p.R735L	WDR63_uc009wcl.2_Missense_Mutation_p.R696L	NM_145172	NP_660155	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	735	WD 4.									upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		TACATCGGCCGAGAAGATGGA	0.488													4	29	---	---	---	---	PASS
HFM1	164045	broad.mit.edu	37	1	91740343	91740343	+	Silent	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91740343A>G	uc001doa.3	-	33	3712	c.3612T>C	c.(3610-3612)AGT>AGC	p.S1204S	HFM1_uc009wdb.2_RNA|HFM1_uc010osu.1_Silent_p.S883S|HFM1_uc001dob.3_Silent_p.S392S|HFM1_uc010osv.1_Silent_p.S888S	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	1204							ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TAAGGTCCACACTTTGAGATT	0.284													17	9	---	---	---	---	PASS
AMY2B	280	broad.mit.edu	37	1	104116374	104116374	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104116374G>T	uc001duq.2	+	6	1174	c.558G>T	c.(556-558)GAG>GAT	p.E186D	AMY2B_uc010ouo.1_RNA|LOC648740_uc001dur.2_Missense_Mutation_p.E186D|AMY2B_uc001dus.1_5'Flank	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor	186					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		TTGCACTGGAGAAAGATTATG	0.403													83	103	---	---	---	---	PASS
AMY2A	279	broad.mit.edu	37	1	104160235	104160235	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104160235G>A	uc001dut.2	+						AMY2A_uc010ouq.1_Intron	NM_000699	NP_000690	P04746	AMYP_HUMAN	pancreatic amylase alpha 2A precursor						carbohydrate catabolic process|polysaccharide digestion	extracellular space	alpha-amylase activity|calcium ion binding|chloride ion binding			ovary(1)|skin(1)	2		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Bentiromide(DB00522)|Icodextrin(DB00702)|Miglitol(DB00491)|Pancrelipase(DB00085)	GTTCAGGTGGGTATGATTCAT	0.413													31	71	---	---	---	---	PASS
KCND3	3752	broad.mit.edu	37	1	112525141	112525141	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112525141C>A	uc001ebu.1	-	2	688	c.208G>T	c.(208-210)GAG>TAG	p.E70*	KCND3_uc001ebv.1_Nonsense_Mutation_p.E70*	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related	70	Cytoplasmic (Potential).					sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)		AACTCCTTCTCCGTGCTGCCC	0.617													10	17	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144882681	144882681	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144882681T>A	uc001elw.3	-	24	3629	c.3338A>T	c.(3337-3339)CAC>CTC	p.H1113L	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Missense_Mutation_p.H120L	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1113	Potential.				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)		GATGATATTGTGGGCATTCTT	0.478			T	PDGFRB	MPD								51	187	---	---	---	---	PASS
RPTN	126638	broad.mit.edu	37	1	152128280	152128280	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152128280C>T	uc001ezs.1	-	3	1360	c.1295G>A	c.(1294-1296)AGA>AAA	p.R432K		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	432	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0						CTGGCCTTGTCTGTCTGTCTG	0.527													163	714	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	154112355	154112355	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154112355C>A	uc001fdw.2	-	5	712	c.640G>T	c.(640-642)GGA>TGA	p.G214*	NUP210L_uc010peh.1_Nonsense_Mutation_p.G214*	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	214						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			ATCACATCTCCTTGTTTCTCC	0.343													9	556	---	---	---	---	PASS
ATP8B2	57198	broad.mit.edu	37	1	154321553	154321553	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154321553A>T	uc001fex.2	+	28	3631	c.3631A>T	c.(3631-3633)AGT>TGT	p.S1211C		NM_020452	NP_065185	P98198	AT8B2_HUMAN	ATPase, class I, type 8B, member 2 isoform a	1197	Cytoplasmic (Potential).				ATP biosynthetic process	plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(1)|skin(1)	2	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGACAGTGCCAGTAGCCCCAG	0.637													17	20	---	---	---	---	PASS
IQGAP3	128239	broad.mit.edu	37	1	156542282	156542282	+	Intron	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156542282C>G	uc001fpf.2	-						IQGAP3_uc009wsb.1_Intron	NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3						small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCTCCGCACTCACAGGCTGCC	0.667													62	135	---	---	---	---	PASS
OR10R2	343406	broad.mit.edu	37	1	158450386	158450386	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158450386G>C	uc010pik.1	+	1	719	c.719G>C	c.(718-720)TGC>TCC	p.C240S	uc001fso.1_RNA	NM_001004472	NP_001004472	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R,	240	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)					TCTTATCTCTGCATTCTGAGG	0.438													49	109	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158622411	158622411	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158622411C>T	uc001fst.1	-	23	3420	c.3221G>A	c.(3220-3222)CGC>CAC	p.R1074H		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1074					actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					ACGACGTCTGCGTTCTTCTGC	0.438													47	61	---	---	---	---	PASS
PPOX	5498	broad.mit.edu	37	1	161140943	161140943	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161140943C>A	uc001fyj.2	+	13	1701	c.1411C>A	c.(1411-1413)CTG>ATG	p.L471M	PPOX_uc001fyn.2_Missense_Mutation_p.L179M|PPOX_uc001fyg.2_Missense_Mutation_p.L471M|PPOX_uc001fyl.2_Missense_Mutation_p.L437M|PPOX_uc001fym.2_RNA|PPOX_uc001fyk.2_Missense_Mutation_p.L309M|PPOX_uc001fyh.2_Missense_Mutation_p.L309M|PPOX_uc010pkg.1_Missense_Mutation_p.L309M|PPOX_uc009wuc.1_Missense_Mutation_p.L272M|PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron	NM_001122764	NP_001116236	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	471					heme biosynthetic process	intrinsic to mitochondrial inner membrane|mitochondrial intermembrane space	flavin adenine dinucleotide binding|oxygen-dependent protoporphyrinogen oxidase activity			ovary(1)	1	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AGTCAGTGTCCTGGGCACAGA	0.507									Porphyria_Variegata				7	261	---	---	---	---	PASS
FCGR2C	9103	broad.mit.edu	37	1	161559371	161559371	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161559371G>T	uc001gav.2	+	3	252	c.153G>T	c.(151-153)GTG>GTT	p.V51V	FCGR2C_uc009wuj.2_RNA|FCGR2C_uc009wuk.2_RNA	NM_201563	NP_963857			Fc fragment of IgG, low affinity IIc, receptor												0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			CAAAGGCTGTGCTGAAACTCG	0.572													38	57	---	---	---	---	PASS
ALDH9A1	223	broad.mit.edu	37	1	165636578	165636578	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165636578G>T	uc001gdh.1	-	9	1422	c.1317C>A	c.(1315-1317)ACC>ACA	p.T439T	ALDH9A1_uc010pky.1_Silent_p.T345T|ALDH9A1_uc010pkz.1_Silent_p.T429T	NM_000696	NP_000687	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9A1	415					carnitine biosynthetic process|cellular aldehyde metabolic process|hormone metabolic process|neurotransmitter biosynthetic process	cytosol|plasma membrane	3-chloroallyl aldehyde dehydrogenase activity|4-trimethylammoniobutyraldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aminobutyraldehyde dehydrogenase activity				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				NADH(DB00157)	GTCCAAAAGTGGTATCATTGG	0.458													5	89	---	---	---	---	PASS
SELP	6403	broad.mit.edu	37	1	169563946	169563946	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169563946G>A	uc001ggi.3	-	13	2336	c.2271C>T	c.(2269-2271)ACC>ACT	p.T757T	SELP_uc001ggh.2_Silent_p.T592T|SELP_uc009wvr.2_Silent_p.T757T	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor	757	Extracellular (Potential).|Sushi 9.				platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)	AGGTTGGCACGGTAGTTGACC	0.428													23	33	---	---	---	---	PASS
SELE	6401	broad.mit.edu	37	1	169698355	169698355	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169698355C>T	uc001ggm.3	-	7	1219	c.1062G>A	c.(1060-1062)CAG>CAA	p.Q354Q	C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441	P16581	LYAM2_HUMAN	selectin E precursor	354	Extracellular (Potential).|Sushi 3.				actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)|skin(2)	5	all_hematologic(923;0.208)					GCTGTGTCCACTGCCCTTGAG	0.448													22	35	---	---	---	---	PASS
C1orf156	92342	broad.mit.edu	37	1	169762072	169762072	+	Silent	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169762072T>C	uc001ggn.2	-	2	1043	c.765A>G	c.(763-765)CCA>CCG	p.P255P	C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggo.2_5'Flank|uc010plt.1_5'Flank|C1orf112_uc001ggp.2_5'Flank|C1orf112_uc001ggq.2_5'Flank|C1orf112_uc009wvt.2_5'Flank	NM_033418	NP_219486	O95568	MET18_HUMAN	hypothetical protein MGC9084	255						cytoplasm	protein methyltransferase activity				0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GTGTTACTTTTGGTTTCCTGC	0.333													39	69	---	---	---	---	PASS
DARS2	55157	broad.mit.edu	37	1	173806114	173806114	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173806114G>T	uc001gjh.1	+	8	1110	c.700G>T	c.(700-702)GGA>TGA	p.G234*		NM_018122	NP_060592	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	234					tRNA aminoacylation for protein translation	mitochondrial matrix|nucleus	aspartate-tRNA ligase activity|ATP binding|nucleic acid binding			central_nervous_system(2)	2					L-Aspartic Acid(DB00128)	CAGGGAACCTGGAAAGTTTTA	0.393													18	280	---	---	---	---	PASS
RGS18	64407	broad.mit.edu	37	1	192153562	192153562	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192153562G>T	uc001gsg.2	+	5	762	c.586G>T	c.(586-588)GAC>TAC	p.D196Y		NM_130782	NP_570138	Q9NS28	RGS18_HUMAN	regulator of G-protein signalling 18	196	RGS.				negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)	3						TCTGAAATCTGACATCTATTT	0.413													42	24	---	---	---	---	PASS
IL20	50604	broad.mit.edu	37	1	207039697	207039697	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207039697G>A	uc001her.2	+	2	257	c.213G>A	c.(211-213)TTG>TTA	p.L71L	IL20_uc010pry.1_Silent_p.L142L|IL20_uc009xby.2_Silent_p.L71L	NM_018724	NP_061194	Q9NYY1	IL20_HUMAN	interleukin 20 precursor	71					positive regulation of keratinocyte differentiation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of inflammatory response	extracellular space	cytokine activity|interleukin-20 receptor binding				0	Breast(84;0.201)			OV - Ovarian serous cystadenocarcinoma(81;0.00459)		CTGAGTCTTTGCAAGACACAA	0.488													86	44	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216166399	216166399	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216166399G>T	uc001hku.1	-	35	7155	c.6768C>A	c.(6766-6768)TCC>TCA	p.S2256S		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2256	Fibronectin type-III 9.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AGACATTAAAGGAGTCAGGTG	0.468										HNSCC(13;0.011)	OREG0014251	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	191	---	---	---	---	PASS
SPATA17	128153	broad.mit.edu	37	1	217915451	217915451	+	Intron	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217915451C>A	uc001hlh.1	+						SPATA17_uc009xdr.1_Intron|SPATA17_uc001hli.2_Intron	NM_138796	NP_620151	Q96L03	SPT17_HUMAN	spermatogenesis associated 17							cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		GTTGGTTTACCTGTCCCTGAC	0.463													7	154	---	---	---	---	PASS
RAB3GAP2	25782	broad.mit.edu	37	1	220359061	220359061	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220359061C>T	uc010puk.1	-	18	1966	c.1802G>A	c.(1801-1803)AGT>AAT	p.S601N	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_Missense_Mutation_p.S181N	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	601					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)		TAAACGTTCACTTGCCAAAAT	0.328													16	24	---	---	---	---	PASS
KCNK1	3775	broad.mit.edu	37	1	233802474	233802474	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233802474G>T	uc010pxo.1	+	2	657	c.489G>T	c.(487-489)AGG>AGT	p.R163S	KCNK1_uc001hvw.2_RNA|KCNK1_uc001hvx.2_RNA	NM_002245	NP_002236	O00180	KCNK1_HUMAN	potassium channel, subfamily K, member 1	163	Cytoplasmic (Potential).					voltage-gated potassium channel complex	inward rectifier potassium channel activity			central_nervous_system(1)	1		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine(DB00908)	TCACCCGCAGGCCGGTCCTCT	0.592													23	25	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235969140	235969140	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235969140G>T	uc001hxj.2	-	6	3471	c.3296C>A	c.(3295-3297)TCA>TAA	p.S1099*	LYST_uc009xgb.1_RNA|LYST_uc010pxs.1_RNA|LYST_uc001hxl.1_Nonsense_Mutation_p.S1099*	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	1099					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ACTTTGAAGTGAGGTCTCACT	0.423									Chediak-Higashi_syndrome				6	44	---	---	---	---	PASS
RGS7	6000	broad.mit.edu	37	1	240977014	240977014	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240977014G>A	uc001hyv.2	-	13	1190	c.860C>T	c.(859-861)ACG>ATG	p.T287M	RGS7_uc010pyh.1_Missense_Mutation_p.T261M|RGS7_uc010pyj.1_Missense_Mutation_p.T203M|RGS7_uc001hyu.2_Missense_Mutation_p.T287M|RGS7_uc009xgn.1_Missense_Mutation_p.T234M|RGS7_uc001hyw.2_Missense_Mutation_p.T287M|RGS7_uc001hyt.2_Missense_Mutation_p.T119M	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7	287	G protein gamma.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			ATACTGTTCCGTGTAACTTAG	0.428													8	23	---	---	---	---	PASS
KMO	8564	broad.mit.edu	37	1	241753535	241753535	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241753535G>T	uc009xgp.2	+	14	1295	c.1230G>T	c.(1228-1230)GAG>GAT	p.E410D	KMO_uc001hyy.2_Missense_Mutation_p.E397D|KMO_uc009xgo.1_Missense_Mutation_p.E410D	NM_003679	NP_003670	O15229	KMO_HUMAN	kynurenine 3-monooxygenase	410					pyridine nucleotide biosynthetic process|response to salt stress	cytosol|integral to membrane|mitochondrial outer membrane	electron carrier activity|flavin adenine dinucleotide binding|kynurenine 3-monooxygenase activity|NAD(P)H oxidase activity			ovary(2)	2	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			GATACCATGAGGCTGTGCAGC	0.318													17	83	---	---	---	---	PASS
WDR64	128025	broad.mit.edu	37	1	241886728	241886728	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241886728C>A	uc001hze.1	+	9	1361	c.1154C>A	c.(1153-1155)TCC>TAC	p.S385Y	WDR64_uc001hzf.1_Missense_Mutation_p.S105Y			B1ANS9	WDR64_HUMAN	RecName: Full=WD repeat-containing protein 64;	385	WD 4.									skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			GTCAGCCTTTCCTCTGCAAAG	0.383													11	31	---	---	---	---	PASS
SCCPDH	51097	broad.mit.edu	37	1	246890254	246890254	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246890254C>T	uc001ibr.2	+	2	598	c.251C>T	c.(250-252)TCG>TTG	p.S84L		NM_016002	NP_057086	Q8NBX0	SCPDH_HUMAN	saccharopine dehydrogenase (putative)	84						midbody	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity			ovary(1)	1	all_cancers(71;6.8e-05)|all_epithelial(71;7.93e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0545)|Lung NSC(105;0.0618)	all_cancers(173;0.0343)	OV - Ovarian serous cystadenocarcinoma(106;0.00323)	GBM - Glioblastoma multiforme(49;0.0896)		AATCCAGCCTCGCTTGATGAA	0.383													18	48	---	---	---	---	PASS
VN1R5	317705	broad.mit.edu	37	1	247419455	247419455	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247419455C>A	uc010pyu.1	+	1	82	c.82C>A	c.(82-84)CTT>ATT	p.L28I		NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	vomeronasal 1 receptor 5	28	Cytoplasmic (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	OV - Ovarian serous cystadenocarcinoma(106;0.00854)			CACAGATATCCTTTGCTTTAA	0.328													23	74	---	---	---	---	PASS
OR2M5	127059	broad.mit.edu	37	1	248309295	248309295	+	Silent	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248309295T>C	uc010pze.1	+	1	846	c.846T>C	c.(844-846)ACT>ACC	p.T282T		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	282	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CCATCCTCACTCCCATGCTGA	0.502													39	39	---	---	---	---	PASS
OR2M3	127062	broad.mit.edu	37	1	248366447	248366447	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248366447C>A	uc010pzg.1	+	1	78	c.78C>A	c.(76-78)TTC>TTA	p.F26L		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	26	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CCCACACCTTCCTCTTCTTTC	0.507													65	104	---	---	---	---	PASS
FKBP1B	2281	broad.mit.edu	37	2	24276774	24276774	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24276774A>G	uc002rer.2	+	2	176	c.40A>G	c.(40-42)AGG>GGG	p.R14G	FKBP1B_uc002res.2_Missense_Mutation_p.R14G|FKBP1B_uc002ret.2_RNA|FKBP1B_uc002reu.2_RNA	NM_004116	NP_004107	P68106	FKB1B_HUMAN	FK506 binding protein 1B, 12.6 kDa isoform a	14					'de novo' protein folding|negative regulation of heart rate|negative regulation of protein phosphatase type 2B activity|protein maturation by protein folding|protein refolding|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|regulation of ryanodine-sensitive calcium-release channel activity|response to redox state	calcium channel complex|sarcoplasmic reticulum membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCTGCAGGAAGGACATTCCC	0.557													19	89	---	---	---	---	PASS
OTOF	9381	broad.mit.edu	37	2	26717816	26717816	+	Nonsense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26717816G>C	uc002rhk.2	-	9	1018	c.891C>G	c.(889-891)TAC>TAG	p.Y297*		NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	297	Cytoplasmic (Potential).|C2 1.				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)					TGACCTCGTTGTAATAGGGGC	0.572													21	51	---	---	---	---	PASS
GCKR	2646	broad.mit.edu	37	2	27724107	27724107	+	Intron	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27724107T>C	uc002rky.2	+						GCKR_uc010ezd.2_Intron|GCKR_uc010ylu.1_Intron	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein						carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)					GTGAGCCTTCTGGAATGACTG	0.358													13	52	---	---	---	---	PASS
C2orf16	84226	broad.mit.edu	37	2	27800102	27800102	+	Silent	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27800102A>G	uc002rkz.3	+	1	714	c.663A>G	c.(661-663)TTA>TTG	p.L221L		NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	221										large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)					CAAAATTCTTAGGATTAACTC	0.443													11	47	---	---	---	---	PASS
GALNT14	79623	broad.mit.edu	37	2	31133823	31133823	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31133823C>T	uc002rnr.2	-	15	2222	c.1603G>A	c.(1603-1605)GTC>ATC	p.V535I	GALNT14_uc002rnq.2_Missense_Mutation_p.V515I|GALNT14_uc002rns.2_Missense_Mutation_p.V540I|GALNT14_uc010ymr.1_Missense_Mutation_p.V500I	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	535	Lumenal (Potential).|Ricin B-type lectin.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					CATGGGTTGACGACGATTTCC	0.562													17	84	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32774511	32774511	+	Silent	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32774511C>G	uc010ezu.2	+	65	13241	c.13107C>G	c.(13105-13107)CTC>CTG	p.L4369L		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	4369					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					AGTCCTGCCTCATCCCAGCCA	0.418													21	69	---	---	---	---	PASS
THADA	63892	broad.mit.edu	37	2	43520275	43520275	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43520275C>A	uc002rsw.3	-	32	4868	c.4516G>T	c.(4516-4518)GCC>TCC	p.A1506S	THADA_uc010far.2_Missense_Mutation_p.A701S|THADA_uc002rsx.3_Missense_Mutation_p.A1506S|THADA_uc002rsy.3_RNA	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1506							binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				ACCTTGAAGGCCCAAGGGAAT	0.557													20	60	---	---	---	---	PASS
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48873715	48873715	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48873715G>C	uc010yol.1	+	5	2530	c.2483G>C	c.(2482-2484)AGT>ACT	p.S828T	STON1-GTF2A1L_uc002rwp.1_Missense_Mutation_p.S875T|GTF2A1L_uc002rws.1_Missense_Mutation_p.S171T|GTF2A1L_uc010yom.1_Missense_Mutation_p.S137T|GTF2A1L_uc002rwt.2_Missense_Mutation_p.S171T	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	828					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATACAAACTAGTGTTCCACAA	0.433													53	34	---	---	---	---	PASS
GPR75	10936	broad.mit.edu	37	2	54081850	54081850	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54081850G>T	uc002rxo.3	-	2	315	c.44C>A	c.(43-45)TCG>TAG	p.S15*	ASB3_uc002rxi.3_Intron	NM_006794	NP_006785	O95800	GPR75_HUMAN	G protein-coupled receptor 75	15	Extracellular (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|skin(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CACATGGAGCGAGGTGGCATT	0.522													5	149	---	---	---	---	PASS
BCL11A	53335	broad.mit.edu	37	2	60687618	60687618	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60687618C>A	uc002sae.1	-	4	2657	c.2429G>T	c.(2428-2430)AGC>ATC	p.S810I	BCL11A_uc002sab.2_Intron|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Intron|BCL11A_uc010ypj.1_Intron|BCL11A_uc002sad.1_Missense_Mutation_p.S658I|BCL11A_uc002saf.1_Missense_Mutation_p.S776I	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1	810	C2H2-type 6.				negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			ACTGTACACGCTAAAAGGCAT	0.428			T	IGH@	B-CLL								221	58	---	---	---	---	PASS
KIAA1841	84542	broad.mit.edu	37	2	61298890	61298890	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61298890G>T	uc002saw.3	+	4	603	c.300G>T	c.(298-300)CAG>CAT	p.Q100H	KIAA1841_uc002sax.3_Translation_Start_Site|KIAA1841_uc002say.2_Missense_Mutation_p.Q100H|KIAA1841_uc002sav.3_Missense_Mutation_p.Q100H	NM_001129993	NP_001123465	Q6NSI8	K1841_HUMAN	KIAA1841 protein isoform a	100											0			Epithelial(17;0.193)			GAGAATTTCAGGAGACTCCAG	0.363													7	200	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61597467	61597467	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61597467C>A	uc002sbe.2	-	10	1262	c.1240G>T	c.(1240-1242)GCT>TCT	p.A414S		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	414					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			TGTGCTGCAGCCCAAATACAG	0.224													51	514	---	---	---	---	PASS
FAM161A	84140	broad.mit.edu	37	2	62065688	62065688	+	Intron	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62065688C>A	uc010ypo.1	-						FAM161A_uc002sbm.3_Missense_Mutation_p.R579I|FAM161A_uc002sbn.3_Intron|FAM161A_uc010fcm.1_RNA|FAM161A_uc010fcn.1_Intron	NM_032180	NP_115556	Q3B820	F161A_HUMAN	hypothetical protein LOC84140						response to stimulus|visual perception	centrosome				large_intestine(2)|ovary(1)	3						ACATTTTACTCTGGATTTAGA	0.343													9	439	---	---	---	---	PASS
NAGK	55577	broad.mit.edu	37	2	71300618	71300618	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71300618G>T	uc002shp.3	+	6	879	c.473G>T	c.(472-474)TGG>TTG	p.W158L	NAGK_uc010fea.2_RNA|NAGK_uc002shq.3_Missense_Mutation_p.W9L|NAGK_uc002shr.2_Missense_Mutation_p.W107L	NM_017567	NP_060037	Q9UJ70	NAGK_HUMAN	N-Acetylglucosamine kinase	158					N-acetylglucosamine metabolic process|N-acetylmannosamine metabolic process		ATP binding|N-acetylglucosamine kinase activity|protein binding				0					N-Acetyl-D-glucosamine(DB00141)	GCAGCCTACTGGATCGCACAC	0.512													10	374	---	---	---	---	PASS
SLC4A5	57835	broad.mit.edu	37	2	74482935	74482935	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74482935A>T	uc002sko.1	-	8	994	c.992T>A	c.(991-993)CTG>CAG	p.L331Q	SLC4A5_uc002skl.2_RNA|SLC4A5_uc002skn.2_Missense_Mutation_p.L331Q|SLC4A5_uc010ffc.1_Missense_Mutation_p.L331Q|SLC4A5_uc002skp.1_Missense_Mutation_p.L267Q|SLC4A5_uc002sks.1_Missense_Mutation_p.L331Q	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a	331	Cytoplasmic (Potential).					apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9						CACTCCTCCCAGCATGGCCGA	0.612													10	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	89986939	89986939	+	Intron	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89986939T>A	uc010fhm.2	+						uc002stn.1_RNA					Parts of antibodies, mostly variable regions.																		GCTCCTGATCTATGAAGTTTC	0.527													19	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90154142	90154142	+	RNA	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90154142G>C	uc010fhm.2	+	20		c.2607G>C								Parts of antibodies, mostly variable regions.																		CAGGGCCACTGGCATCCCAGC	0.557													22	35	---	---	---	---	PASS
ARID5A	10865	broad.mit.edu	37	2	97217381	97217381	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97217381G>A	uc002swe.2	+	7	1216	c.1116G>A	c.(1114-1116)TTG>TTA	p.L372L	ARID5A_uc010yuq.1_Silent_p.L320L|ARID5A_uc002swf.2_Silent_p.L208L|ARID5A_uc002swg.2_Silent_p.L320L	NM_212481	NP_997646	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A	372					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding				0						GGGTGCTATTGGGGCCTCCTG	0.587													8	9	---	---	---	---	PASS
REV1	51455	broad.mit.edu	37	2	100079080	100079080	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100079080C>T	uc002tad.2	-	3	271	c.59G>A	c.(58-60)GGG>GAG	p.G20E	REV1_uc002tac.2_Missense_Mutation_p.G20E|REV1_uc002tae.1_5'UTR	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1	20					DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2						AGCCATATACCCACCCTAGAA	0.353								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					31	80	---	---	---	---	PASS
MYO7B	4648	broad.mit.edu	37	2	128387373	128387373	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128387373C>A	uc002top.2	+	34	4753	c.4700C>A	c.(4699-4701)ACG>AAG	p.T1567K	MYO7B_uc002tor.1_Missense_Mutation_p.T420K	NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	1567	SH3 1.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		ACCATCCCCACGGTCACTAAG	0.647													11	34	---	---	---	---	PASS
UBXN4	23190	broad.mit.edu	37	2	136530083	136530083	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136530083G>C	uc002tur.2	+	9	1227	c.916G>C	c.(916-918)GAA>CAA	p.E306Q	UBXN4_uc002tus.2_Missense_Mutation_p.E72Q	NM_014607	NP_055422	Q92575	UBXN4_HUMAN	UBX domain containing 2	306	Cytoplasmic (Potential).				response to unfolded protein	endoplasmic reticulum membrane|nuclear envelope	protein binding			skin(2)	2						GGCAGAAATGGAAGTCAAGAG	0.443													14	50	---	---	---	---	PASS
THSD7B	80731	broad.mit.edu	37	2	138208577	138208577	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138208577T>A	uc002tva.1	+	14	3029	c.3029T>A	c.(3028-3030)CTG>CAG	p.L1010Q	THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		TGTCCCAAACTGGATCTCAAG	0.373													9	11	---	---	---	---	PASS
NXPH2	11249	broad.mit.edu	37	2	139429176	139429176	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139429176T>A	uc002tvi.2	-	2	111	c.111A>T	c.(109-111)AAA>AAT	p.K37N		NM_007226	NP_009157	O95156	NXPH2_HUMAN	neurexophilin 2 precursor	37	II.				neuropeptide signaling pathway	extracellular region				ovary(3)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(221;0.101)		CTGGAGCATCTTTGTCTTCCC	0.512													22	57	---	---	---	---	PASS
ZEB2	9839	broad.mit.edu	37	2	145161578	145161578	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145161578C>A	uc002tvu.2	-	6	1192	c.712G>T	c.(712-714)GAA>TAA	p.E238*	ZEB2_uc002tvv.2_Nonsense_Mutation_p.E232*|ZEB2_uc010zbm.1_Nonsense_Mutation_p.E209*|ZEB2_uc010fnp.2_Nonsense_Mutation_p.E146*|ZEB2_uc010fnq.1_Nonsense_Mutation_p.E267*	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	238						cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)		AAGTTCTCTTCATTCTTCTCG	0.557													9	43	---	---	---	---	PASS
ACVR2A	92	broad.mit.edu	37	2	148602722	148602722	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148602722A>G	uc002twg.2	+	2	270	c.1A>G	c.(1-3)ATG>GTG	p.M1V	ACVR2A_uc010zbn.1_Intron|ACVR2A_uc002twh.2_Missense_Mutation_p.M1V	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	1					activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)		CCTCGGGAAAATGGGAGCTGC	0.592													16	46	---	---	---	---	PASS
NEB	4703	broad.mit.edu	37	2	152580773	152580773	+	Splice_Site	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152580773C>A	uc010fnx.2	-	8	803	c.612_splice	c.e8+1	p.K204_splice		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		CAGACCCTTACCTTGCTGAAC	0.458													8	24	---	---	---	---	PASS
DPP4	1803	broad.mit.edu	37	2	162865781	162865781	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162865781C>A	uc002ubz.2	-	21	2418	c.1857G>T	c.(1855-1857)GTG>GTT	p.V619V	DPP4_uc010fpb.2_Silent_p.V295V	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV	619	Extracellular (Potential).				cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)	GTTTGTTGTCCACAAATCCCA	0.368													5	63	---	---	---	---	PASS
GCA	25801	broad.mit.edu	37	2	163212958	163212958	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163212958G>T	uc002ucg.2	+	4	449	c.273G>T	c.(271-273)TTG>TTT	p.L91F	GCA_uc010zcu.1_Missense_Mutation_p.L72F	NM_012198	NP_036330	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	91	EF-hand 2.				cellular membrane fusion	cytoplasm|plasma membrane	calcium ion binding|protein homodimerization activity				0						CCTTCAGTTTGGAAACCTGCA	0.299													5	57	---	---	---	---	PASS
KCNH7	90134	broad.mit.edu	37	2	163693137	163693137	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163693137C>A	uc002uch.1	-	2	429	c.217G>T	c.(217-219)GAG>TAG	p.E73*	KCNH7_uc002uci.2_Nonsense_Mutation_p.E73*	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	73	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	CTCTTGGTCTCGGGTCCATGG	0.483													13	22	---	---	---	---	PASS
SCN7A	6332	broad.mit.edu	37	2	167297992	167297992	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167297992C>G	uc002udu.1	-	14	2198	c.2071G>C	c.(2071-2073)GAG>CAG	p.E691Q	SCN7A_uc010fpm.1_RNA	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	691					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1						CACAAGGTCTCTACCCACTCT	0.448													17	52	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168115829	168115829	+	3'UTR	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168115829G>T	uc002udx.2	+	10					XIRP2_uc010fpn.2_Nonsense_Mutation_p.E958*|XIRP2_uc010fpo.2_Nonsense_Mutation_p.E925*|XIRP2_uc010fpp.2_Nonsense_Mutation_p.E925*|XIRP2_uc010fpq.2_3'UTR|XIRP2_uc010fpr.2_Nonsense_Mutation_p.E703*	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						ACTCACGGTGGAAGAGCAGAT	0.443													15	57	---	---	---	---	PASS
SCRN3	79634	broad.mit.edu	37	2	175265857	175265857	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175265857A>G	uc002uiq.2	+	4	569	c.481A>G	c.(481-483)AGG>GGG	p.R161G	SCRN3_uc010zen.1_Missense_Mutation_p.R154G|SCRN3_uc010zeo.1_Intron	NM_024583	NP_078859	Q0VDG4	SCRN3_HUMAN	secernin 3	161					proteolysis		dipeptidase activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.229)			GATAGCTGATAGGAATGAAGC	0.398													16	35	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178098944	178098944	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178098944C>T	uc002ulh.3	-	2	656	c.101G>A	c.(100-102)CGA>CAA	p.R34Q	NFE2L2_uc002ulg.3_Missense_Mutation_p.R18Q|NFE2L2_uc010zfa.1_Missense_Mutation_p.R18Q|NFE2L2_uc002uli.3_Missense_Mutation_p.R18Q|NFE2L2_uc010fra.2_Missense_Mutation_p.R18Q|NFE2L2_uc010frb.2_Missense_Mutation_p.R18Q	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1	34					transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AAATACTTCTCGACTTACTCC	0.373			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			12	34	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179582536	179582536	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179582536C>T	uc010zfg.1	-	84	21557	c.21333G>A	c.(21331-21333)GCG>GCA	p.A7111A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.A3772A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							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)			GAAGTTTGCGCGCTGTAAAGA	0.378													8	27	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179591833	179591833	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179591833G>T	uc010zfg.1	-	66	16751	c.16527C>A	c.(16525-16527)ACC>ACA	p.T5509T	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.T2170T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6436							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)			CTATAACCTTGGTACTGCAGC	0.418													5	86	---	---	---	---	PASS
CCDC141	285025	broad.mit.edu	37	2	179718255	179718255	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179718255G>T	uc002unf.1	-	10	1489	c.1432C>A	c.(1432-1434)CAG>AAG	p.Q478K		NM_173648	NP_775919	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	478							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)			TTAAACTGCTGGTGGAGAATT	0.428													36	58	---	---	---	---	PASS
ZNF804A	91752	broad.mit.edu	37	2	185798417	185798417	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185798417C>G	uc002uph.2	+	3	937	c.343C>G	c.(343-345)CAA>GAA	p.Q115E		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	115						intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11						AAAGGCACTCCAACGCCTGCA	0.383													13	30	---	---	---	---	PASS
ZNF804A	91752	broad.mit.edu	37	2	185800721	185800721	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185800721G>T	uc002uph.2	+	4	1192	c.598G>T	c.(598-600)GTT>TTT	p.V200F		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	200						intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11						AAATAACCAAGTTGGGGATCA	0.403													17	39	---	---	---	---	PASS
PMS1	5378	broad.mit.edu	37	2	190719768	190719768	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190719768C>A	uc002urh.3	+	9	2299	c.1770C>A	c.(1768-1770)CTC>CTA	p.L590L	PMS1_uc010zga.1_Silent_p.L551L|PMS1_uc010zgb.1_Silent_p.L529L|PMS1_uc002urk.3_Silent_p.L551L|PMS1_uc002uri.3_Silent_p.L590L|PMS1_uc010zgc.1_Silent_p.L414L|PMS1_uc010zgd.1_Silent_p.L414L|PMS1_uc002urj.2_RNA|PMS1_uc010fry.1_Silent_p.L551L|PMS1_uc010frz.2_Intron|PMS1_uc002url.2_Silent_p.L375L|PMS1_uc002urm.2_RNA|PMS1_uc002urn.1_Silent_p.L258L	NM_000534	NP_000525	P54277	PMS1_HUMAN	postmeiotic segregation 1 isoform a	590	HMG box.				mismatch repair|reciprocal meiotic recombination	MutLalpha complex	ATP binding|ATPase activity|mismatched DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			CTCAGTTTCTCATAGAAAATC	0.373			Mis|N			colorectal|endometrial|ovarian		Direct_reversal_of_damage|MMR					6	70	---	---	---	---	PASS
MFSD6	54842	broad.mit.edu	37	2	191301381	191301381	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191301381C>A	uc002urz.2	+	3	950	c.626C>A	c.(625-627)TCA>TAA	p.S209*		NM_017694	NP_060164	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing	209					transmembrane transport	integral to membrane				ovary(2)	2						CTCAATGTCTCAGACACCGTT	0.428													5	67	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196746728	196746728	+	Intron	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196746728T>A	uc002utj.3	-							NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TGTTTATAATTAACAACCAAG	0.323													7	17	---	---	---	---	PASS
PLCL1	5334	broad.mit.edu	37	2	198950685	198950685	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198950685C>T	uc010fsp.2	+	2	2735	c.2444C>T	c.(2443-2445)CCA>CTA	p.P815L	PLCL1_uc002uuv.3_Missense_Mutation_p.P736L	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	815					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)	TATACGATACCATTTGAATGT	0.438													14	50	---	---	---	---	PASS
FAM134A	79137	broad.mit.edu	37	2	220045906	220045906	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220045906C>T	uc002vjw.3	+	6	899	c.763C>T	c.(763-765)CAT>TAT	p.H255Y	FAM134A_uc010fwc.2_Missense_Mutation_p.H48Y|FAM134A_uc002vjx.2_Missense_Mutation_p.H48Y	NM_024293	NP_077269	Q8NC44	F134A_HUMAN	hypothetical protein LOC79137	255						endoplasmic reticulum|integral to membrane				ovary(1)|central_nervous_system(1)	2		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAATGCCCTGCATCACAAACA	0.562													29	69	---	---	---	---	PASS
IRS1	3667	broad.mit.edu	37	2	227662338	227662338	+	Missense_Mutation	SNP	G	A	A	rs147944503		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227662338G>A	uc002voh.3	-	1	1169	c.1117C>T	c.(1117-1119)CGC>TGC	p.R373C		NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1	373	Ser-rich.				fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		GGGATGGAGCGGCTGTGGTTG	0.697											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	10	18	---	---	---	---	PASS
TRPM8	79054	broad.mit.edu	37	2	234863887	234863887	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234863887G>T	uc002vvh.2	+	11	1395	c.1355G>T	c.(1354-1356)CGA>CTA	p.R452L	TRPM8_uc010fyj.2_Missense_Mutation_p.R140L	NM_024080	NP_076985	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel,	452	Cytoplasmic (Potential).					integral to membrane				skin(4)	4		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	AATGACCGCCGATGGGAGGTA	0.502													21	35	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238250716	238250716	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238250716A>G	uc002vwl.2	-	37	8042	c.7757T>C	c.(7756-7758)GTT>GCT	p.V2586A	COL6A3_uc002vwo.2_Missense_Mutation_p.V2380A|COL6A3_uc010znj.1_Missense_Mutation_p.V1979A|COL6A3_uc002vwj.2_5'UTR	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2586	Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		ACCCAAGCAAACATGACACGT	0.453													9	18	---	---	---	---	PASS
CNTN4	152330	broad.mit.edu	37	3	3030128	3030128	+	Silent	SNP	T	C	C	rs78171908	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3030128T>C	uc003bpc.2	+	13	1679	c.1458T>C	c.(1456-1458)GCT>GCC	p.A486A	CNTN4_uc003bpb.1_Silent_p.A158A|CNTN4_uc003bpd.1_Silent_p.A486A|CNTN4_uc003bpe.2_Silent_p.A158A|CNTN4_uc003bpf.2_Silent_p.A158A	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	486	Ig-like C2-type 5.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TTGGAACTGCTAGCAGTACTG	0.378													11	22	---	---	---	---	PASS
LRRN1	57633	broad.mit.edu	37	3	3886844	3886844	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3886844C>G	uc003bpt.3	+	2	1280	c.519C>G	c.(517-519)CAC>CAG	p.H173Q	SUMF1_uc003bps.1_Intron	NM_020873	NP_065924	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1 precursor	173	LRR 5.|Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		TAAGGCTCCACCTGAACTCCA	0.398													27	33	---	---	---	---	PASS
CCR5	1234	broad.mit.edu	37	3	46415167	46415167	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46415167C>A	uc003cpo.3	+	3	896	c.774C>A	c.(772-774)AAC>AAA	p.N258K	CCR5_uc010hjd.2_Missense_Mutation_p.N258K	NM_001100168	NP_001093638	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5	258	Helical; Name=6; (Potential).				cell-cell signaling|cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|immune response|inflammatory response|initiation of viral infection	endosome|external side of plasma membrane|integral to plasma membrane	actin binding|C-C chemokine receptor activity|coreceptor activity|phosphatidylinositol phospholipase C activity			lung(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	TTCTCCTGAACACCTTCCAGG	0.468													65	105	---	---	---	---	PASS
LAMB2	3913	broad.mit.edu	37	3	49166717	49166717	+	Missense_Mutation	SNP	C	A	A	rs148333147		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49166717C>A	uc003cwe.2	-	12	1858	c.1559G>T	c.(1558-1560)CGC>CTC	p.R520L	LAMB2_uc003cwf.1_Missense_Mutation_p.R520L	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	520	Laminin EGF-like 4.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTCACAGGGGCGGCAGCCGAG	0.622													12	10	---	---	---	---	PASS
DOCK3	1795	broad.mit.edu	37	3	51265418	51265418	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51265418G>T	uc011bds.1	+	17	1569	c.1546G>T	c.(1546-1548)GAC>TAC	p.D516Y		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	516	DHR-1.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		TACAGCAAAGGACAAAGGGGA	0.428													16	15	---	---	---	---	PASS
SPCS1	28972	broad.mit.edu	37	3	52740666	52740666	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52740666A>T	uc011bei.1	+	2	449	c.244A>T	c.(244-246)AAG>TAG	p.K82*	GLT8D1_uc003dfj.2_5'Flank|GLT8D1_uc003dfk.2_5'Flank|GLT8D1_uc003dfl.2_5'Flank|GLT8D1_uc003dfm.2_5'Flank|GLT8D1_uc003dfn.2_5'Flank|GLT8D1_uc003dfo.1_5'Flank|GLT8D1_uc010hmm.1_5'Flank	NM_014041	NP_054760	Q9Y6A9	SPCS1_HUMAN	signal peptidase complex subunit 1 homolog	82	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	integral to endoplasmic reticulum membrane|microsome|signal peptidase complex	peptidase activity				0				BRCA - Breast invasive adenocarcinoma(193;6.51e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)|OV - Ovarian serous cystadenocarcinoma(275;0.0469)		CCAGGATTACAAGGGCCAGAA	0.478													15	19	---	---	---	---	PASS
ADAMTS9	56999	broad.mit.edu	37	3	64636807	64636807	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64636807C>A	uc003dmg.2	-	9	1381	c.1349G>T	c.(1348-1350)TGT>TTT	p.C450F	ADAMTS9_uc011bfo.1_Missense_Mutation_p.C422F|ADAMTS9_uc003dmh.1_Missense_Mutation_p.C279F|ADAMTS9_uc003dmk.1_Missense_Mutation_p.C450F	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	450	Peptidase M12B.				glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		TTCTTCTTTACATTTGTTGTT	0.408													6	33	---	---	---	---	PASS
CRYBG3	131544	broad.mit.edu	37	3	97596805	97596805	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97596805G>T	uc003drx.2	+	1	987	c.923G>T	c.(922-924)GGT>GTT	p.G308V		NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0						GCCAGATTTGGTGGAATTTTT	0.373													15	55	---	---	---	---	PASS
OR5K1	26339	broad.mit.edu	37	3	98189081	98189081	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98189081A>G	uc003dsm.2	+	1	661	c.661A>G	c.(661-663)ATT>GTT	p.I221V		NM_001004736	NP_001004736	Q8NHB7	OR5K1_HUMAN	olfactory receptor, family 5, subfamily K,	221	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)	1						TTATCTCTATATTCTTCTTAC	0.348													19	65	---	---	---	---	PASS
ABI3BP	25890	broad.mit.edu	37	3	100523636	100523636	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100523636C>A	uc003dun.2	-	20	1832	c.1747G>T	c.(1747-1749)GCT>TCT	p.A583S	ABI3BP_uc003duj.2_Missense_Mutation_p.A138S|ABI3BP_uc003duk.2_Missense_Mutation_p.A267S|ABI3BP_uc003dul.2_Missense_Mutation_p.A388S|ABI3BP_uc011bhd.1_Missense_Mutation_p.A537S|ABI3BP_uc003dum.2_5'UTR	NM_015429	NP_056244	Q7Z7G0	TARSH_HUMAN	ABI gene family, member 3 (NESH) binding protein	583	Pro-rich.					extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4						AAGCATTTACCAGGTGTGGTG	0.418													28	34	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108211452	108211452	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108211452G>A	uc003dxa.1	-							NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						TCTGGATGATGAGAAATGAAT	0.284													7	26	---	---	---	---	PASS
DPPA2	151871	broad.mit.edu	37	3	109028010	109028010	+	Intron	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109028010T>C	uc003dxo.2	-							NM_138815	NP_620170	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2							nucleus	nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)	3						CACCCAAGTGTACTAACCTTG	0.418													70	190	---	---	---	---	PASS
FBXO40	51725	broad.mit.edu	37	3	121345583	121345583	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121345583G>T	uc003eeg.2	+	4	2166	c.1956G>T	c.(1954-1956)TGG>TGT	p.W652C		NM_016298	NP_057382	Q9UH90	FBX40_HUMAN	F-box protein 40	652					muscle cell differentiation	centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)		TCAAGAGCTGGGAGTTTAATG	0.453													9	207	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	124281726	124281726	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124281726G>T	uc003ehg.2	+	34	5093	c.4966G>T	c.(4966-4968)GAC>TAC	p.D1656Y	KALRN_uc003ehi.2_Missense_Mutation_p.D29Y	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	1656	SH3 1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						GGTCCTCCAGGACTTCAGTGC	0.493													4	13	---	---	---	---	PASS
HEG1	57493	broad.mit.edu	37	3	124738123	124738123	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124738123G>T	uc003ehs.3	-	5	1639	c.1571C>A	c.(1570-1572)CCA>CAA	p.P524Q	HEG1_uc011bke.1_Missense_Mutation_p.P524Q	NM_020733	NP_065784	Q9ULI3	HEG1_HUMAN	HEG homolog 1 precursor	524	Extracellular (Potential).|Ser-rich.					extracellular region|integral to membrane	calcium ion binding			ovary(2)	2						TTCTCCACGTGGTGCTGATGA	0.443													5	99	---	---	---	---	PASS
DBR1	51163	broad.mit.edu	37	3	137880959	137880959	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137880959C>A	uc003erv.2	-	8	1543	c.1407G>T	c.(1405-1407)AGG>AGT	p.R469S	DBR1_uc003eru.2_Missense_Mutation_p.R418S|DBR1_uc003ert.2_Missense_Mutation_p.R237S	NM_016216	NP_057300	Q9UK59	DBR1_HUMAN	debranching enzyme homolog 1	469						nucleus	metal ion binding|RNA lariat debranching enzyme activity				0						CTGGCAAGATCCTGACATCAG	0.443													47	96	---	---	---	---	PASS
CLSTN2	64084	broad.mit.edu	37	3	140122641	140122641	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140122641G>T	uc003etn.2	+	3	593	c.403G>T	c.(403-405)GAG>TAG	p.E135*	CLSTN2_uc003etm.2_Nonsense_Mutation_p.E135*	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	135	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						TGGGCCCCACGAGACAGCCTG	0.592										HNSCC(16;0.037)			22	77	---	---	---	---	PASS
CPA3	1359	broad.mit.edu	37	3	148586807	148586807	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148586807C>A	uc003ewm.2	+	3	302	c.250C>A	c.(250-252)CAA>AAA	p.Q84K		NM_001870	NP_001861	P15088	CBPA3_HUMAN	carboxypeptidase A3 precursor	84					proteolysis	stored secretory granule|transport vesicle	metallocarboxypeptidase activity|zinc ion binding			breast(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			TGCCTTGGATCAAAATAAAAT	0.418													57	56	---	---	---	---	PASS
IGSF10	285313	broad.mit.edu	37	3	151161171	151161171	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151161171G>T	uc011bod.1	-	5	5564	c.5564C>A	c.(5563-5565)ACT>AAT	p.T1855N	IGSF10_uc011bob.1_5'Flank|IGSF10_uc011boc.1_5'Flank	NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	1855	Ig-like C2-type 5.				cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTCACCCCAAGTGCCTACAAT	0.488													20	71	---	---	---	---	PASS
VEPH1	79674	broad.mit.edu	37	3	157099055	157099055	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157099055G>T	uc003fbj.1	-	7	1334	c.1017C>A	c.(1015-1017)TCC>TCA	p.S339S	VEPH1_uc003fbk.1_Silent_p.S339S|VEPH1_uc010hvu.1_Silent_p.S339S	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1	339						plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			CCAAGATTGAGGAGAAGGTGT	0.512													7	136	---	---	---	---	PASS
RSRC1	51319	broad.mit.edu	37	3	157841731	157841731	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157841731G>C	uc003fbt.2	+	3	382	c.271G>C	c.(271-273)GGG>CGG	p.G91R	RSRC1_uc011bou.1_Missense_Mutation_p.G91R|RSRC1_uc003fbu.1_Missense_Mutation_p.G91R|RSRC1_uc003fbv.2_Missense_Mutation_p.G91R	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	91	Arg/Ser-rich.				nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)			AAGGGGTCGAGGGAAATCCTA	0.343													92	74	---	---	---	---	PASS
MFSD1	64747	broad.mit.edu	37	3	158545131	158545131	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158545131G>T	uc003fcl.1	+						MFSD1_uc003fcm.1_Intron|MFSD1_uc003fcn.1_Intron|MFSD1_uc011bow.1_Intron|MFSD1_uc011box.1_Intron	NM_022736	NP_073573	Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing						transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TACTGAGTAAGTATTAAAAGG	0.264													12	73	---	---	---	---	PASS
IQCJ	654502	broad.mit.edu	37	3	158983023	158983023	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158983023G>T	uc003fcp.1	+	5	416	c.311G>T	c.(310-312)GGG>GTG	p.G104V	SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|IQCJ_uc010hvy.1_Missense_Mutation_p.G77V	NM_001042705	NP_001036170	Q1A5X6	IQCJ_HUMAN	IQ motif containing J isoform CaMBPv1	104											0			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			GCCCCTGTTGGGAAGATTCAT	0.448													8	267	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164709970	164709970	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164709970G>T	uc003fei.2	-	43	5040	c.4978C>A	c.(4978-4980)CAT>AAT	p.H1660N		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1660	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	CTTACTGTATGGTAGTCAAAC	0.353										HNSCC(35;0.089)			7	217	---	---	---	---	PASS
MYNN	55892	broad.mit.edu	37	3	169501285	169501285	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169501285G>T	uc003fft.2	+	6	1849	c.1420G>T	c.(1420-1422)GGT>TGT	p.G474C	MYNN_uc011bpm.1_Missense_Mutation_p.G360C|MYNN_uc003ffu.2_Missense_Mutation_p.G474C|MYNN_uc003ffv.2_Missense_Mutation_p.G201C|MYNN_uc010hwo.2_Missense_Mutation_p.G474C|MYNN_uc003ffw.1_RNA	NM_018657	NP_061127	Q9NPC7	MYNN_HUMAN	myoneurin	474	C2H2-type 7.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			ATACATATGTGGTATTTGTGG	0.333													6	151	---	---	---	---	PASS
PLD1	5337	broad.mit.edu	37	3	171406667	171406667	+	Splice_Site	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171406667C>G	uc003fhs.2	-	14	1455	c.1339_splice	c.e14-1	p.V447_splice	PLD1_uc003fht.2_Splice_Site_p.V447_splice	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GTCTCATCACCTTGAGAGGGA	0.438													4	60	---	---	---	---	PASS
PLD1	5337	broad.mit.edu	37	3	171427430	171427430	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171427430G>A	uc003fhs.2	-	10	1097	c.981C>T	c.(979-981)ATC>ATT	p.I327I	PLD1_uc003fht.2_Silent_p.I327I	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a	327	PH.				cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	CATGTTTCTGGATGAATTCTT	0.368													23	123	---	---	---	---	PASS
TTC14	151613	broad.mit.edu	37	3	180327705	180327705	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180327705G>T	uc003fkk.2	+	12	1820	c.1688G>T	c.(1687-1689)AGG>ATG	p.R563M	TTC14_uc003fkl.2_3'UTR|TTC14_uc003fkm.2_Missense_Mutation_p.R563M	NM_133462	NP_597719	Q96N46	TTC14_HUMAN	tetratricopeptide repeat domain 14 isoform a	563							RNA binding			ovary(1)	1	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			AAGCAGGATAGGTTACAGTAT	0.398													9	374	---	---	---	---	PASS
ATP11B	23200	broad.mit.edu	37	3	182553841	182553841	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182553841C>T	uc003flb.2	+	5	591	c.334C>T	c.(334-336)CGG>TGG	p.R112W	ATP11B_uc003fla.2_Missense_Mutation_p.R112W	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	112	Cytoplasmic (Potential).				aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			AGATTGGTTACGGCATAACTC	0.308													30	72	---	---	---	---	PASS
EPHB3	2049	broad.mit.edu	37	3	184294818	184294818	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184294818C>A	uc003foz.2	+	5	1638	c.1201C>A	c.(1201-1203)CGG>AGG	p.R401R		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	401	Fibronectin type-III 1.|Extracellular (Potential).					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)			GTTTGTGCCTCGGCAGCTGGG	0.627													5	161	---	---	---	---	PASS
MSX1	4487	broad.mit.edu	37	4	4864840	4864840	+	Silent	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4864840T>C	uc003gif.2	+	2	1117	c.882T>C	c.(880-882)CAT>CAC	p.H294H		NM_002448	NP_002439	P28360	MSX1_HUMAN	msh homeobox 1	288					apoptotic nuclear change|face morphogenesis|negative regulation of cell growth|odontogenesis of dentine-containing tooth|positive regulation of apoptosis|protein localization to nucleus|protein stabilization	nucleus	p53 binding|sequence-specific DNA binding transcription factor activity				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		ACACGGCCCATGTGGGCTACA	0.697													3	7	---	---	---	---	PASS
CPZ	8532	broad.mit.edu	37	4	8607752	8607752	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8607752G>A	uc003glm.2	+	5	872	c.746G>A	c.(745-747)GGC>GAC	p.G249D	CPZ_uc003gll.2_RNA|CPZ_uc003gln.2_Missense_Mutation_p.G112D|CPZ_uc003glo.2_Missense_Mutation_p.G238D|CPZ_uc003glp.2_RNA	NM_001014447	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	249					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3						AACATTCATGGCAACGAGGTG	0.602													9	16	---	---	---	---	PASS
GBA3	57733	broad.mit.edu	37	4	22729006	22729006	+	Intron	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22729006G>C	uc003gqp.3	+						GBA3_uc010iep.2_Intron|GBA3_uc011bxo.1_Intron	NM_020973	NP_066024	Q9H227	GBA3_HUMAN	cytosolic beta-glucosidase isoform a						glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity				0						GTTCATAGCAGCACACACCTG	0.423													16	18	---	---	---	---	PASS
ATP8A1	10396	broad.mit.edu	37	4	42487624	42487624	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42487624T>A	uc003gwr.2	-	25	2445	c.2213A>T	c.(2212-2214)AAT>ATT	p.N738I	ATP8A1_uc003gwq.2_Intron|ATP8A1_uc003gws.2_Missense_Mutation_p.N723I	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	738	Cytoplasmic (Potential).				ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	AGCAAAATCATTCTCTTTCCG	0.408													14	15	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79403008	79403008	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79403008G>C	uc003hlb.2	+	57	8934	c.8494G>C	c.(8494-8496)GCA>CCA	p.A2832P		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	2827	Calx-beta 3.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						CTCTACTTTCGCATCTGTCTG	0.488													50	88	---	---	---	---	PASS
HNRPDL	9987	broad.mit.edu	37	4	83349603	83349603	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83349603G>T	uc003hmr.2	-						ENOPH1_uc003hmv.2_5'Flank|ENOPH1_uc003hmw.2_5'Flank|ENOPH1_uc003hmx.2_5'Flank|HNRPDL_uc003hmq.2_Intron|HNRPDL_uc003hms.2_Intron|HNRPDL_uc003hmt.2_Intron	NM_031372	NP_112740	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like						regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|heterogeneous nuclear ribonucleoprotein complex	double-stranded DNA binding|nucleotide binding|poly(A) RNA binding|protein binding|single-stranded DNA binding			skin(1)	1		Hepatocellular(203;0.114)				CATTTTACTAGAAATAAAAGT	0.328													11	17	---	---	---	---	PASS
SMARCAD1	56916	broad.mit.edu	37	4	95162117	95162117	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95162117T>A	uc003htc.3	+	6	920	c.665T>A	c.(664-666)TTT>TAT	p.F222Y	SMARCAD1_uc003htb.3_Missense_Mutation_p.F222Y|SMARCAD1_uc003htd.3_Missense_Mutation_p.F222Y|SMARCAD1_uc010ila.2_Missense_Mutation_p.F85Y	NM_020159	NP_064544	Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated	222					chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		GAAGATGAATTTAATGATGAT	0.358													8	11	---	---	---	---	PASS
MANBA	4126	broad.mit.edu	37	4	103644062	103644062	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103644062T>C	uc003hwg.2	-	4	615	c.515A>G	c.(514-516)CAG>CGG	p.Q172R	MANBA_uc011ces.1_Intron	NM_005908	NP_005899	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal precursor	172					carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		TTCACCCTTCTGCACAAGTGG	0.512													19	19	---	---	---	---	PASS
NHEDC1	150159	broad.mit.edu	37	4	103822328	103822328	+	Silent	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103822328G>C	uc003hww.2	-	12	1616	c.1494C>G	c.(1492-1494)CGC>CGG	p.R498R	NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Silent_p.R271R	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1	498						integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		GATCATAATGGCGTGTAAGCA	0.378													5	127	---	---	---	---	PASS
ENPEP	2028	broad.mit.edu	37	4	111482595	111482595	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111482595G>T	uc003iab.3	+	20	3097	c.2755G>T	c.(2755-2757)GGA>TGA	p.G919*		NM_001977	NP_001968	Q07075	AMPE_HUMAN	glutamyl aminopeptidase	919	Extracellular (Potential).				cell migration|cell proliferation|cell-cell signaling|proteolysis	integral to plasma membrane	aminopeptidase activity|metalloexopeptidase activity|zinc ion binding			skin(3)|ovary(1)|breast(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)	L-Glutamic Acid(DB00142)	TCCACAAGCTGGAGCAGGAGA	0.358													4	28	---	---	---	---	PASS
ADAD1	132612	broad.mit.edu	37	4	123317446	123317446	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123317446T>C	uc003ieo.2	+	7	870	c.638T>C	c.(637-639)GTT>GCT	p.V213A	ADAD1_uc003iep.2_Missense_Mutation_p.V213A|ADAD1_uc003ieq.2_Missense_Mutation_p.V195A	NM_139243	NP_640336	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1	213					multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0						TCACAGATCGTTAAAGAAAGA	0.308													13	20	---	---	---	---	PASS
TKTL2	84076	broad.mit.edu	37	4	164393684	164393684	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164393684G>A	uc003iqp.3	-	1	1364	c.1203C>T	c.(1201-1203)TTC>TTT	p.F401F		NM_032136	NP_115512	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	401						cytoplasm	metal ion binding|transketolase activity			ovary(2)|skin(2)|pancreas(1)	5	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GGAGCTGATCGAATGCTCTAG	0.488													11	14	---	---	---	---	PASS
MORF4	10934	broad.mit.edu	37	4	174537470	174537470	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174537470A>T	uc011cke.1	-	1	325	c.325T>A	c.(325-327)TAT>AAT	p.Y109N		NM_006792	NP_006783			mortality factor 4												0		Prostate(90;0.00201)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0765)|all_hematologic(60;0.107)		all cancers(43;1.88e-18)|Epithelial(43;1.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		TAATTTGCATAGTCCTCAAGA	0.393													57	75	---	---	---	---	PASS
GPM6A	2823	broad.mit.edu	37	4	176622806	176622806	+	Silent	SNP	C	T	T	rs144181937		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176622806C>T	uc003iuf.2	-	2	954	c.150G>A	c.(148-150)GCG>GCA	p.A50A	GPM6A_uc011ckj.1_Silent_p.A43A|GPM6A_uc003iug.2_Silent_p.A50A|GPM6A_uc003iuh.2_Silent_p.A39A	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2	50	Extracellular (Potential).					cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		TTCCAGAAAGCGCTTCATGAC	0.493													26	44	---	---	---	---	PASS
NSUN2	54888	broad.mit.edu	37	5	6620317	6620317	+	Silent	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6620317G>C	uc003jdu.2	-	7	782	c.717C>G	c.(715-717)GTC>GTG	p.V239V	NSUN2_uc003jdt.2_Silent_p.V3V|NSUN2_uc011cmk.1_Silent_p.V204V|NSUN2_uc003jdv.2_Silent_p.V3V	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2	239						cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						CATCATGGTTGACCACCATGA	0.507													11	83	---	---	---	---	PASS
MARCH6	10299	broad.mit.edu	37	5	10382034	10382034	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10382034G>T	uc003jet.1	+	4	496	c.313G>T	c.(313-315)GGA>TGA	p.G105*	MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_5'UTR|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6	105	Helical; (Potential).				protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						TGCATGGTTGGGAGTTGTTCC	0.363													7	170	---	---	---	---	PASS
CTNND2	1501	broad.mit.edu	37	5	11159741	11159741	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11159741C>T	uc003jfa.1	-	12	2251	c.2106G>A	c.(2104-2106)CGG>CGA	p.R702R	CTNND2_uc010itt.2_Silent_p.R611R|CTNND2_uc011cmy.1_Silent_p.R365R|CTNND2_uc011cmz.1_Silent_p.R269R|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Silent_p.R269R	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	702	ARM 5.				multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						GCTGTATTTTCCGATCATCCT	0.552													44	58	---	---	---	---	PASS
RNASEN	29102	broad.mit.edu	37	5	31521266	31521266	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31521266T>G	uc003jhg.2	-	5	1270	c.911A>C	c.(910-912)GAA>GCA	p.E304A	RNASEN_uc003jhh.2_Missense_Mutation_p.E304A|RNASEN_uc003jhi.2_Missense_Mutation_p.E304A|RNASEN_uc010iui.1_Intron	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1	304	Arg-rich.				gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0						GTAGGACCTTTCCAGAGATGG	0.413													58	164	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41015478	41015478	+	Intron	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41015478A>G	uc003jmj.3	-						HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2								binding			ovary(6)|central_nervous_system(2)	8						CTCCATATTTATTACCTTAGC	0.408													16	46	---	---	---	---	PASS
HEATR7B2	133558	broad.mit.edu	37	5	41018458	41018458	+	Silent	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41018458C>G	uc003jmj.3	-	27	3238	c.2748G>C	c.(2746-2748)CTG>CTC	p.L916L	HEATR7B2_uc003jmi.3_Silent_p.L471L	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	916							binding			ovary(6)|central_nervous_system(2)	8						TATCATTTGTCAGCACTTTCG	0.403													11	18	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45267343	45267343	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45267343A>T	uc003jok.2	-	7	1656	c.1631T>A	c.(1630-1632)CTG>CAG	p.L544Q		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	544	cAMP.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						TCCTTTGGTCAGCAGGCAAAT	0.393													18	48	---	---	---	---	PASS
GPBP1	65056	broad.mit.edu	37	5	56557016	56557016	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56557016G>T	uc003jrh.3	+	11	2444	c.1170G>T	c.(1168-1170)AAG>AAT	p.K390N	GPBP1_uc010iwg.2_Missense_Mutation_p.K410N|GPBP1_uc003jri.3_Missense_Mutation_p.K219N|GPBP1_uc003jrj.3_Missense_Mutation_p.K382N|GPBP1_uc003jrk.3_Missense_Mutation_p.K397N|GPBP1_uc003jrl.3_RNA	NM_022913	NP_075064	Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1 isoform 1	390					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		GATTGTTAAAGGAAATGGGCT	0.358													5	69	---	---	---	---	PASS
IPO11	51194	broad.mit.edu	37	5	61923053	61923053	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61923053G>A	uc003jtc.2	+	30	3026	c.2836G>A	c.(2836-2838)GAG>AAG	p.E946K	IPO11_uc011cqr.1_Missense_Mutation_p.E986K|IPO11_uc010iwr.2_3'UTR|IPO11_uc003jte.2_Missense_Mutation_p.E65K	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2	946						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)		GGCACAGCAGGAGATGCTAGG	0.502													14	45	---	---	---	---	PASS
SFRS12	140890	broad.mit.edu	37	5	65470820	65470820	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65470820A>G	uc003juo.2	+	11	1843	c.1183A>G	c.(1183-1185)ACA>GCA	p.T395A	SFRS12_uc003jun.2_Missense_Mutation_p.T511A|SFRS12_uc010iwy.2_Missense_Mutation_p.T395A	NM_139168	NP_631907	Q8WXA9	SREK1_HUMAN	splicing factor, arginine/serine-rich 12 isoform	395	Arg/Glu/Lys/Ser-rich.				mRNA processing|RNA splicing	spliceosomal complex	nucleic acid binding|nucleotide binding|protein binding				0		Lung NSC(167;9.34e-06)|Prostate(74;0.00187)|Ovarian(174;0.0545)|Breast(144;0.0928)|Colorectal(97;0.234)		Lung(70;0.00449)		ATCGCCAAGAACATCAAAAAC	0.393													6	20	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82841392	82841392	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82841392G>T	uc003kii.3	+	9	9658	c.9302G>T	c.(9301-9303)GGA>GTA	p.G3101V	VCAN_uc003kij.3_Missense_Mutation_p.G2114V|VCAN_uc010jau.2_Missense_Mutation_p.G1347V|VCAN_uc003kik.3_Missense_Mutation_p.G360V|VCAN_uc003kil.3_Missense_Mutation_p.G1765V	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	3101	EGF-like 1.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		TGCCTTAACGGAGGCACCTGT	0.458													82	152	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82875859	82875859	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82875859G>T	uc003kii.3	+	14	10297	c.9941G>T	c.(9940-9942)CGT>CTT	p.R3314L	VCAN_uc003kij.3_Missense_Mutation_p.R2327L|VCAN_uc010jau.2_Missense_Mutation_p.R1560L|VCAN_uc003kik.3_Missense_Mutation_p.R573L|VCAN_uc003kil.3_Missense_Mutation_p.R1978L	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	3314	Sushi.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		ATGAAACCTCGTTATGAAATC	0.423													19	64	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90025489	90025489	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90025489G>T	uc003kju.2	+	50	10553	c.10457G>T	c.(10456-10458)TGG>TTG	p.W3486L	GPR98_uc003kjt.2_Missense_Mutation_p.W1192L|GPR98_uc003kjv.2_Missense_Mutation_p.W1086L	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	3486	Extracellular (Potential).|EAR 5.				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATTTTCATCTGGGAGATGGGA	0.353													4	20	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90074906	90074906	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90074906C>A	uc003kju.2	+	64	13170	c.13074C>A	c.(13072-13074)CTC>CTA	p.L4358L	GPR98_uc003kjt.2_Silent_p.L2064L|GPR98_uc003kjw.2_5'Flank	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4358	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGGTGGAACTCCAGGGAAGGT	0.398													16	27	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127614475	127614475	+	Silent	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127614475G>C	uc003kuu.2	-	57	7636	c.7197C>G	c.(7195-7197)TCC>TCG	p.S2399S		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	2399	TB 9.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TGCGACTACTGGATGCCATTT	0.517													4	18	---	---	---	---	PASS
AFF4	27125	broad.mit.edu	37	5	132240074	132240074	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132240074C>G	uc003kyd.2	-	6	1481	c.1073G>C	c.(1072-1074)GGC>GCC	p.G358A	AFF4_uc011cxk.1_Missense_Mutation_p.G36A|AFF4_uc003kye.1_Missense_Mutation_p.G358A	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	358	Ser-rich.				transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTCTCCAGTGCCAAAATTGGA	0.289													5	17	---	---	---	---	PASS
PCDHA4	56144	broad.mit.edu	37	5	140188634	140188634	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188634C>T	uc003lhi.2	+	1	1963	c.1862C>T	c.(1861-1863)CCG>CTG	p.P621L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.P621L|PCDHA4_uc011daa.1_Missense_Mutation_p.P621L	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	621	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGCATCCCGTTCCGCGTG	0.672													10	58	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140209210	140209210	+	Missense_Mutation	SNP	G	A	A	rs138462086	byFrequency	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209210G>A	uc003lho.2	+	1	1561	c.1534G>A	c.(1534-1536)GCG>ACG	p.A512T	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_Missense_Mutation_p.A512T|PCDHA6_uc011dab.1_Missense_Mutation_p.A512T	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	512	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCGGTGCACGCGGAGAGCGG	0.697													8	36	---	---	---	---	PASS
PCDHA8	56140	broad.mit.edu	37	5	140222505	140222505	+	Silent	SNP	C	T	T	rs147542523		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140222505C>T	uc003lhs.2	+	1	1599	c.1599C>T	c.(1597-1599)TTC>TTT	p.F533F	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_uc003lhr.1_Silent_p.F533F	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	533	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGCAGTTCCAGGTGAGCG	0.672													6	73	---	---	---	---	PASS
PCDHB13	56123	broad.mit.edu	37	5	140596009	140596009	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140596009C>A	uc003lja.1	+	1	2501	c.2314C>A	c.(2314-2316)CCC>ACC	p.P772T		NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor	772	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCCGATTATCCCCAACTTCCC	0.493													29	63	---	---	---	---	PASS
PCDHGB1	56104	broad.mit.edu	37	5	140732021	140732021	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140732021G>A	uc003ljo.1	+	1	2194	c.2194G>A	c.(2194-2196)GGG>AGG	p.G732R	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA4_uc003ljq.1_5'Flank|PCDHGB1_uc011daq.1_Missense_Mutation_p.G732R|PCDHGA4_uc003ljp.1_5'Flank	NM_018922	NP_061745	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1 isoform 1	732	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCAAGTCTGGGCCCGGGGT	0.547													34	67	---	---	---	---	PASS
PCDHGA5	56110	broad.mit.edu	37	5	140744378	140744378	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140744378G>T	uc003lju.1	+	1	481	c.481G>T	c.(481-483)GAT>TAT	p.D161Y	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc011das.1_Missense_Mutation_p.D161Y	NM_018918	NP_061741	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5 isoform 1	161	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGGATGCGGATGTGGGTGT	0.507													10	23	---	---	---	---	PASS
FAM114A2	10827	broad.mit.edu	37	5	153406071	153406071	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153406071G>C	uc003lvb.2	-	8	1389	c.801C>G	c.(799-801)ATC>ATG	p.I267M	FAM114A2_uc003lvc.2_Missense_Mutation_p.I267M|FAM114A2_uc003lvd.2_Missense_Mutation_p.I267M|FAM114A2_uc003lve.2_Missense_Mutation_p.I83M|FAM114A2_uc011dda.1_Missense_Mutation_p.I197M	NM_018691	NP_061161	Q9NRY5	F1142_HUMAN	hypothetical protein LOC10827	267							purine nucleotide binding				0						GAGAATTAAGGATAGATTTCA	0.318													10	12	---	---	---	---	PASS
GEMIN5	25929	broad.mit.edu	37	5	154308114	154308114	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154308114G>T	uc003lvx.3	-	6	970	c.887C>A	c.(886-888)CCA>CAA	p.P296Q	GEMIN5_uc011ddk.1_Missense_Mutation_p.P295Q	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	296	WD 5.				ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CAGCTGTGTTGGTTGATTGCT	0.428													7	139	---	---	---	---	PASS
ITK	3702	broad.mit.edu	37	5	156608051	156608051	+	Silent	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156608051T>A	uc003lwo.1	+	1	145	c.63T>A	c.(61-63)ACT>ACA	p.T21T		NM_005546	NP_005537	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	21	PH.				cellular defense response|intracellular signal transduction|T cell receptor signaling pathway	cytosol|plasma membrane	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(12)|ovary(8)|skin(4)|stomach(1)|central_nervous_system(1)	26	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AGAGAAGAACTTCTCCCTCGA	0.438			T	SYK	peripheral T-cell lymphoma								19	56	---	---	---	---	PASS
FBXW11	23291	broad.mit.edu	37	5	171297857	171297857	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171297857C>G	uc003mbm.1	-	10	1654	c.1283G>C	c.(1282-1284)TGG>TCG	p.W428S	FBXW11_uc011dey.1_Missense_Mutation_p.W396S|FBXW11_uc003mbl.1_Missense_Mutation_p.W415S|FBXW11_uc003mbn.1_Missense_Mutation_p.W394S	NM_012300	NP_036432	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11 isoform	428	WD 5.				cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of circadian rhythm|positive regulation of proteolysis|positive regulation of transcription, DNA-dependent|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	centrosome|cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTCAATATCCCAGAGCCTTGA	0.408													15	53	---	---	---	---	PASS
CD83	9308	broad.mit.edu	37	6	14118260	14118260	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14118260G>T	uc003nbi.2	+	2	295	c.117G>T	c.(115-117)TGG>TGT	p.W39C	CD83_uc003nbh.2_Missense_Mutation_p.W39C	NM_004233	NP_004224	Q01151	CD83_HUMAN	CD83 antigen isoform a	39	Extracellular (Potential).|Ig-like V-type.				defense response|humoral immune response|signal transduction	integral to plasma membrane					0	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				CCGCCCCCTGGGATCCGCAGG	0.622													4	12	---	---	---	---	PASS
ZNF165	7718	broad.mit.edu	37	6	28053949	28053949	+	Splice_Site	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28053949G>A	uc003nkg.2	+	4	1496	c.412_splice	c.e4-1	p.V138_splice	ZNF165_uc003nkh.2_Splice_Site_p.V138_splice|ZNF165_uc003nki.3_Splice_Site_p.V138_splice	NM_003447	NP_003438	P49910	ZN165_HUMAN	zinc finger protein 165						viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						ATTTTTCTCAGGTTCAAGCCC	0.413													16	51	---	---	---	---	PASS
SCAND3	114821	broad.mit.edu	37	6	28543760	28543760	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28543760G>T	uc003nlo.2	-	3	1340	c.722C>A	c.(721-723)ACT>AAT	p.T241N		NM_052923	NP_443155	Q6R2W3	SCND3_HUMAN	SCAN domain containing 3	241					DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1						AAATATCTTAGTATTATTACT	0.353													14	40	---	---	---	---	PASS
GNL1	2794	broad.mit.edu	37	6	30515028	30515028	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30515028G>A	uc003nqh.2	-	10	2330	c.1302C>T	c.(1300-1302)ATC>ATT	p.I434I	GNL1_uc011dmi.1_Silent_p.I231I|GNL1_uc011dmj.1_Silent_p.I432I|GNL1_uc011dmk.1_Silent_p.I89I	NM_005275	NP_005266	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	434					response to DNA damage stimulus|signal transduction|T cell mediated immunity	extracellular space|intracellular	GTP binding|structural molecule activity			ovary(3)	3						GGATCTGGGCGATAGGGTAGA	0.602													37	83	---	---	---	---	PASS
SLC44A4	80736	broad.mit.edu	37	6	31842560	31842560	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31842560C>T	uc010jti.2	-	6	472	c.406G>A	c.(406-408)GTT>ATT	p.V136I	SLC44A4_uc011dol.1_Missense_Mutation_p.V60I|SLC44A4_uc011dom.1_Intron	NM_025257	NP_079533	Q53GD3	CTL4_HUMAN	choline transporter-like protein 4	136	Extracellular (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4					Choline(DB00122)	ACTTCCCCAACAGTCTGTGAG	0.512													7	45	---	---	---	---	PASS
HLA-DMB	3109	broad.mit.edu	37	6	32905190	32905190	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32905190C>A	uc003ocl.1	-	3	614	c.381G>T	c.(379-381)ACG>ACT	p.T127T	HLA-DMB_uc003ocj.1_3'UTR|HLA-DMB_uc003ock.1_5'Flank|HLA-DMB_uc010jud.1_5'UTR|HLA-DMB_uc010jue.1_5'UTR|HLA-DMB_uc010juf.1_5'UTR|HLA-DMB_uc011dql.1_Silent_p.T127T	NM_002118	NP_002109	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM	127	Lumenal (Potential).|Ig-like C1-type.|Beta-2.				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	integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CAGGCTCCCTCGTGTTAAAAG	0.512													5	121	---	---	---	---	PASS
TCP11	6954	broad.mit.edu	37	6	35090020	35090020	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35090020T>A	uc003okd.2	-	5	672	c.491A>T	c.(490-492)CAT>CTT	p.H164L	TCP11_uc003ojz.1_Missense_Mutation_p.H89L|TCP11_uc003oka.2_Missense_Mutation_p.H89L|TCP11_uc003okb.2_Missense_Mutation_p.H88L|TCP11_uc003okc.2_Missense_Mutation_p.H88L|TCP11_uc011dsu.1_Missense_Mutation_p.H146L|TCP11_uc011dsv.1_Missense_Mutation_p.H113L|TCP11_uc011dsw.1_Missense_Mutation_p.H118L	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	151					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5						CAGGGCCCCATGTTCTGCCTC	0.488													29	49	---	---	---	---	PASS
C6orf130	221443	broad.mit.edu	37	6	41037854	41037854	+	Silent	SNP	C	A	A	rs144524444	byFrequency	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41037854C>A	uc003opm.2	-	4	376	c.204G>T	c.(202-204)GTG>GTT	p.V68V	UNC5CL_uc010jxe.1_5'UTR|C6orf130_uc010jxg.2_Silent_p.V68V|C6orf130_uc003opn.2_Silent_p.V68V|C6orf130_uc010jxh.1_Silent_p.V68V|NFYA_uc003opo.2_5'Flank|NFYA_uc003opp.2_5'Flank	NM_145063	NP_659500	Q9Y530	CF130_HUMAN	hypothetical protein LOC221443	68	Macro.										0	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCAGAACAGCCACTTCTCCAG	0.313													15	38	---	---	---	---	PASS
CUL9	23113	broad.mit.edu	37	6	43155591	43155591	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43155591G>A	uc003ouk.2	+	7	1797	c.1722G>A	c.(1720-1722)CTG>CTA	p.L574L	CUL9_uc003ouj.1_Silent_p.L464L|CUL9_uc003oul.2_Silent_p.L574L|CUL9_uc010jyk.2_5'UTR|CUL9_uc003oum.1_Silent_p.L32L	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	574					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12						AGTATGGGCTGCTGTCTAATG	0.522													18	50	---	---	---	---	PASS
ZNF318	24149	broad.mit.edu	37	6	43306887	43306887	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43306887G>C	uc003oux.2	-	10	4927	c.4849C>G	c.(4849-4851)CCT>GCT	p.P1617A	ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1617					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CTGTTCAAAGGAGAAGTAGAA	0.473													34	68	---	---	---	---	PASS
SUPT3H	8464	broad.mit.edu	37	6	44921148	44921148	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44921148C>G	uc003oxo.2	-	11	1051	c.733G>C	c.(733-735)GAT>CAT	p.D245H	SUPT3H_uc003oxn.1_Missense_Mutation_p.D234H|SUPT3H_uc011dvv.1_Missense_Mutation_p.D82H|SUPT3H_uc003oxp.2_Missense_Mutation_p.D234H|SUPT3H_uc011dvw.1_Missense_Mutation_p.D148H	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2	316					histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3						AGAGCCAGATCCACTAACTAG	0.433													12	32	---	---	---	---	PASS
RHAG	6005	broad.mit.edu	37	6	49604511	49604511	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49604511G>A	uc003ozk.3	-	1	77	c.15C>T	c.(13-15)TTC>TTT	p.F5F	RHAG_uc010jzl.2_Silent_p.F5F|RHAG_uc010jzm.2_Silent_p.F5F	NM_000324	NP_000315	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	5	Helical; (Potential).				carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)|skin(1)	2	Lung NSC(77;0.0255)					CCATGAGAGGGAATGTGAACC	0.438													43	44	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51882299	51882299	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51882299G>T	uc003pah.1	-	34	5785	c.5509C>A	c.(5509-5511)CTC>ATC	p.L1837I	PKHD1_uc003pai.2_Missense_Mutation_p.L1837I	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1837	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)					CAAATGTAGAGGTAAGGCCAC	0.498													8	271	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51941139	51941139	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51941139G>T	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						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)					AAACTGTTTAGAAAATAGTAC	0.378													21	7	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54805608	54805608	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54805608C>A	uc003pck.2	+	5	1955	c.1839C>A	c.(1837-1839)ACC>ACA	p.T613T		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	613										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					AAATGCACACCTTGCAGGTTC	0.428													6	94	---	---	---	---	PASS
PRIM2	5558	broad.mit.edu	37	6	57398208	57398208	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57398208G>A	uc003pdx.2	+	10	998	c.911G>A	c.(910-912)GGA>GAA	p.G304E		NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2	304					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)		CTTTGTCATGGAGGCCGAATG	0.393													26	258	---	---	---	---	PASS
COL19A1	1310	broad.mit.edu	37	6	70873266	70873266	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70873266C>A	uc003pfc.1	+	36	2495	c.2378C>A	c.(2377-2379)CCC>CAC	p.P793H	COL19A1_uc010kam.1_Missense_Mutation_p.P689H	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	793	Triple-helical region 4 (COL4).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						CATCCTGGTCCCACAGGAGCA	0.448													5	31	---	---	---	---	PASS
PHIP	55023	broad.mit.edu	37	6	79672925	79672925	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79672925C>A	uc003pir.2	-	30	3650	c.3424G>T	c.(3424-3426)GGT>TGT	p.G1142C	PHIP_uc003piq.2_Missense_Mutation_p.G166C|PHIP_uc011dyp.1_Missense_Mutation_p.G1141C|PHIP_uc003pio.3_Missense_Mutation_p.G28C	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1142					insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CTGCACTCACCATCAGTTAAA	0.383													6	203	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90440607	90440607	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90440607C>T	uc003pnn.1	-	35	5094	c.4978G>A	c.(4978-4980)GCA>ACA	p.A1660T		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	1660					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCTTTTCGTGCCAAAAGGGCT	0.403													37	33	---	---	---	---	PASS
ENPP1	5167	broad.mit.edu	37	6	132206132	132206132	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132206132C>A	uc011ecf.1	+	23	2393	c.2373C>A	c.(2371-2373)GTC>GTA	p.V791V		NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	791	Nuclease.|Extracellular (Potential).				3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	GAAATGGTGTCAATGTCGTCA	0.378													13	17	---	---	---	---	PASS
ECT2L	345930	broad.mit.edu	37	6	139175174	139175174	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139175174G>T	uc003qif.1	+	8	1184	c.1081G>T	c.(1081-1083)GGT>TGT	p.G361C	ECT2L_uc011edq.1_Missense_Mutation_p.G292C	NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	epithelial cell transforming sequence 2	361					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0						CTATAAAATTGGTGTTAAAAA	0.363													5	83	---	---	---	---	PASS
ARID1B	57492	broad.mit.edu	37	6	157522468	157522468	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157522468G>T	uc003qqn.2	+	18	4838	c.4686G>T	c.(4684-4686)ATG>ATT	p.M1562I	ARID1B_uc003qqo.2_Missense_Mutation_p.M1522I|ARID1B_uc003qqp.2_Missense_Mutation_p.M1509I	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1567	Pro-rich.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CTATGAAGATGCAGAAGGTCA	0.597													34	44	---	---	---	---	PASS
PLG	5340	broad.mit.edu	37	6	161139439	161139439	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161139439G>T	uc003qtm.3	+	8	964	c.901G>T	c.(901-903)GCA>TCA	p.A301S		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	301	Kringle 3.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	GCACTGGAGTGCACAGACCCC	0.527													27	24	---	---	---	---	PASS
AGPAT4	56895	broad.mit.edu	37	6	161587445	161587445	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161587445C>A	uc003qtr.1	-	3	410	c.183G>T	c.(181-183)CTG>CTT	p.L61L	AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron|AGPAT4_uc003qtt.1_RNA|AGPAT4_uc011egc.1_Silent_p.L61L|AGPAT4_uc011egd.1_5'UTR|AGPAT4_uc011ege.1_Intron	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	61					phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		GCAGCATCACCAGCTCTGGAA	0.572													12	17	---	---	---	---	PASS
USP42	84132	broad.mit.edu	37	7	6189676	6189676	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6189676G>A	uc011jwo.1	+	13	1972	c.1849G>A	c.(1849-1851)GAG>AAG	p.E617K	USP42_uc010kth.1_Missense_Mutation_p.E550K|USP42_uc011jwp.1_Missense_Mutation_p.E617K|USP42_uc011jwq.1_Missense_Mutation_p.E424K|USP42_uc011jwr.1_Missense_Mutation_p.E462K	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	617					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		GGACTCTGACGAGGAGTCAAA	0.597													9	13	---	---	---	---	PASS
MEOX2	4223	broad.mit.edu	37	7	15725863	15725863	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15725863G>T	uc003stc.2	-	1	446	c.165C>A	c.(163-165)AAC>AAA	p.N55K	MEOX2_uc011jxw.1_Missense_Mutation_p.N55K	NM_005924	NP_005915	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	55					blood circulation|multicellular organismal development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		TGCCCTCTTCGTTGGGGTATC	0.398													10	8	---	---	---	---	PASS
BMPER	168667	broad.mit.edu	37	7	34094843	34094843	+	Silent	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34094843T>C	uc011kap.1	+	9	969	c.855T>C	c.(853-855)TGT>TGC	p.C285C		NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor	285	VWFC 4.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						AGGAGGGCTGTTGTGAAGAGT	0.498													31	74	---	---	---	---	PASS
SEPT7	989	broad.mit.edu	37	7	35919506	35919506	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35919506G>T	uc010kxc.2	+	6	779	c.586G>T	c.(586-588)GCA>TCA	p.A196S	SEPT7_uc011kat.1_Missense_Mutation_p.A195S|SEPT7_uc011kau.1_Missense_Mutation_p.A160S|SEPT7_uc011kav.1_Missense_Mutation_p.A143S|SEPT7_uc003tey.2_Missense_Mutation_p.A44S	NM_001788	NP_001779	Q16181	SEPT7_HUMAN	cell division cycle 10 isoform 1	196	GTP (By similarity).				cilium morphogenesis|cytokinesis|mitosis|protein heterooligomerization|regulation of embryonic cell shape	cilium axoneme|cleavage furrow|condensed chromosome kinetochore|midbody|nucleus|septin complex|spindle|stress fiber	GTP binding|protein binding|structural molecule activity				0						TATTGCCAAAGCAGACACACT	0.363													18	25	---	---	---	---	PASS
AOAH	313	broad.mit.edu	37	7	36634000	36634000	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36634000C>A	uc003tfh.3	-	12	1284	c.883G>T	c.(883-885)GAG>TAG	p.E295*	AOAH_uc010kxf.2_Nonsense_Mutation_p.E295*|AOAH_uc011kba.1_Nonsense_Mutation_p.E263*	NM_001637	NP_001628	P28039	AOAH_HUMAN	acyloxyacyl hydrolase precursor	295					inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity			skin(1)	1						CAGTCAAGCTCGTTGGTAAGG	0.403													4	107	---	---	---	---	PASS
GPR141	353345	broad.mit.edu	37	7	37780665	37780665	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37780665C>A	uc003tfm.1	+	1	670	c.670C>A	c.(670-672)CAG>AAG	p.Q224K	uc003tfl.2_Intron	NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	224	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3						GTTCTGGGCTCAGCTGAAAAA	0.438													28	74	---	---	---	---	PASS
TBRG4	9238	broad.mit.edu	37	7	45148416	45148416	+	Intron	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45148416C>T	uc003tmv.2	-						TBRG4_uc003tmu.2_5'Flank|TBRG4_uc003tmw.2_Intron|TBRG4_uc003tmx.2_Intron|TBRG4_uc011kcd.1_Intron|SNORA5B_uc003tna.3_5'Flank	NM_004749	NP_004740	Q969Z0	TBRG4_HUMAN	cell cycle progression 2 protein isoform 1						apoptosis|cell cycle arrest|cellular respiration|G1 phase of mitotic cell cycle|positive regulation of cell proliferation	mitochondrion	ATP binding|protein binding|protein kinase activity				0						GACCACACTCCGGCACCCACC	0.517													6	140	---	---	---	---	PASS
ZNF479	90827	broad.mit.edu	37	7	57187643	57187643	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57187643G>T	uc010kzo.2	-	5	1750	c.1479C>A	c.(1477-1479)TAC>TAA	p.Y493*		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	493	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(1)	4			GBM - Glioblastoma multiforme(1;9.18e-12)			CTTCACATTTGTAGGGTTTCT	0.388													11	24	---	---	---	---	PASS
GUSB	2990	broad.mit.edu	37	7	65444483	65444483	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65444483G>A	uc003tun.2	-	4	703	c.627C>T	c.(625-627)TTC>TTT	p.F209F	GUSB_uc011kdt.1_Intron|GUSB_uc010kzw.1_Missense_Mutation_p.S38L	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor	209					glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						CAGCGTAGTTGAAAAAGTCAA	0.532													26	38	---	---	---	---	PASS
WBSCR17	64409	broad.mit.edu	37	7	71177096	71177096	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71177096G>T	uc003tvy.2	+	11	1762	c.1762G>T	c.(1762-1764)GGT>TGT	p.G588C	WBSCR17_uc003tvz.2_Missense_Mutation_p.G287C	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	588	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CAGCTGCACAGGTCAGAGGTG	0.627													12	39	---	---	---	---	PASS
BAZ1B	9031	broad.mit.edu	37	7	72913032	72913032	+	Intron	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72913032T>C	uc003tyc.2	-							NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B						ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)				TCCCAACCTATAAAGGAGGTA	0.393													14	22	---	---	---	---	PASS
HIP1	3092	broad.mit.edu	37	7	75168666	75168666	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75168666C>A	uc003uds.1	-	30	3079	c.3038G>T	c.(3037-3039)GGT>GTT	p.G1013V	HIP1_uc011kfz.1_Missense_Mutation_p.G839V	NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1	1013					activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8						CTCAGCAACACCAGCAAGCTC	0.532			T	PDGFRB	CMML								99	234	---	---	---	---	PASS
CACNA2D1	781	broad.mit.edu	37	7	81978881	81978881	+	Intron	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81978881C>G	uc003uhr.1	-							NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	GGATTTTACTCACATCAACAA	0.358													21	55	---	---	---	---	PASS
CACNA2D1	781	broad.mit.edu	37	7	81978903	81978903	+	Missense_Mutation	SNP	C	T	T	rs79543314		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81978903C>T	uc003uhr.1	-	2	414	c.158G>A	c.(157-159)GGA>GAA	p.G53E		NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	53	Extracellular (Potential).					voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)	CTGATTGACTCCACTTGCTGT	0.368													22	54	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82764209	82764209	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82764209C>A	uc003uhx.2	-	3	2946	c.2657G>T	c.(2656-2658)GGC>GTC	p.G886V	PCLO_uc003uhv.2_Missense_Mutation_p.G886V	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	832	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						GACAGTTTGGCCAGCGGTAGG	0.527													54	114	---	---	---	---	PASS
ZNF804B	219578	broad.mit.edu	37	7	88965101	88965101	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88965101G>C	uc011khi.1	+	4	3343	c.2805G>C	c.(2803-2805)AAG>AAC	p.K935N		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	935						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TACAAGCCAAGAAATGTCAAG	0.418										HNSCC(36;0.09)			57	144	---	---	---	---	PASS
COL1A2	1278	broad.mit.edu	37	7	94057744	94057744	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94057744C>G	uc003ung.1	+	50	4137	c.3666C>G	c.(3664-3666)GAC>GAG	p.D1222E	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	1222	Fibrillar collagen NC1.				axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	GCTCCAAGGACAAGAAACACG	0.463										HNSCC(75;0.22)			18	34	---	---	---	---	PASS
SMURF1	57154	broad.mit.edu	37	7	98645444	98645444	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98645444C>A	uc003upu.1	-	11	1413	c.1093G>T	c.(1093-1095)GAG>TAG	p.E365*	SMURF1_uc003upv.1_Nonsense_Mutation_p.E339*|SMURF1_uc003upt.2_Nonsense_Mutation_p.E339*	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform	365					BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TCCTCGTCCTCCAGAGAGCCC	0.572													7	136	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100683152	100683152	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100683152C>A	uc003uxp.1	+	3	8508	c.8455C>A	c.(8455-8457)CAC>AAC	p.H2819N	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2819	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|45.					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)					GCCTGTCAACCACACGCCAGT	0.493													8	319	---	---	---	---	PASS
CUX1	1523	broad.mit.edu	37	7	101840336	101840336	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101840336G>T	uc003uyx.3	+	15	1683	c.1645G>T	c.(1645-1647)GAG>TAG	p.E549*	CUX1_uc003uys.3_Nonsense_Mutation_p.E560*|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a	549	CUT 1.				negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						CTCCGAGGGCGAGGAGATGGA	0.522													5	139	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103237091	103237091	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103237091C>A	uc003vca.2	-	25	3511	c.3351G>T	c.(3349-3351)CTG>CTT	p.L1117L	RELN_uc010liz.2_Silent_p.L1117L	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1117					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CCCAACTCACCAGCTGTCTTT	0.448													20	35	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116340287	116340287	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116340287G>T	uc003vij.2	+	2	1336	c.1149G>T	c.(1147-1149)GTG>GTT	p.V383V	MET_uc010lkh.2_Silent_p.V383V|MET_uc011knc.1_Silent_p.V383V|MET_uc011knd.1_Silent_p.V383V|MET_uc011kne.1_Silent_p.V383V|MET_uc011knf.1_Silent_p.V383V|MET_uc011kng.1_Silent_p.V383V|MET_uc011knh.1_Silent_p.V383V|MET_uc011kni.1_Silent_p.V383V|MET_uc003vii.1_Silent_p.V402V|MET_uc010lkg.2_Silent_p.V383V|MET_uc011kmz.1_Silent_p.V383V|MET_uc011kna.1_Silent_p.V383V|MET_uc011knb.1_Silent_p.V383V	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	383	Extracellular (Potential).|Sema.				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			AAAACAATGTGAGATGTCTCC	0.408			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				17	50	---	---	---	---	PASS
KCND2	3751	broad.mit.edu	37	7	119914843	119914843	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119914843C>G	uc003vjj.1	+	1	1122	c.157C>G	c.(157-159)CAG>GAG	p.Q53E		NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related	53	Cytoplasmic (Potential).				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)					CACCCGCTTCCAGACGTGGCA	0.562													38	93	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	121081131	121081131	+	IGR	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121081131C>A								FAM3C (44709 upstream) : PTPRZ1 (432028 downstream)																							GGCTGCGGGCCCGGCTGGTCA	0.612													12	16	---	---	---	---	PASS
FLNC	2318	broad.mit.edu	37	7	128485260	128485260	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128485260G>A	uc003vnz.3	+	21	3950	c.3741G>A	c.(3739-3741)GCG>GCA	p.A1247A	FLNC_uc003voa.3_Silent_p.A1247A	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1247	Filamin 11.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12						TGCAGCCTGCGGTCGATACCA	0.602													17	29	---	---	---	---	PASS
DGKI	9162	broad.mit.edu	37	7	137172389	137172389	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137172389C>G	uc003vtt.2	-	23	2350	c.2349G>C	c.(2347-2349)GAG>GAC	p.E783D	DGKI_uc003vtu.2_Missense_Mutation_p.E483D	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	783					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3						TACGGCAAGTCTCCAAATCAC	0.363													55	145	---	---	---	---	PASS
KIAA1549	57670	broad.mit.edu	37	7	138603107	138603107	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138603107G>T	uc011kql.1	-	2	1314	c.1265C>A	c.(1264-1266)GCG>GAG	p.A422E	KIAA1549_uc003vuk.3_Missense_Mutation_p.A372E|KIAA1549_uc011kqj.1_Missense_Mutation_p.A422E	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	422						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						AGTGCAGGCCGCACACCAAGT	0.557			O	BRAF	pilocytic astrocytoma								4	100	---	---	---	---	PASS
RP1L1	94137	broad.mit.edu	37	8	10464585	10464585	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10464585G>T	uc003wtc.2	-	4	7252	c.7023C>A	c.(7021-7023)ACC>ACA	p.T2341T		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2341					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)		GGTACATCCTGGTGGCCTTCC	0.542													5	102	---	---	---	---	PASS
CNOT7	29883	broad.mit.edu	37	8	17090016	17090016	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17090016C>G	uc003wxf.1	-	6	817	c.649G>C	c.(649-651)GAG>CAG	p.E217Q	CNOT7_uc003wxg.1_Missense_Mutation_p.E217Q|CNOT7_uc003wxh.1_Missense_Mutation_p.E217Q	NM_013354	NP_037486	Q9UIV1	CNOT7_HUMAN	CCR4-NOT transcription complex, subunit 7	217					carbohydrate metabolic process|nuclear-transcribed mRNA poly(A) tail shortening	CCR4-NOT complex|cytoplasmic mRNA processing body|cytosol	nucleic acid binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1				Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209)		CGTTCCAGCTCTAACTGTTCT	0.388													34	45	---	---	---	---	PASS
VPS37A	137492	broad.mit.edu	37	8	17137762	17137762	+	Silent	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17137762T>C	uc003wxj.2	+	8	1209	c.856T>C	c.(856-858)TTG>CTG	p.L286L	VPS37A_uc003wxk.2_Silent_p.L261L|VPS37A_uc003wxl.2_Silent_p.L63L	NM_152415	NP_689628	Q8NEZ2	VP37A_HUMAN	hepatocellular carcinoma related protein 1	286					cellular membrane organization|endosome transport|protein transport	centrosome|late endosome membrane|nucleus					0				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		AAATCTCCTTTTGGAGCCCAG	0.318													16	17	---	---	---	---	PASS
LGI3	203190	broad.mit.edu	37	8	22012074	22012074	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22012074G>A	uc003xav.2	-	3	638	c.349C>T	c.(349-351)CTC>TTC	p.L117F	LGI3_uc010ltu.2_Missense_Mutation_p.L117F	NM_139278	NP_644807	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	117	LRR 2.				exocytosis	cell junction|extracellular region|synaptic vesicle|synaptosome				ovary(1)	1				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		CCCACACACAGATACTGCAGG	0.557													24	27	---	---	---	---	PASS
MIR320A	407037	broad.mit.edu	37	8	22102500	22102500	+	RNA	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22102500C>T	hsa-mir-320a|MI0000542	-			c.57C>T			uc011kzd.1_RNA|POLR3D_uc003xbl.2_5'Flank|POLR3D_uc003xbm.2_5'Flank|POLR3D_uc011kze.1_5'Flank																	0						GCCCTCTCAACCCAGCTTTTC	0.647													26	24	---	---	---	---	PASS
EBF2	64641	broad.mit.edu	37	8	25718560	25718560	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25718560G>T	uc003xes.1	-						PPP2R2A_uc003xek.2_Intron|EBF2_uc010lug.1_Intron	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		TAAGAAAGGTGGTACCTTGAT	0.463													4	34	---	---	---	---	PASS
LYPLA1	10434	broad.mit.edu	37	8	54963627	54963627	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54963627G>A	uc003xry.2	-	8	778	c.584C>T	c.(583-585)CCA>CTA	p.P195L	LYPLA1_uc011ldx.1_Missense_Mutation_p.P156L|LYPLA1_uc003xrz.2_Missense_Mutation_p.P174L	NM_006330	NP_006321	O75608	LYPA1_HUMAN	lysophospholipase 1	195					fatty acid metabolic process|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytosol	lysophospholipase activity|palmitoyl-(protein) hydrolase activity			central_nervous_system(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)			CACATTGGCTGGATTCACCAA	0.423													31	69	---	---	---	---	PASS
XKR4	114786	broad.mit.edu	37	8	56270408	56270408	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56270408T>G	uc003xsf.2	+	2	1009	c.977T>G	c.(976-978)GTA>GGA	p.V326G		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	326	Helical; (Potential).					integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)			TGCATTATCGTACAGACTCAT	0.463													10	21	---	---	---	---	PASS
TRIM55	84675	broad.mit.edu	37	8	67040529	67040529	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67040529G>T	uc003xvv.2	+						TRIM55_uc003xvu.2_Intron|TRIM55_uc003xvw.2_Intron|TRIM55_uc003xvx.2_Intron	NM_184085	NP_908973	Q9BYV6	TRI55_HUMAN	tripartite motif-containing 55 isoform 1							cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			TTCTTACTTGGCAAGAACAGG	0.463													24	38	---	---	---	---	PASS
PREX2	80243	broad.mit.edu	37	8	68939562	68939562	+	Intron	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68939562T>A	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						TTTGAAGGTATTTTATGTGCT	0.333													15	34	---	---	---	---	PASS
TRPA1	8989	broad.mit.edu	37	8	72973999	72973999	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72973999G>A	uc003xza.2	-							NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	CTTCCCTTCTGTAAAGGGTTT	0.388													16	30	---	---	---	---	PASS
CNBD1	168975	broad.mit.edu	37	8	88249239	88249239	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88249239C>A	uc003ydy.2	+	6	718	c.670C>A	c.(670-672)CCA>ACA	p.P224T		NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	224										ovary(3)	3						AAGTGATTCACCAGACTCGTT	0.373													22	67	---	---	---	---	PASS
RIMS2	9699	broad.mit.edu	37	8	104922734	104922734	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104922734G>T	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Nonsense_Mutation_p.E412*|RIMS2_uc003ylt.2_5'Flank	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			AACCCTTAACGAGGAGCATAG	0.448										HNSCC(12;0.0054)			4	43	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113484877	113484877	+	Nonsense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113484877T>A	uc003ynu.2	-	32	5497	c.5338A>T	c.(5338-5340)AAA>TAA	p.K1780*	CSMD3_uc003yns.2_Nonsense_Mutation_p.K1052*|CSMD3_uc003ynt.2_Nonsense_Mutation_p.K1740*|CSMD3_uc011lhx.1_Nonsense_Mutation_p.K1676*	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1780	Extracellular (Potential).|CUB 10.					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						CTGTAATTTTTTGGATAGTTT	0.353										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			18	40	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113694737	113694737	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113694737C>T	uc003ynu.2	-	16	2770	c.2611G>A	c.(2611-2613)GAA>AAA	p.E871K	CSMD3_uc003yns.2_Missense_Mutation_p.E143K|CSMD3_uc003ynt.2_Missense_Mutation_p.E831K|CSMD3_uc011lhx.1_Missense_Mutation_p.E767K	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	871	Sushi 4.|Extracellular (Potential).					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						GTAATTGTTTCTGTTCCCTGG	0.373										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			14	43	---	---	---	---	PASS
ENPP2	5168	broad.mit.edu	37	8	120594825	120594825	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120594825G>A	uc003yot.1	-	18	1647	c.1561C>T	c.(1561-1563)CCA>TCA	p.P521S	ENPP2_uc011lic.1_Missense_Mutation_p.P38S|ENPP2_uc003yor.1_Missense_Mutation_p.P160S|ENPP2_uc003yos.1_Missense_Mutation_p.P573S|ENPP2_uc010mdd.1_Missense_Mutation_p.P521S	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein	521					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TTAGGAGCTGGCTTCAATCCC	0.413													35	93	---	---	---	---	PASS
COL14A1	7373	broad.mit.edu	37	8	121292969	121292969	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121292969G>T	uc003yox.2	+	30	3931	c.3666G>T	c.(3664-3666)AAG>AAT	p.K1222N	COL14A1_uc003yoz.2_Missense_Mutation_p.K187N	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	1222	Nonhelical region (NC4).				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TGGTACACAAGGATGGCATTG	0.373													15	22	---	---	---	---	PASS
SNTB1	6641	broad.mit.edu	37	8	121706117	121706117	+	Silent	SNP	C	T	T	rs140148929	byFrequency	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121706117C>T	uc010mdg.2	-	2	829	c.603G>A	c.(601-603)GTG>GTA	p.V201V	SNTB1_uc003ype.2_Silent_p.V201V	NM_021021	NP_066301	Q13884	SNTB1_HUMAN	basic beta 1 syntrophin	201	PH 1.				muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)			ATCCTTTCTTCACATAGGGCG	0.517													13	59	---	---	---	---	PASS
FER1L6	654463	broad.mit.edu	37	8	125109611	125109611	+	Intron	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125109611T>A	uc003yqw.2	+						uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			GTATGTCAGCTGTAGCCCCAG	0.512													13	36	---	---	---	---	PASS
OC90	729330	broad.mit.edu	37	8	133036764	133036764	+	Silent	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133036764C>G	uc003ytg.2	-	13	1398	c.1398G>C	c.(1396-1398)CTG>CTC	p.L466L	OC90_uc011lix.1_Silent_p.L466L	NM_001080399	NP_001073868	Q02509	OC90_HUMAN	otoconin 90	482					lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			CCAAGGGACCCAGTGACTTCC	0.597													5	13	---	---	---	---	PASS
OC90	729330	broad.mit.edu	37	8	133053809	133053809	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133053809A>C	uc003ytg.2	-	3	259	c.259T>G	c.(259-261)TTT>GTT	p.F87V	OC90_uc011lix.1_Missense_Mutation_p.F103V	NM_001080399	NP_001073868	Q02509	OC90_HUMAN	otoconin 90	103	Phospholipase A2-like 1.				lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			TCCATCTCAAACCTGCAGGTG	0.498													21	39	---	---	---	---	PASS
TOPORS	10210	broad.mit.edu	37	9	32541567	32541567	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32541567G>A	uc003zrb.2	-	3	3123	c.2956C>T	c.(2956-2958)CCA>TCA	p.P986S	TOPORS_uc003zrc.2_Missense_Mutation_p.P919S	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	986					DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		GCCAGAGGTGGAATATTATCT	0.398													113	43	---	---	---	---	PASS
RASEF	158158	broad.mit.edu	37	9	85607851	85607851	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85607851G>A	uc004amo.1	-	15	2271	c.2010C>T	c.(2008-2010)GTC>GTT	p.V670V		NM_152573	NP_689786	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	670					protein transport|small GTPase mediated signal transduction	perinuclear region of cytoplasm	calcium ion binding|GTP binding			upper_aerodigestive_tract(1)|lung(1)|breast(1)	3						AGTGCCCTGGGACACATTTTT	0.493													25	46	---	---	---	---	PASS
CTSL3	392360	broad.mit.edu	37	9	90388065	90388065	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90388065A>T	uc004apm.1	+	2	136	c.130A>T	c.(130-132)AGG>TGG	p.R44W		NR_027917				RecName: Full=Putative cathepsin L-like protein 3;          Short=Cathepsin L-like protein; AltName: Full=HCTSL-s;											ovary(1)	1						CCAGAAGCACAGGAAGGGGAA	0.438													26	53	---	---	---	---	PASS
FBP2	8789	broad.mit.edu	37	9	97333785	97333785	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97333785G>A	uc004auv.2	-	4	593	c.526C>T	c.(526-528)CTC>TTC	p.L176F	uc004auu.2_Intron	NM_003837	NP_003828	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	176					fructose metabolic process|gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)				CCTGTGGAGAGAGCCACCAGG	0.567													7	26	---	---	---	---	PASS
C9orf102	375748	broad.mit.edu	37	9	98669439	98669439	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98669439C>G	uc004avt.3	+	4	1095	c.707C>G	c.(706-708)ACT>AGT	p.T236S	C9orf102_uc010mrx.1_RNA|C9orf102_uc011lum.1_Intron|C9orf102_uc010mry.1_Intron|C9orf102_uc010mrz.2_Missense_Mutation_p.T47S	NM_001010895	NP_001010895	Q5T890	RAD26_HUMAN	RAD26L hypothetical protein	236	Helicase ATP-binding.				DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)				TTCAGAGTCACTGTTTTACAT	0.348													14	26	---	---	---	---	PASS
CTSL2	1515	broad.mit.edu	37	9	99797040	99797040	+	Silent	SNP	C	T	T	rs145877427		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99797040C>T	uc004awt.2	-	7	1070	c.873G>A	c.(871-873)TCG>TCA	p.S291S	CTSL2_uc010msi.2_Silent_p.S291S|CTSL2_uc004awu.2_Silent_p.S236S|CTSL2_uc010msj.1_Silent_p.S236S	NM_001333	NP_001324	O60911	CATL2_HUMAN	cathepsin L2 preproprotein	291						lysosome	cysteine-type endopeptidase activity				0		Acute lymphoblastic leukemia(62;0.0559)				TGCTGTTATTCGAATTTGCTC	0.383													14	39	---	---	---	---	PASS
ALG2	85365	broad.mit.edu	37	9	101980956	101980956	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101980956C>T	uc004azf.2	-	2	581	c.511G>A	c.(511-513)GAC>AAC	p.D171N	ALG2_uc004azg.2_Missense_Mutation_p.D78N	NM_033087	NP_149078	Q9H553	ALG2_HUMAN	alpha-1,3-mannosyltransferase ALG2	171					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in endoplasmic reticulum|protein N-linked glycosylation via asparagine|response to calcium ion	endoplasmic reticulum membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	alpha-1,3-mannosyltransferase activity|calcium-dependent protein binding|glycolipid 3-alpha-mannosyltransferase activity|protein anchor|protein heterodimerization activity|protein N-terminus binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0559)				AAGATGCAGTCTGCCATGCCT	0.448													13	36	---	---	---	---	PASS
RNF20	56254	broad.mit.edu	37	9	104309415	104309415	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104309415G>A	uc004bbn.2	+							NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20						histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TGTGTTCTCTGTAGGTGAATT	0.418													29	54	---	---	---	---	PASS
CYLC2	1539	broad.mit.edu	37	9	105767646	105767646	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105767646G>T	uc004bbs.2	+	5	803	c.733G>T	c.(733-735)GAG>TAG	p.E245*		NM_001340	NP_001331	Q14093	CYLC2_HUMAN	cylicin 2	245	31 X 3 AA repeats of K-K-X.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			skin(1)	1		all_hematologic(171;0.125)				AAAGAAGGATGAGGATGGAAA	0.368													6	103	---	---	---	---	PASS
ZNF883	169834	broad.mit.edu	37	9	115760266	115760266	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115760266T>C	uc011lwy.1	-	5	1513	c.274A>G	c.(274-276)ACT>GCT	p.T92A		NM_001101338	NP_001094808	P0CG24	ZN883_HUMAN	hypothetical protein LOC169834	92					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTCTCCCCAGTATGGACTCTT	0.363													15	27	---	---	---	---	PASS
AKNA	80709	broad.mit.edu	37	9	117122322	117122322	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117122322G>T	uc004biq.3	-	9	2280	c.2145C>A	c.(2143-2145)GCC>GCA	p.A715A	AKNA_uc004bin.3_5'UTR|AKNA_uc004bio.3_Silent_p.A175A|AKNA_uc004bip.3_Silent_p.A634A|AKNA_uc004bir.3_Silent_p.A715A|AKNA_uc004bis.3_Silent_p.A715A|AKNA_uc010mve.2_Silent_p.A596A|AKNA_uc004biu.1_Silent_p.A456A|AKNA_uc004biv.1_Silent_p.A715A	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	715					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6						CAGTGCTGGCGGCGGCAGTGG	0.587													4	18	---	---	---	---	PASS
CDK5RAP2	55755	broad.mit.edu	37	9	123220895	123220895	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123220895C>G	uc004bkf.2	-	20	2389	c.2208G>C	c.(2206-2208)ATG>ATC	p.M736I	CDK5RAP2_uc004bke.2_Missense_Mutation_p.M21I|CDK5RAP2_uc004bkg.2_Missense_Mutation_p.M736I|CDK5RAP2_uc011lxw.1_Missense_Mutation_p.M1I|CDK5RAP2_uc011lxx.1_RNA|CDK5RAP2_uc011lxy.1_RNA|CDK5RAP2_uc011lxz.1_Missense_Mutation_p.M1I|CDK5RAP2_uc011lya.1_Missense_Mutation_p.M1I|CDK5RAP2_uc004bkh.1_Intron|CDK5RAP2_uc004bki.2_Missense_Mutation_p.M503I	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	736					brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4						AAAGGTCTTTCATAATCTGCA	0.453													8	68	---	---	---	---	PASS
PHF19	26147	broad.mit.edu	37	9	123636960	123636960	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123636960G>T	uc004bks.1	-	2	313	c.60C>A	c.(58-60)CTC>CTA	p.L20L	PHF19_uc004bkt.2_Silent_p.L20L|PHF19_uc010mvk.2_Silent_p.L20L	NM_015651	NP_056466	Q5T6S3	PHF19_HUMAN	PHD finger protein 19 isoform a	20					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|breast(1)	2						CCTTGTTGGGGAGGTGGCTGG	0.567													6	85	---	---	---	---	PASS
TTC16	158248	broad.mit.edu	37	9	130489368	130489368	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130489368C>A	uc004brq.1	+	11	1612	c.1545C>A	c.(1543-1545)GCC>GCA	p.A515A	PTRH1_uc011mah.1_5'Flank|TTC16_uc011mai.1_Silent_p.A502A|TTC16_uc004brr.1_Intron|TTC16_uc010mxn.1_Silent_p.A111A	NM_144965	NP_659402	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	515							binding				0						GCCTGCAGGCCGGCAGCCCAC	0.662													3	14	---	---	---	---	PASS
SLC25A25	114789	broad.mit.edu	37	9	130869708	130869708	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130869708C>A	uc004bte.2	+	10	1424	c.1395C>A	c.(1393-1395)GGC>GGA	p.G465G	SLC25A25_uc004btb.2_Silent_p.G499G|SLC25A25_uc004btc.2_Silent_p.G485G|SLC25A25_uc004btd.2_Silent_p.G497G|SLC25A25_uc004btf.2_Silent_p.G362G	NM_052901	NP_443133	Q6KCM7	SCMC2_HUMAN	solute carrier family 25, member 25 isoform a	465	Mitochondrial intermembrane (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding				0						TCACCCTGGGCGTGCAGTCGC	0.637													22	83	---	---	---	---	PASS
GOLGA2	2801	broad.mit.edu	37	9	131021485	131021485	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131021485C>T	uc011maw.1	-	19	1990	c.1977G>A	c.(1975-1977)GCG>GCA	p.A659A	GOLGA2_uc010mxw.2_Intron|GOLGA2_uc004buh.2_Silent_p.A132A	NM_004486	NP_004477	Q08379	GOGA2_HUMAN	Golgi autoantigen, golgin subfamily a, 2	659	Potential.					Golgi cisterna membrane	protein binding			ovary(1)	1						TCTCGGCCACCGCTTTGCCCT	0.617													7	20	---	---	---	---	PASS
OBP2A	29991	broad.mit.edu	37	9	138439740	138439740	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138439740C>A	uc004cgb.2	+	4	343	c.301C>A	c.(301-303)CTG>ATG	p.L101M	OBP2A_uc004cgc.2_Missense_Mutation_p.L101M|OBP2A_uc010nau.2_RNA|OBP2A_uc010nav.2_Missense_Mutation_p.P56H	NM_014582	NP_055397	Q9NY56	OBP2A_HUMAN	odorant binding protein 2A precursor	101					response to stimulus|sensory perception of smell	extracellular region	odorant binding|transporter activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		GCTCATATACCTGCAGGAGCT	0.587													10	24	---	---	---	---	PASS
NOTCH1	4851	broad.mit.edu	37	9	139402784	139402784	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139402784C>T	uc004chz.2	-	20	3225	c.3225G>A	c.(3223-3225)TGG>TGA	p.W1075*	NOTCH1_uc004cia.1_Nonsense_Mutation_p.W305*	NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	1075	Extracellular (Potential).|EGF-like 28.				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGTGGGTCTGCCAGCATTTGC	0.662			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			13	68	---	---	---	---	PASS
GPR158	57512	broad.mit.edu	37	10	25885705	25885705	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25885705C>A	uc001isj.2	+	10	2192	c.2132C>A	c.(2131-2133)CCA>CAA	p.P711Q	GPR158_uc001isk.2_Missense_Mutation_p.P86Q	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	711	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8						AGCTTGGATCCAGAGGACATT	0.483													19	27	---	---	---	---	PASS
ARMC4	55130	broad.mit.edu	37	10	28228919	28228919	+	Silent	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28228919T>A	uc009xky.2	-	14	2102	c.2004A>T	c.(2002-2004)GCA>GCT	p.A668A	ARMC4_uc010qds.1_Silent_p.A193A|ARMC4_uc010qdt.1_Silent_p.A360A|ARMC4_uc001itz.2_Silent_p.A668A	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	668	ARM 4.|HEAT.						binding			ovary(4)|skin(2)	6						CTGCTTTGATTGCAGCCCGGT	0.388													11	19	---	---	---	---	PASS
MPP7	143098	broad.mit.edu	37	10	28345494	28345494	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28345494G>T	uc001iua.1	-	18	1870	c.1466C>A	c.(1465-1467)CCA>CAA	p.P489Q	MPP7_uc009xkz.1_RNA|MPP7_uc001iub.1_Missense_Mutation_p.P489Q|MPP7_uc009xla.2_Missense_Mutation_p.P489Q|MPP7_uc010qdv.1_RNA	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7	489	Guanylate kinase-like.				establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1						CTCTATTGATGGAGGCTTTAT	0.358													7	87	---	---	---	---	PASS
ZNF33A	7581	broad.mit.edu	37	10	38344482	38344482	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38344482C>A	uc001izh.2	+	5	1605	c.1427C>A	c.(1426-1428)TCC>TAC	p.S476Y	ZNF33A_uc001izg.2_Missense_Mutation_p.S477Y|ZNF33A_uc010qev.1_Missense_Mutation_p.S483Y|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	476	C2H2-type 6.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						TGTGGGAAATCCTTTAGTGAA	0.383													17	23	---	---	---	---	PASS
ZNF33A	7581	broad.mit.edu	37	10	38344544	38344544	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38344544G>A	uc001izh.2	+	5	1667	c.1489G>A	c.(1489-1491)GAA>AAA	p.E497K	ZNF33A_uc001izg.2_Missense_Mutation_p.E498K|ZNF33A_uc010qev.1_Missense_Mutation_p.E504K|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	497	C2H2-type 7.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3						TAAATCTTATGAATGTAATGC	0.368													8	39	---	---	---	---	PASS
ZNF37A	7587	broad.mit.edu	37	10	38406785	38406785	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38406785A>T	uc001izk.2	+	8	1525	c.706A>T	c.(706-708)ACC>TCC	p.T236S	ZNF37A_uc001izl.2_Missense_Mutation_p.T236S|ZNF37A_uc001izm.2_Missense_Mutation_p.T236S	NM_001007094	NP_001007095	P17032	ZN37A_HUMAN	zinc finger protein 37a	236						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)	1						AATTCAGAGAACCCACTCAAT	0.333													15	25	---	---	---	---	PASS
ZNF485	220992	broad.mit.edu	37	10	44111890	44111890	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44111890G>T	uc010qfc.1	+	5	593	c.399G>T	c.(397-399)AAG>AAT	p.K133N	ZNF485_uc010qfd.1_Missense_Mutation_p.K42N	NM_145312	NP_660355	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	133	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ATAAGTGCAAGGAATGTGGGA	0.448													5	65	---	---	---	---	PASS
RASSF4	83937	broad.mit.edu	37	10	45480357	45480357	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45480357G>A	uc001jbo.2	+	6	604	c.470G>A	c.(469-471)GGT>GAT	p.G157D	RASSF4_uc001jbp.2_Missense_Mutation_p.G188D|RASSF4_uc009xmn.2_Missense_Mutation_p.G87D|RASSF4_uc001jbq.2_Missense_Mutation_p.G54D|RASSF4_uc001jbt.2_Missense_Mutation_p.G114D	NM_032023	NP_114412	Q9H2L5	RASF4_HUMAN	Ras association domain family 4	157					cell cycle|signal transduction		protein binding			large_intestine(1)	1						CGCGCCCCCGGTGAGGCCCAG	0.677													17	48	---	---	---	---	PASS
IPMK	253430	broad.mit.edu	37	10	59986886	59986886	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59986886G>A	uc001jkb.2	-	3	614	c.291C>T	c.(289-291)GAC>GAT	p.D97D		NM_152230	NP_689416	Q8NFU5	IPMK_HUMAN	inositol polyphosphate multikinase	97						nucleus	ATP binding|inositol trisphosphate 6-kinase activity			ovary(1)	1						CATCAAAACAGTCAGCAGCAT	0.353													18	47	---	---	---	---	PASS
USP54	159195	broad.mit.edu	37	10	75276843	75276843	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75276843C>A	uc001juo.2	-	18	3358	c.3341G>T	c.(3340-3342)AGT>ATT	p.S1114I	USP54_uc010qkk.1_Missense_Mutation_p.S296I|USP54_uc001juk.2_Missense_Mutation_p.S202I|USP54_uc001jul.2_Missense_Mutation_p.S202I|USP54_uc001jum.2_RNA|USP54_uc001jun.2_RNA	NM_152586	NP_689799	Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1114					ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)					GGTCTCCTCACTGCCTCTGTC	0.498													23	35	---	---	---	---	PASS
MYST4	23522	broad.mit.edu	37	10	76790376	76790376	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76790376C>A	uc001jwn.1	+	18	6287	c.5794C>A	c.(5794-5796)CTG>ATG	p.L1932M	MYST4_uc001jwo.1_Missense_Mutation_p.L1640M|MYST4_uc001jwp.1_Missense_Mutation_p.L1749M	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	1932	Interaction with RUNX1 and RUNX2.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)					GTCAGCGTCTCTGTCACCAGC	0.532			T	CREBBP	AML								5	60	---	---	---	---	PASS
SFTPD	6441	broad.mit.edu	37	10	81701710	81701710	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81701710C>A	uc001kbh.2	-	5	593	c.550G>T	c.(550-552)GGG>TGG	p.G184W	MBL1P_uc001kbf.2_Intron	NM_003019	NP_003010	P35247	SFTPD_HUMAN	pulmonary surfactant-associated protein D	184	Collagen-like.				cell junction assembly|innate immune response|lung alveolus development|macrophage chemotaxis|negative regulation of interleukin-2 biosynthetic process|negative regulation of T cell proliferation|positive regulation of phagocytosis|reactive oxygen species metabolic process|receptor-mediated endocytosis|respiratory gaseous exchange|surfactant homeostasis	collagen|endocytic vesicle|extracellular space|lysosome	bacterial cell surface binding|protein binding|sugar binding			skin(1)	1	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			CACTGCTCACCTGCTGCCCCT	0.642													5	50	---	---	---	---	PASS
MARCH5	54708	broad.mit.edu	37	10	94109448	94109448	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94109448C>A	uc001khx.1	+	5	906	c.574C>A	c.(574-576)CGA>AGA	p.R192R	MARCH5_uc010qno.1_Silent_p.R88R	NM_017824	NP_060294	Q9NX47	MARH5_HUMAN	membrane-associated ring finger (C3HC4) 5	192					cell aging|protein autoubiquitination|protein localization in mitochondrion|protein polyubiquitination|regulation of mitochondrial fission	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane	GTPase binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1						TCCTGTTCCTCGAATTCCAGC	0.418													8	289	---	---	---	---	PASS
ABCC2	1244	broad.mit.edu	37	10	101604082	101604082	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101604082C>A	uc001kqf.2	+	28	3986	c.3847C>A	c.(3847-3849)CCC>ACC	p.P1283T		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	1283	Cytoplasmic (By similarity).					apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	TTGCCAGGCACCCTGGGTGAC	0.527													15	30	---	---	---	---	PASS
AS3MT	57412	broad.mit.edu	37	10	104638234	104638234	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104638234A>T	uc001kwk.2	+	8	849	c.709A>T	c.(709-711)ACA>TCA	p.T237S	AS3MT_uc001kwj.2_Missense_Mutation_p.T239S|AS3MT_uc009xxh.2_Missense_Mutation_p.T237S	NM_020682	NP_065733	Q9HBK9	AS3MT_HUMAN	arsenic (+3 oxidation state) methyltransferase	237					arsonoacetate metabolic process|toxin metabolic process	cytosol	arsenite methyltransferase activity|methylarsonite methyltransferase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)		CAATCTCATTACAATTCAAAA	0.418													24	73	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	114063077	114063077	+	IGR	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114063077G>T								TECTB (7 upstream) : GUCY2GP (4860 downstream)																							ATAGGAGTTAGCCAGGCAGCT	0.498													13	29	---	---	---	---	PASS
ADRB1	153	broad.mit.edu	37	10	115804389	115804389	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115804389C>A	uc001lba.2	+	1	584	c.498C>A	c.(496-498)TAC>TAA	p.Y166*		NM_000684	NP_000675	P08588	ADRB1_HUMAN	beta-1-adrenergic receptor	166	Cytoplasmic (By similarity).				positive regulation of cAMP biosynthetic process	integral to plasma membrane	alpha-2A adrenergic receptor binding|beta1-adrenergic receptor activity|protein heterodimerization activity				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Arbutamine(DB01102)|Atenolol(DB00335)|Betaxolol(DB00195)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Desipramine(DB01151)|Dobutamine(DB00841)|Dopamine(DB00988)|Epinephrine(DB00668)|Esmolol(DB00187)|Isoetharine(DB00221)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Metoprolol(DB00264)|Nadolol(DB01203)|Norepinephrine(DB00368)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Practolol(DB01297)|Propranolol(DB00571)|Risperidone(DB00734)|Timolol(DB00373)|Ziprasidone(DB00246)	CCTTCCGCTACCAGAGCCTGC	0.572													16	32	---	---	---	---	PASS
PNLIPRP1	5407	broad.mit.edu	37	10	118363606	118363606	+	Silent	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118363606T>A	uc001lco.1	+	11	1146	c.1128T>A	c.(1126-1128)GCT>GCA	p.A376A	PNLIPRP1_uc001lcp.2_Silent_p.A376A	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor	376	PLAT.				lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)		TCAAAGTTGCTTTGTTTGGAA	0.413													5	16	---	---	---	---	PASS
KCNK18	338567	broad.mit.edu	37	10	118957018	118957018	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118957018C>G	uc010qsr.1	+	1	19	c.19C>G	c.(19-21)CCC>GCC	p.P7A		NM_181840	NP_862823	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	7	Cytoplasmic (Potential).					integral to membrane|plasma membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;0.19)		all cancers(201;0.0211)		CTCGGGGCACCCCCAGGCCAG	0.632													11	22	---	---	---	---	PASS
EIF3A	8661	broad.mit.edu	37	10	120797901	120797901	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120797901G>T	uc001ldu.2	-	20	3723	c.3577C>A	c.(3577-3579)CGA>AGA	p.R1193R	EIF3A_uc010qsu.1_Silent_p.R1159R|EIF3A_uc009xzg.1_Silent_p.R232R	NM_003750	NP_003741	Q14152	EIF3A_HUMAN	eukaryotic translation initiation factor 3,	1193	Asp-rich.				formation of translation initiation complex	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|structural molecule activity|translation initiation factor activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		CTTGATTCTCGAGGTGGACCC	0.244													6	152	---	---	---	---	PASS
PPAPDC1A	196051	broad.mit.edu	37	10	122263319	122263319	+	Intron	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122263319T>C	uc001lev.1	+						PPAPDC1A_uc010qtd.1_Intron|PPAPDC1A_uc009xzl.1_Intron|PPAPDC1A_uc001lew.1_Intron|PPAPDC1A_uc001lex.1_Intron|PPAPDC1A_uc001ley.1_Intron	NM_001030059	NP_001025230	Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain						phospholipid dephosphorylation	integral to membrane	phosphatidate phosphatase activity			breast(1)	1		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)		ACTTTTCTTTTTATGTTTCAG	0.468													6	14	---	---	---	---	PASS
CUZD1	50624	broad.mit.edu	37	10	124594350	124594350	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124594350C>T	uc001lgq.2	-	7	1586	c.1254G>A	c.(1252-1254)TTG>TTA	p.L418L	CUZD1_uc001lgp.2_Silent_p.L137L|CUZD1_uc009yad.2_Silent_p.L137L|CUZD1_uc009yaf.2_Silent_p.L52L|CUZD1_uc001lgr.2_Silent_p.L137L|CUZD1_uc010qty.1_Silent_p.L137L|CUZD1_uc009yae.2_Silent_p.L137L|CUZD1_uc001lgs.2_Silent_p.L418L|CUZD1_uc010qtz.1_Silent_p.L418L	NM_022034	NP_071317	Q86UP6	CUZD1_HUMAN	CUB and zona pellucida-like domains 1 precursor	418	Extracellular (Potential).|ZP.				cell cycle|cell division|cell proliferation|substrate-dependent cell migration, cell attachment to substrate|trypsinogen activation	integral to membrane|transport vesicle membrane|zymogen granule membrane				ovary(1)|skin(1)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)		GAGTTTGGTTCAAATCCACAT	0.383													10	25	---	---	---	---	PASS
SIRT3	23410	broad.mit.edu	37	11	218844	218844	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:218844C>A	uc001lok.3	-	6	1201	c.1167G>T	c.(1165-1167)CGG>CGT	p.R389R	SIRT3_uc001loj.3_Silent_p.R247R|SIRT3_uc010qvm.1_Silent_p.R325R|SIRT3_uc010qvn.1_Silent_p.R308R|SIRT3_uc010qvo.1_Silent_p.R389R|SIRT3_uc010qvp.1_Silent_p.R335R|SIRT3_uc010qvq.1_Silent_p.R247R	NM_012239	NP_036371	Q9NTG7	SIRT3_HUMAN	sirtuin 3 isoform a	389					chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding			urinary_tract(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		TCCCAGTTTCCCGCTGCACAA	0.607													13	35	---	---	---	---	PASS
ATHL1	80162	broad.mit.edu	37	11	292014	292014	+	Silent	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:292014A>G	uc010qvu.1	+	5	1060	c.945A>G	c.(943-945)CCA>CCG	p.P315P	ATHL1_uc001lor.3_Silent_p.P138P|ATHL1_uc001los.1_Silent_p.P315P|ATHL1_uc001lou.3_5'Flank|ATHL1_uc001lov.3_5'Flank	NM_025092	NP_079368	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1	315					carbohydrate metabolic process		hydrolase activity, acting on glycosyl bonds			liver(1)|central_nervous_system(1)|skin(1)	3		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		TGTTCCACCCAGAAGCCGCCA	0.672													5	10	---	---	---	---	PASS
TRPM5	29850	broad.mit.edu	37	11	2426276	2426276	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2426276G>T	uc001lwm.3	-						TRPM5_uc010qxl.1_Intron|TRPM5_uc009ydn.2_Intron	NM_014555	NP_055370	Q9NZQ8	TRPM5_HUMAN	transient receptor potential cation channel,							integral to membrane|plasma membrane	receptor activity|voltage-gated ion channel activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		CTGAGAGCCTGCTGGGAAGGA	0.672													9	13	---	---	---	---	PASS
OR51F1	256892	broad.mit.edu	37	11	4790944	4790944	+	Silent	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4790944T>C	uc010qyl.1	-	1	204	c.204A>G	c.(202-204)CTA>CTG	p.L68L		NM_001004752	NP_001004752	A6NLW9	A6NLW9_HUMAN	olfactory receptor, family 51, subfamily F,	68						integral to membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		CAGTGGCTGATAGCCTGAAGA	0.448													11	25	---	---	---	---	PASS
OR51S1	119692	broad.mit.edu	37	11	4870257	4870257	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4870257G>A	uc010qyo.1	-	1	182	c.182C>T	c.(181-183)CCC>CTC	p.P61L		NM_001004758	NP_001004758	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S,	61	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGCAGGGCGGGCTGCAGGGC	0.562													22	38	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	5220956	5220956	+	IGR	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5220956C>A								OR52A1 (47357 upstream) : OR51V1 (10 downstream)																							CAATACATCTCAATATCTCTC	0.303													13	34	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6644526	6644526	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6644526G>A	uc001mem.1	-	21	8791	c.8381C>T	c.(8380-8382)TCA>TTA	p.S2794L		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	2794	Cadherin 26.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GACAGAGGCTGAGAGATTCCC	0.567													4	8	---	---	---	---	PASS
OR5P2	120065	broad.mit.edu	37	11	7818157	7818157	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7818157C>A	uc001mfp.1	-	1	333	c.333G>T	c.(331-333)CTG>CTT	p.L111L		NM_153444	NP_703145	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P,	111	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCATGGCAGCCAGAAGGACGC	0.473													40	86	---	---	---	---	PASS
MICALCL	84953	broad.mit.edu	37	11	12316029	12316029	+	Missense_Mutation	SNP	C	T	T	rs113400332		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12316029C>T	uc001mkg.1	+	3	1342	c.1051C>T	c.(1051-1053)CGG>TGG	p.R351W		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	351					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding			skin(1)	1				Epithelial(150;0.00177)		TTTGCCCAATCGGCCATCCAA	0.552													35	80	---	---	---	---	PASS
ANO3	63982	broad.mit.edu	37	11	26574888	26574888	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26574888C>A	uc001mqt.3	+	13	1527	c.1382C>A	c.(1381-1383)GCC>GAC	p.A461D	ANO3_uc010rdr.1_Missense_Mutation_p.A445D|ANO3_uc010rds.1_Missense_Mutation_p.A300D|ANO3_uc010rdt.1_Missense_Mutation_p.A315D	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	461	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TGTATCTATGCCAAGGTGAGT	0.458													58	107	---	---	---	---	PASS
NAT10	55226	broad.mit.edu	37	11	34158541	34158541	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34158541G>T	uc001mvk.2	+	21	2423	c.2179G>T	c.(2179-2181)GGA>TGA	p.G727*	NAT10_uc010ren.1_Nonsense_Mutation_p.G655*	NM_024662	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 isoform a	727	N-acetyltransferase.|Required for localization to the nucleolus and midbody.					nucleolus	ATP binding|N-acetyltransferase activity|protein binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				GAAACGAGCTGGATTTGTTCC	0.512													4	18	---	---	---	---	PASS
CRY2	1408	broad.mit.edu	37	11	45889225	45889225	+	Silent	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45889225A>T	uc010rgn.1	+	6	889	c.867A>T	c.(865-867)ACA>ACT	p.T289T	CRY2_uc009ykw.2_Silent_p.T207T|CRY2_uc010rgo.1_Silent_p.T11T	NM_021117	NP_066940	Q49AN0	CRY2_HUMAN	cryptochrome 2 (photolyase-like) isoform 1	268	FAD-binding.				DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	blue light photoreceptor activity|damaged DNA binding|DNA photolyase activity|nucleotide binding|protein binding|single-stranded DNA binding			central_nervous_system(1)	1						CCAGCCCCACAGGCCTCAGCC	0.572													21	53	---	---	---	---	PASS
KBTBD4	55709	broad.mit.edu	37	11	47595308	47595308	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47595308C>A	uc001nfx.2	-	4	902	c.731G>T	c.(730-732)GGG>GTG	p.G244V	NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_Missense_Mutation_p.G269V|KBTBD4_uc001nfz.2_Missense_Mutation_p.G260V|KBTBD4_uc001nfy.2_Missense_Mutation_p.G244V	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	244	Kelch 1.									ovary(1)|central_nervous_system(1)	2						TGACTCTTTCCCAATCAGGTA	0.433													5	75	---	---	---	---	PASS
AGBL2	79841	broad.mit.edu	37	11	47712000	47712000	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47712000C>A	uc001ngg.2	-	9	1359	c.1259G>T	c.(1258-1260)TGC>TTC	p.C420F	AGBL2_uc001ngf.2_RNA|AGBL2_uc010rhq.1_Missense_Mutation_p.C382F|AGBL2_uc001ngh.1_Missense_Mutation_p.C364F	NM_024783	NP_079059	Q5U5Z8	CBPC2_HUMAN	carboxypeptidase 2, cytosolic	420					proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2						TTGGAGCTTGCAGAACTGAGA	0.478													22	40	---	---	---	---	PASS
OR4C12	283093	broad.mit.edu	37	11	50003265	50003265	+	Missense_Mutation	SNP	C	G	G	rs141386333		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50003265C>G	uc010ria.1	-	1	773	c.773G>C	c.(772-774)CGC>CCC	p.R258P		NM_001005270	NP_001005270	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C,	258	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3						GGTCACTGAGCGCAGATACAC	0.433													5	30	---	---	---	---	PASS
OR8K1	390157	broad.mit.edu	37	11	56113634	56113634	+	Silent	SNP	A	T	T	rs149499466		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56113634A>T	uc010rjg.1	+	1	120	c.120A>T	c.(118-120)ATA>ATT	p.I40I		NM_001002907	NP_001002907	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K,	40	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)					TCCTCATCATATATCTGGTCA	0.463										HNSCC(65;0.19)			14	33	---	---	---	---	PASS
FADS2	9415	broad.mit.edu	37	11	61624947	61624947	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61624947C>G	uc001nsl.1	+	7	977	c.827C>G	c.(826-828)CCC>CGC	p.P276R	FADS2_uc001nsj.2_Missense_Mutation_p.P254R|FADS2_uc010rlo.1_Missense_Mutation_p.P245R|FADS2_uc001nsk.2_Missense_Mutation_p.P276R	NM_004265	NP_004256	O95864	FADS2_HUMAN	fatty acid desaturase 2	276	Helical; (Potential).				electron transport chain|transport|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	heme binding			ovary(1)|pancreas(1)	2					Alpha-Linolenic Acid(DB00132)	CTGCTCATCCCCATGTATTTC	0.592													11	48	---	---	---	---	PASS
SPTBN2	6712	broad.mit.edu	37	11	66463960	66463960	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66463960C>A	uc001ojd.2	-	20	4138	c.4066G>T	c.(4066-4068)GAG>TAG	p.E1356*		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1356	Spectrin 10.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						CTCAGCTTCTCCGACACCAGG	0.577													6	131	---	---	---	---	PASS
CPT1A	1374	broad.mit.edu	37	11	68552317	68552317	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68552317C>A	uc001oog.3	-	10	1299	c.1129G>T	c.(1129-1131)GAG>TAG	p.E377*	CPT1A_uc001oof.3_Nonsense_Mutation_p.E377*|CPT1A_uc009ysj.2_Intron	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform	377	Cytoplasmic (Potential).				carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)	AGCCTGGCCTCCCCGGGCTGA	0.657													5	16	---	---	---	---	PASS
MAP6	4135	broad.mit.edu	37	11	75299068	75299068	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75299068G>T	uc001owu.2	-	4	1543	c.1478C>A	c.(1477-1479)CCA>CAA	p.P493Q		NM_033063	NP_149052	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6 isoform 1	493	Pro-rich.					Golgi apparatus|microtubule|perinuclear region of cytoplasm	calmodulin binding				0	Ovarian(111;0.11)					TAGATCCTTTGGAGGCCCTGG	0.512													6	109	---	---	---	---	PASS
DLG2	1740	broad.mit.edu	37	11	83182671	83182671	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83182671G>C	uc001paj.2	-	19	2432	c.2129C>G	c.(2128-2130)CCT>CGT	p.P710R	DLG2_uc001pai.2_Missense_Mutation_p.P589R|DLG2_uc010rsy.1_Missense_Mutation_p.P659R|DLG2_uc010rsz.1_Missense_Mutation_p.P706R|DLG2_uc010rta.1_Missense_Mutation_p.P692R|DLG2_uc001pak.2_Missense_Mutation_p.P815R|DLG2_uc010rtb.1_Missense_Mutation_p.P677R|DLG2_uc010rsw.1_Missense_Mutation_p.P174R|DLG2_uc010rsx.1_Missense_Mutation_p.P187R	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2	710	Guanylate kinase-like.					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)				ACACTTACGAGGCACACAGGA	0.428													11	27	---	---	---	---	PASS
DLG2	1740	broad.mit.edu	37	11	83673930	83673930	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83673930G>A	uc001paj.2	-	9	1326	c.1023C>T	c.(1021-1023)ACC>ACT	p.T341T	DLG2_uc001pai.2_Silent_p.T290T|DLG2_uc010rsy.1_Silent_p.T308T|DLG2_uc010rsz.1_Silent_p.T341T|DLG2_uc010rta.1_Silent_p.T341T|DLG2_uc001pak.2_Silent_p.T446T|DLG2_uc010rtb.1_Silent_p.T308T|DLG2_uc001pal.1_Silent_p.T341T|DLG2_uc001pam.1_Silent_p.T380T	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2	341						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)				TATCTGACCTGGTGTAGTCGT	0.418													22	54	---	---	---	---	PASS
HEPHL1	341208	broad.mit.edu	37	11	93800724	93800724	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93800724T>A	uc001pep.2	+	5	1028	c.871T>A	c.(871-873)TCC>ACC	p.S291T	uc001pen.1_RNA	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	291	Plastocyanin-like 2.|Extracellular (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				AGAATCTGTGTCCTGGCACCT	0.473													53	98	---	---	---	---	PASS
KIAA1377	57562	broad.mit.edu	37	11	101829038	101829038	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101829038C>A	uc001pgm.2	+	5	916	c.646C>A	c.(646-648)CAG>AAG	p.Q216K	KIAA1377_uc001pgn.2_Missense_Mutation_p.Q172K|KIAA1377_uc010run.1_Missense_Mutation_p.Q17K|KIAA1377_uc009yxa.1_Missense_Mutation_p.Q17K	NM_020802	NP_065853	Q9P2H0	K1377_HUMAN	hypothetical protein LOC57562	216							protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AAATGTGTTCCAGCTTAAACT	0.338													6	180	---	---	---	---	PASS
OR4D5	219875	broad.mit.edu	37	11	123810587	123810587	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123810587C>T	uc001pzk.1	+	1	264	c.264C>T	c.(262-264)GGC>GGT	p.G88G		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	88	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		TGCTCTCAGGCAACCCTACCA	0.473													23	42	---	---	---	---	PASS
OR10G9	219870	broad.mit.edu	37	11	123894342	123894342	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123894342G>T	uc010sad.1	+	1	623	c.623G>T	c.(622-624)GGC>GTC	p.G208V		NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,	208	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GTGGCCTCGGGCTGCTTTCTC	0.552													25	57	---	---	---	---	PASS
OR10G8	219869	broad.mit.edu	37	11	123900599	123900599	+	Silent	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123900599T>C	uc001pzp.1	+	1	270	c.270T>C	c.(268-270)GCT>GCC	p.A90A		NM_001004464	NP_001004464	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G,	90	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GTGGCAGGGCTATCTCCTTCC	0.517													21	59	---	---	---	---	PASS
ROBO4	54538	broad.mit.edu	37	11	124766101	124766101	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124766101G>A	uc001qbg.2	-	4	812	c.672C>T	c.(670-672)TCC>TCT	p.S224S	ROBO4_uc010sas.1_Silent_p.S79S|ROBO4_uc001qbh.2_Silent_p.S114S|ROBO4_uc001qbi.2_5'Flank|ROBO4_uc010sat.1_5'Flank	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	224	Ig-like C2-type 2.				angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		TACCCTGGATGGAAACCCGGG	0.602													12	33	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2566724	2566724	+	Intron	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2566724C>A	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	TCTCTTTCCTCTCTTCTAGGC	0.527													5	60	---	---	---	---	PASS
DYRK4	8798	broad.mit.edu	37	12	4705872	4705872	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4705872C>A	uc001qmx.2	+	6	697	c.537C>A	c.(535-537)TTC>TTA	p.F179L	DYRK4_uc009zeh.1_Missense_Mutation_p.F294L|DYRK4_uc001qmy.1_Missense_Mutation_p.F179L	NM_003845	NP_003836	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	179	Protein kinase.					Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)			GCAATCACTTCTGCATCACCT	0.423													14	39	---	---	---	---	PASS
AKAP3	10566	broad.mit.edu	37	12	4735746	4735746	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4735746T>A	uc001qnb.3	-	4	2551	c.2322A>T	c.(2320-2322)CAA>CAT	p.Q774H		NM_006422	NP_006413	O75969	AKAP3_HUMAN	A-kinase anchor protein 3	774					acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding			skin(3)|large_intestine(1)|ovary(1)|kidney(1)	6						GAAGGACGGCTTGGAGTTGCT	0.502													17	45	---	---	---	---	PASS
PRICKLE1	144165	broad.mit.edu	37	12	42863376	42863376	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42863376T>A	uc010skv.1	-	4	547	c.260A>T	c.(259-261)CAG>CTG	p.Q87L	PRICKLE1_uc001rnl.2_Missense_Mutation_p.Q87L|PRICKLE1_uc010skw.1_Missense_Mutation_p.Q87L|PRICKLE1_uc001rnm.2_Missense_Mutation_p.Q87L|PRICKLE1_uc009zka.2_Missense_Mutation_p.Q83L	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	87	PET.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		ACTCAAAGACTGGCAATACCG	0.458													19	37	---	---	---	---	PASS
OR8S1	341568	broad.mit.edu	37	12	48921715	48921715	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48921715C>G	uc010slu.1	+	2	909	c.909C>G	c.(907-909)GAC>GAG	p.D303E		NM_001005203	NP_001005203	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S,	303	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						GCCTCCGGGACAGCAGTCATT	0.502													7	23	---	---	---	---	PASS
ESPL1	9700	broad.mit.edu	37	12	53671270	53671270	+	Missense_Mutation	SNP	G	T	T	rs146530110		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53671270G>T	uc001sck.2	+	10	2193	c.2102G>T	c.(2101-2103)CGG>CTG	p.R701L	ESPL1_uc001scj.2_Missense_Mutation_p.R376L|ESPL1_uc010soe.1_5'Flank	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase	701					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						GAGCGGGATCGGAGAGCCCAG	0.343													3	12	---	---	---	---	PASS
OR6C70	390327	broad.mit.edu	37	12	55863538	55863538	+	Missense_Mutation	SNP	G	T	T	rs141132100		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55863538G>T	uc010spn.1	-	1	385	c.385C>A	c.(385-387)CGT>AGT	p.R129S		NM_001005499	NP_001005499	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C,	129	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						GACATATAACGCAAAGGTTTG	0.388													26	48	---	---	---	---	PASS
SMARCC2	6601	broad.mit.edu	37	12	56568479	56568479	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56568479G>A	uc001skb.2	-	16	1558	c.1452C>T	c.(1450-1452)ACC>ACT	p.T484T	SMARCC2_uc001skd.2_Silent_p.T484T|SMARCC2_uc001ska.2_Silent_p.T484T|SMARCC2_uc001skc.2_Silent_p.T484T|SMARCC2_uc010sqf.1_Silent_p.T373T	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	484	SWIRM.				chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)			GGCGGCAGGCGGTAGAGGTAA	0.512													24	47	---	---	---	---	PASS
LRIG3	121227	broad.mit.edu	37	12	59271448	59271448	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59271448G>T	uc001sqr.2	-	15	2516	c.2270C>A	c.(2269-2271)TCA>TAA	p.S757*	LRIG3_uc009zqh.2_Nonsense_Mutation_p.S697*|LRIG3_uc010ssh.1_RNA	NM_153377	NP_700356	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like	757	Ig-like C2-type 3.					integral to membrane				skin(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;1.17e-18)			ACTGACATCTGAGTCCACAAT	0.502													6	101	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	80663896	80663896	+	IGR	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80663896G>T								PPP1R12A (334661 upstream) : PTPRQ (174230 downstream)																							TGTTCAAATGGGACTGTGAAA	0.373													5	20	---	---	---	---	PASS
MYBPC1	4604	broad.mit.edu	37	12	102067366	102067366	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102067366C>A	uc001tii.2	+	24	2856	c.2754C>A	c.(2752-2754)TTC>TTA	p.F918L	MYBPC1_uc001tig.2_Missense_Mutation_p.F925L|MYBPC1_uc010svq.1_Missense_Mutation_p.F887L|MYBPC1_uc001tih.2_Missense_Mutation_p.F925L|MYBPC1_uc001tij.2_Missense_Mutation_p.F900L|MYBPC1_uc010svr.1_Missense_Mutation_p.F900L|MYBPC1_uc010svs.1_Missense_Mutation_p.F918L|MYBPC1_uc010svt.1_Missense_Mutation_p.F888L|MYBPC1_uc010svu.1_Missense_Mutation_p.F881L|MYBPC1_uc001tik.2_Missense_Mutation_p.F874L|MYBPC1_uc001til.2_5'UTR|MYBPC1_uc001tim.2_5'UTR	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	918	Ig-like C2-type 6.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4						TGGACAAATTCGTGGAGACCG	0.418													5	169	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124305213	124305213	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124305213G>T	uc001uft.3	+	23	3758	c.3733G>T	c.(3733-3735)GAT>TAT	p.D1245Y		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1245	TPR 1.|Stem (By similarity).|Potential.				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GAAACTTTTCGATCTTCCTAT	0.423													5	123	---	---	---	---	PASS
DHX37	57647	broad.mit.edu	37	12	125435086	125435086	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125435086G>A	uc001ugy.2	-	23	3093	c.2994C>T	c.(2992-2994)AGC>AGT	p.S998S	DHX37_uc001ugz.1_Silent_p.S85S	NM_032656	NP_116045	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	998							ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GGACCTCCACGCTAGAGACGC	0.701													5	9	---	---	---	---	PASS
C13orf23	80209	broad.mit.edu	37	13	39600451	39600451	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39600451G>T	uc001uwy.2	-	6	1316	c.443C>A	c.(442-444)CCC>CAC	p.P148H	C13orf23_uc001uwz.2_Missense_Mutation_p.P126H	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	148								p.P148P(1)		ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)		TCTTCCTTTGGGATATGGATT	0.408													5	57	---	---	---	---	PASS
KLHL1	57626	broad.mit.edu	37	13	70681669	70681669	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70681669G>C	uc001vip.2	-	1	957	c.163C>G	c.(163-165)CGC>GGC	p.R55G	KLHL1_uc010thm.1_Missense_Mutation_p.R55G|ATXN8OS_uc010aej.1_RNA	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	55	Ser-rich.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TTGAGCAGGCGACTCTGGCTG	0.488													9	28	---	---	---	---	PASS
PIBF1	10464	broad.mit.edu	37	13	73372080	73372080	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73372080G>T	uc001vjc.2	+	5	893	c.588G>T	c.(586-588)AAG>AAT	p.K196N	PIBF1_uc001vja.1_Missense_Mutation_p.K196N|PIBF1_uc010aeo.1_RNA|PIBF1_uc001vjb.2_Missense_Mutation_p.K196N|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337	Q8WXW3	PIBF1_HUMAN	progesterone-induced blocking factor 1	196						centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		CATTAAGAAAGGAAATCTGTG	0.299													6	155	---	---	---	---	PASS
LMO7	4008	broad.mit.edu	37	13	76416980	76416980	+	Intron	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76416980C>G	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc001vjt.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjw.1_Intron	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CTTTTTCTATCTTTTAGGCCT	0.333													14	34	---	---	---	---	PASS
SLITRK5	26050	broad.mit.edu	37	13	88330288	88330288	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88330288G>T	uc001vln.2	+	2	2864	c.2645G>T	c.(2644-2646)TGC>TTC	p.C882F	SLITRK5_uc010tic.1_Missense_Mutation_p.C641F	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5 precursor	882	Cytoplasmic (Potential).					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)					AAATTCCCGTGCAGCCCCGCT	0.602													11	42	---	---	---	---	PASS
MYO16	23026	broad.mit.edu	37	13	109459146	109459146	+	Silent	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109459146T>C	uc001vqt.1	+	7	921	c.795T>C	c.(793-795)TAT>TAC	p.Y265Y	MYO16_uc010agk.1_Silent_p.Y287Y|MYO16_uc001vqu.1_Silent_p.Y65Y	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	265	ANK 7.				cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity	p.Y265H(1)		ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CAGCCAAATATGGCCAGGTAG	0.328													10	27	---	---	---	---	PASS
COL4A1	1282	broad.mit.edu	37	13	110819570	110819570	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110819570C>T	uc001vqw.3	-	44	4006	c.3884G>A	c.(3883-3885)GGT>GAT	p.G1295D	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	1295	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			TGGAGAGCCACCAATACCCTA	0.507													37	94	---	---	---	---	PASS
TFDP1	7027	broad.mit.edu	37	13	114290914	114290914	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114290914G>A	uc001vtw.2	+	10	1117	c.905G>A	c.(904-906)CGG>CAG	p.R302Q	TFDP1_uc010tkd.1_Missense_Mutation_p.R207Q|TFDP1_uc010tke.1_Missense_Mutation_p.R207Q|TFDP1_uc001vty.3_Missense_Mutation_p.R302Q|TFDP1_uc001vtx.2_Missense_Mutation_p.R182Q	NM_007111	NP_009042	Q14186	TFDP1_HUMAN	transcription factor Dp-1	302	DCB2.|Enhances binding of RB protein to E2F.				cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding			lung(4)|ovary(2)|skin(1)	7	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			GTGCTGAAGCGGATGGGCATG	0.507										TSP Lung(29;0.18)			16	64	---	---	---	---	PASS
RASA3	22821	broad.mit.edu	37	13	114778717	114778717	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114778717C>A	uc001vui.2	-	15	1544	c.1413G>T	c.(1411-1413)CCG>CCT	p.P471P	RASA3_uc010tkk.1_Silent_p.P439P|RASA3_uc001vuj.2_Silent_p.P88P	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	471	Ras-GAP.				intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			ACCTGACGTCCGGGTCATCTG	0.637													3	13	---	---	---	---	PASS
OR4N2	390429	broad.mit.edu	37	14	20295919	20295919	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20295919G>C	uc010tkv.1	+	1	312	c.312G>C	c.(310-312)TTG>TTC	p.L104F		NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N,	104	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCTTTTTCTTGCACTTCCTTG	0.522													18	89	---	---	---	---	PASS
OR4K5	79317	broad.mit.edu	37	14	20389170	20389170	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20389170C>A	uc010tkw.1	+	1	405	c.405C>A	c.(403-405)ATC>ATA	p.I135I		NM_001005483	NP_001005483	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K,	135	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATGTGGTCATCATGAGCCGAA	0.443													31	148	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22315246	22315246	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22315246G>T	uc010tmf.1	+						uc001wbw.2_Intron|uc010tmg.1_Intron|uc001wby.2_Intron|uc010ait.1_Nonsense_Mutation_p.G43*|uc001wbz.1_Nonsense_Mutation_p.G62*					SubName: Full=Putative uncharacterized protein ENSP00000374943;																		CCCCAACAAAGGACTCCAGCT	0.498											OREG0022570	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	198	---	---	---	---	PASS
MIPOL1	145282	broad.mit.edu	37	14	37717084	37717084	+	5'UTR	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37717084A>T	uc001wuc.2	+	4					MIPOL1_uc010amr.2_RNA|MIPOL1_uc001wub.3_5'UTR|MIPOL1_uc001wud.2_5'UTR|MIPOL1_uc010ams.2_5'UTR|MIPOL1_uc001wue.2_5'UTR|MIPOL1_uc010amt.2_Intron	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1											ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		AAACAAGAACAGAAATACAAA	0.368													16	51	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44975852	44975852	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44975852C>A	uc001wvn.2	-	1	648	c.339G>T	c.(337-339)CAG>CAT	p.Q113H		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	113						cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		TTTCTACATCCTGAACACTCT	0.428													46	79	---	---	---	---	PASS
SLC35F4	341880	broad.mit.edu	37	14	58060845	58060845	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58060845G>A	uc001xdb.1	-						SLC35F4_uc010aoz.1_Intron|SLC35F4_uc010apa.1_Intron	NM_001080455	NP_001073924			solute carrier family 35, member F4											ovary(2)	2						GGAGGTACCTGGAAAGACAGA	0.383													11	26	---	---	---	---	PASS
GPR65	8477	broad.mit.edu	37	14	88477826	88477826	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88477826A>T	uc001xvv.2	+	2	1165	c.635A>T	c.(634-636)CAC>CTC	p.H212L		NM_003608	NP_003599	Q8IYL9	PSYR_HUMAN	G protein-coupled receptor 65	212	Cytoplasmic (Potential).				actin cytoskeleton reorganization|activation of Rho GTPase activity|apoptosis|immune response|multicellular organismal development|positive regulation of cAMP biosynthetic process|positive regulation of stress fiber assembly|response to acidity	integral to plasma membrane	G-protein coupled receptor activity				0						GCTGTGCGGCACAATAAAGCC	0.428													22	29	---	---	---	---	PASS
SERPINA3	12	broad.mit.edu	37	14	95085702	95085702	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95085702G>A	uc001ydp.2	+	3	893	c.814G>A	c.(814-816)GCC>ACC	p.A272T	SERPINA3_uc001ydo.3_Missense_Mutation_p.A297T|SERPINA3_uc001ydr.2_Intron|SERPINA3_uc001ydq.2_Missense_Mutation_p.A272T|SERPINA3_uc001yds.2_Missense_Mutation_p.A272T|SERPINA3_uc010avg.2_Missense_Mutation_p.A272T	NM_001085	NP_001076	P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A, member 3	272					acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|skin(1)	6		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		CACAGGCAATGCCAGCGCACT	0.547													11	15	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102506598	102506598	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102506598C>A	uc001yks.2	+	63	11880	c.11716C>A	c.(11716-11718)CAG>AAG	p.Q3906K		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	3906					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						TGCAGAATTCCAGCACTTCTT	0.562													5	70	---	---	---	---	PASS
CDC42BPB	9578	broad.mit.edu	37	14	103416919	103416919	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103416919C>A	uc001ymi.1	-	25	3425	c.3193G>T	c.(3193-3195)GTG>TTG	p.V1065L	CDC42BPB_uc001ymj.1_Missense_Mutation_p.V167L	NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	1065	Phorbol-ester/DAG-type.				actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		TTGCAGGACACGTGGCAAGCA	0.582													4	4	---	---	---	---	PASS
SNORD115-20	100033460	broad.mit.edu	37	15	25475980	25475980	+	Intron	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25475980G>C	uc001yzq.1	+						SNORD115-26_uc001yzw.1_Intron|SNORD115-33_uc001zab.1_5'Flank	NR_003313				Homo sapiens small nucleolar RNA, C/D box 115-15 (SNORD115-15), non-coding RNA.												0						GGGGTGCCCTGGGTTGGGTCA	0.542													45	80	---	---	---	---	PASS
ATP10A	57194	broad.mit.edu	37	15	25926071	25926071	+	Intron	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25926071A>T	uc010ayu.2	-							NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CCTGAAAGACAGTGGGGTCCT	0.547													19	31	---	---	---	---	PASS
GREM1	26585	broad.mit.edu	37	15	33023383	33023383	+	Silent	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33023383T>A	uc001zhe.1	+	2	651	c.492T>A	c.(490-492)CCT>CCA	p.P164P	GREM1_uc001zhd.1_Silent_p.P94P|GREM1_uc010uby.1_Silent_p.P123P	NM_013372	NP_037504	O60565	GREM1_HUMAN	gremlin-1 precursor	164	CTCK.				negative regulation of BMP signaling pathway|nervous system development|regulation of epithelial to mesenchymal transition	extracellular space	cytokine activity				0		all_lung(180;1.49e-09)		all cancers(64;2.97e-18)|Epithelial(43;3.15e-12)|GBM - Glioblastoma multiforme(186;2.32e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0107)		TACAGCCACCTACCAAGAAGA	0.498													30	48	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34109158	34109158	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34109158C>T	uc001zhi.2	+	75	10668	c.10598C>T	c.(10597-10599)GCT>GTT	p.A3533V	RYR3_uc010bar.2_Missense_Mutation_p.A3528V	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3533					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)		CAGGATTTGGCTGTAAGTACT	0.418													5	15	---	---	---	---	PASS
DISP2	85455	broad.mit.edu	37	15	40656136	40656136	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40656136C>T	uc001zlk.1	+	2	519	c.430C>T	c.(430-432)CAC>TAC	p.H144Y		NM_033510	NP_277045	A7MBM2	DISP2_HUMAN	dispatched B	144					smoothened signaling pathway	integral to membrane				ovary(2)	2		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		CGCTGTGCAGCACCATGTGGT	0.657													7	22	---	---	---	---	PASS
CDAN1	146059	broad.mit.edu	37	15	43024584	43024584	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43024584C>T	uc001zql.2	-	10	1597	c.1480G>A	c.(1480-1482)GCA>ACA	p.A494T	CDAN1_uc001zqj.2_5'Flank|CDAN1_uc001zqk.2_5'UTR|CDAN1_uc010bcx.1_RNA	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	494						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		CTGCAGGCTGCGGAGAGCTGA	0.517													5	38	---	---	---	---	PASS
VPS13C	54832	broad.mit.edu	37	15	62265707	62265707	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62265707C>A	uc002agz.2	-	26	2637	c.2563G>T	c.(2563-2565)GGT>TGT	p.G855C	VPS13C_uc002aha.2_Missense_Mutation_p.G812C|VPS13C_uc002ahb.1_Missense_Mutation_p.G855C|VPS13C_uc002ahc.1_Missense_Mutation_p.G812C	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	855					protein localization					ovary(2)	2						TTTGTACCACCTGAAATAATA	0.328													5	63	---	---	---	---	PASS
ZNF609	23060	broad.mit.edu	37	15	64791652	64791652	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64791652G>A	uc002ann.2	+	1	34	c.34G>A	c.(34-36)GGA>AGA	p.G12R	ZNF609_uc010bgy.2_Missense_Mutation_p.G12R	NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609	12						nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						CGGAGGGAAAGGAGTGGATGC	0.517													9	104	---	---	---	---	PASS
SMAD3	4088	broad.mit.edu	37	15	67457287	67457287	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67457287C>A	uc002aqj.2	+	2	559	c.261C>A	c.(259-261)ATC>ATA	p.I87I	SMAD3_uc010ujr.1_5'UTR|SMAD3_uc010ujs.1_Silent_p.I43I|SMAD3_uc010ujt.1_5'Flank	NM_005902	NP_005893	P84022	SMAD3_HUMAN	mothers against decapentaplegic homolog 3	87	MH1.				activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding			large_intestine(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		CTCATGTCATCTACTGCCGCC	0.602													24	46	---	---	---	---	PASS
PARP6	56965	broad.mit.edu	37	15	72554003	72554003	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72554003A>T	uc002auc.2	-	8	900	c.441T>A	c.(439-441)AAT>AAA	p.N147K	PARP6_uc002aua.2_Missense_Mutation_p.N12K|PARP6_uc002aub.2_RNA|PARP6_uc002aud.3_RNA|PARP6_uc002auf.1_Missense_Mutation_p.N147K	NM_020214	NP_064599	Q2NL67	PARP6_HUMAN	poly (ADP-ribose) polymerase family, member 6	147							NAD+ ADP-ribosyltransferase activity				0						TCAAGAAATCATTGCTCAGAT	0.468													115	214	---	---	---	---	PASS
MAN2C1	4123	broad.mit.edu	37	15	75651097	75651097	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75651097C>T	uc002baf.2	-	19	2211	c.2194G>A	c.(2194-2196)GTC>ATC	p.V732I	MAN2C1_uc002bag.2_Missense_Mutation_p.V732I|MAN2C1_uc002bah.2_Missense_Mutation_p.V749I|MAN2C1_uc010bkk.2_Missense_Mutation_p.V633I	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	732					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0						TACAAGGGGACATCATCAAAT	0.572													6	17	---	---	---	---	PASS
CSPG4	1464	broad.mit.edu	37	15	75981901	75981901	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75981901C>T	uc002baw.2	-	3	1598	c.1505G>A	c.(1504-1506)CGC>CAC	p.R502H		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	502	Extracellular (Potential).|CSPG 1.|Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3						GCGGGCCTTGCGGTTCACCAC	0.652													14	41	---	---	---	---	PASS
SCAPER	49855	broad.mit.edu	37	15	76673733	76673733	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76673733G>A	uc002bby.2	-	27	3750	c.3691C>T	c.(3691-3693)CTG>TTG	p.L1231L	SCAPER_uc010bkr.2_Silent_p.L539L|SCAPER_uc002bbx.2_Silent_p.L985L|SCAPER_uc002bbz.1_Silent_p.L1102L	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	1230						endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						AAAGCAGGCAGATGAAGAGCT	0.413													13	33	---	---	---	---	PASS
PSMA4	5685	broad.mit.edu	37	15	78837990	78837990	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78837990G>T	uc002bdu.3	+	7	549	c.391G>T	c.(391-393)GGT>TGT	p.G131C	PSMA4_uc010blf.2_Missense_Mutation_p.G131C|PSMA4_uc002bdv.3_Missense_Mutation_p.G60C|PSMA4_uc002bdw.3_Missense_Mutation_p.G107C|PSMA4_uc002bdx.3_Missense_Mutation_p.G60C	NM_002789	NP_002780	P25789	PSA4_HUMAN	proteasome alpha 4 subunit isoform 1	131					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity				0						ACGTCCCTTTGGTGTTTCATT	0.403													6	128	---	---	---	---	PASS
CHRNA3	1136	broad.mit.edu	37	15	78894195	78894195	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78894195G>T	uc002bec.2	-	5	975	c.789C>A	c.(787-789)TTC>TTA	p.F263L	CHRNA3_uc002bea.2_RNA|CHRNA3_uc002beb.2_Missense_Mutation_p.F263L	NM_000743	NP_000734	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3	263	Helical; (Potential).				activation of transmembrane receptor protein tyrosine kinase activity|behavioral response to nicotine|locomotory behavior|regulation of acetylcholine secretion|regulation of dendrite morphogenesis|regulation of excitatory postsynaptic membrane potential|regulation of smooth muscle contraction|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|dendrite|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic density|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(3)|ovary(1)	4						AGGGCAGGTAGAAGACGAGCA	0.557													17	27	---	---	---	---	PASS
TMC3	342125	broad.mit.edu	37	15	81636343	81636343	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81636343G>A	uc002bgo.1	-	14	1562	c.1562C>T	c.(1561-1563)GCG>GTG	p.A521V	TMC3_uc010blr.1_RNA|TMC3_uc002bgp.2_Missense_Mutation_p.A521V	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	521	Helical; (Potential).					integral to membrane				ovary(1)|liver(1)	2						CAGAATGCTCGCCACGGTGAA	0.517													20	31	---	---	---	---	PASS
TMC3	342125	broad.mit.edu	37	15	81638754	81638754	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81638754G>T	uc002bgo.1	-	12	1224	c.1224C>A	c.(1222-1224)TAC>TAA	p.Y408*	TMC3_uc010blr.1_RNA|TMC3_uc002bgp.2_Nonsense_Mutation_p.Y408*	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	408	Helical; (Potential).					integral to membrane				ovary(1)|liver(1)	2						TGATCAGGCTGTAGAGATTTC	0.522													15	33	---	---	---	---	PASS
BNC1	646	broad.mit.edu	37	15	83926460	83926460	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83926460G>T	uc002bjt.1	-	5	2807	c.2719C>A	c.(2719-2721)CCC>ACC	p.P907T	BNC1_uc010uos.1_Missense_Mutation_p.P895T	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	907					epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						ACACAGATGGGGTACTCATCT	0.542													7	167	---	---	---	---	PASS
TTC23	64927	broad.mit.edu	37	15	99696512	99696512	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99696512G>A	uc002bur.2	-						TTC23_uc002bus.2_Intron|TTC23_uc002but.2_Intron|TTC23_uc002buu.2_Intron|TTC23_uc002buv.2_Intron|TTC23_uc002bux.2_Intron|TTC23_uc002buw.2_Intron|TTC23_uc010boq.2_Intron|TTC23_uc002buy.2_Intron|TTC23_uc010bor.2_Intron|TTC23_uc002buz.2_Intron	NM_022905	NP_075056	Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23								binding				0	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)			TCTGTGAAAGGAACAAAAAGC	0.488													32	41	---	---	---	---	PASS
PIGQ	9091	broad.mit.edu	37	16	633304	633304	+	3'UTR	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:633304C>T	uc010bqw.2	+	12					PIGQ_uc002chn.2_3'UTR|PIGQ_uc002cho.2_Silent_p.G651G|PIGQ_uc010uui.1_3'UTR|PIGQ_uc002chp.2_Silent_p.G221G|uc010uuj.1_Missense_Mutation_p.R161H	NM_004204	NP_004195	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)				ACCATGGTGGCGAGCACAGCA	0.677													15	24	---	---	---	---	PASS
FBXL16	146330	broad.mit.edu	37	16	746775	746775	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:746775C>A	uc002cjc.2	-	3	834	c.631G>T	c.(631-633)GAG>TAG	p.E211*	FBXL16_uc002cja.2_5'Flank|FBXL16_uc002cjb.2_5'Flank	NM_153350	NP_699181	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	211											0		Hepatocellular(780;0.0218)				GTGCACACCTCGAGGCCTGCG	0.637													4	19	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3828795	3828795	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3828795G>C	uc002cvv.2	-	9	2051	c.1847C>G	c.(1846-1848)CCT>CGT	p.P616R	CREBBP_uc002cvw.2_Missense_Mutation_p.P578R	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	616	KIX.				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)		TGCGGGATCAGGTGTTGGGAA	0.433			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				26	62	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9892214	9892214	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9892214G>T	uc002czo.3	-	11	2824	c.2276C>A	c.(2275-2277)ACC>AAC	p.T759N	GRIN2A_uc010uym.1_Missense_Mutation_p.T759N|GRIN2A_uc010uyn.1_Missense_Mutation_p.T602N|GRIN2A_uc002czr.3_Missense_Mutation_p.T759N	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	759	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TCCATAACCGGTGGTGGCAAA	0.552													11	28	---	---	---	---	PASS
KIAA0556	23247	broad.mit.edu	37	16	27629747	27629747	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27629747G>T	uc002dow.2	+	3	89	c.65G>T	c.(64-66)GGT>GTT	p.G22V		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	22										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8						TCATTTCAGGGTTACGCTAAG	0.512													15	34	---	---	---	---	PASS
MMP2	4313	broad.mit.edu	37	16	55539304	55539304	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55539304C>G	uc002ehz.3	+	13	2244	c.1933C>G	c.(1933-1935)CTG>GTG	p.L645V	MMP2_uc010vhd.1_Missense_Mutation_p.L569V|MMP2_uc010ccc.2_Missense_Mutation_p.L595V|MMP2_uc002eia.3_Missense_Mutation_p.L142V	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	645	Required for inhibitor TIMP2 binding.|Hemopexin-like 4.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)	GAACCAAAGTCTGAAGAGCGT	0.532													46	99	---	---	---	---	PASS
CES1	1066	broad.mit.edu	37	16	55844887	55844887	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55844887C>A	uc002eim.2	-	10	1227	c.1119G>T	c.(1117-1119)CTG>CTT	p.L373L	CES1_uc010ccf.2_Silent_p.L48L|CES1_uc002eil.2_Silent_p.L374L|CES1_uc002ein.2_Silent_p.L372L	NM_001025194	NP_001020365	P23141	EST1_HUMAN	carboxylesterase 1 isoform b precursor	373					response to toxin	endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.13)|Epithelial(162;0.137)	Aminoglutethimide(DB00357)|Bezafibrate(DB01393)|Cholestyramine(DB01432)|Moexipril(DB00691)	TCTTCTGGTCCAGTTGCCCTT	0.358													7	26	---	---	---	---	PASS
CIAPIN1	57019	broad.mit.edu	37	16	57465090	57465090	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57465090C>T	uc002ell.1	-	7	890	c.719G>A	c.(718-720)GGG>GAG	p.G240E	CIAPIN1_uc002elk.1_RNA|CIAPIN1_uc002elm.1_Missense_Mutation_p.G227E|CIAPIN1_uc002eln.1_Intron|CIAPIN1_uc010cda.1_Missense_Mutation_p.G240E|CIAPIN1_uc002elo.1_Intron	NM_020313	NP_064709	Q6FI81	CPIN1_HUMAN	cytokine induced apoptosis inhibitor 1	240					anti-apoptosis|apoptosis	cytoplasm|nucleolus					0						CCTCTTTTTCCCTTCCCCACA	0.542													37	72	---	---	---	---	PASS
PRSS54	221191	broad.mit.edu	37	16	58327644	58327644	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58327644G>A	uc002enf.2	-	3	472	c.77C>T	c.(76-78)TCT>TTT	p.S26F	PRSS54_uc002eng.2_Missense_Mutation_p.S26F|PRSS54_uc010vie.1_5'UTR	NM_001080492	NP_001073961	Q6PEW0	PRS54_HUMAN	plasma kallikrein-like protein 4 precursor	26					proteolysis	extracellular region	serine-type endopeptidase activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						ACTGGTGGAAGAATAGAGAAG	0.572													3	9	---	---	---	---	PASS
KCTD19	146212	broad.mit.edu	37	16	67327991	67327991	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67327991G>T	uc002esu.2	-	12	1725	c.1674C>A	c.(1672-1674)TCC>TCA	p.S558S	KCTD19_uc002est.2_Silent_p.S330S|KCTD19_uc010vjj.1_Silent_p.S301S	NM_001100915	NP_001094385	Q17RG1	KCD19_HUMAN	potassium channel tetramerisation domain	558						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)		CCATCTGGTTGGACCTGACCA	0.572													6	159	---	---	---	---	PASS
SF3B3	23450	broad.mit.edu	37	16	70597869	70597869	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70597869G>T	uc002ezf.2	+	18	2590	c.2379G>T	c.(2377-2379)GAG>GAT	p.E793D		NM_012426	NP_036558	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3	793					protein complex assembly	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(1)	1		Ovarian(137;0.0694)				TCCACCCTGAGAGTAACAACC	0.458													6	103	---	---	---	---	PASS
DHX38	9785	broad.mit.edu	37	16	72142152	72142152	+	Silent	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72142152C>A	uc002fcb.2	+	22	3346	c.2991C>A	c.(2989-2991)ATC>ATA	p.I997I	DHX38_uc010vmp.1_Silent_p.I309I	NM_014003	NP_054722	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	997					mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1		Ovarian(137;0.125)				GTGATCAAATCCGGGAGAAGT	0.493													4	30	---	---	---	---	PASS
MBTPS1	8720	broad.mit.edu	37	16	84104333	84104333	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84104333C>T	uc002fhi.2	-	13	2144	c.1642G>A	c.(1642-1644)GCC>ACC	p.A548T	MBTPS1_uc002fhh.2_Missense_Mutation_p.A52T	NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1	548	Lumenal (Potential).				cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2						TAGGAGAAGGCAACTTCAATG	0.512													18	54	---	---	---	---	PASS
KCNG4	93107	broad.mit.edu	37	16	84270969	84270969	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84270969G>T	uc010voc.1	-	2	244	c.123C>A	c.(121-123)TAC>TAA	p.Y41*	KCNG4_uc002fhu.1_Nonsense_Mutation_p.Y41*	NM_172347	NP_758857	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G,	41	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(3)	3						GCACCCTCCGGTAGTAAAGGC	0.632													10	19	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7578457	7578457	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578457C>A	uc002gim.2	-	5	667	c.473G>T	c.(472-474)CGC>CTC	p.R158L	TP53_uc002gig.1_Missense_Mutation_p.R158L|TP53_uc002gih.2_Missense_Mutation_p.R158L|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R26L|TP53_uc010cng.1_Missense_Mutation_p.R26L|TP53_uc002gii.1_Missense_Mutation_p.R26L|TP53_uc010cnh.1_Missense_Mutation_p.R158L|TP53_uc010cni.1_Missense_Mutation_p.R158L|TP53_uc002gij.2_Missense_Mutation_p.R158L|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R65L|TP53_uc002gio.2_Missense_Mutation_p.R26L|TP53_uc010vug.1_Missense_Mutation_p.R119L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	158	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> F (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R158H(58)|p.R158L(55)|p.R158C(17)|p.R158G(10)|p.R158P(9)|p.0?(7)|p.R158R(6)|p.R158fs*12(5)|p.R158_A159insX(4)|p.R158_A159delRA(2)|p.R156_I162delRVRAMAI(2)|p.V157fs*9(2)|p.P153fs*22(2)|p.R158fs*11(2)|p.V157fs*22(2)|p.V157_C176del20(1)|p.R156_A161delRVRAMA(1)|p.R158F(1)|p.P151_V173del23(1)|p.R158fs*24(1)|p.R65L(1)|p.R156_R158delRVR(1)|p.R156fs*18(1)|p.R156_A161del(1)|p.R158_A159insXX(1)|p.V157_M160delVRAM(1)|p.V157_R158delVR(1)|p.S149fs*72(1)|p.A159fs*21(1)|p.T155_A161delTRVRAMA(1)|p.G154fs*22(1)|p.R156fs*20(1)|p.V157_I162delVRAMAI(1)|p.R26L(1)|p.V157fs*21(1)|p.R158fs*8(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)		GGCCATGGCGCGGACGCGGGT	0.627		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)			10	17	---	---	---	---	PASS
KRBA2	124751	broad.mit.edu	37	17	8272906	8272906	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8272906C>A	uc002glf.1	-	2	1031	c.1025G>T	c.(1024-1026)TGG>TTG	p.W342L	KRBA2_uc002glg.1_Missense_Mutation_p.W259L	NM_213597	NP_998762	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	342	Integrase catalytic.				DNA integration|regulation of transcription, DNA-dependent	intracellular	DNA binding				0						TAGGTCTGGCCACAACTCATT	0.463													4	22	---	---	---	---	PASS
GLP2R	9340	broad.mit.edu	37	17	9760734	9760734	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9760734G>A	uc002gmd.1	+							NM_004246	NP_004237	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor precursor						G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane				lung(2)|ovary(1)	3					Glucagon recombinant(DB00040)	TTTTCTCCTCGCACAGAAAAC	0.483													12	17	---	---	---	---	PASS
GAS7	8522	broad.mit.edu	37	17	9828857	9828857	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9828857C>T	uc002gmg.1	-	11	1235	c.1074G>A	c.(1072-1074)GAG>GAA	p.E358E	GAS7_uc010vvc.1_Silent_p.E172E|GAS7_uc002gmh.1_Silent_p.E218E|GAS7_uc010vvd.1_Silent_p.E310E|GAS7_uc002gmi.2_Silent_p.E294E|GAS7_uc002gmj.1_Silent_p.E298E|GAS7_uc010coh.1_Silent_p.E298E	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c	358	Potential.				cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2						TCAGCTTGATCTCCAGCTGCT	0.602			T	MLL	AML*						OREG0024170	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	27	20	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10439902	10439902	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10439902T>C	uc010coi.2	-	17	2047	c.1919A>G	c.(1918-1920)AAG>AGG	p.K640R	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.K640R|MYH2_uc010coj.2_Missense_Mutation_p.K640R	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	640	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						ACCACCTTTCTTGGCCCCTCC	0.418													7	13	---	---	---	---	PASS
C17orf103	256302	broad.mit.edu	37	17	21147437	21147437	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21147437G>A	uc010vzx.1	-	3	209	c.207C>T	c.(205-207)ATC>ATT	p.I69I		NM_152914	NP_690878	Q8N6N6	GTL3B_HUMAN	transcript expressed during hematopoiesis 2	69											0						GGTGCTTGGCGATGCCACGCC	0.672													6	13	---	---	---	---	PASS
KCNJ12	3768	broad.mit.edu	37	17	21319497	21319497	+	Silent	SNP	C	T	T	rs139358757	byFrequency	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21319497C>T	uc002gyv.1	+	3	1548	c.843C>T	c.(841-843)TTC>TTT	p.F281F		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	281	Cytoplasmic (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	GCCCGCTCTTCGGCATCAGCC	0.607										Prostate(3;0.18)			10	31	---	---	---	---	PASS
NLK	51701	broad.mit.edu	37	17	26490659	26490659	+	Intron	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26490659C>A	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315	Q9UBE8	NLK_HUMAN	nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		CTAAAGGTAGCTTTTCAGTTT	0.348													8	10	---	---	---	---	PASS
SLC13A2	9058	broad.mit.edu	37	17	26817737	26817737	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26817737G>A	uc002hbh.2	+	4	454	c.387G>A	c.(385-387)ATG>ATA	p.M129I	SLC13A2_uc010wal.1_Missense_Mutation_p.M86I|SLC13A2_uc010wam.1_Missense_Mutation_p.M85I|SLC13A2_uc010wan.1_Missense_Mutation_p.M178I|SLC13A2_uc010wao.1_Missense_Mutation_p.M86I|SLC13A2_uc002hbi.2_Missense_Mutation_p.M58I	NM_003984	NP_003975	Q13183	S13A2_HUMAN	solute carrier family 13, member 2 isoform b	129	Helical; (Potential).					integral to plasma membrane|membrane fraction	low affinity sodium:dicarboxylate symporter activity				0	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	TGGGCTTCATGCTGGTCACGG	0.592													15	61	---	---	---	---	PASS
SUPT6H	6830	broad.mit.edu	37	17	27009836	27009836	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27009836C>T	uc002hby.2	+	14	1779	c.1689C>T	c.(1687-1689)CCC>CCT	p.P563P	SUPT6H_uc010crt.2_Silent_p.P563P	NM_003170	NP_003161	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog	563					chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Lung NSC(42;0.00431)					AGCAGTTTCCCGCGGAGCCCT	0.592													12	54	---	---	---	---	PASS
UTP6	55813	broad.mit.edu	37	17	30213082	30213082	+	Splice_Site	SNP	T	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30213082T>G	uc002hgr.2	-	9	705	c.622_splice	c.e9-1	p.E208_splice	UTP6_uc002hgq.2_Splice_Site_p.E24_splice|UTP6_uc010cst.2_Splice_Site_p.E57_splice|UTP6_uc010wbw.1_Splice_Site_p.E208_splice	NM_018428	NP_060898	Q9NYH9	UTP6_HUMAN	hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				AGGATTCTCCTAAAGAGTGTT	0.313													38	45	---	---	---	---	PASS
CCL7	6354	broad.mit.edu	37	17	32598747	32598747	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32598747G>A	uc002hhz.2	+	3	296	c.226G>A	c.(226-228)GCT>ACT	p.A76T	CCL7_uc010ctf.2_RNA	NM_006273	NP_006264	P80098	CCL7_HUMAN	chemokine (C-C motif) ligand 7 precursor	76					cell-cell signaling|cellular calcium ion homeostasis|chemotaxis|immune response|inflammatory response|signal transduction	extracellular space	chemokine activity|heparin binding			ovary(1)	1	Breast(3;0.00224)	Breast(31;0.151)|Ovarian(249;0.17)		BRCA - Breast invasive adenocarcinoma(366;0.155)		GGAGATCTGTGCTGACCCCAC	0.483													19	77	---	---	---	---	PASS
PEX12	5193	broad.mit.edu	37	17	33902880	33902880	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33902880C>A	uc002hjp.2	-	3	1617	c.1001G>T	c.(1000-1002)AGG>ATG	p.R334M		NM_000286	NP_000277	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	334	Cytoplasmic (Potential).|RING-type; degenerate.				protein import into peroxisome matrix	integral to peroxisomal membrane	protein C-terminus binding|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTGGTGACTCCTCACATAATG	0.448													6	92	---	---	---	---	PASS
FBXL20	84961	broad.mit.edu	37	17	37425100	37425100	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37425100C>A	uc010wed.1	-	12	1134	c.913G>T	c.(913-915)GAC>TAC	p.D305Y	FBXL20_uc002hrt.2_Missense_Mutation_p.D305Y|FBXL20_uc010cvu.2_Missense_Mutation_p.D273Y	NM_032875	NP_116264	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20	305	LRR 9.					cytoplasm				ovary(1)	1			LUAD - Lung adenocarcinoma(14;0.146)			TCTTCCAGGTCCATCTTTTCA	0.318													39	46	---	---	---	---	PASS
MED24	9862	broad.mit.edu	37	17	38178199	38178199	+	Intron	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38178199C>T	uc002htt.2	-						MED24_uc010weq.1_5'Flank|MED24_uc002htr.2_Intron|MED24_uc010wer.1_Intron|MED24_uc010wes.1_Intron|MED24_uc010wet.1_Intron|MED24_uc002hts.2_Intron|MED24_uc002htu.2_Intron|MED24_uc010cwn.2_Intron|MED24_uc010weu.1_Intron	NM_014815	NP_055630	O75448	MED24_HUMAN	mediator complex subunit 24 isoform 1						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1	Colorectal(19;0.000442)					GGCCAGCCCACACACTCACTG	0.607													20	26	---	---	---	---	PASS
MED24	9862	broad.mit.edu	37	17	38209752	38209752	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38209752C>A	uc002htt.2	-	2	413	c.100G>T	c.(100-102)GGA>TGA	p.G34*	MED24_uc010wet.1_RNA|MED24_uc002hts.2_Nonsense_Mutation_p.G59*|MED24_uc002htu.2_Nonsense_Mutation_p.G34*|MED24_uc010cwn.2_Nonsense_Mutation_p.G34*|MED24_uc010weu.1_Translation_Start_Site|MED24_uc010wev.1_Intron|MED24_uc010wew.1_Intron|MED24_uc010wex.1_5'Flank|MED24_uc010wfa.1_5'Flank|MED24_uc010wfb.1_Nonsense_Mutation_p.G59*|MED24_uc010wfc.1_5'Flank	NM_014815	NP_055630	O75448	MED24_HUMAN	mediator complex subunit 24 isoform 1	34					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1	Colorectal(19;0.000442)					CAGGTGGCTCCTTTAGGAAAG	0.463													8	337	---	---	---	---	PASS
KRT20	54474	broad.mit.edu	37	17	39034579	39034579	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39034579G>T	uc002hvl.2	-	6	999	c.957C>A	c.(955-957)GCC>GCA	p.A319A		NM_019010	NP_061883	P35900	K1C20_HUMAN	keratin 20	319	Rod.|Coil 2.				apoptosis|intermediate filament organization	Golgi apparatus|intermediate filament	protein binding|structural constituent of cytoskeleton			large_intestine(1)|kidney(1)|skin(1)	3		Breast(137;0.000301)|Ovarian(249;0.15)				TGCTGTAACGGGCCTTGGTCT	0.483													47	56	---	---	---	---	PASS
ATXN7L3	56970	broad.mit.edu	37	17	42272026	42272026	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42272026C>A	uc002iga.2	-	11	845	c.754G>T	c.(754-756)GAG>TAG	p.E252*	ATXN7L3_uc010wiv.1_Nonsense_Mutation_p.E34*|ATXN7L3_uc002ifz.2_Nonsense_Mutation_p.E259*	NM_001098833	NP_001092303	Q14CW9	AT7L3_HUMAN	ataxin 7-like 3 isoform b	252	SCA7.				histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	SAGA complex	ligand-dependent nuclear receptor transcription coactivator activity|metal ion binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)		AGGGAGCTCTCGACCTCTGGA	0.557													4	64	---	---	---	---	PASS
C17orf104	284071	broad.mit.edu	37	17	42744414	42744414	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42744414C>T	uc010czv.2	+	5	1135	c.1135C>T	c.(1135-1137)CAG>TAG	p.Q379*	C17orf104_uc002igy.1_Nonsense_Mutation_p.Q213*|C17orf104_uc002igz.3_Nonsense_Mutation_p.Q213*|C17orf104_uc010wja.1_RNA|C17orf104_uc002iha.2_Nonsense_Mutation_p.Q213*	NM_001145080	NP_001138552	A2RUB1	CQ104_HUMAN	hypothetical protein LOC284071	379										central_nervous_system(1)	1						GCCAGCGAATCAGAAAAAAAT	0.403													38	39	---	---	---	---	PASS
CRHR1	1394	broad.mit.edu	37	17	43912064	43912064	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43912064C>T	uc010dap.2	+	14	1534	c.1269C>T	c.(1267-1269)GCC>GCT	p.A423A	CRHR1_uc010wjx.1_Silent_p.A219A|CRHR1_uc002ijp.2_Missense_Mutation_p.P248L|CRHR1_uc002ijm.2_Silent_p.A394A|CRHR1_uc002ijn.2_Silent_p.A354A|CRHR1_uc010dar.2_Silent_p.A380A|CRHR1_uc010dao.2_Silent_p.A293A|CRHR1_uc010daq.2_Silent_p.A219A	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	423	Cytoplasmic (Potential).				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)		TGGCCCGTGCCATGTCCATCC	0.632													28	22	---	---	---	---	PASS
MAPT	4137	broad.mit.edu	37	17	44101454	44101454	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44101454G>A	uc002ijr.3	+	14	2514	c.2194G>A	c.(2194-2196)GGC>AGC	p.G732S	MAPT_uc010dau.2_Missense_Mutation_p.G750S|MAPT_uc002ijs.3_Missense_Mutation_p.G415S|MAPT_uc002ijx.3_Missense_Mutation_p.G386S|MAPT_uc002ijt.3_Missense_Mutation_p.G357S|MAPT_uc002iju.3_Missense_Mutation_p.G326S|MAPT_uc002ijv.3_Missense_Mutation_p.G333S	NM_016835	NP_058519	P10636	TAU_HUMAN	microtubule-associated protein tau isoform 1	732					cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)				CTCCTCCACCGGCAGCATCGA	0.637													45	44	---	---	---	---	PASS
HOXB9	3219	broad.mit.edu	37	17	46703155	46703155	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46703155T>G	uc002inx.2	-	1	681	c.477A>C	c.(475-477)AAA>AAC	p.K159N		NM_024017	NP_076922	P17482	HXB9_HUMAN	homeobox B9	159					canonical Wnt receptor signaling pathway|cell chemotaxis	mitochondrion|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						CTTCGCAAATTTTATTGTCCC	0.567													18	58	---	---	---	---	PASS
ITGA3	3675	broad.mit.edu	37	17	48165101	48165101	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48165101G>T	uc010dbl.2	+						ITGA3_uc010dbm.2_Intron	NM_002204	NP_002195	P26006	ITA3_HUMAN	integrin alpha 3 isoform a precursor						blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3						TCCTCTCCCCGCTCCAGTTCT	0.642													11	39	---	---	---	---	PASS
KIF2B	84643	broad.mit.edu	37	17	51900675	51900675	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51900675C>A	uc002iua.2	+	1	437	c.281C>A	c.(280-282)CCC>CAC	p.P94H	uc010wna.1_RNA	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	94					blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8						CCGCCCCCGCCCTTATCCCCC	0.572													44	90	---	---	---	---	PASS
KIF2B	84643	broad.mit.edu	37	17	51901022	51901022	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51901022C>G	uc002iua.2	+	1	784	c.628C>G	c.(628-630)CAA>GAA	p.Q210E	uc010wna.1_RNA	NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	210	Kinesin-motor.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)|skin(3)	8						GGAGCCCCCGCAAGAACATCG	0.537													20	39	---	---	---	---	PASS
AKAP1	8165	broad.mit.edu	37	17	55184062	55184062	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55184062G>T	uc002iux.2	+	2	1468	c.1237G>T	c.(1237-1239)GCC>TCC	p.A413S	AKAP1_uc010wnl.1_Missense_Mutation_p.A413S|AKAP1_uc002iuy.2_RNA|AKAP1_uc010dcm.2_Missense_Mutation_p.A413S	NM_003488	NP_003479	Q92667	AKAP1_HUMAN	A-kinase anchor protein 1 precursor	413					blood coagulation	cytosol|integral to membrane|mitochondrial outer membrane	protein binding|RNA binding			ovary(1)	1	Breast(9;5.46e-08)					GGCAGCTGTTGCCCCGCCGGA	0.622													12	12	---	---	---	---	PASS
SFRS1	6426	broad.mit.edu	37	17	56084313	56084313	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56084313C>A	uc002ivi.2	-	1	395	c.186G>T	c.(184-186)GAG>GAT	p.E62D	SFRS1_uc002ivj.2_Missense_Mutation_p.E62D	NM_006924	NP_008855	Q07955	SRSF1_HUMAN	splicing factor, arginine/serine-rich 1 isoform	62	RRM 1.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA 5'-splice site recognition|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytoplasm|nuclear speck	nucleotide binding|RNA binding				0		Colorectal(1115;0.0691)		LUAD - Lung adenocarcinoma(1115;0.247)		ACCGCGGGTCCTCGAACTCAA	0.597													46	45	---	---	---	---	PASS
TEX14	56155	broad.mit.edu	37	17	56634390	56634390	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56634390C>A	uc010dcz.1	-	33	4594	c.4476G>T	c.(4474-4476)CAG>CAT	p.Q1492H	TEX14_uc002iwr.1_Missense_Mutation_p.Q1486H|TEX14_uc002iws.1_Missense_Mutation_p.Q1446H|TEX14_uc010dda.1_Missense_Mutation_p.Q1226H	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	1492						cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACAAGTCACTCTGATCCAGCA	0.408													43	46	---	---	---	---	PASS
MRC2	9902	broad.mit.edu	37	17	60742095	60742095	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60742095A>G	uc002jad.2	+	2	707	c.305A>G	c.(304-306)AAC>AGC	p.N102S	MRC2_uc002jac.2_Missense_Mutation_p.N102S	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	102	Extracellular (Potential).|Ricin B-type lectin.				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3						CCAGGCACCAACACCACGGCC	0.612													23	31	---	---	---	---	PASS
MARCH10	162333	broad.mit.edu	37	17	60821758	60821758	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60821758C>A	uc010ddr.2	-	5	752	c.514G>T	c.(514-516)GTG>TTG	p.V172L	MARCH10_uc002jag.3_Missense_Mutation_p.V172L|MARCH10_uc010dds.2_Missense_Mutation_p.V210L|MARCH10_uc002jah.2_Missense_Mutation_p.V171L	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN	ring finger protein 190	172							ligase activity|zinc ion binding				0						GGAACCGGCACCTTTGCAGGC	0.557													21	81	---	---	---	---	PASS
BPTF	2186	broad.mit.edu	37	17	65900897	65900897	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65900897G>T	uc002jgf.2	+	9	2814	c.2753G>T	c.(2752-2754)AGG>ATG	p.R918M	BPTF_uc002jge.2_Missense_Mutation_p.R1044M|BPTF_uc010wqm.1_Missense_Mutation_p.R981M	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1044					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)			CATGTTTATAGGTTTGTTCCT	0.353													5	60	---	---	---	---	PASS
KCNJ2	3759	broad.mit.edu	37	17	68171704	68171704	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68171704T>C	uc010dfg.2	+	2	925	c.524T>C	c.(523-525)ATC>ACC	p.I175T	KCNJ2_uc002jir.2_Missense_Mutation_p.I175T	NM_000891	NP_000882	P63252	IRK2_HUMAN	potassium inwardly-rectifying channel J2	175	Helical; Name=M2; (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity|protein binding				0	Breast(10;1.64e-08)					GATGCTTTCATCATTGGCGCA	0.488													48	52	---	---	---	---	PASS
SDK2	54549	broad.mit.edu	37	17	71348719	71348719	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71348719G>A	uc010dfm.2	-	41	5651	c.5651C>T	c.(5650-5652)ACG>ATG	p.T1884M	SDK2_uc002jjt.3_Missense_Mutation_p.T1024M|SDK2_uc002jjv.1_RNA	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2	1884	Fibronectin type-III 13.|Extracellular (Potential).				cell adhesion	integral to membrane				ovary(2)	2						CATGCTGAACGTGTAGGAGCT	0.597													8	49	---	---	---	---	PASS
KIAA0195	9772	broad.mit.edu	37	17	73488676	73488676	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73488676C>A	uc002jnz.3	+	15	1993	c.1718C>A	c.(1717-1719)TCC>TAC	p.S573Y	KIAA0195_uc010wsa.1_Missense_Mutation_p.S583Y|KIAA0195_uc010wsb.1_Missense_Mutation_p.S213Y|KIAA0195_uc002job.3_5'Flank	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	573					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTTGATGACTCCAACTGGCAG	0.592													6	73	---	---	---	---	PASS
ENGASE	64772	broad.mit.edu	37	17	77079096	77079096	+	Intron	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77079096C>A	uc002jwv.2	+						ENGASE_uc002jww.2_Intron	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase							cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1						CCCTCTGTCTCTTCAGTCGTT	0.577											OREG0024792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	133	---	---	---	---	PASS
SMCHD1	23347	broad.mit.edu	37	18	2707859	2707859	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2707859C>T	uc002klm.3	+	17	2390	c.2201C>T	c.(2200-2202)CCA>CTA	p.P734L	SMCHD1_uc002klk.3_RNA|SMCHD1_uc002kll.3_RNA	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible	734					chromosome organization		ATP binding				0						CAAAAGCTTCCAGGAACAAGC	0.303													11	21	---	---	---	---	PASS
L3MBTL4	91133	broad.mit.edu	37	18	6301890	6301890	+	Intron	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6301890G>T	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				TGTAAATATTGGTGATAATTA	0.318													5	75	---	---	---	---	PASS
SEH1L	81929	broad.mit.edu	37	18	12948239	12948239	+	Intron	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12948239C>G	uc002krr.2	+						SEH1L_uc002krq.2_Intron	NM_031216	NP_112493	Q96EE3	SEH1_HUMAN	sec13-like protein isoform 2						attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex					0						AAGGTGCGCGCGGCGCTTGCG	0.672													3	8	---	---	---	---	PASS
TCEB3B	51224	broad.mit.edu	37	18	44560934	44560934	+	Missense_Mutation	SNP	T	A	A	rs148199634		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44560934T>A	uc002lcr.1	-	1	1055	c.702A>T	c.(700-702)AAA>AAT	p.K234N	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_016427	NP_057511	Q8IYF1	ELOA2_HUMAN	elongin A2	234					regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter	integral to membrane|nucleus	DNA binding			ovary(2)|large_intestine(1)|pancreas(1)	4						ACAAGGGGCGTTTTTCCTGGC	0.607													13	13	---	---	---	---	PASS
CCDC68	80323	broad.mit.edu	37	18	52586518	52586518	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52586518C>T	uc002lfs.2	-	9	945	c.773G>A	c.(772-774)CGC>CAC	p.R258H	CCDC68_uc002lft.2_Missense_Mutation_p.R258H	NM_001143829	NP_001137301	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	258	Potential.									skin(1)	1				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		GATGACACTGCGCAGGTTCTG	0.468													23	51	---	---	---	---	PASS
CLEC4M	10332	broad.mit.edu	37	19	7830871	7830871	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7830871C>A	uc002mih.2	+	5	611	c.493C>A	c.(493-495)CTG>ATG	p.L165M	CLEC4M_uc010xjv.1_Missense_Mutation_p.L160M|CLEC4M_uc002mhy.2_Missense_Mutation_p.L132M|CLEC4M_uc010xjw.1_Missense_Mutation_p.L167M|CLEC4M_uc010dvt.2_Intron|CLEC4M_uc010dvs.2_Missense_Mutation_p.L164M|CLEC4M_uc010xjx.1_Missense_Mutation_p.L137M|CLEC4M_uc002mhz.2_Intron|CLEC4M_uc002mic.2_Missense_Mutation_p.L160M|CLEC4M_uc002mia.2_Intron	NM_001144910	NP_001138382	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M isoform	165	Extracellular (Probable).|7 X approximate tandem repeats.|3.				cell-cell recognition|endocytosis|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor	cytoplasm|extracellular region|integral to plasma membrane	ICAM-3 receptor activity|mannose binding|metal ion binding|peptide antigen binding|virion binding			pancreas(1)	1						GCTGACCCGGCTGAAGGCTGC	0.582													4	40	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9063042	9063042	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9063042G>T	uc002mkp.2	-	3	24608	c.24404C>A	c.(24403-24405)GCC>GAC	p.A8135D		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8137	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						CATCTCTGTGGCTAAGCTGGT	0.532													34	47	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9063975	9063975	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9063975T>C	uc002mkp.2	-	3	23675	c.23471A>G	c.(23470-23472)GAG>GGG	p.E7824G		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	7826	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGAAGCTAGCTCTGTCTGAAT	0.542													28	36	---	---	---	---	PASS
ZNF562	54811	broad.mit.edu	37	19	9764539	9764539	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9764539C>A	uc010xks.1	-	6	530	c.367G>T	c.(367-369)GGA>TGA	p.G123*	ZNF562_uc002mly.2_Nonsense_Mutation_p.G123*|ZNF562_uc002mlx.2_Nonsense_Mutation_p.G51*|ZNF562_uc010xkt.1_Nonsense_Mutation_p.G86*|ZNF562_uc010xku.1_Nonsense_Mutation_p.G54*|ZNF562_uc010xkv.1_Nonsense_Mutation_p.G122*|ZNF562_uc010xkw.1_Nonsense_Mutation_p.G7*	NM_001130032	NP_001123504	Q6V9R5	ZN562_HUMAN	zinc finger protein 562 isoform a	123					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AGTTTCCATCCACTGTAGCTT	0.393													4	44	---	---	---	---	PASS
NOTCH3	4854	broad.mit.edu	37	19	15302760	15302760	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15302760G>A	uc002nan.2	-						NOTCH3_uc002nao.1_Intron	NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor						Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TCCTGAGTAGGGCTCACTCAC	0.647													8	17	---	---	---	---	PASS
C19orf44	84167	broad.mit.edu	37	19	16612105	16612105	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16612105G>A	uc002neh.1	+	2	575	c.502G>A	c.(502-504)GCG>ACG	p.A168T	MED26_uc002nee.2_Intron|C19orf44_uc002nef.1_Missense_Mutation_p.A168T|C19orf44_uc002neg.2_Missense_Mutation_p.A168T|C19orf44_uc010eai.1_RNA	NM_032207	NP_115583	Q9H6X5	CS044_HUMAN	hypothetical protein LOC84167	168											0						TGCACAGAACGCGAAGGTCAG	0.493													19	80	---	---	---	---	PASS
KIAA1683	80726	broad.mit.edu	37	19	18368721	18368721	+	Missense_Mutation	SNP	G	A	A	rs146173511		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18368721G>A	uc002nin.2	-	4	3028	c.2812C>T	c.(2812-2814)CGT>TGT	p.R938C	PDE4C_uc002nil.3_5'Flank|KIAA1683_uc010ebn.2_Missense_Mutation_p.R1125C|KIAA1683_uc010xqe.1_Missense_Mutation_p.R892C|KIAA1683_uc010xqf.1_RNA	NM_025249	NP_079525	Q9H0B3	K1683_HUMAN	KIAA1683 isoform b	938	IQ 2.					mitochondrion				ovary(2)	2						AGGTAGCCACGGACGCCCGCC	0.682													13	24	---	---	---	---	PASS
ZNF99	7652	broad.mit.edu	37	19	22940719	22940719	+	Silent	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22940719A>T	uc010xrh.1	-	5	1719	c.1719T>A	c.(1717-1719)CTT>CTA	p.L573L		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TATGTCTAGTAAGGTGTGAGG	0.378													16	51	---	---	---	---	PASS
ZNF91	7644	broad.mit.edu	37	19	23543751	23543751	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23543751T>A	uc002nre.2	-	4	2143	c.2030A>T	c.(2029-2031)AAG>ATG	p.K677M	ZNF91_uc002nrd.2_5'Flank|ZNF91_uc010xrj.1_Missense_Mutation_p.K645M	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	677	C2H2-type 19.					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)				ATGAGTTATCTTATGATTAGC	0.353													12	77	---	---	---	---	PASS
ZNF91	7644	broad.mit.edu	37	19	23544675	23544675	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23544675T>A	uc002nre.2	-	4	1219	c.1106A>T	c.(1105-1107)AAG>ATG	p.K369M	ZNF91_uc010xrj.1_Missense_Mutation_p.K337M	NM_003430	NP_003421	Q05481	ZNF91_HUMAN	zinc finger protein 91	369	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)				ATGAGTTATCTTATGATTAGC	0.353													12	33	---	---	---	---	PASS
SLC7A9	11136	broad.mit.edu	37	19	33333196	33333196	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33333196G>T	uc002ntv.3	-	11	1219	c.1102C>A	c.(1102-1104)CCT>ACT	p.P368T	SLC7A9_uc002ntt.3_RNA|SLC7A9_uc002ntu.3_Missense_Mutation_p.P368T|SLC7A9_uc002ntw.3_Missense_Mutation_p.P159T	NM_001126335	NP_001119807	P82251	BAT1_HUMAN	solute carrier family 7, member 9	368	Helical; (Potential).				blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	integral to plasma membrane	L-cystine transmembrane transporter activity|neutral amino acid transmembrane transporter activity|peptide antigen binding			skin(1)	1	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	ATGTCACCAGGGATGATATAA	0.388													6	127	---	---	---	---	PASS
GPATCH1	55094	broad.mit.edu	37	19	33585143	33585143	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33585143G>T	uc002nug.1	+	5	835	c.521G>T	c.(520-522)CGA>CTA	p.R174L		NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	174	G-patch.					catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					GTTGGTCCTCGAGTAAAGAGA	0.368													5	103	---	---	---	---	PASS
EIF3K	27335	broad.mit.edu	37	19	39116734	39116734	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39116734G>T	uc002oiz.1	+	4	533	c.346G>T	c.(346-348)GCC>TCC	p.A116S	EIF3K_uc010xuh.1_Missense_Mutation_p.A116S|EIF3K_uc010xui.1_Missense_Mutation_p.A29S	NM_013234	NP_037366	Q9UBQ5	EIF3K_HUMAN	eukaryotic translation initiation factor 3,	116					regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex|nucleus	protein binding|ribosome binding|translation initiation factor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CCATTTCCAGGCCTTCTGGGT	0.567													77	21	---	---	---	---	PASS
FBL	2091	broad.mit.edu	37	19	40330880	40330880	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40330880G>T	uc002omn.2	-	4	485	c.371C>A	c.(370-372)TCG>TAG	p.S124*	FBL_uc002omm.1_Nonsense_Mutation_p.S38*|FBL_uc002omo.2_Nonsense_Mutation_p.S123*|FBL_uc010egr.2_Nonsense_Mutation_p.S124*	NM_001436	NP_001427	P22087	FBRL_HUMAN	fibrillarin	124					rRNA processing|tRNA processing	box C/D snoRNP complex|Cajal body	methyltransferase activity|protein binding|RNA binding			ovary(1)	1	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		CACCGAAATCGAGACTCTCTT	0.478													4	55	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41383104	41383104	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41383104G>T	uc002opm.2	-	7	1694	c.1152C>A	c.(1150-1152)TTC>TTA	p.F384L	CYP2A7_uc002opo.2_Missense_Mutation_p.F384L|CYP2A7_uc002opn.2_Missense_Mutation_p.F333L	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,	384						endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTTAGGGAGGAAAAAATCCC	0.527													20	77	---	---	---	---	PASS
PSG9	5678	broad.mit.edu	37	19	43772283	43772283	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43772283C>A	uc002owd.3	-	2	182	c.83G>T	c.(82-84)TGG>TTG	p.W28L	PSG9_uc002owe.3_Missense_Mutation_p.W28L|PSG9_uc010xwm.1_Missense_Mutation_p.W28L|PSG9_uc002owf.3_Missense_Mutation_p.W28L|PSG9_uc002owg.2_Missense_Mutation_p.W28L|PSG9_uc002owh.2_Missense_Mutation_p.W28L	NM_002784	NP_002775	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	28					female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				GGGCGGGTTCCAGAAGTTTAA	0.498													6	201	---	---	---	---	PASS
TRPM4	54795	broad.mit.edu	37	19	49692232	49692232	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49692232G>T	uc002pmw.2	+	14	1975	c.1903G>T	c.(1903-1905)GAG>TAG	p.E635*	TRPM4_uc010emu.2_Nonsense_Mutation_p.E635*|TRPM4_uc010yak.1_Nonsense_Mutation_p.E99*|TRPM4_uc002pmx.2_Nonsense_Mutation_p.E461*|TRPM4_uc010emv.2_Nonsense_Mutation_p.E520*|TRPM4_uc010yal.1_Nonsense_Mutation_p.E281*|TRPM4_uc002pmy.2_5'UTR	NM_017636	NP_060106	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel,	635	Cytoplasmic (Potential).				dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production	endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	ATP binding|calcium activated cation channel activity|calmodulin binding			ovary(1)|central_nervous_system(1)	2		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		TCGCAGCAGTGAGGTGAGGGC	0.622													6	96	---	---	---	---	PASS
ZNF432	9668	broad.mit.edu	37	19	52537242	52537242	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52537242T>A	uc002pyk.2	-	5	2008	c.1690A>T	c.(1690-1692)ACA>TCA	p.T564S		NM_014650	NP_055465	O94892	ZN432_HUMAN	zinc finger protein 432	564					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|pancreas(1)	3		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		TTCTCTTCTGTATGAATTTGC	0.398													60	35	---	---	---	---	PASS
ZNF468	90333	broad.mit.edu	37	19	53344201	53344201	+	Missense_Mutation	SNP	T	C	C	rs140223089		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53344201T>C	uc002qaf.2	-	4	1497	c.1346A>G	c.(1345-1347)CAG>CGG	p.Q449R	ZNF468_uc002qae.2_Missense_Mutation_p.Q396R	NM_001008801	NP_001008801	Q5VIY5	ZN468_HUMAN	zinc finger protein ZNF468 isoform 2	449	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0358)		TGAATCCCTCTGGAAAGCCTT	0.438													39	50	---	---	---	---	PASS
LILRB1	10859	broad.mit.edu	37	19	55143986	55143986	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55143986C>A	uc002qgj.2	+	7	1073	c.733C>A	c.(733-735)CAG>AAG	p.Q245K	LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Missense_Mutation_p.Q245K|LILRB1_uc002qgk.2_Missense_Mutation_p.Q245K|LILRB1_uc002qgm.2_Missense_Mutation_p.Q245K|LILRB1_uc010erq.2_Missense_Mutation_p.Q245K|LILRB1_uc010err.2_RNA	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor,	245	Ig-like C2-type 3.|Extracellular (Potential).				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		CCTGACTCTGCAGTGTGGCTC	0.562										HNSCC(37;0.09)			27	45	---	---	---	---	PASS
ZNF304	57343	broad.mit.edu	37	19	57869221	57869221	+	3'UTR	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57869221C>A	uc010ygw.1	+	3					ZNF304_uc010etw.2_3'UTR|ZNF304_uc010etx.2_3'UTR	NM_020657	NP_065708	Q9HCX3	ZN304_HUMAN	zinc finger protein 304						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		TGTTTAACACCAGAAAATTCA	0.438													5	116	---	---	---	---	PASS
CENPB	1059	broad.mit.edu	37	20	3766901	3766901	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3766901A>T	uc002wjk.2	-	1	437	c.230T>A	c.(229-231)CTC>CAC	p.L77H	CDC25B_uc010zqk.1_5'Flank|CDC25B_uc010zql.1_5'Flank|CDC25B_uc010zqm.1_5'Flank	NM_001810	NP_001801	P07199	CENPB_HUMAN	centromere protein B	77	HTH CENPB-type.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	chromatin binding|satellite DNA binding				0						CAAGCCCTCGAGCTTGTCGTA	0.642													17	18	---	---	---	---	PASS
MCM8	84515	broad.mit.edu	37	20	5965433	5965433	+	Silent	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5965433G>T	uc002wmi.2	+	15	2117	c.1740G>T	c.(1738-1740)GGG>GGT	p.G580G	MCM8_uc002wmj.2_Silent_p.G564G|MCM8_uc002wmk.2_Silent_p.G620G|MCM8_uc002wml.2_Silent_p.G580G|MCM8_uc010gbp.2_Silent_p.G533G|MCM8_uc002wmm.2_Silent_p.G118G	NM_032485	NP_115874	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	580	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1						ATAGAATGGGGAGTGCACTAC	0.358													14	44	---	---	---	---	PASS
ANKRD5	63926	broad.mit.edu	37	20	10030131	10030131	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10030131G>T	uc002wno.2	+	7	1307	c.914G>T	c.(913-915)CGA>CTA	p.R305L	uc002wnn.1_Intron|ANKRD5_uc002wnp.2_Missense_Mutation_p.R305L|ANKRD5_uc010gbz.2_Missense_Mutation_p.R116L	NM_022096	NP_071379	Q9NU02	ANKR5_HUMAN	ankyrin repeat domain protein 5	305							calcium ion binding			ovary(1)|breast(1)	2						GAAATACGCCGAGCAGAGAGA	0.488													5	104	---	---	---	---	PASS
TASP1	55617	broad.mit.edu	37	20	13539738	13539738	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13539738T>C	uc002woi.2	-	8	709	c.592A>G	c.(592-594)AGA>GGA	p.R198G	TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Missense_Mutation_p.R175G|TASP1_uc010zrj.1_RNA	NM_017714	NP_060184	Q9H6P5	TASP1_HUMAN	taspase 1 precursor	198					asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0						CTCTTGTTTCTTTTAAATGCA	0.249													16	42	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20505508	20505508	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20505508C>T	uc002wrz.2	-	29	3871	c.3728G>A	c.(3727-3729)AGT>AAT	p.S1243N	RALGAPA2_uc010gcx.2_Missense_Mutation_p.S947N|RALGAPA2_uc010zsg.1_Missense_Mutation_p.S691N|RALGAPA2_uc002wsa.1_Missense_Mutation_p.S15N	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	1243					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						GTACTCTGCACTTGGTAAAAG	0.358													11	18	---	---	---	---	PASS
REM1	28954	broad.mit.edu	37	20	30070289	30070289	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30070289A>T	uc002wwa.2	+	4	907	c.623A>T	c.(622-624)GAA>GTA	p.E208V		NM_014012	NP_054731	O75628	REM1_HUMAN	RAS-like GTP-binding protein REM	208					small GTPase mediated signal transduction	membrane	calmodulin binding|GTP binding|GTPase activity			lung(2)|pancreas(2)	4	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			GTCTCTGTGGAAGGTGAGCCC	0.622													16	27	---	---	---	---	PASS
SULF2	55959	broad.mit.edu	37	20	46288434	46288434	+	Intron	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46288434G>A	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron|SULF2_uc010zyd.1_Intron	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor						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			ovary(2)|breast(2)|pancreas(1)|skin(1)	6						ATAATAAAACGAAATACCTGT	0.398													14	28	---	---	---	---	PASS
DDX27	55661	broad.mit.edu	37	20	47849862	47849862	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47849862G>T	uc002xuh.2	+	10	1205	c.1144G>T	c.(1144-1146)GAG>TAG	p.E382*		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	382	Helicase ATP-binding.					nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TGAGTACTTTGAGGAGCAGAT	0.557													4	35	---	---	---	---	PASS
ZNF831	128611	broad.mit.edu	37	20	57829217	57829217	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57829217G>T	uc002yan.2	+	5	4453	c.4453G>T	c.(4453-4455)GAC>TAC	p.D1485Y		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1485						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					TCCCCACCATGACATTGCTAC	0.493													16	35	---	---	---	---	PASS
ZBTB46	140685	broad.mit.edu	37	20	62407098	62407098	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62407098G>A	uc002ygv.1	-	3	1356	c.1155C>T	c.(1153-1155)GCC>GCT	p.A385A	ZBTB46_uc002ygu.2_RNA	NM_025224	NP_079500	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	385					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CCAGCACGTCGGCCTTCAGCG	0.677											OREG0026130	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	35	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	10921987	10921987	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10921987C>G	uc002yip.1	-	18	1404	c.1036G>C	c.(1036-1038)GGA>CGA	p.G346R	TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_Missense_Mutation_p.G328R|TPTE_uc002yir.1_Missense_Mutation_p.G308R|TPTE_uc010gkv.1_Missense_Mutation_p.G208R	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	346	Phosphatase tensin-type.				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)		ACCATAGTTCCTGTTCTATCT	0.323													5	40	---	---	---	---	PASS
TRPM2	7226	broad.mit.edu	37	21	45815303	45815303	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45815303G>C	uc002zet.1	+	13	2014	c.1801G>C	c.(1801-1803)GGA>CGA	p.G601R	TRPM2_uc002zeu.1_Missense_Mutation_p.G601R|TRPM2_uc002zew.1_Missense_Mutation_p.G601R|TRPM2_uc010gpt.1_Missense_Mutation_p.G601R|TRPM2_uc002zex.1_Missense_Mutation_p.G387R|TRPM2_uc002zey.1_Missense_Mutation_p.G114R	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	601	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						CCAGGTGCAGGGAGTGAGCCT	0.403													24	41	---	---	---	---	PASS
CECR2	27443	broad.mit.edu	37	22	18020401	18020401	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18020401G>A	uc010gqw.1	+	13	1856	c.1730G>A	c.(1729-1731)CGG>CAG	p.R577Q	CECR2_uc010gqv.1_Missense_Mutation_p.R436Q|CECR2_uc002zml.2_Missense_Mutation_p.R436Q	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	619					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		CAGCCCCCGCGGGAGGTGGGC	0.587													17	19	---	---	---	---	PASS
CECR2	27443	broad.mit.edu	37	22	18022205	18022205	+	Silent	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18022205G>A	uc010gqw.1	+	15	2433	c.2307G>A	c.(2305-2307)AAG>AAA	p.K769K	CECR2_uc010gqv.1_Silent_p.K628K|CECR2_uc002zml.2_Silent_p.K628K	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	811					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)		CAGATGAGAAGCCCCACCTGG	0.577													11	15	---	---	---	---	PASS
TUBA8	51807	broad.mit.edu	37	22	18609431	18609431	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18609431G>T	uc002znv.1	+	4	759	c.686G>T	c.(685-687)CGC>CTC	p.R229L	TUBA8_uc002znr.2_Missense_Mutation_p.R163L|TUBA8_uc002znw.1_Missense_Mutation_p.R253L|TUBA8_uc002znx.1_Missense_Mutation_p.R76L	NM_018943	NP_061816	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	229					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0						AACCTCAACCGCCTCATCAGT	0.522													4	45	---	---	---	---	PASS
CSF2RB	1439	broad.mit.edu	37	22	37334270	37334270	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37334270C>T	uc003aqa.3	+	14	2637	c.2420C>T	c.(2419-2421)TCC>TTC	p.S807F	CSF2RB_uc003aqc.3_Missense_Mutation_p.S813F	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	807	Cytoplasmic (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)	TCCCCAACATCCCCACAGCCC	0.657													14	31	---	---	---	---	PASS
TCF20	6942	broad.mit.edu	37	22	42609195	42609195	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42609195C>T	uc003bcj.1	-	1	2251	c.2117G>A	c.(2116-2118)CGC>CAC	p.R706H	TCF20_uc003bck.1_Missense_Mutation_p.R706H|TCF20_uc003bnt.2_Missense_Mutation_p.R706H	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	706					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5						GTAACTATAGCGCAGACTTCC	0.507													36	67	---	---	---	---	PASS
PARVB	29780	broad.mit.edu	37	22	44514978	44514978	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44514978G>T	uc003ben.2	+	4	386	c.334G>T	c.(334-336)GAG>TAG	p.E112*	PARVB_uc003bem.2_Nonsense_Mutation_p.E145*|PARVB_uc010gzn.2_Nonsense_Mutation_p.E60*|PARVB_uc003beo.2_Nonsense_Mutation_p.E75*	NM_013327	NP_037459	Q9HBI1	PARVB_HUMAN	parvin, beta isoform b	112	CH 1.				cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)				GAAGCAGCTGGAGGAAGACCT	0.602													18	39	---	---	---	---	PASS
GLRA2	2742	broad.mit.edu	37	X	14708972	14708972	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14708972G>T	uc010nep.2	+	9	1403	c.1071G>T	c.(1069-1071)AGG>AGT	p.R357S	GLRA2_uc010neq.2_Missense_Mutation_p.R357S|GLRA2_uc004cwe.3_Missense_Mutation_p.R357S|GLRA2_uc011mio.1_Missense_Mutation_p.R268S|GLRA2_uc011mip.1_Missense_Mutation_p.R335S	NM_001118885	NP_001112357	P23416	GLRA2_HUMAN	glycine receptor, alpha 2 isoform A	357	Cytoplasmic (Probable).				neuropeptide signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(1)|lung(1)	2	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)	GACAGAAGAGGCAGAATAAGG	0.468													29	19	---	---	---	---	PASS
CNKSR2	22866	broad.mit.edu	37	X	21545097	21545097	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21545097C>A	uc004czx.1	+	10	1106	c.1070C>A	c.(1069-1071)CCT>CAT	p.P357H	CNKSR2_uc004czw.2_Missense_Mutation_p.P357H|CNKSR2_uc011mjn.1_Missense_Mutation_p.P308H|CNKSR2_uc011mjo.1_Missense_Mutation_p.P357H|CNKSR2_uc004czy.2_Translation_Start_Site	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	357	Poly-Pro.|DUF1170.				regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2						CCCCCTCCTCCTGCAGAACCA	0.473													6	154	---	---	---	---	PASS
CNKSR2	22866	broad.mit.edu	37	X	21609254	21609254	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21609254G>T	uc004czx.1	+	15	1808	c.1772G>T	c.(1771-1773)TGG>TTG	p.W591L	CNKSR2_uc004czw.2_Missense_Mutation_p.W591L|CNKSR2_uc011mjn.1_Missense_Mutation_p.W542L|CNKSR2_uc011mjo.1_Missense_Mutation_p.W561L|CNKSR2_uc004czy.2_Missense_Mutation_p.W183L	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	591	PH.				regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2						TCACAGAAATGGAAAAAATAT	0.378													5	47	---	---	---	---	PASS
MAGEB4	4115	broad.mit.edu	37	X	30260360	30260360	+	Silent	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:30260360A>G	uc004dcb.2	+	1	192	c.108A>G	c.(106-108)GAA>GAG	p.E36E	MAGEB1_uc004dcc.2_5'Flank|MAGEB1_uc004dcd.2_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	36										ovary(1)	1						CAGAGAAAGAAGAGTCTCCTT	0.572													8	6	---	---	---	---	PASS
FAM47C	442444	broad.mit.edu	37	X	37027451	37027451	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37027451C>T	uc004ddl.1	+	1	982	c.968C>T	c.(967-969)TCT>TTT	p.S323F		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	323										ovary(3)	3						CCAGAGCCTTCTGAGACTGGA	0.612													29	14	---	---	---	---	PASS
FAM47C	442444	broad.mit.edu	37	X	37028697	37028697	+	Silent	SNP	C	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37028697C>T	uc004ddl.1	+	1	2228	c.2214C>T	c.(2212-2214)CTC>CTT	p.L738L		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	738										ovary(3)	3						TGTCCCATCTCCGCCCAGAGC	0.632													25	10	---	---	---	---	PASS
KDM6A	7403	broad.mit.edu	37	X	44929602	44929602	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44929602G>A	uc004dge.3	+	17	3077	c.2702G>A	c.(2701-2703)AGG>AAG	p.R901K	KDM6A_uc010nhk.2_Missense_Mutation_p.R867K|KDM6A_uc011mkz.1_Missense_Mutation_p.R953K|KDM6A_uc011mla.1_Missense_Mutation_p.R856K|KDM6A_uc011mlb.1_Missense_Mutation_p.R908K|KDM6A_uc011mlc.1_Missense_Mutation_p.R605K|KDM6A_uc011mld.1_Missense_Mutation_p.R540K	NM_021140	NP_066963	O15550	KDM6A_HUMAN	ubiquitously transcribed tetratricopeptide	901					histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84						AAGGCATGCAGGTTAGTGTGG	0.418			D|N|F|S		renal|oesophageal SCC|MM								8	6	---	---	---	---	PASS
ZNF81	347344	broad.mit.edu	37	X	47774986	47774986	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47774986A>G	uc010nhy.1	+	6	1309	c.941A>G	c.(940-942)AAG>AGG	p.K314R		NM_007137	NP_009068	P51508	ZNF81_HUMAN	zinc finger protein 81	314						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_lung(315;0.0973)				TTTACACAGAAGCCACTACTC	0.353													11	4	---	---	---	---	PASS
TAF1	6872	broad.mit.edu	37	X	70612518	70612518	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70612518G>T	uc004dzu.3	+	19	2929	c.2878G>T	c.(2878-2880)GGT>TGT	p.G960C	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.G981C|TAF1_uc004dzv.3_Missense_Mutation_p.G134C	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	960					G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)				CACGGGGTGTGGTGAAGGATT	0.488													14	10	---	---	---	---	PASS
TAF1	6872	broad.mit.edu	37	X	70612519	70612519	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70612519G>T	uc004dzu.3	+	19	2930	c.2879G>T	c.(2878-2880)GGT>GTT	p.G960V	BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.G981V|TAF1_uc004dzv.3_Missense_Mutation_p.G134V	NM_138923	NP_620278	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 2	960					G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)				ACGGGGTGTGGTGAAGGATTC	0.488													13	10	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91090613	91090613	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91090613A>T	uc004efk.1	+	1	955	c.110A>T	c.(109-111)AAC>ATC	p.N37I	PCDH11X_uc004efl.1_Missense_Mutation_p.N37I|PCDH11X_uc004efo.1_Missense_Mutation_p.N37I|PCDH11X_uc010nmv.1_Missense_Mutation_p.N37I|PCDH11X_uc004efm.1_Missense_Mutation_p.N37I|PCDH11X_uc004efn.1_Missense_Mutation_p.N37I|PCDH11X_uc004efh.1_Missense_Mutation_p.N37I|PCDH11X_uc004efj.1_Missense_Mutation_p.N37I	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	37	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						ATGCCAGAAAACGTCCTGATA	0.493													18	14	---	---	---	---	PASS
ARMCX1	51309	broad.mit.edu	37	X	100808631	100808631	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100808631C>A	uc004ehv.2	+	4	1089	c.718C>A	c.(718-720)CAG>AAG	p.Q240K	ARMCX1_uc004ehw.2_Missense_Mutation_p.Q240K	NM_016608	NP_057692	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	240	ARM 2.					integral to membrane	binding			ovary(3)|pancreas(1)	4						TTCATTTAACCAGAATGCCAT	0.393													5	110	---	---	---	---	PASS
TEX13A	56157	broad.mit.edu	37	X	104464313	104464313	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104464313C>A	uc004ema.2	-	3	677	c.565G>T	c.(565-567)GGA>TGA	p.G189*	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_Nonsense_Mutation_p.G189*	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	189						intracellular	zinc ion binding			ovary(2)	2						CCTTTTCCTCCAGCAGCACCA	0.667													7	9	---	---	---	---	PASS
GLUD2	2747	broad.mit.edu	37	X	120182460	120182460	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120182460G>T	uc004eto.2	+	1	999	c.922G>T	c.(922-924)GGA>TGA	p.G308*		NM_012084	NP_036216	P49448	DHE4_HUMAN	glutamate dehydrogenase 2 precursor	308					glutamate biosynthetic process|glutamate catabolic process	mitochondrial matrix	ADP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|leucine binding			pancreas(1)	1					L-Glutamic Acid(DB00142)|NADH(DB00157)	TGTTGTTCAGGGATTTGGTAA	0.388													5	77	---	---	---	---	PASS
ODZ1	10178	broad.mit.edu	37	X	124097479	124097479	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124097479A>T	uc004euj.2	-	1	188	c.124T>A	c.(124-126)TCC>ACC	p.S42T	ODZ1_uc011muj.1_Missense_Mutation_p.S42T|ODZ1_uc010nqy.2_Missense_Mutation_p.S42T	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	42	Teneurin N-terminal.|Cytoplasmic (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						GTCTCCCTGGAGTTGTATGAC	0.423													8	75	---	---	---	---	PASS
PASD1	139135	broad.mit.edu	37	X	150790039	150790039	+	Silent	SNP	T	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150790039T>A	uc004fev.3	+	6	725	c.393T>A	c.(391-393)ATT>ATA	p.I131I		NM_173493	NP_775764	Q8IV76	PASD1_HUMAN	PAS domain containing 1	131						nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					TGAAATTTATTGTGAATGTAA	0.303													3	4	---	---	---	---	PASS
MIR767	768215	broad.mit.edu	37	X	151561985	151561985	+	RNA	SNP	A	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151561985A>G	hsa-mir-767|MI0003763	-			c.17A>G			GABRA3_uc010ntk.1_Intron|MIR105-1_hsa-mir-105-1|MI0000111_5'Flank|uc004ffo.2_5'Flank																	0						ATGAGCAAAAACCTACAATAT	0.428													5	6	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	1318078	1318078	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1318078delC								AURKAIP1 (7260 upstream) : CCNL2 (3013 downstream)																							ATCCAGAGGTCACCACCCCTT	0.493													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	3725956	3725956	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3725956delT								LRRC47 (12888 upstream) : KIAA0562 (2689 downstream)																							cccggccCACttttttttttt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	9481775	9481776	+	IGR	INS	-	T	T	rs146649778	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9481775_9481776insT								SPSB1 (52187 upstream) : SLC25A33 (117752 downstream)																							tagtgggggagtatttacacca	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	13164130	13164131	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13164130_13164131insA								PRAMEF5 (46379 upstream) : LOC440563 (18830 downstream)																							TTTACTGTAACAAAAAAAAAAG	0.515													6	3	---	---	---	---	
CROCC	9696	broad.mit.edu	37	1	17229819	17229820	+	Intron	INS	-	A	A	rs147278844		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17229819_17229820insA	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)		gaaagaaaaagaaaaagaaAGA	0.094													3	4	---	---	---	---	
IGSF21	84966	broad.mit.edu	37	1	18642041	18642042	+	Intron	INS	-	GATGGATG	GATGGATG	rs143440506	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18642041_18642042insGATGGATG	uc001bau.1	+							NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor							extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		agtggatggatgatggatggat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20725235	20725235	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20725235delA	uc009vpu.1	-						uc001bdf.1_RNA					Homo sapiens cDNA clone IMAGE:5269505.																		ggggacactcaggtagtcaca	0.015													4	2	---	---	---	---	
MDS2	259283	broad.mit.edu	37	1	23957795	23957796	+	Intron	DEL	AA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23957795_23957796delAA	uc001bhi.3	+						MDS2_uc001bhj.3_Intron					Homo sapiens MDS2 gene.											ovary(2)	2						tccagcctctaaaaaaaaaaat	0.000			T	ETV6	MDS								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	27377673	27377673	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27377673delA								FAM46B (38340 upstream) : SLC9A1 (47628 downstream)																							agtccatctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
WDTC1	23038	broad.mit.edu	37	1	27612113	27612114	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27612113_27612114insT	uc009vst.2	+						WDTC1_uc001bno.2_Intron|WDTC1_uc001bnp.1_Intron	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1								protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		tgtttcttttcttttttttttt	0.134													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31128407	31128409	+	IGR	DEL	GAC	-	-	rs72287507	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31128407_31128409delGAC								None (None upstream) : MATN1 (55717 downstream)																							tggtggtggtgacggtggtggtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35394333	35394334	+	IGR	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35394333_35394334delCA								DLGAP3 (23349 upstream) : ZMYM6 (55034 downstream)																							cgcgcacacgcacacacacaca	0.376													4	2	---	---	---	---	
PSMB2	5690	broad.mit.edu	37	1	36109379	36109379	+	5'Flank	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36109379delA	uc001bzf.1	-						PSMB2_uc001bzd.1_5'Flank|PSMB2_uc010ohz.1_5'Flank|PSMB2_uc001bzg.1_5'Flank	NM_002794	NP_002785	P49721	PSB2_HUMAN	proteasome beta 2 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)	actctgtctcaaaaaaaaaaa	0.144													4	2	---	---	---	---	
ZC3H12A	80149	broad.mit.edu	37	1	37949683	37949683	+	3'UTR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37949683delC	uc001cbb.3	+	6					ZC3H12A_uc001cbc.1_3'UTR	NM_025079	NP_079355	Q5D1E8	ZC12A_HUMAN	zinc finger CCCH-type containing 12A						angiogenesis|apoptosis|cell differentiation	cytoplasm|nucleus|plasma membrane	endonuclease activity|metal ion binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GCCAATGAGGCCTCATCTGTG	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38646764	38646764	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38646764delT								POU3F1 (134314 upstream) : RRAGC (658251 downstream)																							ttataaattcttaaggtgatt	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38808274	38808274	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38808274delT								POU3F1 (295824 upstream) : RRAGC (496741 downstream)																							TTCTTACACATTTTtttttta	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	41344724	41344731	+	IGR	DEL	AAGGAAAG	-	-	rs3071111		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41344724_41344731delAAGGAAAG								CITED4 (16706 upstream) : CTPS (100276 downstream)																							gaaagaaagaaaggaaagaaggaaggaa	0.005													4	3	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42010581	42010582	+	Intron	INS	-	ATC	ATC	rs141959984	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42010581_42010582insATC	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)				ccaccaccactaccacctctac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48209043	48209044	+	IGR	INS	-	GGA	GGA	rs143555360	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48209043_48209044insGGA								FOXD2 (302681 upstream) : SKINTL (358343 downstream)																							gtggtggtggtagtggtggtgg	0.000													3	8	---	---	---	---	
PPAP2B	8613	broad.mit.edu	37	1	57025229	57025230	+	Intron	INS	-	TT	TT	rs68061241		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57025229_57025230insTT	uc001cyj.1	-							NM_177414	NP_803133	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B						canonical Wnt receptor signaling pathway involved in positive regulation of cell-cell adhesion|canonical Wnt receptor signaling pathway involved in positive regulation of endothelial cell migration|canonical Wnt receptor signaling pathway involved in positive regulation of wound healing|germ cell migration|homotypic cell-cell adhesion|negative regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|sphingolipid metabolic process	adherens junction|Golgi apparatus|integral to membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|protein binding|sphingosine-1-phosphate phosphatase activity				0						ccagccTTGAATTTTTTTTTTT	0.149													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59179116	59179116	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59179116delG								MYSM1 (13369 upstream) : JUN (67348 downstream)																							ttattggaaaggtgacataag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59237140	59237140	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59237140delG								MYSM1 (71393 upstream) : JUN (9324 downstream)																							gtgctgtggtggggggaggga	0.000													4	2	---	---	---	---	
NEGR1	257194	broad.mit.edu	37	1	72739678	72739679	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72739678_72739679insT	uc001dfw.2	-						NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		ACGTGTTGTTCTTTTTTTTTTT	0.361													4	2	---	---	---	---	
DPYD	1806	broad.mit.edu	37	1	98311257	98311258	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98311257_98311258insT	uc001drv.2	-						DPYD_uc010oub.1_Intron|DPYD_uc001drw.2_Intron	NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	tcgccaggttgtgggagacatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	106278967	106278968	+	IGR	DEL	GA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106278967_106278968delGA								None (None upstream) : None (None downstream)																							AACAGAAGGTgagagagagaga	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	107130492	107130492	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107130492delC								None (None upstream) : PRMT6 (468775 downstream)																							tatgtatataccacttccatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	110327893	110327894	+	IGR	DEL	GT	-	-	rs10612080		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110327893_110327894delGT								EPS8L3 (21329 upstream) : CSF1 (125339 downstream)																							ACTGCCAGGAgtgtgtgtgtgt	0.366													4	2	---	---	---	---	
CEPT1	10390	broad.mit.edu	37	1	111725037	111725038	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111725037_111725038insT	uc001eah.1	+						CEPT1_uc001eai.1_Intron|CEPT1_uc001eaj.1_Intron|CEPT1_uc009wfz.1_Intron	NM_001007794	NP_001007795	Q9Y6K0	CEPT1_HUMAN	choline/ethanolaminephosphotransferase							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	diacylglycerol cholinephosphotransferase activity|ethanolaminephosphotransferase activity|metal ion binding				0		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	TCATTTGTTAATTTATAATTTA	0.178													5	4	---	---	---	---	
CD101	9398	broad.mit.edu	37	1	117548213	117548213	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117548213delA	uc010oxb.1	+						CD101_uc009whd.2_Intron|CD101_uc010oxc.1_Intron|CD101_uc010oxd.1_Intron	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor						cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4						ttccctctgtaagttttgttc	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120677297	120677298	+	IGR	INS	-	G	G	rs138089011	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120677297_120677298insG								NOTCH2 (65021 upstream) : FAM72B (161707 downstream)																							tggaattatttgtttttttttt	0.000													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121134228	121134229	+	IGR	DEL	TC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121134228_121134229delTC								FCGR1B (198284 upstream) : LOC647121 (126681 downstream)																							tttcgctgtttctctttctccc	0.104													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143534418	143534418	+	IGR	DEL	A	-	-	rs2872278	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143534418delA								None (None upstream) : LOC100286793 (113221 downstream)																							gactgcccccacaccattaga	0.000													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143972579	143972579	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143972579delT	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		agtgtttttgttttttttttt	0.104													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144885722	144885722	+	Intron	DEL	A	-	-	rs66777969		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144885722delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	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)		tatctcaacgaaaaaaaaaaa	0.060			T	PDGFRB	MPD								4	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145007452	145007453	+	Intron	INS	-	T	T	rs141963263		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145007452_145007453insT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CATACAttttcttttttttgtt	0.139			T	PDGFRB	MPD								5	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145070603	145070603	+	Intron	DEL	A	-	-	rs151083850		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145070603delA	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						atctacatgcaaaaaaaaaaa	0.000													7	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145135925	145135925	+	Intron	DEL	T	-	-	rs139349677		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145135925delT	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						gttggtgtcctttgaagcaca	0.000													4	3	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145384619	145384620	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145384619_145384620insT	uc001emp.3	+							NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		aggataaagtctttgtctttga	0.000													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	146996768	146996768	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146996768delG								CHD1L (229327 upstream) : BCL9 (16414 downstream)																							TGGTTGTAATGTTTAGCTGCA	0.443													4	2	---	---	---	---	
LOC645166	645166	broad.mit.edu	37	1	148948880	148948881	+	Intron	INS	-	A	A	rs144249846		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148948880_148948881insA	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0						caagactatctaaaaaaaaaaa	0.124													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149032673	149032674	+	IGR	DEL	CA	-	-	rs112278711		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149032673_149032674delCA								LOC645166 (79619 upstream) : LOC388692 (246802 downstream)																							TTACCATCTGCACACACACACA	0.376													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149302689	149302689	+	IGR	DEL	A	-	-	rs140796132		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149302689delA								LOC388692 (10947 upstream) : FCGR1C (66605 downstream)																							aggcagaaataaaaaaaaatt	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	150617002	150617002	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150617002delT								ENSA (14904 upstream) : GOLPH3L (1699 downstream)																							CTGAGttttcttttttttttt	0.204													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152170253	152170254	+	IGR	DEL	CT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152170253_152170254delCT								RPTN (38549 upstream) : HRNR (14304 downstream)																							ttctttcttcctctctgtctct	0.000													9	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152304645	152304645	+	Intron	DEL	C	-	-	rs35971937		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152304645delC	uc001ezv.2	+											Homo sapiens cDNA FLJ31869 fis, clone NT2RP7002151.																		TAGGGGAGGGCTCAGAATAGT	0.428													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	152395655	152395656	+	IGR	DEL	GC	-	-	rs113643562		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152395655_152395656delGC								CRNN (8905 upstream) : LCE5A (87664 downstream)																							tccacacatggcgttattttgg	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	153694218	153694218	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153694218delT								NPR1 (27751 upstream) : INTS3 (6331 downstream)																							AAACCCCAACttttttttttt	0.025													3	3	---	---	---	---	
GATAD2B	57459	broad.mit.edu	37	1	153790790	153790790	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153790790delC	uc001fdb.3	-							NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TCAAGGttttctttttttttt	0.189													9	5	---	---	---	---	
GATAD2B	57459	broad.mit.edu	37	1	153854258	153854259	+	Intron	INS	-	GT	GT	rs146390017	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153854258_153854259insGT	uc001fdb.3	-							NM_020699	NP_065750	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AGGTTTTTTTCgtgtgtgtgtg	0.322													4	2	---	---	---	---	
TPM3	7170	broad.mit.edu	37	1	154165865	154165865	+	5'Flank	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154165865delG	uc001fec.1	-							NM_152263	NP_689476	P06753	TPM3_HUMAN	tropomyosin 3 isoform 1						cellular component movement|muscle filament sliding|regulation of muscle contraction	cytosol|muscle thin filament tropomyosin|stress fiber	actin binding		TPM3/ALK(33)	haematopoietic_and_lymphoid_tissue(22)|soft_tissue(11)|skin(1)	34	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					AGTGGAAAATGGGGGGGGGGT	0.483			T	NTRK1|ALK	papillary thyroid|ALCL								3	4	---	---	---	---	
ADAR	103	broad.mit.edu	37	1	154580199	154580210	+	Intron	DEL	ACACACACACGC	-	-	rs151050554	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154580199_154580210delACACACACACGC	uc001ffh.2	-						ADAR_uc001ffj.2_Intron|ADAR_uc001ffi.2_Intron|ADAR_uc001ffk.2_Intron|ADAR_uc001ffl.1_5'Flank|ADAR_uc001ffm.1_5'Flank|ADAR_uc001ffn.1_Intron	NM_001111	NP_001102	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific isoform a						adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TGGCAAGACTacacacacacgcacacacacac	0.410													2	4	---	---	---	---	
ADAR	103	broad.mit.edu	37	1	154596489	154596490	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154596489_154596490insA	uc001ffk.2	-							NM_001025107	NP_001020278	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific isoform d						adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		gactccatctcaaaaaaaaaaa	0.025													4	2	---	---	---	---	
KCNN3	3782	broad.mit.edu	37	1	154792184	154792184	+	Intron	DEL	G	-	-	rs35589944		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154792184delG	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron|KCNN3_uc009wox.1_Intron	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)			GGGAGGATAAGGGGCTGGGTG	0.587													4	8	---	---	---	---	
DUSP23	54935	broad.mit.edu	37	1	159749041	159749055	+	5'Flank	DEL	CCAGAGGTAGTGCAA	-	-	rs72232656		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159749041_159749055delCCAGAGGTAGTGCAA	uc001ftz.1	+						DUSP23_uc001fua.1_5'Flank|DUSP23_uc001fub.1_5'Flank	NM_017823	NP_060293	Q9BVJ7	DUS23_HUMAN	dual specificity phosphatase 23							cytosol|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			lung(1)	1	all_hematologic(112;0.0537)					AGTCTTGTCTCCAGAGGTAGTGCAACCAGAAATCC	0.484													4	2	---	---	---	---	
SLAMF1	6504	broad.mit.edu	37	1	160605139	160605140	+	Intron	DEL	GC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160605139_160605140delGC	uc001fwl.3	-						SLAMF1_uc010pjk.1_Intron|SLAMF1_uc010pjl.1_Intron|SLAMF1_uc010pjm.1_Intron	NM_003037	NP_003028	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family						interspecies interaction between organisms|lymphocyte activation|positive regulation of cell proliferation	integral to membrane	antigen binding|transmembrane receptor activity			ovary(1)|breast(1)	2	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			gtgtgtgcgtgCGCGCGCGCGC	0.386													6	3	---	---	---	---	
B4GALT3	8703	broad.mit.edu	37	1	161146411	161146411	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161146411delC	uc001fyq.1	-						PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron|B4GALT3_uc001fyo.1_5'Flank|B4GALT3_uc001fyp.1_5'Flank|B4GALT3_uc001fyr.1_Intron|B4GALT3_uc001fys.1_Intron|B4GALT3_uc009wud.1_Intron	NM_003779	NP_003770	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|metal ion binding|N-acetyllactosamine synthase activity				0	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	ACCTGCACCGCCAGAGATCAG	0.552													4	2	---	---	---	---	
MPZ	4359	broad.mit.edu	37	1	161281189	161281190	+	5'Flank	DEL	TG	-	-	rs72062148		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161281189_161281190delTG	uc001gaf.3	-						MPZ_uc010pko.1_5'Flank|SDHC_uc001gag.2_5'Flank|SDHC_uc001gai.2_5'Flank|SDHC_uc001gaj.2_5'Flank|SDHC_uc001gak.2_5'Flank	NM_000530	NP_000521	P25189	MYP0_HUMAN	myelin protein zero						synaptic transmission	integral to plasma membrane	structural molecule activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			AGAGACAGAAtgtgtgtgtgtg	0.312													8	4	---	---	---	---	
DDR2	4921	broad.mit.edu	37	1	162648957	162648957	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162648957delT	uc001gcf.2	+						DDR2_uc001gcg.2_Intron	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2						cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			acccaataggttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	163191279	163191282	+	IGR	DEL	AATC	-	-	rs34713100		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163191279_163191282delAATC								RGS5 (18407 upstream) : NUF2 (100441 downstream)																							acatctcaaaaatcaatcaatcaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165085404	165085406	+	IGR	DEL	CTC	-	-	rs34495148		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165085404_165085406delCTC								PBX1 (231104 upstream) : LMX1A (85699 downstream)																							tcttattcttctcctcctcctcc	0.000													6	4	---	---	---	---	
TMCO1	54499	broad.mit.edu	37	1	165758528	165758528	+	Intron	DEL	A	-	-	rs113963252		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165758528delA	uc001gdn.3	-									Q9UM00	TMCO1_HUMAN	Homo sapiens mRNA for putative membrane protein, complete cds.							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				central_nervous_system(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					GGTGTTATTGAAAAAAAAAAA	0.338													4	2	---	---	---	---	
UCK2	7371	broad.mit.edu	37	1	165838642	165838642	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165838642delT	uc001gdp.2	+						UCK2_uc010plb.1_Intron	NM_012474	NP_036606	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity			ovary(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					CTGtatctacttgagtttcaa	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166008484	166008484	+	IGR	DEL	C	-	-	rs59815510		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166008484delC								UCK2 (131147 upstream) : FAM78B (20932 downstream)																							AATATATGCACAACATTCTGG	0.303													3	4	---	---	---	---	
MPZL1	9019	broad.mit.edu	37	1	167725396	167725397	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167725396_167725397insT	uc001geo.2	+						MPZL1_uc001gen.3_Intron|MPZL1_uc001gep.2_Intron|MPZL1_uc001geq.2_Intron|MPZL1_uc009wvh.2_Intron	NM_003953	NP_003944	O95297	MPZL1_HUMAN	myelin protein zero-like 1 isoform a						cell-cell signaling|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	protein binding|structural molecule activity			ovary(2)	2	all_hematologic(923;0.215)					AAGTACATGGAttttttttttt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168133509	168133513	+	IGR	DEL	ACCTA	-	-	rs145338652		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168133509_168133513delACCTA								GPR161 (26688 upstream) : TIPRL (14658 downstream)																							CTTGCTAGTTACCTAACAAGTACTG	0.371													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	170330659	170330659	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170330659delT								LOC284688 (77310 upstream) : GORAB (170604 downstream)																							tgagatcaacttttttagttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	172988966	172988966	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172988966delT								FASLG (352956 upstream) : TNFSF18 (21394 downstream)																							CTATCAAGCAttttttttttt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	175242173	175242174	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175242173_175242174insT								KIAA0040 (79944 upstream) : TNR (49761 downstream)																							gatctcagggattttttttttt	0.000													4	2	---	---	---	---	
TDRD5	163589	broad.mit.edu	37	1	179631354	179631354	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179631354delC	uc001gnf.1	+	14	2526	c.2276delC	c.(2275-2277)TCCfs	p.S759fs	TDRD5_uc010pnp.1_Frame_Shift_Del_p.S813fs|TDRD5_uc001gnh.1_Frame_Shift_Del_p.S314fs	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	759					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						GATGCTGCCTCCCATCTATTT	0.428													33	27	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	180553723	180553723	+	IGR	DEL	T	-	-	rs71121032		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180553723delT								ACBD6 (81701 upstream) : XPR1 (47423 downstream)																							gacccccccctcctcagcctc	0.065													4	2	---	---	---	---	
XPR1	9213	broad.mit.edu	37	1	180690358	180690358	+	Intron	DEL	A	-	-	rs113624114		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180690358delA	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0						actctgtctcaaaaaaaaaaa	0.119													4	2	---	---	---	---	
RGSL1	353299	broad.mit.edu	37	1	182425434	182425435	+	Intron	INS	-	T	T	rs113276872		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182425434_182425435insT	uc009wxw.2	+						RGSL1_uc010pnu.1_Intron	NM_001137669	NP_001131141	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1							integral to membrane	signal transducer activity			central_nervous_system(1)	1						CAGAAGTAATCttttttttttt	0.213													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193594986	193594986	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193594986delA								CDC73 (371046 upstream) : None (None downstream)																							TTTAATGTAGAAGAAAAGCAG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	194943447	194943448	+	IGR	INS	-	A	A	rs35085275		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194943447_194943448insA								None (None upstream) : None (None downstream)																							GAATAGAGTTGAAAAAAAAAAG	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	195707382	195707382	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195707382delC								None (None upstream) : KCNT2 (487531 downstream)																							gtcctttggacctaactggat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	200690084	200690091	+	IGR	DEL	TCCCTTCC	-	-	rs111388103		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200690084_200690091delTCCCTTCC								DDX59 (50958 upstream) : CAMSAP1L1 (18595 downstream)																							tctcccttcttcccttcctcccttcctc	0.000													2	5	---	---	---	---	
PKP1	5317	broad.mit.edu	37	1	201285261	201285262	+	Intron	INS	-	GGAT	GGAT	rs138676382	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201285261_201285262insGGAT	uc001gwd.2	+						PKP1_uc001gwe.2_Intron|PKP1_uc009wzm.2_Intron	NM_000299	NP_000290	Q13835	PKP1_HUMAN	plakophilin 1 isoform 1b						cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development	desmosome|intermediate filament|nucleus	intermediate filament binding|signal transducer activity|structural constituent of epidermis			ovary(2)	2						gacggacggacggacggatgga	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201988162	201988163	+	IGR	INS	-	CA	CA	rs146201805	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201988162_201988163insCA								ELF3 (1856 upstream) : GPR37L1 (103866 downstream)																							ggaaccaaagtcacacacactc	0.134													3	4	---	---	---	---	
CR1L	1379	broad.mit.edu	37	1	207842739	207842756	+	Intron	DEL	ATTTCAGTTTTCTTCGAG	-	-	rs139825875		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207842739_207842756delATTTCAGTTTTCTTCGAG	uc001hga.3	+						CR1L_uc001hfz.2_Intron	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like							cytoplasm|extracellular region|membrane					0						TTTTCCTCTTATTTCAGTTTTCTTCGAGATCAAATCTG	0.573													5	3	---	---	---	---	
CR1L	1379	broad.mit.edu	37	1	207852342	207852344	+	Intron	DEL	TTT	-	-	rs67388093		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207852342_207852344delTTT	uc001hga.3	+						CR1L_uc001hfz.2_Intron|CR1L_uc001hgb.1_Intron	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like							cytoplasm|extracellular region|membrane					0						tccaaagttcttttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214904515	214904516	+	IGR	INS	-	T	T	rs9793509		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214904515_214904516insT								CENPF (66603 upstream) : KCNK2 (274369 downstream)																							ttttttttttgttttttttttt	0.000													3	3	---	---	---	---	
GPATCH2	55105	broad.mit.edu	37	1	217626015	217626015	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217626015delT	uc001hlf.1	-						GPATCH2_uc009xdq.1_Intron	NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		CTTCTAAACCTTTTTTTTTCC	0.348													4	2	---	---	---	---	
GPATCH2	55105	broad.mit.edu	37	1	217649578	217649579	+	Intron	DEL	GT	-	-	rs141872592		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217649578_217649579delGT	uc001hlf.1	-						GPATCH2_uc009xdq.1_Intron	NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		CCAGATATGAgtgtgtgtgtgt	0.238													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	226154361	226154361	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226154361delA								LEFTY2 (25441 upstream) : C1orf55 (16043 downstream)																							ttactaaaataataaaaataa	0.000													4	2	---	---	---	---	
OBSCN	84033	broad.mit.edu	37	1	228441624	228441624	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228441624delC	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				gcatgagccaccatgcccagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	229830513	229830514	+	IGR	INS	-	T	T	rs111472589		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229830513_229830514insT								URB2 (34567 upstream) : GALNT2 (363022 downstream)																							AAATAATGGAATTTTTTTTTTT	0.351													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	230532305	230532306	+	IGR	INS	-	C	C	rs147949837	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230532305_230532306insC								PGBD5 (18938 upstream) : COG2 (245896 downstream)																							ACATTTTGTTGCCCCCCCTCCC	0.520													3	3	---	---	---	---	
ERO1LB	56605	broad.mit.edu	37	1	236408140	236408141	+	Intron	DEL	AT	-	-	rs66540035		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236408140_236408141delAT	uc001hxt.2	-						ERO1LB_uc010pxt.1_Intron	NM_019891	NP_063944	Q86YB8	ERO1B_HUMAN	endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)			cagTTTGAAGATGGATGCAACA	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	236675421	236675422	+	IGR	INS	-	C	C	rs34811102		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236675421_236675422insC								EDARADD (27413 upstream) : LGALS8 (6143 downstream)																							tttctttctttttttttttttt	0.114													5	4	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237284330	237284331	+	Intron	INS	-	TG	TG	rs146153915	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237284330_237284331insTG	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GTTTAAAATGCtgtgtgtgtgt	0.163													3	4	---	---	---	---	
RYR2	6262	broad.mit.edu	37	1	237592336	237592337	+	Intron	INS	-	T	T	rs138586889	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237592336_237592337insT	uc001hyl.1	+							NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ACTCAGGAATATTGCAGGGCTG	0.545													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	240171282	240171285	+	IGR	DEL	CAGA	-	-	rs72390152		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240171282_240171285delCAGA								CHRM3 (98567 upstream) : FMN2 (83900 downstream)																							taagagggaccagacaaagttcaa	0.000													2	5	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241316766	241316766	+	Intron	DEL	A	-	-	rs113677634		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241316766delA	uc001hyv.2	-						RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			AGATGATTTGAAAAAAAAAAA	0.308													4	2	---	---	---	---	
CEP170	9859	broad.mit.edu	37	1	243336367	243336368	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243336367_243336368insT	uc001hzs.2	-						CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha							centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			AGTAATTATCCttttttttttt	0.173													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	244462517	244462518	+	IGR	DEL	AG	-	-	rs71810240		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244462517_244462518delAG								ZNF238 (241741 upstream) : C1orf100 (53419 downstream)																							AAAAGgagacagagagagagag	0.203													4	2	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245332632	245332633	+	Intron	INS	-	GTGTGGGG	GTGTGGGG			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245332632_245332633insGTGTGGGG	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CGGGCCATGgtgtgtgtgtgtg	0.426													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2910858	2910859	+	Intron	INS	-	T	T	rs149382134	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2910858_2910859insT	uc002qxh.1	-											Homo sapiens cDNA FLJ37991 fis, clone CTONG2011765.																		tccaccccctctccccagccca	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	2910879	2910880	+	Intron	INS	-	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2910879_2910880insC	uc002qxh.1	-											Homo sapiens cDNA FLJ37991 fis, clone CTONG2011765.																		acagccacccaccctacacctc	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	6531873	6531874	+	IGR	INS	-	AA	AA	rs28602613		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6531873_6531874insAA								LOC400940 (403509 upstream) : CMPK2 (448629 downstream)																							tctcaaaaaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
HPCAL1	3241	broad.mit.edu	37	2	10555675	10555675	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10555675delC	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.2_Intron|HPCAL1_uc010exf.2_Intron	NM_002149	NP_002140	P37235	HPCL1_HUMAN	hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)		GTGGTGTCGGCCCCCGAGGCA	0.602													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15279626	15279627	+	IGR	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15279626_15279627delGT								FAM84A (488693 upstream) : NBAS (27405 downstream)																							TTAgtgtatggtgtgtgtgtgt	0.208													4	2	---	---	---	---	
C2orf43	60526	broad.mit.edu	37	2	20943210	20943210	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20943210delA	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744	Q9H6V9	CB043_HUMAN	hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					accactttataagtagtgtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	23426481	23426484	+	IGR	DEL	ACAG	-	-	rs137959221		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23426481_23426484delACAG								None (None upstream) : KLHL29 (328971 downstream)																							acacacaaacacagacaaacacac	0.000													4	2	---	---	---	---	
FKBP1B	2281	broad.mit.edu	37	2	24281074	24281075	+	Intron	DEL	AA	-	-	rs77465113		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24281074_24281075delAA	uc002rer.2	+						FKBP1B_uc002res.2_Intron|FKBP1B_uc002ret.2_Intron|FKBP1B_uc002reu.2_Intron	NM_004116	NP_004107	P68106	FKB1B_HUMAN	FK506 binding protein 1B, 12.6 kDa isoform a						'de novo' protein folding|negative regulation of heart rate|negative regulation of protein phosphatase type 2B activity|protein maturation by protein folding|protein refolding|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|regulation of ryanodine-sensitive calcium-release channel activity|response to redox state	calcium channel complex|sarcoplasmic reticulum membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ctgtctcaggaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
RBKS	64080	broad.mit.edu	37	2	28111657	28111657	+	Intron	DEL	A	-	-	rs111982915		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28111657delA	uc002rlo.1	-						BRE_uc002rlp.1_5'Flank|BRE_uc002rlq.2_5'Flank|BRE_uc002rlr.2_5'Flank|BRE_uc002rls.2_5'Flank|BRE_uc002rlt.2_5'Flank|BRE_uc002rlu.2_5'Flank|RBKS_uc010ezi.1_Intron|RBKS_uc010ymg.1_Intron	NM_022128	NP_071411	Q9H477	RBSK_HUMAN	ribokinase						D-ribose metabolic process		ATP binding|ribokinase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					aaatgttgttaaaaaaaaatg	0.030													3	3	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28411137	28411138	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28411137_28411138insA	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					GCTCACCACTTAAAAAGCCCTA	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	33649443	33649443	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33649443delT								LTBP1 (24870 upstream) : RASGRP3 (11973 downstream)																							ATATTAATGCttttttttttt	0.139													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	35876836	35876837	+	IGR	DEL	AA	-	-	rs111765020		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35876836_35876837delAA								None (None upstream) : CRIM1 (706560 downstream)																							actttgtctcaaaaaaaaaata	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	36313404	36313405	+	IGR	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36313404_36313405delCA								None (None upstream) : CRIM1 (269992 downstream)																							cctattattccacacacacaca	0.158													4	4	---	---	---	---	
FEZ2	9637	broad.mit.edu	37	2	36794409	36794410	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36794409_36794410insA	uc002rph.2	-						FEZ2_uc002rpe.2_Intron|FEZ2_uc002rpf.2_Intron|FEZ2_uc002rpg.2_Intron|FEZ2_uc002rpi.2_Intron|FEZ2_uc002rpj.2_Intron	NM_005102	NP_005093	Q9UHY8	FEZ2_HUMAN	zygin 2 isoform 1						axon guidance|signal transduction		protein binding			ovary(1)	1		all_hematologic(82;0.21)				AGGAGAGAAAGAAAAAAAAAAA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	36913416	36913417	+	IGR	DEL	GT	-	-	rs71398208		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36913416_36913417delGT								FEZ2 (88084 upstream) : VIT (10497 downstream)																							AAgtgtgtgagtgtgtgtgtgt	0.000													2	5	---	---	---	---	
SULT6B1	391365	broad.mit.edu	37	2	37421321	37421322	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37421321_37421322insT	uc002rpv.2	-						SULT6B1_uc010fae.1_Intron|SULT6B1_uc010faf.1_Intron|SULT6B1_uc002rpw.2_Intron|SULT6B1_uc010fag.1_Intron|uc002rpx.1_5'Flank			Q6IMI4	ST6B1_HUMAN	Homo sapiens sulfotransferase SULT6B1 (SULT6B1) mRNA, partial 5'UTR; alternate transcript.							cytoplasm	sulfotransferase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(82;0.248)				CTGTCTGTAGAttttttttttt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43317530	43317532	+	IGR	DEL	AAA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43317530_43317532delAAA								HAAO (297779 upstream) : ZFP36L2 (132010 downstream)																							acactgtgtcaaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
LRPPRC	10128	broad.mit.edu	37	2	44185909	44185909	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44185909delA	uc002rtr.2	-						LRPPRC_uc010yob.1_Intron	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GTGATGTAGTAACCAGTAGTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45297373	45297373	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45297373delA								SIX2 (60830 upstream) : SRBD1 (318447 downstream)																							CAACAAGTATAAAAAAAAAAA	0.403													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45869228	45869229	+	IGR	INS	-	G	G	rs145922094	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45869228_45869229insG								SRBD1 (30795 upstream) : PRKCE (9814 downstream)																							TCAAGGCGAGAGGGGAGACAGC	0.292													3	3	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47686097	47686098	+	Intron	INS	-	A	A	rs35139333		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47686097_47686098insA	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron|MSH2_uc010fbh.1_Intron|MSH2_uc010fbi.1_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(1)		large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACTTACACATTAAAAAAAAAAA	0.050			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				3	3	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47794270	47794271	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47794270_47794271delAC	uc002rvz.2	+						KCNK12_uc002rwb.2_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GGTCTACACAACACACACACAC	0.361			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48391231	48391232	+	IGR	DEL	GT	-	-	rs35338920		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48391231_48391232delGT								FBXO11 (258417 upstream) : FOXN2 (150563 downstream)																							gtgtgtgtacgtgtgtgtgtgt	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	48650240	48650240	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48650240delT								FOXN2 (43806 upstream) : KLRAQ1 (17668 downstream)																							tttgttgttgttttttttttt	0.194													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	53115193	53115194	+	IGR	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53115193_53115194delTT								None (None upstream) : ASB3 (781924 downstream)																							ATACTAAATCtttttttttttt	0.079													4	2	---	---	---	---	
RTN4	57142	broad.mit.edu	37	2	55199932	55199932	+	3'UTR	DEL	T	-	-	rs35013297		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55199932delT	uc002rye.2	-	9					RTN4_uc002ryc.2_3'UTR|RTN4_uc002ryd.2_3'UTR|RTN4_uc002ryf.2_3'UTR|RTN4_uc002ryg.2_3'UTR	NM_020532	NP_065393	Q9NQC3	RTN4_HUMAN	reticulon 4 isoform A						apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration	integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane	protein binding			ovary(2)|large_intestine(1)	3						TGAAAAGGGCTTTTTTTTTTT	0.383													3	3	---	---	---	---	
C2orf63	130162	broad.mit.edu	37	2	55405088	55405089	+	Intron	INS	-	A	A	rs148222697	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55405088_55405089insA	uc002ryi.2	-						C2orf63_uc002ryh.2_Intron|C2orf63_uc002ryj.2_Intron	NM_152385	NP_689598	Q8NHS4	CB063_HUMAN	hypothetical protein LOC130162 isoform 1								binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)			TAGCCCCCGTCAAAAAAAATCA	0.337													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	55499725	55499726	+	IGR	INS	-	AAAAAA	AAAAAA			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55499725_55499726insAAAAAA								MTIF2 (3341 upstream) : PRDXDD1P (9729 downstream)																							TAGAAAGTAGCAAAAAAAAAAA	0.139													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	55989738	55989745	+	IGR	DEL	CCTTTCTT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55989738_55989745delCCTTTCTT								PNPT1 (68727 upstream) : EFEMP1 (103358 downstream)																							tccctttcaccctttcttcctttcttcc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60004209	60004212	+	IGR	DEL	ACAA	-	-	rs71420344		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60004209_60004212delACAA								None (None upstream) : BCL11A (674091 downstream)																							acacacacacacaaacacacacac	0.265													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60068299	60068300	+	IGR	INS	-	A	A	rs138772854	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60068299_60068300insA								None (None upstream) : BCL11A (610003 downstream)																							GTTCTAGGTGGAACTCCAGTCA	0.411													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60400640	60400640	+	IGR	DEL	G	-	-	rs68069352		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60400640delG								None (None upstream) : BCL11A (277663 downstream)																							aaaagaaaaagaaaaaagtag	0.104													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60503021	60503022	+	IGR	INS	-	AAAAC	AAAAC	rs142345133	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60503021_60503022insAAAAC								None (None upstream) : BCL11A (175281 downstream)																							CAAAGAATTGTaaaacaaaaca	0.114													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60827220	60827220	+	IGR	DEL	T	-	-	rs11285050		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60827220delT								BCL11A (46587 upstream) : PAPOLG (156163 downstream)																							ggggagccacttgaggggctt	0.000													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	60940464	60940465	+	IGR	INS	-	A	A	rs151198726	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60940464_60940465insA								BCL11A (159831 upstream) : PAPOLG (42918 downstream)																							ccgtctctactaaaaatacaaa	0.000													5	11	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61588757	61588758	+	Intron	INS	-	G	G	rs143596050	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61588757_61588758insG	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			agaatgaaactggatccttatc	0.000													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64504950	64504952	+	IGR	DEL	TTT	-	-	rs13003134		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64504950_64504952delTTT								PELI1 (133345 upstream) : HSPC159 (176375 downstream)																							tccttccttctttctttctcctt	0.123													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67293618	67293619	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67293618_67293619insT								MEIS1 (493728 upstream) : ETAA1 (330823 downstream)																							TATTACTCACATTTTAACATCA	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67618589	67618590	+	IGR	DEL	AG	-	-	rs10598578		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67618589_67618590delAG								MEIS1 (818699 upstream) : ETAA1 (5852 downstream)																							TACTACCCTTAGAGAGTGTGGC	0.485													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	75159768	75159769	+	Intron	INS	-	T	T	rs112497333		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75159768_75159769insT	uc002sne.1	+											Homo sapiens cDNA FLJ43972 fis, clone TESTI4017961.																		ctagtttaatgttttttttttt	0.129													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82427526	82427526	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82427526delT								None (None upstream) : None (None downstream)																							TCCTGCATGCTTTTTTTTTTC	0.303													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85936613	85936614	+	IGR	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85936613_85936614delAC								GNLY (10739 upstream) : ATOH8 (44295 downstream)																							ATGTTGAGCAACACACACACAG	0.406													4	2	---	---	---	---	
MRPL35	51318	broad.mit.edu	37	2	86435427	86435427	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86435427delT	uc002srg.3	+						MRPL35_uc002srf.3_Intron	NM_016622	NP_057706	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35 isoform a						translation	mitochondrial ribosome	structural constituent of ribosome				0						TGTGTATGTGttttttttttt	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91784574	91784579	+	IGR	DEL	TTAACT	-	-	rs67885824		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91784574_91784579delTTAACT								None (None upstream) : LOC654342 (20613 downstream)																							acttaatacattaactttaaatcccg	0.073													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92267964	92267965	+	IGR	INS	-	ATTCC	ATTCC			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92267964_92267965insATTCC								FKSG73 (137470 upstream) : None (None downstream)																							attccttgctgattccattcca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96617039	96617040	+	Intron	INS	-	C	C	rs74263747		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96617039_96617040insC	uc010yug.1	-											Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																		gaaaaaaaaaaaaaaaacaaaT	0.153													3	4	---	---	---	---	
PDCL3	79031	broad.mit.edu	37	2	101184065	101184067	+	Intron	DEL	AGG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101184065_101184067delAGG	uc002tao.2	+							NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3						apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0						TGAGACCTGAAGGAGGTGAAGAA	0.330													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102250907	102250910	+	IGR	DEL	AGAA	-	-	rs67054911		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102250907_102250910delAGAA								RFX8 (159742 upstream) : MAP4K4 (63578 downstream)																							agaaagagagagaaagaaagaaag	0.000													3	5	---	---	---	---	
MAP4K4	9448	broad.mit.edu	37	2	102460226	102460227	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102460226_102460227insA	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc002tbk.2_5'Flank|MAP4K4_uc002tbj.1_Intron	NM_145687	NP_663720	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						GTTTGCTGAAGAAAAAAAAAGT	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103913375	103913376	+	IGR	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103913375_103913376delCA								TMEM182 (479239 upstream) : None (None downstream)																							acacacacaccacacacacaca	0.287													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	103961187	103961187	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103961187delG								TMEM182 (527051 upstream) : None (None downstream)																							gagagatgttggagactcaaa	0.000													4	2	---	---	---	---	
TGFBRAP1	9392	broad.mit.edu	37	2	105888407	105888407	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105888407delT	uc002tcq.2	-						TGFBRAP1_uc010fjc.2_Intron|TGFBRAP1_uc002tcr.3_Intron	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor						regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						cttttttgcattttggtgctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118884919	118884920	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118884919_118884920insT								INSIG2 (17323 upstream) : EN1 (714828 downstream)																							ACAGGGACCTCtttttttttgt	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	119941978	119941978	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119941978delC								C1QL2 (25507 upstream) : STEAP3 (39406 downstream)																							CATCCCAGGGCAAGCAGGCCt	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121080566	121080567	+	IGR	DEL	AG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121080566_121080567delAG								RALB (28283 upstream) : INHBB (23152 downstream)																							cctaggtgacagagagagagag	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	126073883	126073884	+	IGR	INS	-	AAACA	AAACA			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126073883_126073884insAAACA								CNTNAP5 (401022 upstream) : None (None downstream)																							ggtgtcctttgaaacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	128201604	128201604	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128201604delC								PROC (14788 upstream) : IWS1 (36779 downstream)																							tcgagaccagcatggccaaca	0.000													5	3	---	---	---	---	
GPR17	2840	broad.mit.edu	37	2	128406741	128406744	+	Intron	DEL	AGGA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128406741_128406744delAGGA	uc010yzn.1	+						LIMS2_uc002tow.2_5'Flank|LIMS2_uc002tox.2_Intron|LIMS2_uc010fmb.2_Intron|LIMS2_uc002toy.2_Intron|LIMS2_uc010yzm.1_Intron|LIMS2_uc002tpa.2_Intron|LIMS2_uc002toz.2_Intron|LIMS2_uc002tpb.2_Intron|GPR17_uc002tpc.2_Intron|GPR17_uc010yzo.1_Intron|GPR17_uc002tpd.2_Intron	NM_001161415	NP_001154887	Q13304	GPR17_HUMAN	G protein-coupled receptor 17 isoform a							integral to plasma membrane	chemokine receptor activity|purinergic nucleotide receptor activity, G-protein coupled				0	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)		agaggaaggtaggaaggaaggaag	0.167													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129098917	129098919	+	IGR	DEL	GTG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129098917_129098919delGTG								HS6ST1 (22746 upstream) : None (None downstream)																							ggtattggtagtggtggtgatgg	0.103													4	2	---	---	---	---	
NCRNA00164	554226	broad.mit.edu	37	2	133008479	133008480	+	Intron	INS	-	T	T	rs148481505		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133008479_133008480insT	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0						ATCACTTTTCATTTTTGGGGGT	0.342													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133028130	133028131	+	IGR	DEL	AC	-	-	rs145524384		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133028130_133028131delAC								NCRNA00164 (12588 upstream) : GPR39 (146016 downstream)																							ggacagacagacagagagagag	0.000													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133036727	133036729	+	IGR	DEL	GGG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133036727_133036729delGGG								NCRNA00164 (21185 upstream) : GPR39 (137418 downstream)																							ccctattagtgggtgaacaatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133081485	133081485	+	IGR	DEL	T	-	-	rs113299534		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133081485delT								NCRNA00164 (65943 upstream) : GPR39 (92662 downstream)																							ACTTCCCTTATTTTTTTTCTT	0.249													5	3	---	---	---	---	
MCM6	4175	broad.mit.edu	37	2	136632934	136632935	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136632934_136632935insA	uc002tuw.2	-							NM_005915	NP_005906	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|identical protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.166)	Atorvastatin(DB01076)	aattacgcctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	136657735	136657736	+	IGR	DEL	AA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136657735_136657736delAA								MCM6 (23724 upstream) : DARS (6518 downstream)																							AGAAAAAAAGAAAAAAAAAAAC	0.302													4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	142023275	142023276	+	Intron	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142023275_142023276delTG	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATGAGATAGATGTGTGTGTGTG	0.193										TSP Lung(27;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	157204341	157204342	+	IGR	INS	-	TTG	TTG	rs144856826	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157204341_157204342insTTG								NR4A2 (15054 upstream) : GPD2 (87623 downstream)																							tttttgtttgtttgttgttgtt	0.000													4	2	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160638083	160638086	+	Intron	DEL	GAAA	-	-	rs71923231		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160638083_160638086delGAAA	uc002ubb.3	-						LY75_uc010fos.2_Intron|CD302_uc002uba.2_Intron|CD302_uc010zco.1_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		aaaaaaaagggaaagaaagaaaga	0.054													4	5	---	---	---	---	
FASTKD1	79675	broad.mit.edu	37	2	170411709	170411710	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170411709_170411710delTT	uc002uev.3	-	7	1526_1527	c.1138_1139delAA	c.(1138-1140)AAGfs	p.K380fs	FASTKD1_uc002uew.3_RNA|FASTKD1_uc002uex.3_Frame_Shift_Del_p.K366fs	NM_024622	NP_078898	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	380					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(4)	4						TTGAGTTATCTTCAACAACTCT	0.282													22	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	173241014	173241015	+	IGR	INS	-	AC	AC	rs148638438	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173241014_173241015insAC								DLX2 (273536 upstream) : ITGA6 (51067 downstream)																							cacacagacgtacacacacaca	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174585658	174585659	+	IGR	DEL	CA	-	-	rs66488536		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174585658_174585659delCA								CDCA7 (351940 upstream) : SP3 (187600 downstream)																							GAGacacacgcacacacacaca	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	176156023	176156023	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176156023delA								ATP5G3 (109533 upstream) : KIAA1715 (634387 downstream)																							TTAGAAGGCCAAAAAAAAAAA	0.348													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177357061	177357062	+	IGR	DEL	TG	-	-	rs147440719		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177357061_177357062delTG								MTX2 (154310 upstream) : MIR1246 (108646 downstream)																							GCACTATATAtgtgtgtgtgtg	0.282													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	187646097	187646098	+	IGR	INS	-	T	T	rs144500834		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187646097_187646098insT								FAM171B (15413 upstream) : ZSWIM2 (46109 downstream)																							ttgttttttgattttttttttt	0.000													2	4	---	---	---	---	
ASNSD1	54529	broad.mit.edu	37	2	190533787	190533788	+	Intron	DEL	CT	-	-	rs74416910		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190533787_190533788delCT	uc002uqt.2	+							NM_019048	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1						asparagine biosynthetic process|glutamine metabolic process		asparagine synthase (glutamine-hydrolyzing) activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			ctttctctccctctctctctct	0.307													3	3	---	---	---	---	
ANKRD44	91526	broad.mit.edu	37	2	197915153	197915154	+	Intron	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197915153_197915154delTT	uc002uua.1	-						ANKRD44_uc002utz.3_Intron	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ttgtttttgctttttttttttt	0.089													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201073630	201073631	+	IGR	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201073630_201073631delGT								C2orf47 (244785 upstream) : SPATS2L (96973 downstream)																							gtgcaagccagtgtgtgtgtgc	0.000													2	4	---	---	---	---	
CDK15	65061	broad.mit.edu	37	2	202701524	202701524	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202701524delA	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897	Q96Q40	CDK15_HUMAN	PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)	CTGGTTTAGGAAAAAAAaaaa	0.244													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	204464229	204464229	+	IGR	DEL	A	-	-	rs71408951		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204464229delA								RAPH1 (64171 upstream) : CD28 (106969 downstream)																							actccgtctcaaaaaaaaaaa	0.159													4	2	---	---	---	---	
NRP2	8828	broad.mit.edu	37	2	206607329	206607329	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206607329delC	uc002vaw.2	+						NRP2_uc002vat.2_Intron|NRP2_uc002vau.2_Intron|NRP2_uc002vav.2_Intron|NRP2_uc002vax.2_Intron|NRP2_uc002vay.2_Intron|NRP2_uc010fud.2_Intron	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor						angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4						ggatccaaggcagtaaagagc	0.129													4	2	---	---	---	---	
PLEKHM3	389072	broad.mit.edu	37	2	208784678	208784679	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208784678_208784679delAC	uc002vcl.2	-						PLEKHM3_uc002vcm.2_Intron	NM_001080475	NP_001073944	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1						GTCAGGacagacacacacacac	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	210124606	210124606	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210124606delC								PTH2R (419788 upstream) : MAP2 (164165 downstream)																							GGAATGCACTCCCCACATATG	0.373													4	2	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210422143	210422143	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210422143delT	uc002vdc.1	+						MAP2_uc002vdd.1_Intron	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	AAAAATGTGGTTTTTTTTCCC	0.423													4	2	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210425655	210425655	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210425655delG	uc002vdc.1	+						MAP2_uc002vdd.1_Intron	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	ATTGGACAGAGGACGGAGATG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	217677183	217677184	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217677183_217677184insA								IGFBP5 (116911 upstream) : TNP1 (47000 downstream)																							AAGGACACCACAAAAAAAAAGT	0.287													4	2	---	---	---	---	
DOCK10	55619	broad.mit.edu	37	2	225850347	225850348	+	Intron	INS	-	AAA	AAA	rs72412199		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225850347_225850348insAAA	uc010fwz.1	-						DOCK10_uc002vod.1_Intron	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GGTTAAGGAGGAAAAAAAAAAA	0.406													5	3	---	---	---	---	
AGFG1	3267	broad.mit.edu	37	2	228373404	228373405	+	Intron	INS	-	T	T	rs141926868		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228373404_228373405insT	uc002vpc.2	+						AGFG1_uc002vpd.2_Intron|AGFG1_uc002vpe.2_Intron|AGFG1_uc002vpf.2_Intron	NM_004504	NP_004495	P52594	AGFG1_HUMAN	HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4						CACTGTTGGGATTTTTTTTTTT	0.292													3	4	---	---	---	---	
SP140	11262	broad.mit.edu	37	2	231190580	231190580	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231190580delA	uc010zma.1	+						SP140L_uc010fxm.1_5'Flank	NM_007237		Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1						defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		AATAAACAGCAAAAAAAAAAA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235378751	235378751	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235378751delT								SPP2 (392975 upstream) : ARL4C (22937 downstream)																							TCAGCTCTCCTTTTTTGGTTT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238135052	238135052	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238135052delT								COPS8 (127565 upstream) : COL6A3 (97603 downstream)																							acctaacttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239742073	239742073	+	IGR	DEL	T	-	-	rs71928479		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239742073delT								ASB1 (381183 upstream) : TWIST2 (14600 downstream)																							GTTTGTTTTGTTTTTTTACTA	0.328													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241290179	241290180	+	IGR	INS	-	A	A	rs138807327	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241290179_241290180insA								OTOS (210106 upstream) : GPC1 (84935 downstream)																							taagagaggacacttgtgctgt	0.134													2	4	---	---	---	---	
HRH1	3269	broad.mit.edu	37	3	11238096	11238096	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11238096delT	uc010hdr.2	+						HRH1_uc010hds.2_Intron	NM_001098213	NP_001091683	P35367	HRH1_HUMAN	histamine receptor H1						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	GATTCCTTGAttttttttttc	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	22418297	22418298	+	IGR	INS	-	T	T	rs113484594		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22418297_22418298insT								ZNF385D (4174 upstream) : UBE2E2 (826355 downstream)																							GGAAAAACAAGTTGCAAGAAGC	0.203													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23189700	23189700	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23189700delT								ZNF385D (775577 upstream) : UBE2E2 (54953 downstream)																							ctgagctttattttttttttc	0.005													4	2	---	---	---	---	
LOC152024	152024	broad.mit.edu	37	3	24140763	24140763	+	Intron	DEL	T	-	-	rs112374861		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24140763delT	uc003ccu.3	-											Homo sapiens hypothetical protein LOC152024, mRNA (cDNA clone IMAGE:4829078).												0						cttccttttcttttttttttt	0.065													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	32676648	32676649	+	IGR	INS	-	T	T	rs35155529		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32676648_32676649insT								DYNC1LI1 (64298 upstream) : CNOT10 (50049 downstream)																							gcatctcaatcttTTTTTTTTT	0.153													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	40406005	40406006	+	IGR	DEL	TC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40406005_40406006delTC								EIF1B (52092 upstream) : ENTPD3 (22667 downstream)																							tctctaattttctctctctctc	0.000													4	2	---	---	---	---	
BSN	8927	broad.mit.edu	37	3	49693933	49693933	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49693933delC	uc003cxe.3	+	5	7058	c.6944delC	c.(6943-6945)ACCfs	p.T2315fs		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	2315					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CCCACAACCACCCCTGCTGCC	0.677													8	4	---	---	---	---	
ERC2	26059	broad.mit.edu	37	3	56225889	56225890	+	Intron	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56225889_56225890delCA	uc003dhr.1	-							NM_015576	NP_056391	O15083	ERC2_HUMAN	cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CTGCACAGGCCACACACACACA	0.421													3	3	---	---	---	---	
FAM107A	11170	broad.mit.edu	37	3	58602292	58602292	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58602292delA	uc003dko.2	-							NM_007177	NP_009108	O95990	F107A_HUMAN	downregulated in renal cell carcinoma						regulation of cell growth	nucleus	protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)		acacacacacacaccaccact	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	80321332	80321332	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80321332delA								ROBO1 (504273 upstream) : None (None downstream)																							GAAAAAAATGAAAAAAAATAT	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	86271162	86271162	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86271162delA								CADM2 (153214 upstream) : VGLL3 (715963 downstream)																							GGAGTCTCTTAAGCACACACA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	93505803	93505803	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93505803delA								None (None upstream) : PROS1 (86079 downstream)																							ctacaaaaacagtgtttcaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	95793981	95793982	+	IGR	INS	-	ACACTTCTA	ACACTTCTA	rs139926439	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95793981_95793982insACACTTCTA								LOC255025 (898902 upstream) : EPHA6 (739443 downstream)																							ctaacaccttcacaaggtattt	0.000													4	2	---	---	---	---	
EPHA6	285220	broad.mit.edu	37	3	96888969	96888969	+	Intron	DEL	A	-	-	rs68162597		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96888969delA	uc010how.1	+						EPHA6_uc003drp.1_Intron	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16						gaacttaaagaaaaaaaaaaa	0.169													4	3	---	---	---	---	
ARL6	84100	broad.mit.edu	37	3	97508896	97508897	+	Intron	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97508896_97508897delTG	uc003drv.2	+						ARL6_uc003drw.2_Intron|ARL6_uc003dru.2_Intron|ARL6_uc010hoy.2_Intron	NM_177976	NP_816931	Q9H0F7	ARL6_HUMAN	ADP-ribosylation factor-like 6						cilium assembly|determination of left/right symmetry|melanosome transport|protein polymerization|protein targeting to membrane|small GTPase mediated signal transduction|visual perception|Wnt receptor signaling pathway	axonemal microtubule|cilium axoneme|cilium membrane|membrane coat|microtubule basal body	GTP binding|metal ion binding|phospholipid binding|protein binding				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)		gcatcatgattgtgtgtgtgtg	0.153									Bardet-Biedl_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	97877502	97877503	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97877502_97877503insT								OR5H14 (8340 upstream) : OR5H15 (10041 downstream)																							TTTGCACTAAgtttttttttgt	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	101726594	101726595	+	IGR	INS	-	TT	TT	rs63677661		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101726594_101726595insTT								LOC152225 (9824 upstream) : ZPLD1 (91493 downstream)																							attggacattcttttttttttt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105049227	105049227	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105049227delT								None (None upstream) : ALCAM (36486 downstream)																							TAGGAAACCATAACCGTTGGT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105778223	105778227	+	IGR	DEL	AAAAC	-	-	rs112144589		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105778223_105778227delAAAAC								CBLB (189957 upstream) : LOC100302640 (777433 downstream)																							cgtaaagtaaaaaacaaaacaaaac	0.127													4	3	---	---	---	---	
PLCXD2	257068	broad.mit.edu	37	3	111438552	111438553	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111438552_111438553insA	uc003dya.2	+						PLCXD2_uc003dyb.2_Intron|PLCXD2_uc003dxz.2_Intron	NM_001134478	NP_001127950	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(1)	1						atctacagtggaaaaaaaaatc	0.000													4	2	---	---	---	---	
ATP6V1A	523	broad.mit.edu	37	3	113465473	113465473	+	5'Flank	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113465473delT	uc003eao.2	+						ATP6V1A_uc011bik.1_5'Flank|NAA50_uc011bij.1_5'Flank|NAA50_uc003ean.1_5'Flank	NM_001690	NP_001681	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal V1 subunit A						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(2)|skin(1)	3						AAGTTAGGTGTTTTAAAACAA	0.413													4	2	---	---	---	---	
QTRTD1	79691	broad.mit.edu	37	3	113792606	113792607	+	Intron	INS	-	C	C	rs146591635	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113792606_113792607insC	uc003eay.2	+						QTRTD1_uc003eaz.2_Intron|QTRTD1_uc011biq.1_Intron|QTRTD1_uc011bir.1_Intron|QTRTD1_uc003eba.2_Intron	NM_024638	NP_078914	Q9H974	QTRD1_HUMAN	queuine tRNA-ribosyltransferase domain						queuosine biosynthetic process	mitochondrion	metal ion binding|queuine tRNA-ribosyltransferase activity			central_nervous_system(1)|skin(1)	2						tattaatagtgcccccccattc	0.243													3	4	---	---	---	---	
LSAMP	4045	broad.mit.edu	37	3	115607999	115607999	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115607999delA	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		ACAGGGCTGGAATGGAAAGGT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	116813346	116813346	+	IGR	DEL	T	-	-	rs113183192		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116813346delT								LOC285194 (377461 upstream) : None (None downstream)																							atcttaattcttttttttttt	0.015													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	118562470	118562470	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118562470delC								None (None upstream) : IGSF11 (57011 downstream)																							ctgttgtgctccagttccatt	0.000													4	2	---	---	---	---	
GSK3B	2932	broad.mit.edu	37	3	119751324	119751324	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119751324delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	tccgtctcggaaaaaaaaaaa	0.000													3	3	---	---	---	---	
STXBP5L	9515	broad.mit.edu	37	3	120703362	120703362	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120703362delT	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		tctaacgggattttttttttg	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	121270182	121270183	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121270182_121270183insA								POLQ (5329 upstream) : ARGFX (16595 downstream)																							gactccatctcaaaaaaaaaga	0.168													4	2	---	---	---	---	
PARP15	165631	broad.mit.edu	37	3	122328559	122328559	+	Intron	DEL	A	-	-	rs63276763		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122328559delA	uc003efm.2	+						PARP15_uc003efn.2_Intron|PARP15_uc003efo.1_Intron	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5				GBM - Glioblastoma multiforme(114;0.0531)		aaaaaaaattaaaaaaaaaaa	0.129													4	2	---	---	---	---	
MYLK	4638	broad.mit.edu	37	3	123352677	123352678	+	Intron	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123352677_123352678delTG	uc003ego.2	-						MYLK_uc010hrr.2_Intron|MYLK_uc011bjv.1_Intron|MYLK_uc011bjw.1_Intron|MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CTACACTTTCtgtgtgtgtgtg	0.272													4	2	---	---	---	---	
UMPS	7372	broad.mit.edu	37	3	124450064	124450067	+	Intron	DEL	AAAT	-	-	rs10562112		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124450064_124450067delAAAT	uc003ehl.3	+						UMPS_uc003ehm.3_Intron|UMPS_uc011bka.1_Intron|UMPS_uc011bkb.1_Intron|UMPS_uc011bkc.1_Intron|UMPS_uc003ehn.3_Intron|UMPS_uc011bkd.1_Intron|hsa-mir-544b|MI0014159_5'Flank	NM_000373	NP_000364	P11172	UMPS_HUMAN	uridine monophosphate synthase						'de novo' pyrimidine base biosynthetic process|'de novo' UMP biosynthetic process|pyrimidine nucleoside biosynthetic process	cytosol|nucleus	orotate phosphoribosyltransferase activity|orotidine-5'-phosphate decarboxylase activity			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.146)		aaaaacaaacaaaTAGACCGGGAA	0.127													4	3	---	---	---	---	
SLC41A3	54946	broad.mit.edu	37	3	125732406	125732407	+	Intron	DEL	AA	-	-	rs62745562		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125732406_125732407delAA	uc003eij.2	-						SLC41A3_uc003eii.2_Intron|SLC41A3_uc003eil.2_Intron|SLC41A3_uc003eik.2_Intron|SLC41A3_uc011bkh.1_Intron	NM_001008485	NP_001008485	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3 isoform 1							integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)		actctgtctcaaaaaaaaaaaa	0.252													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126858113	126858114	+	IGR	DEL	GT	-	-	rs111608692	byFrequency	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126858113_126858114delGT								PLXNA1 (101885 upstream) : TPRA1 (433794 downstream)																							agagaTGGGGGTGTGTGTGTGT	0.252													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	126873265	126873266	+	IGR	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126873265_126873266delTG								PLXNA1 (117037 upstream) : TPRA1 (418642 downstream)																							tgtgtgtgactgtgtgtggttg	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	128568960	128568960	+	5'Flank	DEL	G	-	-	rs144888489		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128568960delG	uc003ekz.1	+											DQ576681																		ATGGCCTCCCGGGGGGCTGCA	0.627													3	4	---	---	---	---	
ACAD9	28976	broad.mit.edu	37	3	128614563	128614564	+	Intron	INS	-	CTC	CTC	rs146561372	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128614563_128614564insCTC	uc003ela.3	+						ACAD9_uc010hsw.1_Intron|ACAD9_uc011bks.1_Intron|ACAD9_uc003elb.2_Intron|ACAD9_uc003elc.1_5'Flank	NM_014049	NP_054768	Q9H845	ACAD9_HUMAN	acyl-Coenzyme A dehydrogenase family, member 9							mitochondrion	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(2)|central_nervous_system(1)	3						CTGGAAGTGGTCTCTCCTGAGC	0.604													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	130517109	130517109	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130517109delA								PIK3R4 (51413 upstream) : ATP2C1 (52336 downstream)																							acagaattagaaaaaaaatcc	0.000													4	2	---	---	---	---	
CPNE4	131034	broad.mit.edu	37	3	131646333	131646334	+	Intron	INS	-	T	T	rs74550583	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131646333_131646334insT	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						ATGACATCTCAtgtcattgcag	0.208													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	136499203	136499203	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136499203delT								STAG1 (27958 upstream) : TMEM22 (38658 downstream)																							GCTTTGCCCCTTGACAGGAAC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	138526737	138526737	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138526737delA								PIK3CB (48552 upstream) : FOXL2 (136330 downstream)																							atcctgtctcaaaaaaaaaaa	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	138708574	138708574	+	IGR	DEL	T	-	-	rs113125601		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138708574delT								C3orf72 (35744 upstream) : PRR23A (14231 downstream)																							TTCCCCCAACttttttttttt	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140422206	140422207	+	IGR	INS	-	A	A	rs151336303	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140422206_140422207insA								TRIM42 (2215 upstream) : SLC25A36 (238455 downstream)																							tgctaggaaggaaagaggcatg	0.000													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	140440371	140440371	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140440371delA								TRIM42 (20380 upstream) : SLC25A36 (220291 downstream)																							TCCTGCCTATAATATTCTAGT	0.284													4	2	---	---	---	---	
PCOLCE2	26577	broad.mit.edu	37	3	142571490	142571491	+	Intron	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142571490_142571491delTG	uc003evd.2	-							NM_013363	NP_037495	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2							extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3						cTGATCAAAAtgtgtgtgtgtg	0.010													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	142666682	142666683	+	IGR	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142666682_142666683delTG								PCOLCE2 (58748 upstream) : PAQR9 (1323 downstream)																							GTTTCTGAGTtgtgtgtgtgtg	0.450													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145033577	145033580	+	IGR	DEL	TTGA	-	-	rs111673308		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145033577_145033580delTTGA								None (None upstream) : PLOD2 (753648 downstream)																							ttacctatgtttgattgcctgtat	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145205381	145205382	+	IGR	DEL	TT	-	-	rs67598148		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145205381_145205382delTT								None (None upstream) : PLOD2 (581846 downstream)																							ATGTTTTTACTTTTTTTTTTTT	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145699739	145699739	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145699739delA								None (None upstream) : PLOD2 (87489 downstream)																							ctccatcaacaaaaaaaaaac	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	145752418	145752419	+	IGR	INS	-	A	A	rs113445156		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145752418_145752419insA								None (None upstream) : PLOD2 (34809 downstream)																							CCAATAAACTCAAAAAAAAAAA	0.401													5	4	---	---	---	---	
PLSCR2	57047	broad.mit.edu	37	3	146186597	146186600	+	Intron	DEL	AAAC	-	-	rs150006565		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146186597_146186600delAAAC	uc003evv.1	-						PLSCR2_uc003evw.1_Intron	NM_020359	NP_065092	Q9NRY7	PLS2_HUMAN	phospholipid scramblase 2						phospholipid scrambling	integral to membrane|plasma membrane	calcium ion binding|phospholipid scramblase activity				0						TTTCGTTGAAAAACAAACAAAAAA	0.240													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	148248015	148248016	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148248015_148248016insA								None (None upstream) : AGTR1 (167642 downstream)																							ttaatcatcacaaaaaattgta	0.153													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149994978	149994979	+	IGR	INS	-	T	T	rs140182209	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149994978_149994979insT								PFN2 (306237 upstream) : TSC22D2 (131809 downstream)																							ATTTTGATAGATAATCCAGCTC	0.297													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	150361892	150361892	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150361892delA								SELT (13660 upstream) : FAM194A (15785 downstream)																							actccgtctcaaaaaaaaaaa	0.005													4	2	---	---	---	---	
SIAH2	6478	broad.mit.edu	37	3	150467887	150467887	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150467887delG	uc003eyi.2	-							NM_005067	NP_005058	O43255	SIAH2_HUMAN	seven in absentia homolog 2						apoptosis|axon guidance|cell cycle|negative regulation of canonical Wnt receptor signaling pathway|small GTPase mediated signal transduction|ubiquitin-dependent protein catabolic process	cytosol|nucleus	transcription corepressor activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TTGTGCAAATGGGAGTTGGCA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	150561911	150561912	+	IGR	INS	-	TCTT	TCTT	rs143823850	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150561911_150561912insTCTT								SIAH2 (80648 upstream) : CLRN1OS (8359 downstream)																							ctgtctctttctctctctctct	0.277													5	7	---	---	---	---	
CLRN1OS	116933	broad.mit.edu	37	3	150639158	150639159	+	Intron	INS	-	CA	CA	rs139918092	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150639158_150639159insCA	uc011bny.1	+											Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0						gcacacacgtgcacacacacac	0.322													7	6	---	---	---	---	
MED12L	116931	broad.mit.edu	37	3	150929592	150929592	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150929592delC	uc003eyp.2	+						MED12L_uc011bnz.1_Intron	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			tatgccacgacgcctggctaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151276308	151276308	+	IGR	DEL	T	-	-	rs113104643		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151276308delT								IGSF10 (99811 upstream) : AADACL2 (175396 downstream)																							CATGAATACAttttttttttt	0.204													6	3	---	---	---	---	
MBNL1	4154	broad.mit.edu	37	3	152060343	152060344	+	Intron	DEL	AC	-	-	rs111644138		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152060343_152060344delAC	uc003ezm.2	+						MBNL1_uc003ezh.2_Intron|MBNL1_uc003ezi.2_Intron|MBNL1_uc003ezj.2_Intron|MBNL1_uc003ezl.2_Intron|MBNL1_uc003ezp.2_Intron|MBNL1_uc003ezn.2_Intron|MBNL1_uc003ezo.2_Intron|TMEM14E_uc010hvo.2_5'Flank	NM_207293	NP_997176	Q9NR56	MBNL1_HUMAN	muscleblind-like 1 isoform c						embryonic limb morphogenesis|in utero embryonic development|myoblast differentiation|nervous system development	nucleus|stress granule	double-stranded RNA binding|protein binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			ACTAAACAAAacacacacacac	0.158													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152905561	152905562	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152905561_152905562insA								RAP2B (19300 upstream) : C3orf79 (296722 downstream)																							AGCAGGAATTTAAAAAAAAAAt	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	153735542	153735543	+	IGR	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153735542_153735543delTG								C3orf79 (515059 upstream) : SGEF (103606 downstream)																							tgtgtgtgtatgtgtgtgtgtg	0.277													4	2	---	---	---	---	
SGEF	26084	broad.mit.edu	37	3	153946531	153946531	+	Intron	DEL	A	-	-	rs5853688		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153946531delA	uc011bog.1	+						SGEF_uc011boh.1_Intron|SGEF_uc011boi.1_Intron	NM_015595	NP_056410	Q96DR7	ARHGQ_HUMAN	Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CAAGGAGGCGAACTGCAAATG	0.423													5	5	---	---	---	---	
GPR149	344758	broad.mit.edu	37	3	154077807	154077808	+	Intron	INS	-	G	G	rs72589336	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154077807_154077808insG	uc003faa.2	-							NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			CTCATGCAAAACTTCTAAGAGT	0.416													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	154981296	154981296	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154981296delA								MME (79778 upstream) : PLCH1 (216375 downstream)																							TGCTAGTAAGAAAAAAAATTG	0.353													4	2	---	---	---	---	
KCNAB1	7881	broad.mit.edu	37	3	156094291	156094292	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156094291_156094292insA	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			ATAGTGGAGTGAAAAAAAGCAA	0.396													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157249641	157249641	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157249641delG								VEPH1 (28226 upstream) : C3orf55 (11518 downstream)																							CTCTTTCTGTGGCCCTGATTT	0.527													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	158912899	158912900	+	Intron	INS	-	A	A	rs112153859		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158912899_158912900insA	uc003fcq.1	+						IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			gactctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	159029474	159029474	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159029474delG	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			TTGTATACTTGCAAAGAAATC	0.249													4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	159097584	159097585	+	Intron	INS	-	G	G	rs140351890	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159097584_159097585insG	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			TGGGAAAAAGAAGGTCAGTGCC	0.465													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159746755	159746755	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159746755delT	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		tctaaaaaaaTTTTTAAATAA	0.194													4	2	---	---	---	---	
PPM1L	151742	broad.mit.edu	37	3	160503621	160503622	+	Intron	DEL	TT	-	-	rs112371806		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160503621_160503622delTT	uc003fdr.2	+							NM_139245	NP_640338	Q5SGD2	PPM1L_HUMAN	protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			cggtgcactgtttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163051065	163051066	+	IGR	INS	-	TGTG	TGTG			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163051065_163051066insTGTG								None (None upstream) : MIR1263 (838193 downstream)																							ATATAtgtgtatgtgtgtgtgt	0.188													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163549252	163549253	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163549252_163549253insT								None (None upstream) : MIR1263 (340006 downstream)																							CATCTCCCAAGttttttttttt	0.287													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163673627	163673628	+	IGR	INS	-	CTCT	CTCT	rs147166147	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163673627_163673628insCTCT								None (None upstream) : MIR1263 (215631 downstream)																							gacctctggagctctctctctc	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	163711265	163711265	+	IGR	DEL	C	-	-	rs67677861		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163711265delC								None (None upstream) : MIR1263 (177994 downstream)																							tcttcaccatcccccccactt	0.045													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164087888	164087888	+	IGR	DEL	T	-	-	rs77765413		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164087888delT								MIR720 (28650 upstream) : SI (608799 downstream)																							AATAAACTGGTTGTTATAAAA	0.259													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	164389348	164389349	+	IGR	INS	-	TAGT	TAGT			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164389348_164389349insTAGT								MIR720 (330110 upstream) : SI (307338 downstream)																							agatagatagatagatagatag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165001239	165001239	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165001239delT								SLITRK3 (86770 upstream) : BCHE (489455 downstream)																							CAGGGAAACATTTTTTTTTTT	0.408													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165925462	165925463	+	IGR	INS	-	TGTG	TGTG	rs145797436	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165925462_165925463insTGTG								BCHE (370209 upstream) : None (None downstream)																							atgtgtcttcatgtgtgtgtgt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166240267	166240267	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166240267delT								BCHE (685014 upstream) : ZBBX (717814 downstream)																							aattatagtctactgtatTTA	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	166472636	166472636	+	IGR	DEL	A	-	-	rs112654885		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166472636delA								BCHE (917383 upstream) : ZBBX (485445 downstream)																							caacaacaacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168226397	168226398	+	IGR	INS	-	CA	CA	rs138845776	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168226397_168226398insCA								GOLIM4 (412980 upstream) : MIR551B (43244 downstream)																							TTTTTTTCCTCCAGTTTCTACT	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	168633950	168633950	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168633950delA								C3orf50 (85578 upstream) : MECOM (167337 downstream)																							GAATTAAATTAAAAAAAAAAC	0.294													4	2	---	---	---	---	
MECOM	2122	broad.mit.edu	37	3	169191578	169191578	+	Intron	DEL	C	-	-	rs71634432		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169191578delC	uc011bpj.1	-						MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						aaaacaaaaacaaaaTACCAG	0.154													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	169394790	169394791	+	IGR	INS	-	T	T	rs150538863	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169394790_169394791insT								MECOM (13227 upstream) : TERC (87607 downstream)																							tcttcagtatgtttttttttta	0.119													5	5	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170317536	170317536	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170317536delT	uc011bpt.1	+						uc003fha.1_Intron	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			AAGTACATTGTTTTATATAGG	0.274													4	2	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	171817718	171817718	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171817718delT	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fhx.2_Intron	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B							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)		tgggagacccttgggtactcc	0.129													4	2	---	---	---	---	
FNDC3B	64778	broad.mit.edu	37	3	172080219	172080219	+	Intron	DEL	T	-	-	rs11333442		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172080219delT	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B							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)		TTTTTTGCTATTTTTTTTTTA	0.308													5	5	---	---	---	---	
NLGN1	22871	broad.mit.edu	37	3	173520635	173520635	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173520635delT	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			AATGTATATCttttttttttt	0.209													8	4	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	174997577	174997578	+	Intron	DEL	GT	-	-	rs141845180		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174997577_174997578delGT	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)		TAgtgtgtgagtgtgtgtgtgt	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	175927229	175927230	+	IGR	INS	-	TGTT	TGTT	rs149536455	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175927229_175927230insTGTT								NAALADL2 (403803 upstream) : TBL1XR1 (811313 downstream)																							TAAAATTAACCTGACATTTTTC	0.312													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176975791	176975792	+	IGR	INS	-	T	T	rs80113352		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176975791_176975792insT								TBL1XR1 (60743 upstream) : None (None downstream)																							ggcttattgtcttttttttctt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	177552191	177552194	+	Intron	DEL	AAAC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177552191_177552194delAAAC	uc003fiz.1	+											Homo sapiens cDNA FLJ31690 fis, clone NT2RI2005621.																		acaaataaagaaacaaacaaacaa	0.025													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179000441	179000452	+	IGR	DEL	CAGCCTGGGTGA	-	-	rs145891370		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179000441_179000452delCAGCCTGGGTGA								KCNMB3 (15603 upstream) : ZNF639 (40367 downstream)																							cactgtactccagcctgggtgacagagtgaca	0.005													2	4	---	---	---	---	
USP13	8975	broad.mit.edu	37	3	179501649	179501649	+	Intron	DEL	A	-	-	rs72449152		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179501649delA	uc003fkh.2	+							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)			cttgtctcttaaaaaaaaaaa	0.159													10	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181489110	181489110	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181489110delA								SOX2OT (30107 upstream) : None (None downstream)																							CATCATAAGGAAAAAAATGTG	0.343													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182441748	182441748	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182441748delA								SOX2OT (982745 upstream) : ATP11B (69543 downstream)																							accattgtggaaaaaaaaaAA	0.114													4	2	---	---	---	---	
LAMP3	27074	broad.mit.edu	37	3	182882103	182882103	+	5'Flank	DEL	T	-	-	rs63133763		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182882103delT	uc003flh.3	-							NM_014398	NP_055213	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3						cell proliferation	integral to membrane|lysosomal membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			CACAATATCGttttttttttt	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	183407856	183407856	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183407856delG								KLHL24 (5554 upstream) : YEATS2 (7750 downstream)																							ggctgaggcaggagaattgct	0.000													1	6	---	---	---	---	
ABCC5	10057	broad.mit.edu	37	3	183728844	183728845	+	Intron	INS	-	T	T	rs139079505	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183728844_183728845insT	uc003fmg.2	-						ABCC5_uc011bqt.1_Intron|ABCC5_uc010hxl.2_Intron|ABCC5_uc003fmh.2_Intron|ABCC5_uc010hxm.2_Intron|ABCC5_uc010hxn.2_Intron|ABCC5_uc010hxo.2_Intron|ABCC5_uc003fmi.3_Intron	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5							integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CTCATTCTTAATATCTCCCCAA	0.238													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184472192	184472193	+	IGR	INS	-	TT	TT			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184472192_184472193insTT								MAGEF1 (42356 upstream) : VPS8 (57738 downstream)																							agaagaaggtgatgggagaaga	0.059													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	184472232	184472233	+	IGR	INS	-	AAG	AAG			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184472232_184472233insAAG								MAGEF1 (42396 upstream) : VPS8 (57698 downstream)																							gtggtgggagaaggtggtagga	0.079													3	3	---	---	---	---	
ETV5	2119	broad.mit.edu	37	3	185802072	185802073	+	Intron	DEL	AA	-	-	rs35288935		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185802072_185802073delAA	uc003fpz.2	-						ETV5_uc003fpy.2_Intron	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)						cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			AAGAAATGCTaaaaaaaaaaaa	0.332			T	TMPRSS2|SCL45A3	Prostate 								5	3	---	---	---	---	
DGKG	1608	broad.mit.edu	37	3	185908144	185908144	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185908144delA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	cccaacattgaaaactacatc	0.139													4	2	---	---	---	---	
DGKG	1608	broad.mit.edu	37	3	185952770	185952771	+	Intron	INS	-	CAA	CAA	rs141304537	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185952770_185952771insCAA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	TATAAACAATCCAACAACAACA	0.371													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187353289	187353290	+	IGR	INS	-	T	T	rs33955527		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187353289_187353290insT								RTP4 (263922 upstream) : SST (33406 downstream)																							catattttcagttttttttttt	0.000													2	5	---	---	---	---	
BCL6	604	broad.mit.edu	37	3	187455091	187455091	+	5'Flank	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187455091delA	uc003frp.3	-						BCL6_uc011bsf.1_5'Flank|BCL6_uc010hza.2_5'Flank|BCL6_uc003frq.1_Intron	NM_001130845	NP_001124317	P41182	BCL6_HUMAN	B-cell lymphoma 6 protein isoform 1						negative regulation of B cell apoptosis|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|protein import into nucleus, translocation|regulation of germinal center formation|response to DNA damage stimulus	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|lung(2)|central_nervous_system(1)	5	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		AACAGGAACCAAAAAAAAAAA	0.224			T|Mis	IG loci|ZNFN1A1|LCP1|PIM1|TFRC|MHC2TA|NACA|HSPCB|HSPCA|HIST1H4I|IL21R| POU2AF1|ARHH|EIF4A2|SFRS3	NHL|CLL								6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	187607947	187607947	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187607947delA								BCL6 (144472 upstream) : LPP (263772 downstream)																							AGGCAAACAGAAAAAAAAAAA	0.174													4	4	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188006382	188006383	+	Intron	DEL	AT	-	-	rs71167088	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188006382_188006383delAT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		acacacacacatacacacagat	0.109			T	HMGA2|MLL|C12orf9	lipoma|leukemia								6	4	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188026811	188026811	+	Intron	DEL	T	-	-	rs142243018		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188026811delT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		cttcttcttcttttttttttt	0.000			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189073352	189073353	+	IGR	INS	-	C	C	rs149299822	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189073352_189073353insC								TPRG1 (32082 upstream) : TP63 (275863 downstream)																							CCCTAGAGCTACCCGAGGCCTT	0.495													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189217457	189217458	+	IGR	INS	-	G	G	rs140706404	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189217457_189217458insG								TPRG1 (176187 upstream) : TP63 (131758 downstream)																							gagaaaatggaggggggggatg	0.035													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189625026	189625026	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189625026delT								TP63 (9958 upstream) : LEPREL1 (49493 downstream)																							attgaaatgcttttttttttt	0.065													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	190375844	190375844	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190375844delA								IL1RAP (1 upstream) : LOC647309 (194682 downstream)																							actccatcttaaaaaaaaaaa	0.000													5	3	---	---	---	---	
UTS2D	257313	broad.mit.edu	37	3	191027132	191027132	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191027132delT	uc003fsu.2	-							NM_198152	NP_937795	Q765I0	UTS2B_HUMAN	urotensin 2 domain containing precursor							extracellular region	hormone activity				0	all_cancers(143;1.77e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000214)		ttggtttttcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191396984	191396987	+	IGR	DEL	ACAC	-	-	rs34314089		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191396984_191396987delACAC								PYDC2 (217741 upstream) : FGF12 (462697 downstream)																							AAGCAAGCAAacacacacacacac	0.314													4	2	---	---	---	---	
FGF12	2257	broad.mit.edu	37	3	192289929	192289929	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192289929delA	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)		AGCTTTTAATAAACACAACTT	0.358													4	2	---	---	---	---	
C3orf59	151963	broad.mit.edu	37	3	192548031	192548038	+	Intron	DEL	GTGTGTGT	-	-	rs113287706		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192548031_192548038delGTGTGTGT	uc011bsp.1	-							NM_178496	NP_848591	Q8IYB1	M21D2_HUMAN	hypothetical protein LOC151963												0	all_cancers(143;1.56e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.8e-18)|LUSC - Lung squamous cell carcinoma(58;8.04e-06)|Lung(62;8.62e-06)	GBM - Glioblastoma multiforme(46;3.86e-05)		gtgtgtgtgagtgtgtgtgtgtgtgtgt	0.255													5	4	---	---	---	---	
LOC100128023	100128023	broad.mit.edu	37	3	193713361	193713362	+	5'Flank	INS	-	C	C	rs144302637	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193713361_193713362insC	uc011bss.1	-							NR_027764				Homo sapiens developmental pluripotency associated 2 pseudogene (LOC100128023), non-coding RNA.												0						TCTCTATCTCGCCCCCAGCCCT	0.500													3	6	---	---	---	---	
APOD	347	broad.mit.edu	37	3	195313589	195313589	+	5'Flank	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195313589delT	uc003fur.2	-						APOD_uc011bsx.1_5'Flank	NM_001647	NP_001638	P05090	APOD_HUMAN	apolipoprotein D precursor						lipid metabolic process	extracellular space	lipid binding|lipid transporter activity|protein binding			ovary(2)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		gcccggctaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195366864	195366865	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195366864_195366865insA								APOD (55788 upstream) : SDHAP2 (18045 downstream)																							TTTCTTTATTTAAAAAAAAAAt	0.198													4	2	---	---	---	---	
MUC20	200958	broad.mit.edu	37	3	195462031	195462032	+	3'UTR	INS	-	T	T	rs139052122	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195462031_195462032insT	uc010hzo.2	+	5					MUC20_uc010hzp.2_3'UTR	NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		cctcggcaccgtctttattccc	0.000													13	7	---	---	---	---	
PAK2	5062	broad.mit.edu	37	3	196531334	196531337	+	Intron	DEL	GTGT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196531334_196531337delGTGT	uc003fwy.3	+							NM_002577	NP_002568	Q13177	PAK2_HUMAN	p21-activated kinase 2						axon guidance|cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of apoptosis|regulation of defense response to virus by virus|regulation of growth|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|nucleus|perinuclear region of cytoplasm|plasma membrane	ATP binding|identical protein binding|protein kinase binding|protein serine/threonine kinase activity|protein tyrosine kinase activator activity			ovary(1)|lung(1)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		acgcgcgtgcgtgtgtgtgttttg	0.103													2	4	---	---	---	---	
LOC220729	220729	broad.mit.edu	37	3	197330753	197330753	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197330753delA	uc011bug.1	-											Homo sapiens cDNA FLJ60865 complete cds, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1).												0						CCCCACCCAGAAAAAAAAAAA	0.547													6	4	---	---	---	---	
LRCH3	84859	broad.mit.edu	37	3	197607964	197607967	+	Intron	DEL	TTTC	-	-	rs35420216		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197607964_197607967delTTTC	uc011bul.1	+						LRCH3_uc011bum.1_Intron|LRCH3_uc011bun.1_Intron|LRCH3_uc003fyk.2_Intron	NM_032773	NP_116162	Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH)							extracellular region				ovary(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		TCTGGCCATTTTTCCGTGCCTCAG	0.456													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	37976	37976	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37976delC								None (None upstream) : ZNF595 (15251 downstream)																							aggtcctgtactttttttggt	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	45522	45522	+	IGR	DEL	T	-	-	rs111422431		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45522delT								None (None upstream) : ZNF595 (7705 downstream)																							AATAttttacttttttttttt	0.090													4	2	---	---	---	---	
PCGF3	10336	broad.mit.edu	37	4	709199	709200	+	Intron	INS	-	TG	TG			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:709199_709200insTG	uc011bva.1	+						PCGF3_uc003gbc.1_Intron|PCGF3_uc003gbd.1_Intron|PCGF3_uc003gbe.2_Intron|PCGF3_uc010ibh.2_Intron	NM_006315	NP_006306	Q3KNV8	PCGF3_HUMAN	ring finger protein 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PcG protein complex	zinc ion binding				0						CCTGTAGACACTGAGTGTGAGC	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3753145	3753146	+	IGR	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3753145_3753146delGT								LRPAP1 (218921 upstream) : ADRA2C (14929 downstream)																							TGTCAtgtgcgtgtgtgtgtgt	0.515													4	2	---	---	---	---	
TBC1D14	57533	broad.mit.edu	37	4	6925986	6925990	+	Intron	DEL	AATCC	-	-	rs57881179		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6925986_6925990delAATCC	uc011bwg.1	+						TBC1D14_uc003gjs.3_Intron	NM_001113361	NP_001106832	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14 isoform a							intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2						AGAAGCCCGGAATCCTGTGGGATTG	0.512													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24062680	24062680	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24062680delA								PPARGC1A (170980 upstream) : MIR573 (459135 downstream)																							tttgttctggaaaaaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49648442	49648442	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49648442delG								CWH43 (584349 upstream) : None (None downstream)																							ggaacggaatgggatggaatg	0.000													5	3	---	---	---	---	
UGT2B4	7363	broad.mit.edu	37	4	70361791	70361792	+	5'Flank	INS	-	T	T	rs41299972		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70361791_70361792insT	uc003hek.3	-						UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_5'Flank	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						TTCTTTTTGGATTTTTTTTTTT	0.173													3	4	---	---	---	---	
CSN1S1	1446	broad.mit.edu	37	4	70804857	70804857	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70804857delC	uc003hep.1	+						CSN1S1_uc003heq.1_Intron|CSN1S1_uc003her.1_Intron	NM_001890	NP_001881	P47710	CASA1_HUMAN	casein alpha s1 isoform 1							extracellular region	protein binding|transporter activity				0						TTCTAAAAATCCCAGGGGATA	0.343													18	14	---	---	---	---	
HTN1	3346	broad.mit.edu	37	4	70919455	70919457	+	Intron	DEL	TCC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70919455_70919457delTCC	uc003hex.2	+							NM_002159	NP_002150	P15515	HIS1_HUMAN	histatin 1 precursor						biomineral tissue development|defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			skin(1)	1						CACCGcctcttcctcctcctcct	0.128													4	2	---	---	---	---	
C4orf22	255119	broad.mit.edu	37	4	81283887	81283887	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81283887delA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983	Q6V702	CD022_HUMAN	hypothetical protein LOC255119											skin(2)	2						CCACTCACCTAACAACTGATT	0.398													48	21	---	---	---	---	
SEC31A	22872	broad.mit.edu	37	4	83740163	83740164	+	3'UTR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83740163_83740164insT	uc003hnf.2	-	27					SEC31A_uc003hnd.2_3'UTR|SEC31A_uc003hne.2_3'UTR|SEC31A_uc011ccl.1_3'UTR|SEC31A_uc003hnl.2_3'UTR|SEC31A_uc003hng.2_3'UTR|SEC31A_uc003hnh.2_3'UTR|SEC31A_uc003hni.2_3'UTR|SEC31A_uc003hnj.2_3'UTR|SEC31A_uc011ccm.1_3'UTR|SEC31A_uc011ccn.1_3'UTR|SEC31A_uc003hnk.2_3'UTR|SEC31A_uc003hnm.2_3'UTR	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)				ATGTCTTATAATTTTTTTTTTT	0.376													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	88180872	88180873	+	IGR	INS	-	TTT	TTT	rs33959164		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88180872_88180873insTTT								KLHL8 (39198 upstream) : HSD17B13 (44068 downstream)																							ttctttctttcttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	100074819	100074819	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100074819delG	uc003hum.1	+											Homo sapiens full length insert cDNA clone ZD94A03.																		tttggatactgggattgctgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	116361320	116361321	+	IGR	DEL	GC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116361320_116361321delGC								NDST4 (326288 upstream) : MIR1973 (859560 downstream)																							GTATATTTTTGCACAGTTGTTG	0.282													4	2	---	---	---	---	
SPATA5	166378	broad.mit.edu	37	4	124220273	124220274	+	Intron	DEL	TG	-	-	rs66700040		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124220273_124220274delTG	uc003iez.3	+							NM_145207	NP_660208	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0						CATCTGCCAAtgtgtgtgtgtg	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	139316098	139316098	+	IGR	DEL	T	-	-	rs113120938		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139316098delT								SLC7A11 (152595 upstream) : CCRN4L (620845 downstream)																							AGTGTATCCCTGTTGTCACAC	0.388													0	8	---	---	---	---	
SMARCA5	8467	broad.mit.edu	37	4	144442476	144442477	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144442476_144442477insT	uc003ijg.2	+							NM_003601	NP_003592	O60264	SMCA5_HUMAN	SWI/SNF-related matrix-associated						CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)					ctgtagttctcttttttttttt	0.084													4	3	---	---	---	---	
FAM160A1	729830	broad.mit.edu	37	4	152343706	152343706	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152343706delT	uc003imj.2	+							NM_001109977	NP_001103447	Q05DH4	F16A1_HUMAN	hypothetical protein LOC729830												0						gtccagctaattttaatattt	0.000													4	2	---	---	---	---	
DCHS2	54798	broad.mit.edu	37	4	155411481	155411481	+	Frame_Shift_Del	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155411481delC	uc003inx.2	-	1	1397	c.1027delG	c.(1027-1029)GCGfs	p.A343fs	DCHS2_uc011cik.1_Frame_Shift_Del_p.A343fs	NM_001142552	NP_001136024	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 2	1312	Cadherin 11.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCGCTACCCGCCCCAGGCACT	0.746													4	2	---	---	---	---	
PDGFC	56034	broad.mit.edu	37	4	157846149	157846149	+	Intron	DEL	T	-	-	rs77802931		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157846149delT	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.1_Intron	NM_016205	NP_057289	Q9NRA1	PDGFC_HUMAN	platelet-derived growth factor C precursor						central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		gggctgggcCTTGCAGGAGGC	0.199													2	4	---	---	---	---	
C4orf27	54969	broad.mit.edu	37	4	170670109	170670110	+	Intron	INS	-	T	T	rs76216708		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170670109_170670110insT	uc003isl.3	-							NM_017867	NP_060337	Q9NWY4	CD027_HUMAN	hypothetical protein LOC54969							nucleus				ovary(1)|pancreas(1)	2		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)		TTTTGGAGGCCTTTTTTTTTTT	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179936577	179936578	+	IGR	INS	-	A	A	rs77416869		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179936577_179936578insA								None (None upstream) : None (None downstream)																							aactcagtctgaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190669373	190669375	+	IGR	DEL	ACA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190669373_190669375delACA								None (None upstream) : FRG1 (192599 downstream)																							aaagaaatgcacaacatcactaa	0.000													6	3	---	---	---	---	
LPCAT1	79888	broad.mit.edu	37	5	1501535	1501536	+	Intron	INS	-	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1501535_1501536insC	uc003jcm.2	-							NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1						phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		TGGCCGCGTGACCCCCCCCCAG	0.644													3	4	---	---	---	---	
NSUN2	54888	broad.mit.edu	37	5	6623158	6623158	+	Intron	DEL	A	-	-	rs111573762		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6623158delA	uc003jdu.2	-						NSUN2_uc003jdt.2_5'Flank|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1						GACaaaaaagaaaaaaaaaaa	0.259													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	6681963	6681964	+	IGR	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6681963_6681964delGT								SRD5A1 (12290 upstream) : PAPD7 (32754 downstream)																							tgtgtgtgtggtgtgtgtgtgt	0.059													4	2	---	---	---	---	
SEMA5A	9037	broad.mit.edu	37	5	9353242	9353243	+	Intron	INS	-	G	G	rs148876434	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9353242_9353243insG	uc003jek.2	-							NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						aggaaaggaaaggaaaggaaag	0.000													3	3	---	---	---	---	
ROPN1L	83853	broad.mit.edu	37	5	10454242	10454242	+	Intron	DEL	T	-	-	rs66649527		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10454242delT	uc003jex.3	+							NM_031916	NP_114122	Q96C74	ROP1L_HUMAN	ropporin 1-like						ciliary or flagellar motility|signal transduction	cytoplasm|motile cilium	cAMP-dependent protein kinase regulator activity|protein binding			ovary(1)	1						ttttatttaattttttttttt	0.179													4	2	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11480759	11480760	+	Intron	DEL	TG	-	-	rs71661225		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11480759_11480760delTG	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						AATACATATAtgtgtgtgtgtg	0.297													4	2	---	---	---	---	
FBXL7	23194	broad.mit.edu	37	5	15775493	15775494	+	Intron	INS	-	AC	AC	rs149401468	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15775493_15775494insAC	uc003jfn.1	+							NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3						CCCCACCATATACACACACACA	0.396													6	4	---	---	---	---	
LOC285696	285696	broad.mit.edu	37	5	17160682	17160683	+	Intron	DEL	TG	-	-	rs72420894		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17160682_17160683delTG	uc003jfw.2	-							NR_027253				Homo sapiens cDNA FLJ34047 fis, clone FCBBF3000001.												0						GTTAGGGTTTTGTGTGTGTGTG	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	18633643	18633643	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18633643delT								None (None upstream) : CDH18 (839514 downstream)																							cagcctcatcttgtcctttgg	0.000													0	7	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21537379	21537380	+	Intron	INS	-	AAGG	AAGG	rs71607526		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21537379_21537380insAAGG	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						atgaaacaattaagaattaata	0.000													5	3	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22732577	22732588	+	Intron	DEL	ATATACACACAC	-	-	rs35770175		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22732577_22732588delATATACACACAC	uc003jgk.2	-							NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						atatatatatatatacacacacacacacacac	0.000										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23253563	23253563	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23253563delG								CDH12 (399832 upstream) : PRDM9 (254161 downstream)																							ctatccctccgccctcccccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	25283946	25283947	+	IGR	DEL	GA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25283946_25283947delGA								CDH10 (639035 upstream) : None (None downstream)																							CAGAGGAGGGgagagagagaga	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27963921	27963921	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27963921delG								CDH9 (925232 upstream) : None (None downstream)																							gtggttggctgggagcaagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32111039	32111039	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32111039delT								PDZD2 (2 upstream) : GOLPH3 (13785 downstream)																							TACTACTTGATTTTTTTTTTC	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	32579700	32579701	+	IGR	INS	-	T	T	rs147066812	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32579700_32579701insT								ZFR (134856 upstream) : SUB1 (5904 downstream)																							TATATTGCCCCgtcttagtctg	0.228													4	3	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33627344	33627346	+	Intron	DEL	TGG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33627344_33627346delTGG	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						ggtggagtgatggtggtggtggt	0.000										HNSCC(64;0.19)			2	4	---	---	---	---	
ADAMTS12	81792	broad.mit.edu	37	5	33714755	33714755	+	Intron	DEL	A	-	-	rs68079101		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33714755delA	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9						cacttgcagcaacatggatgg	0.000										HNSCC(64;0.19)			4	3	---	---	---	---	
RAD1	5810	broad.mit.edu	37	5	34906590	34906590	+	3'UTR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34906590delA	uc003jix.2	-	6					RAD1_uc003jiw.2_3'UTR|RAD1_uc003jiy.2_3'UTR	NM_002853	NP_002844	O60671	RAD1_HUMAN	RAD1 homolog						DNA damage checkpoint|DNA repair|DNA replication|meiotic prophase I	nucleoplasm	3'-5' exonuclease activity|damaged DNA binding|exodeoxyribonuclease III activity|protein binding				0	all_lung(31;0.000107)	Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198)	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			caaaaaatacaaaaattagca	0.000								Other_conserved_DNA_damage_response_genes					3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	35503981	35503981	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35503981delA								PRLR (273187 upstream) : SPEF2 (114008 downstream)																							TCTTTGGTGGAAAATAGAAGA	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36386503	36386503	+	IGR	DEL	A	-	-	rs71870732		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36386503delA								RANBP3L (84492 upstream) : SLC1A3 (219954 downstream)																							accctgtcttaaaaaaaaaaa	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	36789117	36789118	+	IGR	DEL	GT	-	-	rs72200833		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36789117_36789118delGT								SLC1A3 (100683 upstream) : NIPBL (87743 downstream)																							ataTCTCCTCgtgtgtgtgtgt	0.277													4	2	---	---	---	---	
WDR70	55100	broad.mit.edu	37	5	37382204	37382204	+	Intron	DEL	T	-	-	rs10074545	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37382204delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATCACTGTTGttttttttttt	0.045													3	3	---	---	---	---	
WDR70	55100	broad.mit.edu	37	5	37544427	37544427	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37544427delA	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTATATTAACAAAAGAAACCA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40856134	40856134	+	IGR	DEL	T	-	-	rs35850416		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40856134delT								CARD6 (680 upstream) : C7 (53465 downstream)																							cagatagttcttttttttttt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42131776	42131778	+	IGR	DEL	CAA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42131776_42131778delCAA								FBXO4 (190113 upstream) : GHR (292248 downstream)																							tcaagaatggcaacaagcccttc	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	42856337	42856338	+	IGR	INS	-	A	A	rs138619493	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42856337_42856338insA								SEPP1 (30339 upstream) : C5orf39 (182845 downstream)																							ATTGAAGAGggaaaaaatgcaa	0.173													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	49437476	49437476	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49437476delA								None (None upstream) : EMB (254557 downstream)																							cagattctacagagtgtttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	51764580	51764580	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51764580delG								None (None upstream) : ITGA1 (319194 downstream)																							TTACCATCTAGGCATATTAAC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	53687261	53687262	+	IGR	INS	-	AC	AC	rs71600830		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53687261_53687262insAC								ARL15 (80858 upstream) : HSPB3 (64183 downstream)																							ACAAAACAAAAACACACACACA	0.292													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56730774	56730774	+	IGR	DEL	T	-	-	rs75199036		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56730774delT								GPBP1 (171364 upstream) : ACTBL2 (45070 downstream)																							tctcgttctcttttttttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56929118	56929119	+	IGR	DEL	AC	-	-	rs35333389		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56929118_56929119delAC								ACTBL2 (150482 upstream) : PLK2 (820693 downstream)																							tgcacacacaacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	62452278	62452278	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62452278delT								ISCA1P1 (379108 upstream) : HTR1A (804001 downstream)																							TAGGAAACCATTTGAATTCCC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63430723	63430723	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63430723delG								HTR1A (173177 upstream) : RNF180 (30948 downstream)																							ctttgactcagaaagggaact	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	66541477	66541478	+	IGR	INS	-	AGGA	AGGA			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66541477_66541478insAGGA								CD180 (48860 upstream) : PIK3R1 (970126 downstream)														p.0?(1)									CGGCAGAAATGaggaaggaagg	0.287													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	66684749	66684750	+	IGR	INS	-	GT	GT	rs71610560		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66684749_66684750insGT								CD180 (192132 upstream) : PIK3R1 (826854 downstream)																							agtattccagcgtgtgtgtttg	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67702262	67702263	+	IGR	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67702262_67702263delGT								PIK3R1 (104615 upstream) : SLC30A5 (687555 downstream)																							aggtatacaggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	71963517	71963518	+	IGR	DEL	TG	-	-	rs3010267		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71963517_71963518delTG								ZNF366 (160268 upstream) : TNPO1 (148900 downstream)																							tatttgtatatgtgtgtgtgtg	0.183													3	3	---	---	---	---	
RGNEF	64283	broad.mit.edu	37	5	73087475	73087476	+	Intron	INS	-	A	A	rs138812145	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73087475_73087476insA	uc011csq.1	+						RGNEF_uc003kcx.2_Intron|RGNEF_uc003kcy.1_Intron|RGNEF_uc010izf.2_Intron	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor						cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)		ATAGAGGTGAGTTTTTTAGGCG	0.386													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	73435766	73435766	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73435766delG								RGNEF (198353 upstream) : ENC1 (487469 downstream)																							gagaaagagtgggagactgaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	73700957	73700958	+	IGR	INS	-	GGAAAACT	GGAAAACT	rs144327243	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73700957_73700958insGGAAAACT								RGNEF (463544 upstream) : ENC1 (222277 downstream)																							GCAGCACTGAAGGAAAACTGGC	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	77965309	77965312	+	IGR	DEL	GAGA	-	-	rs57667593		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77965309_77965312delGAGA								LHFPL2 (20661 upstream) : ARSB (107727 downstream)																							ggaagggggggagagagagagaga	0.010													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	79888488	79888488	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79888488delT								ANKRD34B (22390 upstream) : DHFR (33557 downstream)																							catccaagccttttttttttg	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90839673	90839673	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90839673delT								LOC100129716 (123142 upstream) : None (None downstream)																							ctccttcttcttttttttttt	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	95684368	95684368	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95684368delT								MIR583 (269452 upstream) : PCSK1 (41751 downstream)																							agtaagaggattgaggatggt	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	105353467	105353468	+	IGR	INS	-	TCCT	TCCT			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105353467_105353468insTCCT								RAB9BP1 (917669 upstream) : None (None downstream)																							ccctccccttctccttccttcc	0.089													9	4	---	---	---	---	
C5orf13	9315	broad.mit.edu	37	5	111195550	111195550	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111195550delC	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947	Q16612	NP311_HUMAN	neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)		TAAACATAAACCTAAATTAAT	0.383													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119297678	119297679	+	IGR	INS	-	C	C	rs140251176	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119297678_119297679insC								FAM170A (326162 upstream) : PRR16 (502340 downstream)																							ATGTACACACACCCCCCCAAAC	0.282													4	2	---	---	---	---	
SNCAIP	9627	broad.mit.edu	37	5	121664769	121664769	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121664769delA	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc010jct.2_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|SNCAIP_uc011cwm.1_Intron	NM_005460	NP_005451	Q9Y6H5	SNCAP_HUMAN	synuclein alpha interacting protein						cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		cctcaatgccaggcaccatgt	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	126799781	126799781	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126799781delA								MEGF10 (2873 upstream) : PRRC1 (53528 downstream)																							cacagtttgcaaaaattttcc	0.000													4	2	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	130860301	130860302	+	Intron	DEL	TT	-	-	rs147310442	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130860301_130860302delTT	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvr.2_Intron|RAPGEF6_uc011cxe.1_Intron|RAPGEF6_uc010jdk.2_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		gagagagagattgagagagaga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	135074197	135074200	+	IGR	DEL	ATCT	-	-	rs10579430		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135074197_135074200delATCT								LOC340074 (84573 upstream) : LOC153328 (96165 downstream)																							GACCCAAAGCATCTCCTTTACTCC	0.456													2	5	---	---	---	---	
GFRA3	2676	broad.mit.edu	37	5	137590713	137590716	+	Intron	DEL	AGGA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137590713_137590716delAGGA	uc003lcn.2	-						GFRA3_uc003lco.2_Intron	NM_001496	NP_001487	O60609	GFRA3_HUMAN	GDNF family receptor alpha 3 preproprotein						peripheral nervous system development	anchored to membrane|cytoplasm|extrinsic to membrane|intracellular membrane-bounded organelle	receptor binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			ggagagagagaggaaggaaggaag	0.005													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	137966993	137966993	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137966993delC								HSPA9 (55878 upstream) : CTNNA1 (122114 downstream)																							ATCAGAACTTCCCAGGTTGCT	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139705224	139705224	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139705224delT								PFDN1 (22535 upstream) : HBEGF (7205 downstream)																							CTCTTCTGCCttttttttttt	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139994203	139994204	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139994203_139994204insT								SLC35A4 (45520 upstream) : CD14 (17113 downstream)																							tctttcattccttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	142137009	142137010	+	IGR	DEL	GT	-	-	rs140893047		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142137009_142137010delGT								FGF1 (59374 upstream) : ARHGAP26 (13282 downstream)																							aacagggtgagtgtgtgtgtgt	0.000													4	4	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142539490	142539491	+	Intron	DEL	TT	-	-	rs145258324		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142539490_142539491delTT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGGTATGGGATTTTTTTTTTTT	0.376													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151622055	151622056	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151622055_151622056insT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																		CTGTCTCCATCTTTTTTTTTTC	0.396													3	4	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153652017	153652018	+	Intron	INS	-	GG	GG	rs148342928		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153652017_153652018insGG	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TATGGATAACAGGGAGGGGAAT	0.490													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154410974	154410974	+	IGR	DEL	C	-	-	rs138053612		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154410974delC								KIF4B (13289 upstream) : SGCD (724089 downstream)																							gagtgatgctcttcttattaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	159908469	159908469	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159908469delT	uc003lyl.3	+											Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2005635.																		ctcccttcccttctctccctc	0.040													4	2	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	166873798	166873799	+	Intron	INS	-	CA	CA	rs143921171	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166873798_166873799insCA	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		TTTGAAacacgcacacacacac	0.223													3	4	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167223619	167223622	+	Intron	DEL	GTGT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167223619_167223622delGTGT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		tttggggtgcgtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
WWC1	23286	broad.mit.edu	37	5	167802036	167802043	+	Intron	DEL	CATTTGGA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167802036_167802043delCATTTGGA	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		agcaggagttcatttggacatgtcaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	169606836	169606837	+	IGR	INS	-	AAGA	AAGA	rs141910123	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169606836_169606837insAAGA								FOXI1 (70108 upstream) : C5orf58 (53113 downstream)																							CCTGTGATGACCCAGACAAGAC	0.535													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170920494	170920494	+	IGR	DEL	A	-	-	rs71982385		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170920494delA								FGF18 (36332 upstream) : FBXW11 (368062 downstream)																							ATCTTTCATTAAAAAAAAAAA	0.333													4	3	---	---	---	---	
ATP6V0E1	8992	broad.mit.edu	37	5	172408354	172408355	+	5'Flank	INS	-	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172408354_172408355insC	uc003mcd.1	+							NM_003945	NP_003936	O15342	VA0E1_HUMAN	ATPase, H+ transporting, lysosomal 9kDa, V0						ATP hydrolysis coupled proton transport|cell growth|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport|vacuolar acidification	endosome membrane|integral to membrane|membrane fraction|proton-transporting V-type ATPase, V0 domain|vacuole	proton-transporting ATPase activity, rotational mechanism				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			tgagattccatcaaaaaaagaa	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	172767169	172767170	+	IGR	INS	-	A	A	rs150203655	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172767169_172767170insA								STC2 (10663 upstream) : LOC285593 (239476 downstream)																							ggttttatgagaaaaaaaagac	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	174720446	174720446	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174720446delG								MSX2 (562545 upstream) : DRD1 (147230 downstream)																							CAGGGAGCATGGGGACACCAT	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	178515719	178515726	+	IGR	DEL	GTGTGTGT	-	-	rs112086873		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178515719_178515726delGTGTGTGT								ZNF354C (8030 upstream) : ADAMTS2 (25125 downstream)																							tctagtttccgtgtgtgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
GFPT2	9945	broad.mit.edu	37	5	179763666	179763666	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179763666delC	uc003mlw.1	-							NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	GGGCTGCATGCCCCGGGCTGT	0.527													18	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	180505466	180505466	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180505466delT								BTNL9 (16944 upstream) : OR2V2 (76477 downstream)																							gccatcctcctaccttaatct	0.000													4	2	---	---	---	---	
EXOC2	55770	broad.mit.edu	37	6	519004	519004	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:519004delA	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		CAGAAGTCGTAAAGTGCCAAG	0.483													4	2	---	---	---	---	
EXOC2	55770	broad.mit.edu	37	6	592326	592326	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:592326delA	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		ACCAGTGGCCAAAAAAACCAC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3251855	3251855	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3251855delC	uc003mvi.1	+											Homo sapiens cDNA FLJ38900 fis, clone NT2NE2001021.																		CCGCTTCCTTCCCACCTGCCA	0.502											OREG0017148	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	9162913	9162916	+	IGR	DEL	AAAG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9162913_9162916delAAAG								HULC (508836 upstream) : None (None downstream)																							atagaaagaaaaagaaaggagaat	0.093													4	2	---	---	---	---	
PHACTR1	221692	broad.mit.edu	37	6	12725646	12725647	+	Intron	INS	-	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12725646_12725647insC	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron|PHACTR1_uc003nai.2_Intron	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			CATTGTCACCTCCCCTGTGAAG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	13764110	13764110	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13764110delC								RANBP9 (52314 upstream) : CCDC90A (26911 downstream)																							actcaggactccacatgaatg	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19789442	19789443	+	IGR	DEL	GT	-	-	rs72306808		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19789442_19789443delGT								None (None upstream) : ID4 (48174 downstream)																							AGTTGAAACAgtgtgtgtgtgt	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29516214	29516215	+	IGR	INS	-	GA	GA	rs148301149	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29516214_29516215insGA								MAS1L (60535 upstream) : UBD (7175 downstream)																							ggcacagcagggaggaggagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	29770021	29770021	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29770021delA								HCG4 (9171 upstream) : HLA-G (24735 downstream)																							TAGGGGTGGGAAGAGTGATCC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32441391	32441392	+	IGR	INS	-	T	T	rs28986194		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32441391_32441392insT								HLA-DRA (28570 upstream) : HLA-DRB1 (43771 downstream)																							AAATTATGGGGAGGAGGTTACT	0.505													8	5	---	---	---	---	
GRM4	2914	broad.mit.edu	37	6	34039900	34039901	+	Intron	DEL	AT	-	-	rs139555716		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34039900_34039901delAT	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_Intron	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)	cacaccacacatagacacacat	0.000													5	3	---	---	---	---	
UHRF1BP1	54887	broad.mit.edu	37	6	34816137	34816138	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34816137_34816138insT	uc003oju.3	+						UHRF1BP1_uc010jvm.1_Intron|UHRF1BP1_uc010jvn.2_Intron	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1											ovary(3)	3						aatcccaacactttgggaggct	0.005													4	2	---	---	---	---	
LHFPL5	222662	broad.mit.edu	37	6	35791408	35791409	+	3'UTR	INS	-	G	G	rs147136847	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35791408_35791409insG	uc003olg.1	+	4						NM_182548	NP_872354	Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5							integral to membrane				skin(1)	1						TGCTGCTCAGAGGGGGGTAAGG	0.455													4	2	---	---	---	---	
ZFAND3	60685	broad.mit.edu	37	6	37830294	37830295	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37830294_37830295insA	uc003onx.2	+							NM_021943	NP_068762	Q9H8U3	ZFAN3_HUMAN	zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1						cctatctttccaaaaaaaaaaa	0.000													4	2	---	---	---	---	
GLO1	2739	broad.mit.edu	37	6	38646092	38646093	+	Intron	INS	-	AGAGAA	AGAGAA	rs148661388	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38646092_38646093insAGAGAA	uc003ooc.2	-							NM_006708	NP_006699	Q04760	LGUL_HUMAN	glyoxalase I						anti-apoptosis|carbohydrate metabolic process	cytoplasm	lactoylglutathione lyase activity|metal ion binding			ovary(1)	1					Glutathione(DB00143)	aagaaagaaagagagaaagaga	0.173													6	3	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38768194	38768194	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38768194delT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						attatttgtctttttggtgac	0.000													3	3	---	---	---	---	
MOCS1	4337	broad.mit.edu	37	6	39885595	39885595	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39885595delA	uc003opb.2	-						MOCS1_uc003opa.2_Intron|MOCS1_uc003opc.2_Intron|MOCS1_uc003opd.2_Intron|MOCS1_uc003ope.2_Intron	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein						Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					aaaacttgagaagcagaatga	0.000													4	2	---	---	---	---	
LRFN2	57497	broad.mit.edu	37	6	40475033	40475034	+	Intron	INS	-	T	T	rs141625705	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40475033_40475034insT	uc003oph.1	-							NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III							cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)					CTAAAAGGGGATTTTTTTTACC	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50562309	50562309	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50562309delG								DEFB112 (545945 upstream) : TFAP2D (118948 downstream)																							TTTTTTTTTTGTATCATGGCA	0.353													4	2	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51655930	51655931	+	Intron	DEL	AA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51655930_51655931delAA	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|PKHD1_uc003pai.2_Intron	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1						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)					AACCCTCCCTAAACTCTGTTAA	0.455													13	16	---	---	---	---	
C6orf142	90523	broad.mit.edu	37	6	53942175	53942175	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53942175delA	uc003pcg.3	+						C6orf142_uc003pcf.2_Intron	NM_138569	NP_612636	Q5VWP3	MLIP_HUMAN	hypothetical protein LOC90523							nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)					aaacttcattaaaaaaaaaaa	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	54873907	54873908	+	IGR	INS	-	G	G	rs6908172	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54873907_54873908insG								FAM83B (67090 upstream) : HCRTR2 (135594 downstream)																							gagatcctgcaggaaagcccca	0.000													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	55988838	55988838	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55988838delT	uc003pcs.2	-						COL21A1_uc010jzz.2_Intron|COL21A1_uc011dxg.1_Intron|COL21A1_uc011dxh.1_Intron	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TGTTTTGTCCttttttttttt	0.289													3	5	---	---	---	---	
DST	667	broad.mit.edu	37	6	56340193	56340194	+	Intron	DEL	AC	-	-	rs71707265		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56340193_56340194delAC	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GGCTTTTAAAacacacacacac	0.262													5	3	---	---	---	---	
DST	667	broad.mit.edu	37	6	56734789	56734789	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56734789delT	uc003pdf.2	-							NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ccagctgagattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57128341	57128341	+	5'Flank	DEL	A	-	-	rs67982515		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57128341delA	uc003pdu.2	-											full-length cDNA clone CS0DI039YD12 of Placenta Cot 25-normalized of Homo sapiens (human).																		catcagtcacagtggattgag	0.000													2	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57216138	57216139	+	Intron	INS	-	G	G	rs140899256		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57216138_57216139insG	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)		ttttcaggtttggatgttcaac	0.144													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57231848	57231849	+	Intron	INS	-	AAG	AAG	rs143856525	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57231848_57231849insAAG	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)		TGCTATTAAAAAAACAGTAATA	0.248													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57270722	57270730	+	Intron	DEL	CCCAGCAAG	-	-	rs11276813		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57270722_57270730delCCCAGCAAG	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)		atcatcatcaccCAGCAAGCCAATTCTTC	0.287													4	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57400731	57400733	+	Intron	DEL	ATT	-	-	rs140527998		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57400731_57400733delATT	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)		cattgacatcattatgtattatt	0.138													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57416838	57416839	+	Intron	INS	-	A	A	rs138010997		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57416838_57416839insA	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)		aagcaatggggaaaggactgcc	0.000													3	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57484549	57484549	+	Intron	DEL	C	-	-	rs113067659		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57484549delC	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)		aatatgttctcctattctgta	0.000													5	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57487931	57487931	+	Intron	DEL	T	-	-	rs74294531		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57487931delT	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)		tttgcattaattttttttttg	0.075													7	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57489445	57489446	+	Intron	DEL	CT	-	-	rs75214338		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57489445_57489446delCT	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)		GTTTTTAAAACTCTCTTTTTAT	0.238													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57519622	57519622	+	IGR	DEL	A	-	-	rs66662983		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57519622delA								PRIM2 (6247 upstream) : GUSBL2 (726537 downstream)																							tcTAGGGGGGAAAAAATAGAC	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57523617	57523622	+	IGR	DEL	ATTATT	-	-	rs147467647		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57523617_57523622delATTATT								PRIM2 (10242 upstream) : GUSBL2 (722537 downstream)																							taagcaatacattattattgttttat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57552929	57552929	+	IGR	DEL	A	-	-	rs111299945		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57552929delA								PRIM2 (39554 upstream) : GUSBL2 (693230 downstream)																							aacttttaacaaaaaactttt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57565434	57565436	+	IGR	DEL	TGT	-	-	rs148602557		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57565434_57565436delTGT								PRIM2 (52059 upstream) : GUSBL2 (680723 downstream)																							CTTAAGAAGATGTTTTTttttct	0.167													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	58315871	58315871	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58315871delT								GUSBL2 (28147 upstream) : None (None downstream)																							CCTTCATACATTTTACAGTTC	0.393													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65538963	65538964	+	Intron	INS	-	ATGAC	ATGAC	rs140119069	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65538963_65538964insATGAC	uc011dxu.1	-							NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						ggtagtggcaaatgacatggct	0.000													1	7	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65678723	65678724	+	Intron	INS	-	CCTTTG	CCTTTG	rs145640218	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65678723_65678724insCCTTTG	uc011dxu.1	-							NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						tttgcctaggacctgtccttac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	67777961	67777966	+	IGR	DEL	TGTGTG	-	-	rs72066865		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67777961_67777966delTGTGTG								None (None upstream) : None (None downstream)																							TTAATGTGCTtgtgtgtgtgtgtgtg	0.068													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	67790440	67790440	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67790440delT								None (None upstream) : None (None downstream)																							TCTTATGCACTTTTTCCTATA	0.303													4	2	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70652632	70652633	+	Intron	INS	-	TG	TG	rs138975770	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70652632_70652633insTG	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						cattgtgtgtatgtgtgtgtgt	0.000													2	4	---	---	---	---	
COL19A1	1310	broad.mit.edu	37	6	70898398	70898400	+	Intron	DEL	AAC	-	-	rs72275684		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70898398_70898400delAAC	uc003pfc.1	+							NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4						TGAATATCAGAACAACAAATCTG	0.379													4	2	---	---	---	---	
FAM135A	57579	broad.mit.edu	37	6	71251951	71251952	+	Intron	INS	-	CA	CA	rs142452345	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71251951_71251952insCA	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_Intron	NM_001162529	NP_001156001	Q9P2D6	F135A_HUMAN	hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1						TTTTTATCCTGcacacacacac	0.322													3	3	---	---	---	---	
IMPG1	3617	broad.mit.edu	37	6	76717020	76717020	+	Intron	DEL	T	-	-	rs76741306		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76717020delT	uc003pik.1	-							NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1						visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GATAAGAGAATTTTTTTTTTT	0.279													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	78280967	78280967	+	IGR	DEL	A	-	-	rs79010918		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78280967delA								HTR1B (107847 upstream) : None (None downstream)																							tgaaaattgcaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	78622263	78622264	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78622263_78622264insT								HTR1B (449143 upstream) : IRAK1BP1 (954925 downstream)																							gtggttacatgttttttttggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	79170972	79170972	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79170972delT								HTR1B (997852 upstream) : IRAK1BP1 (406217 downstream)																							ctctgtattatttaaaaaagc	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	79248901	79248901	+	IGR	DEL	A	-	-	rs71743083		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79248901delA								None (None upstream) : IRAK1BP1 (328288 downstream)																							cctttagcttaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	81717709	81717709	+	IGR	DEL	G	-	-	rs68030064		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81717709delG								BCKDHB (661722 upstream) : FAM46A (737739 downstream)																							tctttactatgggtgactcaa	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82050579	82050580	+	IGR	INS	-	A	A	rs141891803	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82050579_82050580insA								BCKDHB (994592 upstream) : FAM46A (404868 downstream)																							acaaatgggataaaaaaaaaag	0.000													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	83060591	83060592	+	IGR	INS	-	A	A	rs111964320		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83060591_83060592insA								IBTK (103143 upstream) : TPBG (12331 downstream)																							gatgctgtctcaaaaaaaaaaG	0.089													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	86582022	86582023	+	IGR	DEL	TC	-	-	rs59114422		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86582022_86582023delTC								SNHG5 (193571 upstream) : None (None downstream)																							ctctctcccttccttccttcct	0.010													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	86742209	86742209	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86742209delT								SNHG5 (353758 upstream) : HTR1E (904815 downstream)																							GTAttttttattttttttttt	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	89947940	89947940	+	IGR	DEL	G	-	-	rs36033576		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89947940delG								GABRR1 (20444 upstream) : GABRR2 (19299 downstream)																							aggctgctctgtctgtccaag	0.035													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	92480951	92480951	+	IGR	DEL	C	-	-	rs79166989	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92480951delC								None (None upstream) : None (None downstream)																							acaactaacaccagaaaaaaa	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	100300189	100300189	+	IGR	DEL	C	-	-	rs11322587		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100300189delC								PRDM13 (236735 upstream) : MCHR2 (67597 downstream)																							TTTTAACTTACAGTAATTTAA	0.358													1	6	---	---	---	---	
TRAF3IP2	10758	broad.mit.edu	37	6	111928114	111928115	+	5'Flank	DEL	AG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111928114_111928115delAG	uc011ebc.1	-						TRAF3IP2_uc003pvg.2_5'Flank|TRAF3IP2_uc003pvf.2_5'Flank|TRAF3IP2_uc010kdw.2_5'Flank|TRAF3IP2_uc010kdx.2_5'Flank	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2						intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		CGATGTGAACAGAGAGAGAGAG	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	115953917	115953918	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115953917_115953918insA								None (None upstream) : FRK (308775 downstream)																							ctttgataaggaaaaaaaaaat	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	116797274	116797274	+	IGR	DEL	A	-	-	rs66783362		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116797274delA								FAM26F (12341 upstream) : BET3L (20379 downstream)																							ctcaaaaaacaaaaaaaaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	131687308	131687308	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131687308delT								AKAP7 (82635 upstream) : ARG1 (207057 downstream)																							AAATATGAGGTTATAAGTCAG	0.308													4	2	---	---	---	---	
VNN3	55350	broad.mit.edu	37	6	133055098	133055099	+	Intron	DEL	GA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133055098_133055099delGA	uc003qdp.2	-						VNN3_uc010kfs.2_Intron|VNN3_uc011ecl.1_Intron|VNN3_uc011ecm.1_Intron|VNN3_uc011ecn.1_Intron|VNN3_uc010kfu.2_Intron|VNN3_uc010kfv.2_Intron|VNN3_uc010kfw.2_Intron|VNN3_uc010kfx.2_Intron|VNN3_uc010kfy.2_Intron|VNN3_uc010kfz.2_Intron	NM_078625	NP_523239			SubName: Full=PAGEL-beta;												0	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00242)|GBM - Glioblastoma multiforme(226;0.0168)		taatagaggggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139872388	139872388	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139872388delT								CITED2 (176603 upstream) : None (None downstream)																							AGGGGACAGCTTTTTTTTTTT	0.438													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141964352	141964352	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141964352delT	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																		TGAAGGTCCATAGACTTCCTT	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	151960035	151960035	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151960035delT								C6orf97 (17708 upstream) : ESR1 (51596 downstream)																							attgcactagttttTTTTTAA	0.139													4	2	---	---	---	---	
ESR1	2099	broad.mit.edu	37	6	152045723	152045726	+	Intron	DEL	ACAC	-	-	rs73780854		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152045723_152045726delACAC	uc003qom.3	+							NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)	acacacacatacacacacacacac	0.299													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156069830	156069830	+	IGR	DEL	G	-	-	rs112042741		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156069830delG								NOX3 (292793 upstream) : MIR1202 (198101 downstream)																							atttgtttttgtttttttttc	0.000													4	3	---	---	---	---	
LPA	4018	broad.mit.edu	37	6	160956626	160956631	+	Intron	DEL	TGGTAA	-	-	rs138119137		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160956626_160956631delTGGTAA	uc003qtl.2	-							NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor						blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	atggtgatggtggtaatgatgttgac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164203617	164203617	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164203617delA								QKI (208725 upstream) : None (None downstream)																							ATGGGAAGTCAAACCTGCATT	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	167697176	167697177	+	IGR	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167697176_167697177delAC								TCP10L2 (100781 upstream) : UNC93A (7626 downstream)																							AGTTTGAGATACACACACACAC	0.436													4	2	---	---	---	---	
MLLT4	4301	broad.mit.edu	37	6	168331698	168331700	+	Intron	DEL	GAC	-	-	rs140325378		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168331698_168331700delGAC	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron|MLLT4_uc003qwg.1_Intron	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		cagtggagatgacgagatggttt	0.000			T	MLL	AL								0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168792932	168792932	+	IGR	DEL	C	-	-	rs35492825		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168792932delC								DACT2 (72530 upstream) : SMOC2 (49099 downstream)																							CTGTCCCCATCCCCCAGCACA	0.637													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1320061	1320063	+	IGR	DEL	GAA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1320061_1320063delGAA								UNCX (43449 upstream) : MICALL2 (153933 downstream)																							tataatgaaggaagaagaagaag	0.000													2	5	---	---	---	---	
INTS1	26173	broad.mit.edu	37	7	1546840	1546840	+	5'Flank	DEL	T	-	-	rs111819550		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1546840delT	uc003skn.2	-						INTS1_uc003skq.2_5'Flank	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1						snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTCAttattcttttttttttt	0.269													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	1634961	1634962	+	IGR	INS	-	ATCC	ATCC	rs141966771	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1634961_1634962insATCC								KIAA1908 (5702 upstream) : TFAMP1 (19144 downstream)																							tccatcctcctatccatccatc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	4310651	4310651	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4310651delG								SDK1 (2022 upstream) : FOXK1 (372737 downstream)																							TTCTGGGCTTGGGGGTCCCAC	0.602													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	5008985	5008989	+	IGR	DEL	AAGGG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5008985_5008989delAAGGG								MMD2 (10141 upstream) : RNF216L (4627 downstream)																							gggaaggagtaagggaagggaaggg	0.034													3	3	---	---	---	---	
TNRC18	84629	broad.mit.edu	37	7	5365060	5365060	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5365060delT	uc003soi.3	-							NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		tttttttttgttttttttttt	0.254													4	2	---	---	---	---	
RNF216	54476	broad.mit.edu	37	7	5666301	5666302	+	Intron	INS	-	A	A	rs71547783		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5666301_5666302insA	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron	NM_207116	NP_996999	Q9NWF9	RN216_HUMAN	ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		aaacttgtgttaaaaaaaaaaa	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	7170465	7170465	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7170465delA								C7orf28B (304604 upstream) : C1GALT1 (51781 downstream)																							TTTAGTTAGTAAAATGTCCGA	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	16774313	16774314	+	IGR	INS	-	A	A	rs68103621		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16774313_16774314insA								BZW2 (28165 upstream) : TSPAN13 (19037 downstream)																							cgtctcaaaagaaaaaaaaaag	0.198													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	17402772	17402772	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17402772delA								AHR (16997 upstream) : SNX13 (427614 downstream)																							TTTGTATATGAAAAAAAAAAC	0.303													4	2	---	---	---	---	
HDAC9	9734	broad.mit.edu	37	7	18154916	18154916	+	Intron	DEL	A	-	-	rs67773503		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18154916delA	uc011jya.1	+							NM_014707	NP_055522	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	actctgtctcaaaaaaaaaaa	0.124													2	5	---	---	---	---	
NUPL2	11097	broad.mit.edu	37	7	23237298	23237298	+	Intron	DEL	T	-	-	rs113208439		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23237298delT	uc003svu.2	+						NUPL2_uc003svv.2_Intron|NUPL2_uc003svw.2_Intron|NUPL2_uc011jyw.1_Intron|NUPL2_uc003svx.2_Intron|NUPL2_uc011jyx.1_Intron	NM_007342	NP_031368	O15504	NUPL2_HUMAN	nucleoporin like 2						carbohydrate metabolic process|glucose transport|mRNA transport|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nuclear pore	nuclear export signal receptor activity|nucleic acid binding|zinc ion binding			skin(2)|ovary(1)	3						CCAGGGCCCCTTCCATAGGTT	0.378													3	4	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23843385	23843385	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23843385delT	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron|STK31_uc003swv.1_Intron	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						gccccgtgtctgttgttccct	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	26037000	26037003	+	IGR	DEL	TGAA	-	-	rs72240185		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26037000_26037003delTGAA								MIR148A (47394 upstream) : NFE2L3 (154844 downstream)																							GAATATTGGTtgaatgaatgaatg	0.260													4	2	---	---	---	---	
HIBADH	11112	broad.mit.edu	37	7	27681314	27681314	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27681314delT	uc003szf.2	-						HIBADH_uc003szg.2_Intron|HIBADH_uc003szh.2_Intron|HIBADH_uc003szi.2_Intron	NM_152740	NP_689953	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase precursor						branched chain family amino acid catabolic process|pentose-phosphate shunt|valine metabolic process	mitochondrial matrix	3-hydroxyisobutyrate dehydrogenase activity|NAD binding|phosphogluconate dehydrogenase (decarboxylating) activity			ovary(2)	2			GBM - Glioblastoma multiforme(3;0.0368)		NADH(DB00157)	agtagtgctcttaggaaatca	0.109													4	2	---	---	---	---	
TAX1BP1	8887	broad.mit.edu	37	7	27849530	27849530	+	Intron	DEL	T	-	-	rs66650174		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27849530delT	uc003szl.2	+						TAX1BP1_uc011jzo.1_Intron|TAX1BP1_uc003szk.2_Intron|TAX1BP1_uc011jzp.1_Intron	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)						anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)			CTTTTGTGCCttttttttttt	0.124													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	31041124	31041125	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31041124_31041125insA								GHRHR (21983 upstream) : ADCYAP1R1 (51017 downstream)																							AAGAACATAGGAAAAAAACAGG	0.441													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	32576150	32576150	+	Intron	DEL	T	-	-	rs34003669		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32576150delT	uc003tcv.1	+						AVL9_uc011kai.1_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						AATAACATTCTTTTTTTTTTC	0.169													4	2	---	---	---	---	
ELMO1	9844	broad.mit.edu	37	7	37144456	37144456	+	Intron	DEL	A	-	-	rs111866765		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37144456delA	uc003tfk.1	-						ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6						AGACTGGTGGAAAAAAAAAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46116145	46116146	+	IGR	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46116145_46116146delCA								IGFBP3 (155274 upstream) : None (None downstream)																							gaaggaactgcacacacacaca	0.000													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46347543	46347543	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46347543delA								IGFBP3 (386672 upstream) : TNS3 (967210 downstream)																							ttgcaattgcaaaaaaagtgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	46639561	46639562	+	IGR	DEL	AG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46639561_46639562delAG								IGFBP3 (678690 upstream) : TNS3 (675191 downstream)																							GCATGGAGGAAGAGAGAGAGAG	0.282													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49031421	49031423	+	IGR	DEL	TTA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49031421_49031423delTTA								CDC14C (64372 upstream) : VWC2 (781834 downstream)																							GGCATGAGatttattattattat	0.281													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55366384	55366384	+	IGR	DEL	A	-	-	rs35951804		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55366384delA								EGFR (91354 upstream) : LANCL2 (66757 downstream)																							tcaaccaaccaaaaaaaaaaa	0.000													3	3	---	---	---	---	
VOPP1	81552	broad.mit.edu	37	7	55641558	55641559	+	5'Flank	DEL	GT	-	-	rs71975614		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55641558_55641559delGT	uc003tqs.2	-						VOPP1_uc011kcr.1_5'Flank	NM_030796	NP_110423	Q96AW1	VOPP1_HUMAN	EGFR-coamplified and overexpressed protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic vesicle membrane|endosome|integral to organelle membrane	signal transducer activity				0						ccattaaaaCgtgtgtgtgtgt	0.163													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57651750	57651751	+	IGR	INS	-	T	T	rs148924254		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57651750_57651751insT								ZNF716 (118485 upstream) : None (None downstream)																							TATGtttgttcttttttgtttg	0.139													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57728682	57728683	+	IGR	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57728682_57728683delTG								ZNF716 (195417 upstream) : None (None downstream)																							cctttatatatgttttctccac	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57996510	57996510	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57996510delG								ZNF716 (463245 upstream) : None (None downstream)																							tggcctcaaagctctccaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61750494	61750495	+	IGR	INS	-	A	A	rs139756826		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61750494_61750495insA								None (None upstream) : None (None downstream)																							gacgcgaatggatcatcattga	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61783453	61783453	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61783453delG								None (None upstream) : LOC643955 (968219 downstream)																							atcatcaaatggactcgaatg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65938419	65938419	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65938419delT								NCRNA00174 (73024 upstream) : LOC493754 (55027 downstream)																							TTTCCATACCTTTTGATTTTC	0.333													4	2	---	---	---	---	
RABGEF1	27342	broad.mit.edu	37	7	66128081	66128083	+	Intron	DEL	AAC	-	-	rs77786247		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66128081_66128083delAAC	uc003tvf.2	+							NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1						endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1						cacaaataataacatgagcgctc	0.000													3	3	---	---	---	---	
TYW1	55253	broad.mit.edu	37	7	66551452	66551453	+	Intron	DEL	GA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66551452_66551453delGA	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)				tgtgtgaggggagagagagaga	0.045													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	66874974	66874974	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66874974delT								STAG3L4 (88462 upstream) : None (None downstream)																							TCtcctcccctccctcctccc	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67729509	67729510	+	IGR	INS	-	TGTGCA	TGTGCA	rs149593356	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67729509_67729510insTGTGCA								STAG3L4 (942997 upstream) : None (None downstream)																							GAAGAAAGGTGTGTGCATGGGG	0.406													5	3	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76627942	76627944	+	Intron	DEL	GTG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76627942_76627944delGTG	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						gtgtataggtgtggtgtctttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	80627350	80627350	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80627350delA								SEMA3C (75675 upstream) : HGF (704095 downstream)																							CAGATGGCATAAAGGCAGTGA	0.378													4	2	---	---	---	---	
DMTF1	9988	broad.mit.edu	37	7	86814123	86814123	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86814123delT	uc003uih.2	+						DMTF1_uc003uii.2_Intron|DMTF1_uc003uij.2_Intron|DMTF1_uc011khb.1_Intron|DMTF1_uc003uik.2_Intron|DMTF1_uc003uil.2_Intron|DMTF1_uc003uin.2_Intron	NM_001142327	NP_001135799	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1						cell cycle	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(14;0.0058)					TGTTTGTTCCTTTTttttttt	0.174													5	3	---	---	---	---	
ZNF804B	219578	broad.mit.edu	37	7	88804619	88804619	+	Intron	DEL	T	-	-	rs146507504		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88804619delT	uc011khi.1	+							NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ggatatccaattttctcagca	0.000										HNSCC(36;0.09)			3	4	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90312300	90312300	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90312300delG	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						tgctaattttgatcatctagt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	91392024	91392024	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91392024delC								FZD1 (493893 upstream) : MTERF (39436 downstream)																							catcctgataccaaaacatgg	0.000													4	2	---	---	---	---	
CDK6	1021	broad.mit.edu	37	7	92331019	92331019	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92331019delA	uc011khw.1	-						CDK6_uc010lez.2_Intron	NM_001259	NP_001250	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6						cell dedifferentiation|cell division|G1 phase of mitotic cell cycle|gliogenesis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|negative regulation of osteoblast differentiation|positive regulation of cell-matrix adhesion|positive regulation of fibroblast proliferation|regulation of erythrocyte differentiation|regulation of gene expression|response to virus	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleus|ruffle	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			central_nervous_system(1)|skin(1)	2	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			gcgcccagccAAAaaaaatat	0.000			T	MLLT10	ALL								4	2	---	---	---	---	
DYNC1I1	1780	broad.mit.edu	37	7	95537087	95537088	+	Intron	DEL	TT	-	-	rs113901047		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95537087_95537088delTT	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			CAATCAACTGTTTTTTTTTTTT	0.327													3	3	---	---	---	---	
TRRAP	8295	broad.mit.edu	37	7	98619596	98619596	+	Intron	DEL	A	-	-	rs112063249		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98619596delA	uc003ups.2	+									Q9Y4A5	TRRAP_HUMAN	Homo sapiens TRRAP protein (TRRAP) mRNA, complete cds.						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			atgaggaaccaaaaaaaaaaa	0.000													3	3	---	---	---	---	
CPSF4	10898	broad.mit.edu	37	7	99036691	99036693	+	5'UTR	DEL	GCC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99036691_99036693delGCC	uc003uqj.2	+	1					PTCD1_uc003uqh.2_5'Flank|PTCD1_uc011kiw.1_Intron|CPSF4_uc003uqi.2_5'UTR|CPSF4_uc003uqk.2_5'UTR|CPSF4_uc011kix.1_5'Flank	NM_006693	NP_006684	O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4,						modification by virus of host mRNA processing|mRNA processing|viral infectious cycle	mRNA cleavage and polyadenylation specificity factor complex	RNA binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ggccggtggggccgccgccgccg	0.537													4	2	---	---	---	---	
ZNF3	7551	broad.mit.edu	37	7	99667789	99667790	+	3'UTR	INS	-	T	T	rs148676350	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99667789_99667790insT	uc003usq.2	-	6					ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_3'UTR|ZNF3_uc010lgj.2_3'UTR|ZNF3_uc003uss.2_3'UTR|ZNF3_uc003ust.3_3'UTR	NM_032924	NP_116313	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 2						cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			ttgtttttttgttttttttttc	0.485													4	2	---	---	---	---	
GATS	352954	broad.mit.edu	37	7	99814393	99814394	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99814393_99814394insA	uc003uua.3	-						GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc011kjl.1_Intron|GATS_uc010lgu.2_Intron|PVRIG_uc003uue.2_5'Flank|PVRIG_uc003uuf.1_5'Flank	NM_178831	NP_849153	Q8NAP1	GATS_HUMAN	GATS, stromal antigen 3 opposite strand												0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					gactccgtttcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101452459	101452460	+	IGR	INS	-	A	A	rs78959117		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101452459_101452460insA								MYL10 (179883 upstream) : CUX1 (6832 downstream)																							ttctcttctctctttttttttt	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	103899769	103899769	+	IGR	DEL	T	-	-	rs111942035		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103899769delT								ORC5L (51306 upstream) : LHFPL3 (69335 downstream)																							tgaaagagaattttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	109701226	109701227	+	IGR	DEL	AC	-	-	rs113595688		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109701226_109701227delAC								EIF3IP1 (100956 upstream) : IMMP2L (601883 downstream)																							acacacacatacacacacacac	0.248													3	3	---	---	---	---	
POT1	25913	broad.mit.edu	37	7	124490960	124490960	+	Intron	DEL	A	-	-	rs145579862		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124490960delA	uc003vlm.2	-						POT1_uc011koe.1_Intron|POT1_uc003vlk.2_Intron|POT1_uc003vll.2_Intron|POT1_uc003vlo.2_Intron|POT1_uc003vln.2_Intron	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1						DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						AGTTAGGTAGAAAAAAAAAAA	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	124776846	124776846	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124776846delT	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																		CTTTCAGGAATTTTTTTTTTA	0.294													4	2	---	---	---	---	
TSGA13	114960	broad.mit.edu	37	7	130362271	130362272	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130362271_130362272insT	uc003vqi.2	-						TSGA13_uc003vqj.2_Intron	NM_052933	NP_443165	Q96PP4	TSG13_HUMAN	testis specific, 13											ovary(2)	2	Melanoma(18;0.0435)					TTTGCtttttcttttttttttt	0.059													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	135467341	135467344	+	IGR	DEL	CCTT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135467341_135467344delCCTT								FAM180A (33747 upstream) : LUZP6 (144161 downstream)																							TGGCTGTCCCCCTTCCTTCCTTGC	0.593													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	135785101	135785102	+	IGR	INS	-	C	C	rs150626195	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135785101_135785102insC								LUZP6 (122897 upstream) : CHRM2 (768297 downstream)																							TGAAGCCAATAGGTGAGGAGGG	0.564													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	136199223	136199223	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136199223delA								LUZP6 (537019 upstream) : CHRM2 (354176 downstream)																							tcttttgggtaaatgccttaa	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142013658	142013659	+	Intron	INS	-	C	C	rs5888044		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142013658_142013659insC	uc011kro.1	+						uc011krp.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		TACATCCTATGACATATTTAGA	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142223659	142223659	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142223659delA	uc011krp.1	+						uc011krr.1_Intron|uc011krx.1_Intron|uc011ksa.1_Intron					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																		ATGTTTTAAGAAAATAGTTCA	0.388													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	145542840	145542840	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145542840delC								None (None upstream) : CNTNAP2 (270613 downstream)																							caggaaatcacgctgttttag	0.000													3	3	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147884202	147884203	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147884202_147884203delAC	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			AAGGAAacatacacacacacac	0.356										HNSCC(39;0.1)			3	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157519032	157519032	+	Intron	DEL	T	-	-	rs57729620		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157519032delT	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)		CAGAGGAGTGTGGCCATACCC	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	158387856	158387858	+	IGR	DEL	ATA	-	-	rs141952618		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158387856_158387858delATA								PTPRN2 (7374 upstream) : NCAPG2 (36145 downstream)																							agagatggtgataatggtggtca	0.000													4	2	---	---	---	---	
ESYT2	57488	broad.mit.edu	37	7	158573989	158573990	+	Intron	INS	-	GTGA	GTGA	rs143518063	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158573989_158573990insGTGA	uc003wob.1	-						ESYT2_uc003woc.1_Intron|ESYT2_uc003wod.1_Intron	NM_020728	NP_065779	A0FGR8	ESYT2_HUMAN	family with sequence similarity 62 (C2 domain							integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3						cagtgtgcggtgtgtgagaaca	0.139													3	3	---	---	---	---	
ESYT2	57488	broad.mit.edu	37	7	158575340	158575341	+	Intron	INS	-	AA	AA	rs145853097	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158575340_158575341insAA	uc003wob.1	-						ESYT2_uc003woc.1_Intron|ESYT2_uc003wod.1_Intron	NM_020728	NP_065779	A0FGR8	ESYT2_HUMAN	family with sequence similarity 62 (C2 domain							integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3						TGAGAACAAAGAAGTATTAAAG	0.421													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	805030	805030	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:805030delG	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																		CGGCAGTAGTGGGTCCGGGAG	0.597													4	2	---	---	---	---	
MFHAS1	9258	broad.mit.edu	37	8	8683757	8683758	+	Intron	INS	-	GTGT	GTGT	rs138177121	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8683757_8683758insGTGT	uc003wsj.1	-							NM_004225	NP_004216	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		AAACACAAAGAgtgtgtgtgtg	0.252													3	3	---	---	---	---	
FAM66D	100132923	broad.mit.edu	37	8	12070093	12070094	+	Intron	INS	-	GA	GA			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12070093_12070094insGA	uc011kxp.1	+						uc003wvm.1_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						GCCCTGACTATgagagagagag	0.297													4	2	---	---	---	---	
PEBP4	157310	broad.mit.edu	37	8	22609102	22609103	+	Intron	DEL	TG	-	-	rs66859652		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22609102_22609103delTG	uc003xcn.1	-							NM_144962	NP_659399	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		GGAgtgtgtctgtgtgtgtgtg	0.243													3	3	---	---	---	---	
C8orf80	389643	broad.mit.edu	37	8	27900223	27900224	+	Intron	DEL	AT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27900223_27900224delAT	uc003xgm.3	-							NM_001010906	NP_001010906	Q68CJ6	SLIP_HUMAN	speckled-like pattern in the germinal center							nucleus	GTP binding|GTPase activity			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.126)|Kidney(114;0.15)|Colorectal(74;0.181)		gctcttagtcatgctcttttat	0.079													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	31054608	31054609	+	IGR	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31054608_31054609delTT								WRN (23332 upstream) : NRG1 (442659 downstream)																							cttttccttcttttttttttct	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	32799301	32799302	+	Intron	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32799301_32799302delCA	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																		tgtctttcttcagtgctttgta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33910393	33910395	+	IGR	DEL	GGA	-	-	rs7823555		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33910393_33910395delGGA								DUSP26 (452954 upstream) : None (None downstream)																							agagggagggggaggaggaggag	0.000													4	2	---	---	---	---	
KCNU1	157855	broad.mit.edu	37	8	36767560	36767561	+	Intron	INS	-	T	T	rs138453074	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36767560_36767561insT	uc010lvw.2	+						KCNU1_uc003xjw.2_Intron	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1							voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TGTGGTATGGCGGTTGCAACTA	0.411													4	2	---	---	---	---	
ERLIN2	11160	broad.mit.edu	37	8	37612354	37612354	+	3'UTR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37612354delT	uc003xke.3	+	12						NM_007175	NP_009106	O94905	ERLN2_HUMAN	ER lipid raft associated 2 isoform 1						ER-associated protein catabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	protein binding				0		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CTGTGATTTGTTTTTTTTTTT	0.408													3	3	---	---	---	---	
C8orf86	389649	broad.mit.edu	37	8	38374478	38374478	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38374478delG	uc003xlx.1	-							NM_207412	NP_997295	Q6ZUL3	CH086_HUMAN	hypothetical protein LOC389649												0						TCCAATGCCAGGGCATGTATG	0.517													4	3	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40538220	40538223	+	Intron	DEL	TACA	-	-	rs35498222		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40538220_40538223delTACA	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)			ATGTCTAATGTacacacacacaca	0.412													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43222361	43222362	+	IGR	DEL	CC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43222361_43222362delCC								POTEA (4033 upstream) : None (None downstream)																							agaaagacatccaaggtcaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43820426	43820426	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43820426delA								POTEA (602098 upstream) : None (None downstream)																							gaatttcttcatataaaaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43824491	43824492	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43824491_43824492insT								POTEA (606163 upstream) : None (None downstream)																							tatgctgaaaaaggaaatatct	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	48068638	48068639	+	IGR	INS	-	A	A	rs142878498	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48068638_48068639insA								BEYLA (301231 upstream) : KIAA0146 (104903 downstream)																							aaatgtacaagaaaaaaacaaa	0.094													4	3	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48400596	48400597	+	Intron	DEL	AA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48400596_48400597delAA	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				acagagacacaaaaaacccttc	0.000													4	2	---	---	---	---	
ATP6V1H	51606	broad.mit.edu	37	8	54758075	54758075	+	5'Flank	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54758075delC	uc003xrl.2	-						ATP6V1H_uc003xrm.2_5'Flank|ATP6V1H_uc003xrn.2_5'Flank|ATP6V1H_uc011ldv.1_5'Flank|ATP6V1H_uc010lyd.2_5'Flank|ATP6V1H_uc003xro.1_5'Flank	NM_213620	NP_998785	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			tcacctcccaccctgtctgtg	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60136021	60136022	+	IGR	INS	-	A	A	rs76235167		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60136021_60136022insA								TOX (104254 upstream) : CA8 (965401 downstream)																							gatcctgtttcaaaaaaaaaaa	0.149													5	3	---	---	---	---	
CHD7	55636	broad.mit.edu	37	8	61664650	61664650	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61664650delT	uc003xue.2	+							NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GCTTTCTGTGTTTAGTTCTAA	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	62128915	62128916	+	IGR	INS	-	AG	AG			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62128915_62128916insAG								CHD7 (349452 upstream) : CLVS1 (71609 downstream)																							CTGGAAGCCACAGAGTGCTCTT	0.436													4	2	---	---	---	---	
NKAIN3	286183	broad.mit.edu	37	8	63495393	63495395	+	Intron	DEL	ATC	-	-	rs66649248		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63495393_63495395delATC	uc010lyq.1	+							NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				GAGGAATGAGATCATCAGTGGGG	0.453													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65747523	65747523	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65747523delC								CYP7B1 (36175 upstream) : ARMC1 (767549 downstream)																							tcctttccttcccttccttcc	0.000													5	3	---	---	---	---	
CRH	1392	broad.mit.edu	37	8	67090397	67090398	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67090397_67090398delAC	uc003xvy.1	-							NM_000756	NP_000747	P06850	CRF_HUMAN	corticotropin releasing hormone precursor						female pregnancy|negative regulation of circadian sleep/wake cycle, REM sleep|parturition|positive regulation of circadian sleep/wake cycle, wakefulness|positive regulation of cortisol secretion|signal transduction|synaptic transmission	extracellular region|soluble fraction	neuropeptide hormone activity				0		all_cancers(86;2.58e-06)|all_epithelial(80;6.27e-09)|all_lung(136;0.000414)|Lung NSC(129;0.0011)	Epithelial(68;0.0136)|all cancers(69;0.0507)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)		Corticotropin(DB01285)	acacatgcatacacacacacac	0.262													4	2	---	---	---	---	
ADHFE1	137872	broad.mit.edu	37	8	67351103	67351103	+	Intron	DEL	A	-	-	rs5892054		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67351103delA	uc003xwb.3	+						ADHFE1_uc003xwd.3_Intron|ADHFE1_uc003xwc.3_Intron|ADHFE1_uc003xwe.3_Intron|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Intron|ADHFE1_uc011leq.1_Intron|ADHFE1_uc011ler.1_Intron	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1						2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			CTTGGGGAAGAAAAAAAAAAG	0.468											OREG0018807	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1	5	---	---	---	---	
NCOA2	10499	broad.mit.edu	37	8	71316083	71316085	+	5'Flank	DEL	CCT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71316083_71316085delCCT	uc003xyn.1	-							NM_006540	NP_006531	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CCCCCAACTCcctcctcctcctc	0.537			T	RUNXBP2	AML								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	71477696	71477696	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71477696delG								NCOA2 (161676 upstream) : TRAM1 (7977 downstream)																							ccaactgcctgggagttaggt	0.000													4	2	---	---	---	---	
ZFHX4	79776	broad.mit.edu	37	8	77610828	77610829	+	Intron	INS	-	GA	GA	rs139208780	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77610828_77610829insGA	uc003yav.2	+						ZFHX4_uc003yat.1_Intron|ZFHX4_uc003yau.1_Intron	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			aagaaaagaatgagagggagaa	0.208										HNSCC(33;0.089)			2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	87785988	87785988	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87785988delA								CNGB3 (30087 upstream) : CNBD1 (92688 downstream)																							gccaccaggtaaaaaaccatg	0.000													4	2	---	---	---	---	
MMP16	4325	broad.mit.edu	37	8	89281057	89281057	+	Intron	DEL	T	-	-	rs35661528		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89281057delT	uc003yeb.3	-						MMP16_uc003yec.2_Intron	NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1						collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8						GTTATTGTTCTTTTTTTTTTA	0.378													4	2	---	---	---	---	
NECAB1	64168	broad.mit.edu	37	8	91969172	91969173	+	3'UTR	DEL	GT	-	-	rs67112732		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91969172_91969173delGT	uc011lgg.1	+	13					NECAB1_uc003yer.2_3'UTR	NM_022351	NP_071746	Q8N987	NECA1_HUMAN	N-terminal EF-hand calcium binding protein 1						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity			central_nervous_system(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.0499)			ACATACACACgtgtgtgtgtgt	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96107894	96107894	+	IGR	DEL	T	-	-	rs35546890		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96107894delT								C8orf38 (19498 upstream) : PLEKHF2 (38144 downstream)																							ATCATTTCGCttttttttttt	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96468903	96468903	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96468903delG								C8orf37 (187466 upstream) : GDF6 (685657 downstream)																							TCAGAAAGTTGGACAGAAATG	0.209													4	2	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100069867	100069867	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100069867delC	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yit.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yis.2_Intron|VPS13B_uc011lgy.1_Intron	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ttcctgaactccagcataaga	0.000													4	2	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100588729	100588729	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100588729delA	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			TTGTTTAACCAAAAAAAAAAG	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	102494532	102494532	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102494532delT								NACAP1 (109597 upstream) : GRHL2 (10136 downstream)																							attcttgtacttttttttttt	0.000													4	2	---	---	---	---	
NCALD	83988	broad.mit.edu	37	8	103054941	103054942	+	Intron	INS	-	GAGCCAGAG	GAGCCAGAG	rs139138233	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103054941_103054942insGAGCCAGAG	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718	P61601	NCALD_HUMAN	neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)			gaatcagtgaagacagagggca	0.000													4	4	---	---	---	---	
UBR5	51366	broad.mit.edu	37	8	103302595	103302596	+	Intron	INS	-	A	A	rs140638834	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103302595_103302596insA	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TGCCTTCAAACAAACAGATAAG	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116818894	116818896	+	IGR	DEL	AAG	-	-	rs139748691		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116818894_116818896delAAG								TRPS1 (137666 upstream) : EIF3H (838160 downstream)																							gaaagaaagaaagaagaagaaaa	0.069													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124490729	124490729	+	IGR	DEL	A	-	-	rs11314932		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124490729delA								WDYHV1 (36469 upstream) : FBXO32 (24630 downstream)																							tttgcaaattatgataagtgc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	124512380	124512380	+	RNA	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124512380delT	uc003yqp.1	-	1		c.1225delA								Homo sapiens cDNA FLJ13329 fis, clone OVARC1001795.																		TGCCATTGGATTTTTTTTTTT	0.393													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125176813	125176813	+	Intron	DEL	C	-	-	rs10717191		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125176813delC	uc003yqy.1	-											Homo sapiens cDNA FLJ32770 fis, clone TESTI2001898.																		TACTCCCATTCCCCAGTGGTA	0.493													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126416352	126416353	+	IGR	DEL	TC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126416352_126416353delTC								NSMCE2 (36985 upstream) : TRIB1 (26210 downstream)																							GTGCTTCCTGTCTCTCTCTCtc	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	126621830	126621830	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126621830delG								TRIB1 (171188 upstream) : FAM84B (942857 downstream)																							atccagctttggggaaactga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	131625131	131625136	+	IGR	DEL	AGAGAG	-	-	rs143668252		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131625131_131625136delAGAGAG								ASAP1 (210915 upstream) : ADCY8 (167412 downstream)																							agagagagacagagagagagagagag	0.146													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138214680	138214680	+	IGR	DEL	G	-	-	rs34331020		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138214680delG								None (None upstream) : FAM135B (927588 downstream)																							AAAAACATACGTTTTTTTTAG	0.209													5	3	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139754749	139754751	+	Intron	DEL	TGA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139754749_139754751delTGA	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			atggtagagttgatgatgatggt	0.000										HNSCC(7;0.00092)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	140606548	140606550	+	IGR	DEL	AAT	-	-	rs67888145		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140606548_140606550delAAT								COL22A1 (680312 upstream) : KCNK9 (6532 downstream)																							GGGAACAGAGAATAGGACTGCCT	0.576													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141227707	141227708	+	Intron	DEL	TG	-	-	rs66464163		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141227707_141227708delTG	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						TACAGACACATGTAAACACCTG	0.470													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	141651395	141651398	+	IGR	DEL	ACAC	-	-	rs35952849		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141651395_141651398delACAC								EIF2C2 (5750 upstream) : PTK2 (17104 downstream)																							ctgtctcaaaacacacacacacac	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142330130	142330130	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142330130delG								SLC45A4 (65905 upstream) : LOC731779 (20518 downstream)																							aaggctctctggaggaggttt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143124363	143124363	+	IGR	DEL	G	-	-	rs142907855		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143124363delG								MIR1302-7 (256689 upstream) : NCRNA00051 (155354 downstream)																							CAGCTGAGCAGGTGCTGAGCA	0.632													2	5	---	---	---	---	
BAI1	575	broad.mit.edu	37	8	143604685	143604686	+	Intron	INS	-	GGAG	GGAG	rs139774464	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143604685_143604686insGGAG	uc003ywm.2	+							NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1						axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					AACCGAGGCTTGAAGGGAGGGC	0.649													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144205840	144205841	+	IGR	DEL	CA	-	-	rs139370233		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144205840_144205841delCA								C8orf31 (70120 upstream) : LY6H (33491 downstream)																							cacacacccccacacacacact	0.035													4	2	---	---	---	---	
CBWD1	55871	broad.mit.edu	37	9	129676	129676	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129676delG	uc003zga.3	-						CBWD1_uc010mgs.2_Intron|CBWD1_uc003zgb.3_Intron|CBWD1_uc003zgc.3_Intron|CBWD1_uc011llr.1_Intron	NM_018491	NP_060961	Q9BRT8	CBWD1_HUMAN	COBW domain containing 1 isoform 1								ATP binding|protein binding			ovary(1)	1	all_lung(41;0.218)	all_cancers(5;3.04e-16)|all_epithelial(5;4.68e-12)|all_lung(10;1.94e-10)|Lung NSC(10;3.61e-10)|Acute lymphoblastic leukemia(5;0.00439)|Breast(48;0.0148)|all_hematologic(5;0.024)|Prostate(43;0.122)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		gacgaaaattggggggggctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	6690932	6690933	+	IGR	INS	-	A	A	rs140370396	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6690932_6690933insA								GLDC (45240 upstream) : KDM4C (25562 downstream)																							tgtctcaaaataaaaaaaaaTG	0.035													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	23401464	23401465	+	IGR	DEL	AC	-	-	rs147862876		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23401464_23401465delAC								DMRTA1 (948992 upstream) : ELAVL2 (288640 downstream)																							atacatacatacacacacacac	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25126139	25126140	+	IGR	DEL	GG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25126139_25126140delGG								None (None upstream) : TUSC1 (550254 downstream)																							tgccactactgggaatggggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25562293	25562296	+	IGR	DEL	TCTG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25562293_25562296delTCTG								None (None upstream) : TUSC1 (114098 downstream)																							cactttgagttctgtctgtccttc	0.000													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	30298774	30298775	+	IGR	DEL	TC	-	-	rs111361112		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30298774_30298775delTC								None (None upstream) : None (None downstream)																							CTTTGCTTTGTCTCTCTCTCTC	0.361													5	4	---	---	---	---	
STOML2	30968	broad.mit.edu	37	9	35104084	35104086	+	5'Flank	DEL	CAA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35104084_35104086delCAA	uc003zwi.2	-						STOML2_uc003zwh.2_5'Flank|STOML2_uc003zwj.2_5'Flank|STOML2_uc011lou.1_5'Flank|STOML2_uc003zwk.2_5'Flank	NM_013442	NP_038470	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2							cytoskeleton	receptor binding				0			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			ACCCTCTCCCcaacaacaacaac	0.409													4	2	---	---	---	---	
UNC13B	10497	broad.mit.edu	37	9	35375841	35375841	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35375841delG	uc003zwq.2	+						UNC13B_uc003zwr.2_Intron	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like						excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			agctgggcatggtagcatgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	35914328	35914331	+	IGR	DEL	AGTG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35914328_35914331delAGTG								LOC158376 (2711 upstream) : OR2S2 (42775 downstream)																							gtatgtgtgtagtgagtgtgtgtg	0.044													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	36420530	36420530	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36420530delA								RNF38 (19335 upstream) : MELK (152375 downstream)																							ctctgtctccaaaaaaaaaaa	0.015													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38362473	38362474	+	IGR	DEL	GT	-	-	rs66817170		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38362473_38362474delGT								SHB (293263 upstream) : ALDH1B1 (30228 downstream)																							GTCtgtgtgcgtgtgtgtgtgt	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	39063303	39063304	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39063303_39063304insA								C9orf122 (440028 upstream) : CNTNAP3 (9462 downstream)																							aactcagtaagaaaaaaaatcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	41885707	41885708	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:41885707_41885708insT								FAM75A5 (558343 upstream) : MGC21881 (62808 downstream)																							ACAGAGCCACCTTTTTTCCTGA	0.416													19	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	42523654	42523654	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:42523654delA								FAM95B1 (49417 upstream) : FOXD4L2 (193580 downstream)																							ttcgagacataaaaaaaaaaa	0.000													4	3	---	---	---	---	
LOC442421	442421	broad.mit.edu	37	9	66495217	66495217	+	5'Flank	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66495217delA	uc004aed.1	+											Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						cgatttgtctatttactctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66797228	66797228	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66797228delA								LOC442421 (294201 upstream) : AQP7P1 (457039 downstream)																							atcttcacataaaaactacac	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66798336	66798336	+	IGR	DEL	G	-	-	rs112257604		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66798336delG								LOC442421 (295309 upstream) : AQP7P1 (455931 downstream)																							tgatagagcagctttgaaaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66990579	66990579	+	IGR	DEL	T	-	-	rs140894478	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66990579delT								LOC442421 (487552 upstream) : AQP7P1 (263688 downstream)																							tgctcaatcataagaaatttt	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67293334	67293334	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67293334delA								AQP7P1 (3842 upstream) : FAM27B (499596 downstream)																							TCTTAACGAGAACCTCCAAAA	0.398													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68742432	68742433	+	Intron	DEL	AA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68742432_68742433delAA	uc004aez.1	+						uc004afa.1_Intron|uc010mnp.1_Intron					Homo sapiens cDNA, FLJ18209.																		actccatctcaaaaaaaaaaaa	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69069523	69069524	+	Intron	INS	-	ACTA	ACTA	rs138568356	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69069523_69069524insACTA	uc004afe.1	+						uc010mnq.1_Intron					Homo sapiens cDNA, FLJ18209.																		actttgtacttactattagttt	0.000													4	3	---	---	---	---	
ANKRD20A4	728747	broad.mit.edu	37	9	69420250	69420251	+	Intron	INS	-	CTTA	CTTA			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69420250_69420251insCTTA	uc004afn.2	+							NM_001098805	NP_001092275	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4												0						TTATTATTCATCTTTTATTAAA	0.257													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69818412	69818412	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69818412delT								LOC100133920 (153463 upstream) : FOXD4L5 (357297 downstream)																							gttctaagtgtttgtccctca	0.000													7	4	---	---	---	---	
TRPM3	80036	broad.mit.edu	37	9	73633195	73633195	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73633195delA	uc004aid.2	-						TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aii.2_Intron	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						aagctaggggaaaaaaagtta	0.000													4	2	---	---	---	---	
TRPM3	80036	broad.mit.edu	37	9	73641859	73641861	+	Intron	DEL	CTG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73641859_73641861delCTG	uc004aid.2	-						TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aii.2_Intron	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						ctacagcaccctgctgctgctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	74176714	74176714	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74176714delA								TRPM3 (114894 upstream) : TMEM2 (121568 downstream)																							ccatccttataaaaaggggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	74876789	74876789	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74876789delT								GDA (8312 upstream) : ZFAND5 (89552 downstream)																							ctcctccttcttctTTTTGCT	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	75054903	75054904	+	IGR	INS	-	T	T	rs148126882		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75054903_75054904insT								ZFAND5 (74740 upstream) : TMC1 (81813 downstream)																							tcttcttcttcttttttttttt	0.173													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	81917112	81917114	+	IGR	DEL	CAT	-	-	rs71504938		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81917112_81917114delCAT								PSAT1 (972105 upstream) : TLE4 (269764 downstream)																							AGGAGGGAGGCATCAAGGAATCA	0.468													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	86841317	86841318	+	IGR	DEL	GT	-	-	rs72455415		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86841317_86841318delGT								RMI1 (222335 upstream) : SLC28A3 (51774 downstream)																							gtgtgagtgcgtgtgtgtgtgt	0.030													4	2	---	---	---	---	
C9orf44	158314	broad.mit.edu	37	9	94917049	94917050	+	Intron	DEL	TT	-	-	rs113728025		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94917049_94917050delTT	uc004arp.1	+						C9orf44_uc004arq.1_5'Flank	NR_027341				Homo sapiens cDNA FLJ13600 fis, clone PLACE1009947.												0						TCACAGCCGAtttttttttttt	0.228													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	98172883	98172883	+	IGR	DEL	A	-	-	rs71366289		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98172883delA								FANCC (92892 upstream) : PTCH1 (32383 downstream)																							GGAGGGGGACAGGGGGTGATC	0.398													4	3	---	---	---	---	
HSD17B3	3293	broad.mit.edu	37	9	99002314	99002315	+	Intron	INS	-	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99002314_99002315insG	uc004awa.1	-						HSD17B3_uc010msc.1_Intron	NM_000197	NP_000188	P37058	DHB3_HUMAN	estradiol 17 beta-dehydrogenase 3						androgen biosynthetic process|male genitalia development	endoplasmic reticulum membrane|microsome	binding|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity				0		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)			NADH(DB00157)	tgagaacacatggacacaggga	0.045													5	3	---	---	---	---	
TMOD1	7111	broad.mit.edu	37	9	100273368	100273369	+	Intron	DEL	AC	-	-	rs112118659		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100273368_100273369delAC	uc004axk.1	+							NM_003275	NP_003266	P28289	TMOD1_HUMAN	tropomodulin 1						muscle filament sliding	cytosol	actin binding				0		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		acacacacagacacacacacac	0.371													4	2	---	---	---	---	
TMEFF1	8577	broad.mit.edu	37	9	103332933	103332934	+	Intron	INS	-	T	T	rs144579680	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103332933_103332934insT	uc004baz.1	+						TMEFF1_uc004bay.1_Intron	NM_003692	NP_003683	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two						multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)				cccACTGCTTGTTTTTTTTTGT	0.257													4	2	---	---	---	---	
LPAR1	1902	broad.mit.edu	37	9	113688976	113688977	+	Intron	INS	-	T	T	rs150593125	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113688976_113688977insT	uc004bfa.2	-						LPAR1_uc011lwm.1_Intron|LPAR1_uc004bfb.2_Intron|LPAR1_uc004bfc.2_Intron|LPAR1_uc011lwn.1_Intron|LPAR1_uc011lwo.1_Intron|LPAR1_uc010mub.2_Intron	NM_057159	NP_476500	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2						GTGGTTTTGTGTTTTTTTTCCC	0.396													2	4	---	---	---	---	
ZNF618	114991	broad.mit.edu	37	9	116812723	116812724	+	3'UTR	DEL	CA	-	-	rs113819665		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116812723_116812724delCA	uc004bid.2	+	15					ZNF618_uc004bic.2_3'UTR|ZNF618_uc011lxi.1_3'UTR|ZNF618_uc011lxj.1_3'UTR|ZNF618_uc010mvb.2_3'UTR	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGcacacacgcacacacacaca	0.465													4	2	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119310385	119310386	+	Intron	INS	-	TGTT	TGTT	rs142574000	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119310385_119310386insTGTT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron|ASTN2_uc004bjp.1_Intron|ASTN2_uc004bjq.1_Intron|ASTN2_uc011lxr.1_Intron|ASTN2_uc011lxs.1_Intron|ASTN2_uc011lxt.1_Intron|uc004bju.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						CCAAAGCACTCTGTTTTCTAAG	0.579													4	2	---	---	---	---	
DBC1	1620	broad.mit.edu	37	9	122024170	122024173	+	Intron	DEL	CTCT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122024170_122024173delCTCT	uc004bkc.2	-						DBC1_uc004bkd.2_Intron	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor						cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8						tcttctcttcctctctctctctct	0.123													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122263499	122263500	+	IGR	INS	-	A	A	rs145397184	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122263499_122263500insA								DBC1 (131760 upstream) : MIR147 (743757 downstream)																							ttgTTCGCTTTAAAAAAAAATA	0.198													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	125001503	125001504	+	IGR	INS	-	T	T	rs146740606	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125001503_125001504insT								LHX6 (10484 upstream) : RBM18 (330 downstream)																							ttttgtttttgttttttttgag	0.168													6	3	---	---	---	---	
NR6A1	2649	broad.mit.edu	37	9	127305209	127305209	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127305209delC	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3						AGAGATATATCCAATTTTCTA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	127599875	127599876	+	IGR	INS	-	CAG	CAG	rs146525347	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127599875_127599876insCAG								OLFML2A (22718 upstream) : WDR38 (15879 downstream)																							AGAACAACAACAAGAAACATTT	0.213													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132557168	132557168	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132557168delG								PTGES (41824 upstream) : TOR1B (8264 downstream)																							CATACGCCTTGGACATAGTAC	0.368													4	2	---	---	---	---	
TTF1	7270	broad.mit.edu	37	9	135280281	135280281	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135280281delT	uc004cbl.2	-						TTF1_uc011mcp.1_Intron|TTF1_uc004cbm.2_Intron	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase						negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		cttttttttcttttttttttg	0.050													4	2	---	---	---	---	
VAV2	7410	broad.mit.edu	37	9	136806049	136806049	+	Intron	DEL	A	-	-	rs67922618		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136806049delA	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		tagctaaaagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	137026355	137026360	+	IGR	DEL	ATGTGT	-	-	rs67843865		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137026355_137026360delATGTGT								WDR5 (1262 upstream) : RNU6ATAC (3202 downstream)																							AAACCACAGCatgtgtatgtgtatgt	0.209													4	2	---	---	---	---	
COL5A1	1289	broad.mit.edu	37	9	137604474	137604474	+	Intron	DEL	C	-	-	rs35270332		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137604474delC	uc004cfe.2	+							NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		ccccttccttcctgttccccc	0.015													5	3	---	---	---	---	
PNPLA7	375775	broad.mit.edu	37	9	140386841	140386841	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140386841delT	uc004cnf.2	-						C9orf167_uc011mew.1_Intron|PNPLA7_uc011mfa.1_Intron|PNPLA7_uc010ncj.1_Intron	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7						lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		AGAGCTTTCCTCCAGTGCTGC	0.498													4	2	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140563846	140563846	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140563846delC	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		ACCCAAGACGCCCCCCACAGC	0.667													7	4	---	---	---	---	
CACNA1B	774	broad.mit.edu	37	9	140968697	140968697	+	Intron	DEL	T	-	-	rs78547363		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140968697delT	uc004cog.2	+						CACNA1B_uc004coi.2_Intron|CACNA1B_uc004cok.1_5'Flank|CACNA1B_uc010ncp.1_5'Flank	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)	tttcttactcttttttttttt	0.020													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	103754	103754	+	IGR	DEL	T	-	-	rs113012935		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103754delT								TUBB8 (8250 upstream) : ZMYND11 (76670 downstream)																							caacacttgctttttttttaa	0.000													3	3	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1255478	1255495	+	Intron	DEL	CCCACACCCATGCCATCA	-	-	rs36221033		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1255478_1255495delCCCACACCCATGCCATCA	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		TACAGCCTCGCCCACACCCATGccatcacccacaccca	0.321													4	3	---	---	---	---	
ADARB2	105	broad.mit.edu	37	10	1320150	1320161	+	Intron	DEL	CTCTTTCTCTCT	-	-	rs139793454		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1320150_1320161delCTCTTTCTCTCT	uc009xhq.2	-							NM_018702	NP_061172	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		cttccttccCCTCtttctctctctctttcttt	0.024													4	2	---	---	---	---	
UCN3	114131	broad.mit.edu	37	10	5412918	5412919	+	Intron	DEL	GG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5412918_5412919delGG	uc001ihx.1	+							NM_053049	NP_444277	Q969E3	UCN3_HUMAN	urocortin 3 preproprotein							extracellular region	hormone activity				0						atgtgtgtaaggtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	5539581	5539584	+	IGR	DEL	ACAG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5539581_5539584delACAG								NET1 (39157 upstream) : CALML5 (1074 downstream)																							agacacagacacagacagacacac	0.000													4	2	---	---	---	---	
SFMBT2	57713	broad.mit.edu	37	10	7206709	7206710	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7206709_7206710delAC	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						ATAAAGGGAAacacacacacac	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	10739082	10739082	+	IGR	DEL	A	-	-	rs111730258		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10739082delA								None (None upstream) : SFTA1P (87320 downstream)																							AGAAGGAGACAAAAAAAAAAA	0.343													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12455529	12455530	+	Intron	INS	-	ATA	ATA			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12455529_12455530insATA	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)		tgataatggtgatgatgatgag	0.139													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	13855236	13855236	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13855236delG	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						cgtgaggtcaggagtttgaga	0.000													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14183580	14183581	+	Intron	INS	-	C	C	rs145322353	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14183580_14183581insC	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						CCCCTTCTCTACCCCTGCCATA	0.525													2	4	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14423847	14423848	+	Intron	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14423847_14423848delCA	uc001imv.2	-						FRMD4A_uc001imw.1_Intron			Q9P2Q2	FRM4A_HUMAN	Homo sapiens mRNA for KIAA1294 protein, partial cds.							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						cacatgcacgcacacacacaca	0.000													4	2	---	---	---	---	
NEBL	10529	broad.mit.edu	37	10	21257269	21257270	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21257269_21257270insA	uc001iqk.2	-							NM_213569	NP_998734	O76041	NEBL_HUMAN	nebulette non-muscle isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2						ccccatctcttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	21652369	21652369	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21652369delT								NEBL (189253 upstream) : C10orf114 (131053 downstream)																							TGGGCTGTCATTGATATTTAG	0.353													4	2	---	---	---	---	
PIP4K2A	5305	broad.mit.edu	37	10	22857259	22857260	+	Intron	INS	-	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22857259_22857260insC	uc001irl.3	-						PIP4K2A_uc010qcu.1_Intron	NM_005028	NP_005019	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type								1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2						AGTGCCTCTTTCCCCACATTAC	0.460													4	2	---	---	---	---	
KIAA1217	56243	broad.mit.edu	37	10	24296068	24296068	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24296068delT	uc001irs.2	+							NM_001098500	NP_001091970	Q5T5P2	SKT_HUMAN	sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						TTTTTTCTGCTTTTTTTTTTT	0.363													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	26005589	26005590	+	Intron	INS	-	A	A	rs150887525		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26005589_26005590insA	uc001isl.1	+											Homo sapiens cDNA FLJ41446 fis, clone BRSTN2003590.																		gagaacaacccccttttgactg	0.000													4	3	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27389840	27389841	+	5'Flank	INS	-	A	A	rs146727302	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27389840_27389841insA	uc001ith.2	-						ANKRD26_uc009xku.1_5'Flank	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						GAGATCGTGGCATATGTGTCAA	0.475													3	3	---	---	---	---	
ARMC4	55130	broad.mit.edu	37	10	28196425	28196426	+	Intron	INS	-	A	A	rs140516962	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28196425_28196426insA	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4								binding			ovary(4)|skin(2)	6						aaactgaccagaaaaaaagcaa	0.139													1	5	---	---	---	---	
MPP7	143098	broad.mit.edu	37	10	28464218	28464219	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28464218_28464219insA	uc001iua.1	-						MPP7_uc009xkz.1_Intron|MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1						gatgtcgtctcaaaaaaaaaaa	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	28776103	28776104	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28776103_28776104insA								MPP7 (184108 upstream) : WAC (45323 downstream)																							tcaggcctctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30083820	30083821	+	IGR	DEL	GA	-	-	rs150828915		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30083820_30083821delGA								SVIL (57956 upstream) : KIAA1462 (217908 downstream)																							agagagagaggagagagagaga	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35145437	35145437	+	IGR	DEL	T	-	-	rs10708611		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35145437delT								PARD3 (41514 upstream) : CUL2 (153371 downstream)																							AACCCCTGTCTTCTggcaggg	0.264													1	5	---	---	---	---	
CCNY	219771	broad.mit.edu	37	10	35630590	35630590	+	Intron	DEL	A	-	-	rs111426338		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35630590delA	uc001iyw.3	+						CCNY_uc001iyu.3_Intron|CCNY_uc001iyv.3_Intron|CCNY_uc001iyx.3_Intron|CCNY_uc009xmb.2_Intron|CCNY_uc010qet.1_Intron	NM_145012	NP_659449	Q8ND76	CCNY_HUMAN	cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0						TTATTGGGTGAGGGGAAACAG	0.338													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36331781	36331781	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36331781delG								FZD8 (401419 upstream) : None (None downstream)																							tttttcttttgtcactcatgc	0.000													4	2	---	---	---	---	
ANKRD30A	91074	broad.mit.edu	37	10	37520278	37520278	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37520278delG	uc001iza.1	+							NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						ACGGCTTAATGGGAAATGTTA	0.279													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38780609	38780609	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38780609delG								LOC399744 (39529 upstream) : None (None downstream)																							tggaatggaagggaatggaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42614713	42614714	+	IGR	INS	-	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42614713_42614714insC								None (None upstream) : LOC441666 (212601 downstream)																							atattattcagccttaaacatg	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42654253	42654255	+	IGR	DEL	TAT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42654253_42654255delTAT								None (None upstream) : LOC441666 (173060 downstream)																							caaatttgcatattattactaat	0.034													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42660976	42660976	+	IGR	DEL	C	-	-	rs150779290	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42660976delC								None (None upstream) : LOC441666 (166339 downstream)																							tatttagagacagaaaacaaa	0.000													4	2	---	---	---	---	
MARCH8	220972	broad.mit.edu	37	10	46032040	46032040	+	5'Flank	DEL	A	-	-	rs35718772		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46032040delA	uc001jci.1	-						MARCH8_uc001jch.2_5'Flank|MARCH8_uc001jcj.1_Intron|MARCH8_uc001jck.1_Intron	NM_001002266	NP_001002266	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						tataaatgttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46188893	46188894	+	IGR	INS	-	TT	TT			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46188893_46188894insTT								ANUBL1 (20642 upstream) : FAM21C (33773 downstream)																							CTTATGCAAGGTTTTTTTCAAA	0.396													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47123573	47123574	+	Intron	INS	-	A	A	rs138486529		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47123573_47123574insA	uc001jed.3	-						uc001jef.2_Intron			P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						ggttctgtctcaaaaaaaaaaa	0.277													6	3	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	53072443	53072444	+	Intron	INS	-	TG	TG	rs149089655	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53072443_53072444insTG	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron|PRKG1_uc010qhp.1_Intron	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		AGATGGATATATGTGTGTGTGT	0.322													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54444918	54444918	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54444918delT								DKK1 (367502 upstream) : MBL2 (80223 downstream)																							CCTTCCGGGATTTTTTTTTTT	0.363													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	54724656	54724658	+	IGR	DEL	CTT	-	-	rs137877332		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54724656_54724658delCTT								MBL2 (193196 upstream) : PCDH15 (837877 downstream)																							ctcttctctccttctcattgccc	0.000													4	3	---	---	---	---	
CTNNA3	29119	broad.mit.edu	37	10	68178314	68178315	+	Intron	INS	-	AC	AC	rs149031846	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68178314_68178315insAC	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856	Q9UI47	CTNA3_HUMAN	catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8						agcacacagggacacacacaca	0.000													5	3	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73303708	73303708	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73303708delA	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jrv.2_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						TGAGAAGGAGAAAAAAAAAAG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	74861795	74861795	+	IGR	DEL	A	-	-	rs34855882		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74861795delA								P4HA1 (5063 upstream) : NUDT13 (8415 downstream)																							actccgtctcaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81086574	81086575	+	IGR	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81086574_81086575delTG								ZMIZ1 (10289 upstream) : PPIF (20645 downstream)																							tttctgtatctgtgtgtgtgtg	0.104													4	2	---	---	---	---	
STAMBPL1	57559	broad.mit.edu	37	10	90652111	90652112	+	Intron	DEL	GT	-	-	rs112774452		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90652111_90652112delGT	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_RNA	NM_020799	NP_065850	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		gtgcgtgtgcgtgtgtgtgtgt	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	92752984	92752985	+	IGR	INS	-	T	T	rs141559563	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92752984_92752985insT								ANKRD1 (71952 upstream) : NUDT9P1 (158776 downstream)																							tacattaacagttttttttttg	0.000													2	4	---	---	---	---	
RRP12	23223	broad.mit.edu	37	10	99127787	99127788	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99127787_99127788insT	uc001knf.2	-						RRP12_uc001kne.2_5'Flank|RRP12_uc009xvl.2_Intron|RRP12_uc009xvm.2_Intron|RRP12_uc010qou.1_Intron|RRP12_uc009xvn.2_Intron	NM_015179	NP_055994	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog isoform 1							integral to membrane|nuclear membrane|nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		ctgtgcctggcttttttttttt	0.000													4	2	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100984178	100984179	+	Intron	DEL	AC	-	-	rs141220632		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100984178_100984179delAC	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		TTTCTCTCTGacacacacacac	0.307													4	2	---	---	---	---	
CALHM2	51063	broad.mit.edu	37	10	105208932	105208932	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105208932delA	uc001kwz.2	-						CALHM2_uc001kxa.2_Intron|CALHM2_uc001kxc.2_Intron|CALHM2_uc001kxb.2_Intron|CALHM2_uc001kxd.1_3'UTR	NM_015916	NP_057000	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2							integral to membrane				skin(1)	1						GATTTACAGTAAAAAAAAAAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107039127	107039128	+	IGR	INS	-	TTCT	TTCT	rs10628728		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107039127_107039128insTTCT								SORCS3 (14134 upstream) : None (None downstream)																							tcttttctttcttctttctttc	0.030													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107372803	107372804	+	IGR	INS	-	G	G	rs149945293	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107372803_107372804insG								SORCS3 (347810 upstream) : SORCS1 (960618 downstream)																							catatgaatttggggggggatg	0.134													2	4	---	---	---	---	
SORCS1	114815	broad.mit.edu	37	10	108359126	108359126	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108359126delA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a							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)		actctaattcaaaaaaaaaaa	0.075													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	111449017	111449018	+	IGR	INS	-	T	T	rs143370278	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111449017_111449018insT								None (None upstream) : XPNPEP1 (175506 downstream)																							ctttggagaaatatttgttcaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	115809947	115809948	+	IGR	INS	-	T	T	rs72354355		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115809947_115809948insT								ADRB1 (3282 upstream) : C10orf118 (72026 downstream)																							ttctttttttgttttttttttt	0.193													4	2	---	---	---	---	
TDRD1	56165	broad.mit.edu	37	10	115946026	115946027	+	Intron	INS	-	TTTG	TTTG	rs140211890	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115946026_115946027insTTTG	uc001lbg.1	+						TDRD1_uc001lbf.2_Intron|TDRD1_uc001lbh.1_Intron|TDRD1_uc001lbi.1_Intron	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1						DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		CCTGGAGtttttttgtttgttt	0.193													3	3	---	---	---	---	
ABLIM1	3983	broad.mit.edu	37	10	116243038	116243039	+	Intron	INS	-	T	T	rs61001282	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116243038_116243039insT	uc010qsg.1	-						ABLIM1_uc010qsh.1_Intron|ABLIM1_uc010qsi.1_Intron|ABLIM1_uc010qsk.1_Intron|ABLIM1_uc009xyp.2_Intron|ABLIM1_uc010qsf.1_Intron|ABLIM1_uc009xyn.2_Intron|ABLIM1_uc010qsj.1_Intron|ABLIM1_uc009xyo.2_Intron	NM_002313	NP_002304	O14639	ABLM1_HUMAN	actin-binding LIM protein 1 isoform a						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		TCCAtttttggtttttttttga	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	119324159	119324170	+	IGR	DEL	GCACGCGCCGGG	-	-	rs112835128		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119324159_119324170delGCACGCGCCGGG								EMX2 (15103 upstream) : RAB11FIP2 (440259 downstream)																							GCCCCTGGGAGCACGCGCCGGGGAGGAGGGAG	0.448													3	3	---	---	---	---	
GRK5	2869	broad.mit.edu	37	10	121046760	121046770	+	Intron	DEL	AGGGAGAGAGG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121046760_121046770delAGGGAGAGAGG	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		ggagggaggaagggagagaggaggaagggaa	0.000													4	2	---	---	---	---	
GRK5	2869	broad.mit.edu	37	10	121051646	121051651	+	Intron	DEL	CTCCTT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121051646_121051651delCTCCTT	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		cctcatcttcctccttctcctcctct	0.000													7	5	---	---	---	---	
GRK5	2869	broad.mit.edu	37	10	121133851	121133851	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121133851delG	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		CATCCACTGTGGTGTCCTTGG	0.358													4	2	---	---	---	---	
RGS10	6001	broad.mit.edu	37	10	121277185	121277186	+	Intron	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121277185_121277186delCA	uc001lee.2	-						RGS10_uc001lef.2_Intron|RGS10_uc001leg.2_Intron	NM_002925	NP_002916	O43665	RGS10_HUMAN	regulator of G-protein signaling 10 isoform b						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|protein binding|signal transducer activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00105)|GBM - Glioblastoma multiforme(135;0.195)		CATTcacacgcacacacacacg	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125014922	125014924	+	IGR	DEL	CAA	-	-	rs144817793	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125014922_125014924delCAA								BUB3 (90036 upstream) : GPR26 (410947 downstream)																							ccaccaccaccaacattaccatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130179375	130179376	+	IGR	DEL	GC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130179375_130179376delGC								MKI67 (254907 upstream) : None (None downstream)																							CTGCAGACCTGCCCTCCTCTGC	0.584													4	2	---	---	---	---	
EBF3	253738	broad.mit.edu	37	10	131700992	131700992	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131700992delA	uc001lki.1	-							NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		TAACTGTACGAAAAGAACTCC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	132139029	132139029	+	IGR	DEL	C	-	-	rs66499808		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132139029delC								GLRX3 (156245 upstream) : TCERG1L (751627 downstream)																							ggatttagggcccgccctaga	0.000													2	4	---	---	---	---	
PPP2R2D	55844	broad.mit.edu	37	10	133758447	133758447	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133758447delG	uc001lks.2	+						PPP2R2D_uc001lkr.2_Intron|PPP2R2D_uc001lkt.2_Intron|PPP2R2D_uc009yay.2_Intron	NM_018461	NP_060931	Q66LE6	2ABD_HUMAN	protein phosphatase 2, regulatory subunit B,						cell division|exit from mitosis|mitosis|signal transduction	cytoplasm|protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			skin(1)	1		all_cancers(35;2.16e-12)|all_epithelial(44;2.77e-09)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Colorectal(31;0.0124)|Breast(234;0.023)|all_neural(114;0.0299)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.86e-05)|Epithelial(32;8.82e-05)|all cancers(32;0.000106)|BRCA - Breast invasive adenocarcinoma(275;0.21)		GTGGGAGTGTGGGATTTTGCA	0.373													4	2	---	---	---	---	
SCGB1C1	147199	broad.mit.edu	37	11	191811	191824	+	5'Flank	DEL	CCCTAACCCCTAAC	-	-	rs4890206		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:191811_191824delCCCTAACCCCTAAC	uc001loa.1	+							NM_145651	NP_663626	Q8TD33	SG1C1_HUMAN	secretoglobin, family 1C, member 1 precursor							extracellular region	binding			skin(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		ctaaccctaaccctaacccctaacccctaaccct	0.075													3	4	---	---	---	---	
RPL27A	6157	broad.mit.edu	37	11	8702004	8702005	+	5'Flank	INS	-	G	G	rs146354873	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8702004_8702005insG	uc001mgs.3	+						uc001mgo.2_5'Flank	NM_000990	NP_000981	P46776	RL27A_HUMAN	ribosomal protein L27a						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0				Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		gaatgaaggcagggcactaagg	0.000													4	2	---	---	---	---	
ST5	6764	broad.mit.edu	37	11	8853059	8853060	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8853059_8853060delAC	uc001mgv.2	-						ST5_uc001mgw.1_Intron	NM_005418	NP_005409	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1						positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CCACTTCCAGACACACACACAC	0.465													4	2	---	---	---	---	
LYVE1	10894	broad.mit.edu	37	11	10588026	10588027	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10588026_10588027delAC	uc001miv.2	-						uc001miu.2_Intron|LYVE1_uc010rca.1_Intron	NM_006691	NP_006682	Q9Y5Y7	LYVE1_HUMAN	lymphatic vessel endothelial hyaluronan receptor						anatomical structure morphogenesis|cell-matrix adhesion|cellular component movement|response to wounding|transport	integral to plasma membrane|membrane fraction				central_nervous_system(1)|skin(1)	2				all cancers(16;7.22e-08)|Epithelial(150;1.03e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0609)		ACACACACAGACACACACACAC	0.386													4	2	---	---	---	---	
PARVA	55742	broad.mit.edu	37	11	12449150	12449151	+	Intron	INS	-	T	T	rs113337456		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12449150_12449151insT	uc001mki.2	+						PARVA_uc001mkh.2_Intron|PARVA_uc010rck.1_Intron	NM_018222	NP_060692	Q9NVD7	PARVA_HUMAN	parvin, alpha						cell adhesion|cell junction assembly|cilium morphogenesis	actin cytoskeleton|cytosol|focal adhesion	actin binding			breast(3)	3				Epithelial(150;0.00624)		tacaacagacatttttttttaa	0.079													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	13917892	13917893	+	IGR	DEL	GT	-	-	rs72232591		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13917892_13917893delGT								FAR1 (164001 upstream) : SPON1 (66021 downstream)																							gtgtgcatgagtgtgtgtgtgt	0.158													6	3	---	---	---	---	
PRMT3	10196	broad.mit.edu	37	11	20415987	20415988	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20415987_20415988insT	uc001mqb.2	+						PRMT3_uc001mqc.2_Intron|PRMT3_uc010rdn.1_Intron	NM_005788	NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3 isoform 1								zinc ion binding				0						CCTTAGGAATGTTTTTTTTTTC	0.188													3	3	---	---	---	---	
LUZP2	338645	broad.mit.edu	37	11	24849577	24849578	+	Intron	DEL	AC	-	-	rs71868703		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24849577_24849578delAC	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909	Q86TE4	LUZP2_HUMAN	leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2						TTTAGGAGAAacacacacacac	0.252													4	2	---	---	---	---	
ABTB2	25841	broad.mit.edu	37	11	34310300	34310304	+	Intron	DEL	CTCCT	-	-	rs140806969		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34310300_34310304delCTCCT	uc001mvl.1	-							NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing								DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				GCAGAAATCACTCCTCTCCTGGGTG	0.551													3	4	---	---	---	---	
PAMR1	25891	broad.mit.edu	37	11	35546637	35546637	+	Intron	DEL	T	-	-	rs111913054		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35546637delT	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						tattcctttctttctttccct	0.403													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	35583686	35583687	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35583686_35583687insT								PAMR1 (31838 upstream) : FJX1 (56048 downstream)																							GGAGCAGGGACTTTTTTTTGCT	0.391													4	2	---	---	---	---	
LDLRAD3	143458	broad.mit.edu	37	11	36115470	36115470	+	Intron	DEL	T	-	-	rs113152603		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36115470delT	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.1_Intron	NM_174902	NP_777562	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain							integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				aaggttaaagttgaagacacc	0.000													2	4	---	---	---	---	
LRRC4C	57689	broad.mit.edu	37	11	40158714	40158717	+	Intron	DEL	GTGT	-	-	rs71936348		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40158714_40158717delGTGT	uc001mxa.1	-						LRRC4C_uc001mxc.1_Intron|LRRC4C_uc001mxd.1_Intron|LRRC4C_uc001mxb.1_Intron	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)				ACGTGGGCACgtgtgtgtgtgtgt	0.255													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	41960792	41960793	+	IGR	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41960792_41960793delCA								LRRC4C (479469 upstream) : None (None downstream)																							Tacacacacgcacacacacaca	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43155421	43155422	+	IGR	INS	-	A	A	rs112722467		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43155421_43155422insA								None (None upstream) : API5 (178083 downstream)																							gactccgtttcaaaaaaaaaaa	0.218													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	47969956	47969956	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47969956delT								NUP160 (99899 upstream) : PTPRJ (32154 downstream)																							agagtcagaatttggactgga	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	50723058	50723058	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50723058delA								LOC646813 (343255 upstream) : OR4A5 (688390 downstream)																							tgaagtttttatgtgaagata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	55025910	55025910	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55025910delC								None (None upstream) : TRIM48 (3748 downstream)																							aatgcacacaccacaaagtag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	60096241	60096242	+	IGR	DEL	AG	-	-	rs34809259		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60096241_60096242delAG								MS4A4A (19797 upstream) : MS4A6E (6113 downstream)																							gggtagaagaagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	60935409	60935410	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60935409_60935410insA								VPS37C (6493 upstream) : PGA3 (35574 downstream)																							CTCAGGCTGCCAAAAAAAAAAG	0.124													4	2	---	---	---	---	
FTH1	2495	broad.mit.edu	37	11	61737542	61737542	+	5'Flank	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61737542delT	uc001nsu.2	-							NM_002032	NP_002023	P02794	FRIH_HUMAN	ferritin, heavy polypeptide 1						cell proliferation|cellular membrane organization|immune response|intracellular sequestering of iron ion|iron ion transport|negative regulation of cell proliferation|post-Golgi vesicle-mediated transport	cytosol|intracellular ferritin complex	ferric iron binding|ferroxidase activity|protein binding			ovary(1)	1					Iron Dextran(DB00893)	tgggacagtattttttttttt	0.000													4	2	---	---	---	---	
TTC9C	283237	broad.mit.edu	37	11	62500084	62500085	+	Intron	INS	-	A	A	rs63749207		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62500084_62500085insA	uc001nuy.2	+						TTC9C_uc001nux.2_Intron	NM_173810	NP_776171	Q8N5M4	TTC9C_HUMAN	tetratricopeptide repeat domain 9C								binding			ovary(1)|pancreas(1)	2						aactccgtctcaaaaaaaaaaa	0.010													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	62795735	62795735	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62795735delG								SLC22A8 (12424 upstream) : SLC22A24 (51679 downstream)																							CGGGCTGGGAGGGGGGCaggg	0.169													4	2	---	---	---	---	
C11orf95	65998	broad.mit.edu	37	11	63533335	63533337	+	In_Frame_Del	DEL	TCC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63533335_63533337delTCC	uc010rmv.1	-	2	598_600	c.579_581delGGA	c.(577-582)GAGGAA>GAA	p.193_194EE>E	C11orf95_uc001nxr.2_Intron|C11orf95_uc001nxs.2_In_Frame_Del_p.79_80EE>E	NM_001144936	NP_001138408	C9JLR9	CK095_HUMAN	hypothetical protein LOC65998	193_194	Glu-rich.					intracellular	zinc ion binding				0						ctcctcttcttcctcctcctcct	0.532													4	2	---	---	---	---	
C11orf84	144097	broad.mit.edu	37	11	63583241	63583241	+	Intron	DEL	T	-	-	rs111368092		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63583241delT	uc001nxt.2	+							NM_138471	NP_612480	Q9BUA3	CK084_HUMAN	hypothetical protein LOC144097												0						tggtcatggattttttttttt	0.000													4	2	---	---	---	---	
AIP	9049	broad.mit.edu	37	11	67247845	67247845	+	5'Flank	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67247845delT	uc001olv.2	+							NM_003977	NP_003968	O00170	AIP_HUMAN	aryl hydrocarbon receptor interacting protein						protein maturation by protein folding|protein targeting to mitochondrion	nucleus	signal transducer activity|transcription coactivator activity|transcription factor binding|unfolded protein binding				0						AAAAAAAttcttttttttttt	0.010									Familial_Isolated_Pituitary_Adenoma_				3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69405804	69405804	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69405804delA								MYEOV (249355 upstream) : CCND1 (50069 downstream)																							ctcacatgttaaaaaaaaaaa	0.005													4	2	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	69949370	69949371	+	Intron	INS	-	A	A	rs142425384	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69949370_69949371insA	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						CTGAGTTTTATAAAAAAAAAAC	0.545													2	4	---	---	---	---	
PPFIA1	8500	broad.mit.edu	37	11	70130603	70130604	+	Intron	INS	-	AGAC	AGAC	rs138935612	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70130603_70130604insAGAC	uc001opo.2	+						PPFIA1_uc001opn.1_Intron|PPFIA1_uc001opp.2_Intron	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b						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)			GTCAGTGGTAGAGACAGGGTCT	0.470													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71306151	71306153	+	IGR	DEL	TTT	-	-	rs34026937		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71306151_71306153delTTT								KRTAP5-11 (12230 upstream) : FAM86C (192404 downstream)																							AGTATGTGGATTTTTTTTTTTTT	0.207													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	81944016	81944016	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81944016delC	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																		tcctcctcctcctcctccACC	0.294													4	2	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83319751	83319752	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83319751_83319752delAC	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_uc010rsw.1_Intron|DLG2_uc010rsx.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)				ATAAATCAGGacacacacacac	0.114													4	2	---	---	---	---	
FAT3	120114	broad.mit.edu	37	11	92232890	92232891	+	Intron	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92232890_92232891delTG	uc001pdj.3	+							NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3						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)				tgtgtgtgtatgtgtgtgtgtg	0.208										TCGA Ovarian(4;0.039)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93750236	93750236	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93750236delG								C11orf90 (166568 upstream) : HEPHL1 (4142 downstream)																							aaaaccttctggaaataattc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	94486473	94486473	+	IGR	DEL	T	-	-	rs2015017		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94486473delT								PIWIL4 (131887 upstream) : AMOTL1 (15035 downstream)																							GCTTTCCTGCTTTTTTTTTTT	0.234													5	3	---	---	---	---	
CWC15	51503	broad.mit.edu	37	11	94696474	94696475	+	3'UTR	INS	-	A	A	rs140103829	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94696474_94696475insA	uc001pfd.3	-	8						NM_016403	NP_057487	Q9P013	CWC15_HUMAN	CWC15 homolog						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CAGGGGAAAAGAAAAAAAAAAC	0.307													3	4	---	---	---	---	
ENDOD1	23052	broad.mit.edu	37	11	94823634	94823635	+	Intron	INS	-	T	T	rs143522584		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94823634_94823635insT	uc001pfh.2	+							NM_015036	NP_055851	O94919	ENDD1_HUMAN	endonuclease domain containing 1 precursor							extracellular region	endonuclease activity|metal ion binding|nucleic acid binding				0		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				ATGAGCTGCAGGGCGGGAGGTC	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	97511258	97511258	+	IGR	DEL	A	-	-	rs57290777		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97511258delA								None (None upstream) : None (None downstream)																							atcattcaggacataggcatt	0.000													3	3	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	103130763	103130763	+	Intron	DEL	A	-	-	rs58492880		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103130763delA	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GATTTAACGTAATATTTATAG	0.269													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	103645762	103645762	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103645762delG								DYNC2H1 (295171 upstream) : PDGFD (132153 downstream)																							TATCTGAGAAGATTGCAGTTA	0.423													4	2	---	---	---	---	
ZBTB16	7704	broad.mit.edu	37	11	114106514	114106514	+	Intron	DEL	T	-	-	rs2511238		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114106514delT	uc001pop.2	+						ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		ttccttcTCCTTTTTTTTTTT	0.194													4	2	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117610512	117610512	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117610512delG	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TAGCTGCAATGGGCAAATCTG	0.383													3	4	---	---	---	---	
C2CD2L	9854	broad.mit.edu	37	11	118984224	118984225	+	Intron	DEL	CT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118984224_118984225delCT	uc001pvo.2	+						C2CD2L_uc001pvn.2_Intron	NM_014807	NP_055622	O14523	C2C2L_HUMAN	transmembrane protein 24							integral to membrane					0						CATTCTTGCCCTCTGAGTCACC	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	121202420	121202420	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121202420delA								SC5DL (18303 upstream) : SORL1 (120541 downstream)																							tgtctctaccaaaaaaaaaaa	0.000													4	3	---	---	---	---	
UBASH3B	84959	broad.mit.edu	37	11	122597058	122597058	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122597058delT	uc001pyi.3	+							NM_032873	NP_116262	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing,							cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		cttcttcttcttttttttttt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129216250	129216251	+	IGR	INS	-	A	A	rs36009298		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129216250_129216251insA								ARHGAP32 (154157 upstream) : BARX2 (29630 downstream)																							agataactggtaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129448339	129448339	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129448339delC								BARX2 (126166 upstream) : TMEM45B (237402 downstream)																							GAAGCGACCTCCCCTCCTTGC	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	129576737	129576738	+	IGR	INS	-	CA	CA	rs145544583	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129576737_129576738insCA								BARX2 (254564 upstream) : TMEM45B (109003 downstream)																							ATGCGCTCATGcacacacacac	0.064													3	3	---	---	---	---	
C12orf5	57103	broad.mit.edu	37	12	4432269	4432270	+	Intron	DEL	AA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4432269_4432270delAA	uc001qmp.2	+							NM_020375	NP_065108	Q9NQ88	TIGAR_HUMAN	TP53-induced glycolysis and apoptosis regulator							intracellular	fructose-2,6-bisphosphate 2-phosphatase activity			skin(1)	1			all cancers(3;1.15e-07)|Colorectal(7;0.00165)|OV - Ovarian serous cystadenocarcinoma(31;0.00596)|COAD - Colon adenocarcinoma(12;0.0229)|GBM - Glioblastoma multiforme(3;0.0266)|STAD - Stomach adenocarcinoma(119;0.206)			tcctctctacaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
KCNA6	3742	broad.mit.edu	37	12	4936366	4936370	+	Intron	DEL	CCTTC	-	-	rs12316421		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4936366_4936370delCCTTC	uc001qng.2	+							NM_002235	NP_002226	P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(2)|ovary(1)	3						ttccttccttccttccctccttcct	0.010										HNSCC(72;0.22)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	6291666	6291666	+	IGR	DEL	G	-	-	rs68072398		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6291666delG								VWF (57830 upstream) : CD9 (17207 downstream)																							CAGGATGGGCGGGGGAAGGAC	0.637													3	5	---	---	---	---	
LRP6	4040	broad.mit.edu	37	12	12408237	12408238	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12408237_12408238insA	uc001rah.3	-						LRP6_uc010shl.1_Intron	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)				gctgactgcagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	12760296	12760296	+	IGR	DEL	T	-	-	rs34961324		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12760296delT								DUSP16 (44979 upstream) : CREBL2 (4535 downstream)																							GCAGCAATAATTACTCTTTTG	0.383													3	6	---	---	---	---	
DDX47	51202	broad.mit.edu	37	12	12961892	12961893	+	Intron	INS	-	TT	TT	rs138849119		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12961892_12961893insTT	uc001rav.2	+							NM_016355	NP_057439	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47							nucleolus|nucleolus	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding				0		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		AGAGACTTGGCttttttttttt	0.203													4	2	---	---	---	---	
GSG1	83445	broad.mit.edu	37	12	13256065	13256065	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13256065delC	uc001rbn.2	-						GSG1_uc001rbo.2_Intron|GSG1_uc001rbp.2_Intron|GSG1_uc001rbq.1_Intron	NM_001080555	NP_001074024	Q2KHT4	GSG1_HUMAN	germ cell associated 1 isoform 4							endoplasmic reticulum membrane|integral to membrane					0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		GGGAATAATGCAGATGAAAGG	0.478													4	2	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	13892669	13892669	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13892669delG	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)	TTTTGGAACTGGGCTGAATTT	0.453											OREG0021692	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	16458861	16458861	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16458861delC								DERA (268547 upstream) : MGST1 (41215 downstream)																							acaccacccaccaccctgaca	0.000													4	2	---	---	---	---	
ITPR2	3709	broad.mit.edu	37	12	26493926	26493927	+	Intron	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26493926_26493927delTG	uc001rhg.2	-							NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					GTAGGTGTTTTGTGTGTGTGTG	0.416													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	29946795	29946796	+	IGR	INS	-	AC	AC	rs145392899	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29946795_29946796insAC								TMTC1 (9103 upstream) : IPO8 (835127 downstream)																							ACATGCTTACTATAGTTGCAAC	0.257													3	6	---	---	---	---	
DENND5B	160518	broad.mit.edu	37	12	31555178	31555181	+	Intron	DEL	AGTA	-	-	rs67565625		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31555178_31555181delAGTA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2						ccctgaaaataGTAGGAGAAGACC	0.289													3	3	---	---	---	---	
PRICKLE1	144165	broad.mit.edu	37	12	42976951	42976952	+	Intron	DEL	GT	-	-	rs148361094		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42976951_42976952delGT	uc001rnm.2	-						PRICKLE1_uc009zka.2_Intron	NM_153026	NP_694571	Q96MT3	PRIC1_HUMAN	prickle homolog 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		AGATTGAAACgtgtgtgtgtgt	0.292													4	2	---	---	---	---	
ADAMTS20	80070	broad.mit.edu	37	12	43935569	43935569	+	Intron	DEL	G	-	-	rs75747861		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43935569delG	uc010skx.1	-							NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TAAGGgttttgttttgttttg	0.284													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48226926	48226941	+	IGR	DEL	GTGTGCGCGCGCGCGC	-	-	rs56179729	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48226926_48226941delGTGTGCGCGCGCGCGC								HDAC7 (13163 upstream) : VDR (8381 downstream)																							gtgtgtgtgtgtgtgcgcgcgcgcgcgtgcgcgcgc	0.412													6	3	---	---	---	---	
DDX23	9416	broad.mit.edu	37	12	49239922	49239923	+	Intron	INS	-	T	T	rs142401519	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49239922_49239923insT	uc001rsm.2	-							NM_004818	NP_004809	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)|skin(1)	6						tagctaatttattttttttata	0.000													4	3	---	---	---	---	
KRT85	3891	broad.mit.edu	37	12	52760516	52760517	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52760516_52760517delAC	uc001sag.2	-							NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85						epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		acacaccgctacacacacacac	0.149													4	2	---	---	---	---	
KRT8	3856	broad.mit.edu	37	12	53328020	53328021	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53328020_53328021insA	uc009zml.1	-						KRT8_uc009zmm.1_Intron	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ctcagaaaaggaaaaaaaataa	0.000													4	2	---	---	---	---	
SP1	6667	broad.mit.edu	37	12	53806715	53806716	+	3'UTR	DEL	TG	-	-	rs139677198		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53806715_53806716delTG	uc001scw.2	+	6					SP1_uc010sog.1_3'UTR	NM_138473	NP_612482	P08047	SP1_HUMAN	Sp1 transcription factor isoform a						positive regulation by host of viral transcription|positive regulation of transcription from RNA polymerase II promoter	cytoplasm	double-stranded DNA binding|histone deacetylase binding|HMG box domain binding|protein C-terminus binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(357;0.00527)		AAAATAGCTCtgtgtgtgtgtg	0.327													3	4	---	---	---	---	
FLJ12825	440101	broad.mit.edu	37	12	54502132	54502133	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54502132_54502133delAC	uc001sey.2	+							NR_026655				Homo sapiens cDNA FLJ12825 fis, clone NT2RP2002800.												0						ATCAGGTTAGacacacacacac	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	59723712	59723713	+	IGR	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59723712_59723713delCA								LRIG3 (409450 upstream) : SLC16A7 (266135 downstream)																							CTCTCTCTTGCACACACACACA	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	61618980	61618981	+	IGR	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61618980_61618981delTG								None (None upstream) : FAM19A2 (483062 downstream)																							tatgtgtgtttgtgtgtgtgtg	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	63670141	63670141	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63670141delT								AVPR1A (123551 upstream) : DPY19L2 (282552 downstream)																							CTAGCTCTTCTTTTTTTTTTG	0.353													4	3	---	---	---	---	
GNS	2799	broad.mit.edu	37	12	65133389	65133389	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65133389delA	uc001ssg.3	-						GNS_uc001ssf.2_Intron|GNS_uc010ssq.1_Intron|GNS_uc010ssr.1_Intron	NM_002076	NP_002067	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase precursor							lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		aCCCCCGTTTAAAAAAAAAAA	0.348													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70472447	70472448	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70472447_70472448insT								RAB3IP (255465 upstream) : CNOT2 (164329 downstream)																							TGCATATTCTCTTTTTTTGGAC	0.327													4	2	---	---	---	---	
LOC283392	283392	broad.mit.edu	37	12	72666481	72666483	+	Intron	DEL	AAG	-	-	rs111457826		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72666481_72666483delAAG	uc010stv.1	-						TRHDE_uc001sxa.2_5'Flank	NR_026836				Homo sapiens thyrotropin-releasing hormone degrading enzyme, mRNA (cDNA clone IMAGE:4992272).												0						gaagaagaaaaagaagaggaaga	0.488													4	3	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78237178	78237179	+	Intron	DEL	TG	-	-	rs113904325		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78237178_78237179delTG	uc001syp.2	+						NAV3_uc001syo.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						GTTAATCATTtgtgtgtgtgtg	0.272										HNSCC(70;0.22)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	79225308	79225311	+	IGR	DEL	GATA	-	-	rs72005288		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79225308_79225311delGATA								NAV3 (618520 upstream) : SYT1 (32462 downstream)																							atagatagatgatagatagatgat	0.147													4	4	---	---	---	---	
LRRIQ1	84125	broad.mit.edu	37	12	85459090	85459090	+	Frame_Shift_Del	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85459090delG	uc001tac.2	+	9	2553	c.2442delG	c.(2440-2442)CTGfs	p.L814fs	LRRIQ1_uc001tab.1_Frame_Shift_Del_p.L814fs	NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	814										ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)		TCTCCACACTGGCAGAGTGTA	0.388													39	21	---	---	---	---	
CEP290	80184	broad.mit.edu	37	12	88530707	88530707	+	Intron	DEL	T	-	-	rs112841615		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88530707delT	uc001tar.2	-						CEP290_uc009zsl.1_Intron	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						GCTTAAGAACTTTTTTTTTTT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91037938	91037938	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91037938delT								LOC338758 (932210 upstream) : C12orf12 (308055 downstream)																							TACTTTTACATTTGCATGGGA	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	91072865	91072866	+	IGR	INS	-	AA	AA	rs146634153	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91072865_91072866insAA								LOC338758 (967137 upstream) : C12orf12 (273127 downstream)																							caaattctcttctctaccttga	0.054													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	93412228	93412229	+	IGR	INS	-	T	T	rs147284938		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93412228_93412229insT								EEA1 (89121 upstream) : NUDT4 (359472 downstream)																							accatgctaacttttttttttt	0.000													4	2	---	---	---	---	
CRADD	8738	broad.mit.edu	37	12	94232333	94232334	+	Intron	DEL	TC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94232333_94232334delTC	uc001tda.2	+						CRADD_uc010sur.1_Intron|CRADD_uc010sus.1_Intron	NM_003805	NP_003796	P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1						CTTCTCTCTTTCTCTCTCTTTT	0.178													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	97457792	97457792	+	IGR	DEL	G	-	-	rs80163813		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97457792delG								NEDD1 (110331 upstream) : RMST (401007 downstream)																							ttcaggtagaggcaacagcat	0.010													4	2	---	---	---	---	
CCDC53	51019	broad.mit.edu	37	12	102439758	102439758	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102439758delA	uc010svw.1	-						CCDC53_uc010svx.1_Intron|CCDC53_uc010svy.1_Intron|CCDC53_uc010svz.1_Intron	NM_016053	NP_057137	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53							WASH complex	protein binding				0						AAATGCAATGAAAATTAAGTA	0.308													4	2	---	---	---	---	
IGF1	3479	broad.mit.edu	37	12	102869159	102869159	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102869159delG	uc001tjp.3	-						IGF1_uc001tjn.2_Intron|IGF1_uc001tjm.2_Intron|IGF1_uc001tjo.2_Intron	NM_001111285	NP_001104755	P05019	IGF1_HUMAN	insulin-like growth factor 1 isoform 3						anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2						ATAGTGAGGTGGATCATAATA	0.383													4	3	---	---	---	---	
BTBD11	121551	broad.mit.edu	37	12	108031564	108031569	+	Intron	DEL	TGTGTG	-	-	rs72303396		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108031564_108031569delTGTGTG	uc001tmk.1	+						BTBD11_uc001tmj.2_Intron|BTBD11_uc001tml.1_Intron|BTBD11_uc001tmm.1_Intron	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3						gcacTGATTTtgtgtgtgtgtgtgtg	0.136													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108417920	108417921	+	IGR	INS	-	T	T	rs141636596	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108417920_108417921insT								ASCL4 (247500 upstream) : WSCD2 (105590 downstream)																							GCTTTTAGTGGTTTCTGGTATT	0.347													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	109159393	109159393	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109159393delG								CORO1C (34098 upstream) : SSH1 (17074 downstream)																							AGCAGCCAGTGGCCATCTCCA	0.617													4	2	---	---	---	---	
CUX2	23316	broad.mit.edu	37	12	111704837	111704837	+	Intron	DEL	A	-	-	rs112232121	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111704837delA	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						ctgtctctacaaaaaaaatac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	112068917	112068917	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112068917delA								ATXN2 (31437 upstream) : BRAP (11034 downstream)																							actctatctcaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116338993	116338994	+	IGR	DEL	TC	-	-	rs77579617		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116338993_116338994delTC								None (None upstream) : MED13L (57389 downstream)																							tttttccctgtcttatcctgtc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	120398136	120398136	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120398136delT								CIT (83044 upstream) : CCDC64 (29512 downstream)																							ggccggctaattttttttgta	0.000													4	2	---	---	---	---	
MLXIP	22877	broad.mit.edu	37	12	122523846	122523847	+	Intron	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122523846_122523847delTT	uc001ubq.2	+							NM_014938	NP_055753	Q9HAP2	MLXIP_HUMAN	MLX interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial outer membrane|nucleus	DNA binding			ovary(2)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		tctactgaccttaacataggga	0.000													4	2	---	---	---	---	
PITPNM2	57605	broad.mit.edu	37	12	123480901	123480901	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123480901delT	uc001uej.1	-						PITPNM2_uc001uek.1_Intron	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,						metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		TTCTGCTTGGTGGACACAGCC	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	124522577	124522577	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124522577delA								ZNF664 (22610 upstream) : FAM101A (251133 downstream)																							gagactccggaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	126602284	126602284	+	IGR	DEL	A	-	-	rs75314807	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126602284delA								TMEM132B (458695 upstream) : LOC100128554 (324743 downstream)																							AGCATTACACATGGACATGGA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127704620	127704622	+	IGR	DEL	TCT	-	-	rs141390414		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127704620_127704622delTCT								LOC100128554 (747290 upstream) : None (None downstream)																							agtttccttgtcttcttcttctc	0.000													3	3	---	---	---	---	
GLT1D1	144423	broad.mit.edu	37	12	129339579	129339579	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129339579delC	uc001uhx.1	+						GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270	Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		GTTGGATGAACCAGCATCCCA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19240492	19240492	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19240492delC								None (None upstream) : LOC284232 (168051 downstream)																							CCTTGTTGATCCGGGAGCGCA	0.597													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19320620	19320620	+	5'Flank	DEL	T	-	-	rs113823012		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19320620delT	uc001ulv.1	-											DQ586768																		taggcctcactgaccaagtcc	0.139													2	4	---	---	---	---	
ZMYM2	7750	broad.mit.edu	37	13	20602949	20602949	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20602949delT	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc010tco.1_Intron|ZMYM2_uc001umv.2_Intron|ZMYM2_uc001umw.2_Intron	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		tgcaatcatcttttttttttt	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21935625	21935626	+	IGR	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21935625_21935626delTT								MRP63 (182407 upstream) : ZDHHC20 (14884 downstream)																							GTTCTAGGGCTTTTTTTTTTCT	0.406													4	2	---	---	---	---	
HMGB1	3146	broad.mit.edu	37	13	31086078	31086078	+	Intron	DEL	T	-	-	rs35026251		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31086078delT	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)		CTGATTCTTCTTTGTGGGGGC	0.423													3	4	---	---	---	---	
C13orf23	80209	broad.mit.edu	37	13	39598699	39598699	+	Intron	DEL	A	-	-	rs72207318		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39598699delA	uc001uwy.2	-						C13orf23_uc001uwz.2_Intron	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1											ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)		GTTCCCTATTAAAAAAAAAAA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	45428653	45428653	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45428653delC								TSC22D1 (277952 upstream) : NUFIP1 (84731 downstream)																							TCAACATTCTCCCTCTCTTAT	0.453													4	2	---	---	---	---	
CPB2	1361	broad.mit.edu	37	13	46674620	46674620	+	Intron	DEL	T	-	-	rs11359529		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46674620delT	uc001vaw.2	-						uc001vau.1_RNA|uc001vav.1_RNA|CPB2_uc001vax.2_Intron	NM_001872	NP_001863	Q96IY4	CBPB2_HUMAN	plasma carboxypeptidase B2 isoform a						blood coagulation|fibrinolysis|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		gatttgtgaattttttttttt	0.005													4	2	---	---	---	---	
LRCH1	23143	broad.mit.edu	37	13	47211848	47211848	+	Intron	DEL	T	-	-	rs67739248		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47211848delT	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		cacttcgtagttttttttttc	0.000													4	2	---	---	---	---	
DLEU1	10301	broad.mit.edu	37	13	51091105	51091106	+	Intron	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51091105_51091106delTG	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						tgtgcacatttgtgtgtgtgtg	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51687703	51687704	+	IGR	DEL	TG	-	-	rs66568876		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51687703_51687704delTG								GUCY1B2 (32705 upstream) : FAM124A (108803 downstream)																							AAGTGTATTTtgtgtgtgtgtg	0.198													4	2	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52840286	52840286	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52840286delA	uc001vgm.1	-											Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						actccatctcaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	59709829	59709830	+	IGR	INS	-	CCCCCTA	CCCCCTA	rs138050394	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59709829_59709830insCCCCCTA								None (None upstream) : DIAPH3 (529895 downstream)																							TGGCACATAAGCCTTACTCAGC	0.446													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	63635859	63635859	+	IGR	DEL	T	-	-	rs67758040		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63635859delT								None (None upstream) : OR7E156P (675709 downstream)																							TATTTATTACTTTTTTTAAAA	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71741626	71741627	+	IGR	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71741626_71741627delAC								None (None upstream) : DACH1 (270471 downstream)																							acacacagaaacacacacacaC	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73209462	73209462	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73209462delG								DACH1 (768132 upstream) : C13orf37 (73033 downstream)																							aatttactaaggggttgccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75260139	75260139	+	IGR	DEL	A	-	-	rs112331922		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75260139delA								KLF12 (551745 upstream) : LOC647288 (551751 downstream)																							caaaaaaaacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
SLAIN1	122060	broad.mit.edu	37	13	78321725	78321725	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78321725delG	uc010thy.1	+						SLAIN1_uc001vkk.1_Intron|SLAIN1_uc001vkl.1_Intron|SLAIN1_uc010thz.1_Intron|SLAIN1_uc010aex.1_Intron|SLAIN1_uc010aey.1_Intron|SLAIN1_uc001vkm.2_Intron	NM_144595	NP_653196	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1 B											ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)		CACAGAGTGAGGTTGTAAGCA	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	79050916	79050916	+	Intron	DEL	A	-	-	rs36059502		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79050916delA	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																		GTTCAAGGAGAAAAAAAAAAA	0.393													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	82265214	82265214	+	IGR	DEL	A	-	-	rs34280872		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82265214delA								None (None upstream) : None (None downstream)																							GAGTTGTTCTAAAAAAAAAAA	0.174													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	86214184	86214184	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86214184delG								None (None upstream) : SLITRK6 (152738 downstream)																							GGCTTTTATAGGATTTCTTTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	95311368	95311369	+	IGR	DEL	AG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95311368_95311369delAG								GPR180 (29424 upstream) : SOX21 (50513 downstream)																							TACATAGTTCagagagagagag	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106337720	106337721	+	IGR	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106337720_106337721delGT								DAOA (194338 upstream) : EFNB2 (804377 downstream)																							TCCTATCTGGGTGTGTGTGTGT	0.376													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106943327	106943330	+	IGR	DEL	AGAG	-	-	rs831915	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106943327_106943330delAGAG								DAOA (799945 upstream) : EFNB2 (198768 downstream)																							aggaaggaaaagagggagagaggg	0.000													4	2	---	---	---	---	
ARHGEF7	8874	broad.mit.edu	37	13	111877859	111877860	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111877859_111877860insT	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Intron|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron|ARHGEF7_uc010tjo.1_Intron	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			ttgtttttttgttttttttttt	0.144													4	2	---	---	---	---	
CUL4A	8451	broad.mit.edu	37	13	113902450	113902453	+	Intron	DEL	TAAG	-	-	rs112437453		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113902450_113902453delTAAG	uc010tjy.1	+						CUL4A_uc010tjx.1_Intron|CUL4A_uc010agu.2_Intron|CUL4A_uc010tjz.1_Intron	NM_001008895	NP_001008895	Q13619	CUL4A_HUMAN	cullin 4A isoform 1						cell cycle arrest|DNA repair|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	ubiquitin protein ligase binding			central_nervous_system(2)|skin(1)	3	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;0.112)			ttgtaatcactaagtaatctgtga	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	114440888	114440891	+	IGR	DEL	TCCT	-	-	rs36177381		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114440888_114440891delTCCT								GRK1 (2252 upstream) : LOC100130386 (10593 downstream)																							CCACTCTTTCtccttccttccttc	0.304													6	4	---	---	---	---	
CDC16	8881	broad.mit.edu	37	13	115020863	115020863	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115020863delT	uc001vuk.1	+						CDC16_uc001vul.1_Intron|CDC16_uc001vum.1_Intron|CDC16_uc001vun.1_Intron|CDC16_uc001vuo.1_Intron	NM_003903	NP_003894	Q13042	CDC16_HUMAN	anaphase-promoting complex, subunit 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|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|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			ccgcttcctattacactgtta	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19012414	19012415	+	IGR	DEL	TA	-	-	rs113187065		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19012414_19012415delTA								None (None upstream) : OR11H12 (365179 downstream)																							tgttcaactctatatgagttga	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19040400	19040400	+	IGR	DEL	T	-	-	rs113500961		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19040400delT								None (None upstream) : OR11H12 (337194 downstream)																							ggttcaactctgtgagttgaa	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21185719	21185720	+	IGR	INS	-	C	C	rs142440729	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21185719_21185720insC								RNASE4 (16962 upstream) : EDDM3A (14140 downstream)																							tgaaacctcagcccccacacca	0.000													2	4	---	---	---	---	
DHRS4L1	728635	broad.mit.edu	37	14	24507240	24507240	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24507240delA	uc010alc.2	+						DHRS4L1_uc010tnu.1_Intron	NM_001082488	NP_001075957	P0CG22	DR4L1_HUMAN	dehydrogenase/reductase (SDR family) member 4								binding|oxidoreductase activity				0						CAGTGATGTTAACTAAAACAT	0.468													4	2	---	---	---	---	
DCAF11	80344	broad.mit.edu	37	14	24584376	24584376	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24584376delT	uc001wlv.2	+						NRL_uc001wlq.2_5'Flank|DCAF11_uc001wlw.2_5'UTR|DCAF11_uc001wlz.2_5'UTR|DCAF11_uc001wly.2_5'UTR|DCAF11_uc001wme.2_5'Flank|DCAF11_uc010tny.1_5'Flank|DCAF11_uc001wmd.2_5'Flank|DCAF11_uc001wmc.2_5'Flank|DCAF11_uc001wmb.3_5'Flank|DCAF11_uc001wma.3_5'Flank	NM_001163484	NP_001156956	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11 isoform 1							CUL4 RING ubiquitin ligase complex	protein binding				0						TTCTAATTGGTTAGATGAGAT	0.537													4	2	---	---	---	---	
NOVA1	4857	broad.mit.edu	37	14	26923374	26923374	+	Intron	DEL	A	-	-	rs76289069	byFrequency	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26923374delA	uc001wpy.2	-						NOVA1_uc001wpz.2_Intron|NOVA1_uc001wqa.2_Intron	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1						locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)		aaatgcaaagaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	30840135	30840135	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30840135delT								PRKD1 (443236 upstream) : G2E3 (188194 downstream)																							ATGTTCTCCATTTTTTACCTC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	31243280	31243280	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31243280delT								SCFD1 (38262 upstream) : COCH (100461 downstream)																							GGTTTCTTGATTTTTTTCTGG	0.388													4	3	---	---	---	---	
HECTD1	25831	broad.mit.edu	37	14	31647112	31647112	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31647112delT	uc001wrc.1	-							NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		tttttagaaattttttttttt	0.318													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	32674329	32674329	+	IGR	DEL	T	-	-	rs33970411		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32674329delT								ARHGAP5 (45397 upstream) : AKAP6 (124150 downstream)																							TCCAATCACGTTTTTTTTTAG	0.299													4	3	---	---	---	---	
SNX6	58533	broad.mit.edu	37	14	35039579	35039580	+	Intron	INS	-	T	T	rs147036265		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35039579_35039580insT	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)		gtcttaccagcttttttttttt	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35821751	35821752	+	IGR	INS	-	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35821751_35821752insG								KIAA0391 (35078 upstream) : NFKBIA (48965 downstream)																							GAATGGAGGCTGGGGGGCAATG	0.579													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	39323375	39323376	+	Intron	INS	-	ACAC	ACAC	rs139580923	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39323375_39323376insACAC	uc001wun.2	-						uc001wuo.2_Intron					Homo sapiens cDNA FLJ43028 fis, clone BRTHA3000297.																		CTCTCTCTCTTacacacacaca	0.446													4	3	---	---	---	---	
LRFN5	145581	broad.mit.edu	37	14	42171665	42171668	+	Intron	DEL	TTTG	-	-	rs67033957		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42171665_42171668delTTTG	uc001wvm.2	+						LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III							integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TGGTGAAGGttttgtttgtttgtt	0.181										HNSCC(30;0.082)			3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	45165191	45165191	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45165191delA								FSCB (188692 upstream) : C14orf28 (201316 downstream)																							tcctaacatcacaattaaaag	0.000													4	2	---	---	---	---	
MDGA2	161357	broad.mit.edu	37	14	47776920	47776922	+	Intron	DEL	GAA	-	-	rs72179606		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47776920_47776922delGAA	uc001wwj.3	-						MDGA2_uc001wwi.3_Intron|MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						AAAAAAATATGAAGATTTGAAGA	0.251													4	2	---	---	---	---	
SOS2	6655	broad.mit.edu	37	14	50670809	50670810	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50670809_50670810insT	uc001wxs.3	-						SOS2_uc010tql.1_Intron	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					gttgttctaagttttttttttt	0.030													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51427983	51427984	+	IGR	INS	-	A	A	rs146708481	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51427983_51427984insA								PYGL (16735 upstream) : TRIM9 (13998 downstream)																							gactctgtctcaaaaaaaaaag	0.099													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51905598	51905599	+	IGR	INS	-	A	A	rs142716401	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51905598_51905599insA								TMX1 (181228 upstream) : FRMD6 (50256 downstream)																							ACTGGCTATGTAAAATGTGGCC	0.411													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	58133428	58133429	+	IGR	INS	-	T	T	rs143372288		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58133428_58133429insT								SLC35F4 (69813 upstream) : C14orf37 (337380 downstream)																							AAAGGAACTTCTTTTTTTTTTT	0.233													3	3	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58540316	58540317	+	Intron	INS	-	A	A	rs142586195	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58540316_58540317insA	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						ACTTCACTGGGAAAAAAAAATA	0.342													4	2	---	---	---	---	
PPP2R5E	5529	broad.mit.edu	37	14	63960201	63960202	+	Intron	INS	-	GT	GT	rs147393671	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63960201_63960202insGT	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237	Q16537	2A5E_HUMAN	epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		ACCGCGCGCGCGTGTGTGTGTG	0.317													2	5	---	---	---	---	
SPTB	6710	broad.mit.edu	37	14	65266041	65266043	+	Intron	DEL	AAG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65266041_65266043delAAG	uc001xht.2	-						SPTB_uc001xhr.2_Intron|SPTB_uc001xhs.2_Intron|SPTB_uc001xhu.2_Intron	NM_000347	NP_000338	P11277	SPTB1_HUMAN	spectrin beta isoform b						actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GGGAGAGAAAAAGAAGGATGAAC	0.532													3	3	---	---	---	---	
UPF0639	400224	broad.mit.edu	37	14	69991737	69991737	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69991737delG	uc010ttf.1	+							NM_001161498	NP_001154970	B9EJC2	B9EJC2_HUMAN	similar to pleckstrin homology domain protein												0						ttctctgcttggagaacttct	0.000													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79679969	79679969	+	Intron	DEL	G	-	-	rs75083405		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79679969delG	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)		CTTTTTTTTTGGGGGGGGGTG	0.433													4	2	---	---	---	---	
STON2	85439	broad.mit.edu	37	14	81758713	81758713	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81758713delG	uc010tvu.1	-						STON2_uc001xvk.1_Intron	NM_033104	NP_149095	Q8WXE9	STON2_HUMAN	stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)		cttgacCCATGCCAGGtgata	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88836910	88836910	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88836910delC								KCNK10 (43654 upstream) : SPATA7 (15102 downstream)																							cctagtgcctcctgacagaga	0.000													4	2	---	---	---	---	
FOXN3	1112	broad.mit.edu	37	14	90059526	90059526	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90059526delA	uc001xxo.3	-						FOXN3_uc010atk.2_Intron|FOXN3_uc001xxp.2_Intron	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3						aggagggaggaaggaaggagg	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	93158367	93158367	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93158367delG								RIN3 (3035 upstream) : LGMN (11790 downstream)																							ctgggggttagggctgcgaca	0.224													4	2	---	---	---	---	
WDR25	79446	broad.mit.edu	37	14	100886649	100886650	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100886649_100886650insT	uc010avx.2	+						WDR25_uc001yhm.2_Intron|WDR25_uc001yhn.2_Intron|WDR25_uc010avy.2_Intron|WDR25_uc001yho.2_Intron	NM_001161476	NP_001154948	Q64LD2	WDR25_HUMAN	WD repeat domain 25												0		Melanoma(154;0.212)				TTGTAAGCACATTTTTTTTTTA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	104811970	104811970	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104811970delG								KIF26A (164736 upstream) : C14orf180 (234086 downstream)																							TTTCCAAAGAGGGCACCCAAG	0.592													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	105369790	105369790	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105369790delC								KIAA0284 (6704 upstream) : PLD4 (21397 downstream)																							tgtttcttctctgctgctctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	105468278	105468278	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105468278delA								C14orf79 (6423 upstream) : CDCA4 (7632 downstream)																							actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107032793	107032794	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107032793_107032794insT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						cagcttcctgctttttcagaaa	0.079													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107127417	107127418	+	Intron	DEL	AT	-	-	rs142028166		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107127417_107127418delAT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						GAAAGAAAAGATAGAGATCCCA	0.406													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20016203	20016203	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20016203delC								None (None upstream) : GOLGA6L6 (720891 downstream)																							gcagatcctacaaaaagagtt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20110539	20110540	+	IGR	INS	-	AT	AT			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20110539_20110540insAT								None (None upstream) : GOLGA6L6 (626554 downstream)																							TTTTTATGCAAATATATATATA	0.262													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20558347	20558348	+	IGR	DEL	TT	-	-	rs3041773		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20558347_20558348delTT								None (None upstream) : GOLGA6L6 (178746 downstream)																							tgggaggcaatttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20602019	20602020	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20602019_20602020insA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																		TTTTTAGACATAAAATATGGGT	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20866888	20866889	+	IGR	INS	-	A	A	rs148671060		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20866888_20866889insA								GOLGA8C (85862 upstream) : BCL8 (3167 downstream)																							ATCACCAACTGAAAAAAAACGA	0.332													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21925810	21925811	+	IGR	DEL	GC	-	-	rs140368944		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21925810_21925811delGC								NF1P1 (791185 upstream) : LOC646214 (6703 downstream)																							gcgcgcgcgtgCGCGCGCACGC	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23163381	23163382	+	IGR	INS	-	A	A	rs140902706		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23163381_23163382insA								NIPA1 (76538 upstream) : WHAMML1 (24349 downstream)																							ctgtgtgtaccaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23685218	23685220	+	IGR	DEL	CTC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23685218_23685220delCTC								GOLGA8E (236795 upstream) : MKRN3 (125234 downstream)																							cccgcatcttctcctcctgctcc	0.000													3	3	---	---	---	---	
SNORD116-4	100033416	broad.mit.edu	37	15	25344465	25344465	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25344465delG	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-28_uc001yxy.2_Intron|IPW_uc001yyb.3_Intron|uc001yyd.2_Intron|SNORD116-26_uc001yyl.2_5'Flank|SNORD116-27_uc001yym.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0						TTTCCTCTTAGGGAATCATAA	0.473													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	26364141	26364141	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26364141delG	uc001zay.2	+											Homo sapiens hypothetical LOC503519, mRNA (cDNA clone IMAGE:5271234).																		ACAGCCATTTGGGATGCTCAC	0.512													4	2	---	---	---	---	
C15orf41	84529	broad.mit.edu	37	15	36895416	36895417	+	Intron	INS	-	C	C	rs144620263	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36895416_36895417insC	uc001zje.3	+						C15orf41_uc001zjd.2_Intron|C15orf41_uc010bbb.1_Intron|C15orf41_uc001zjf.2_Intron	NM_001130010	NP_001123482	Q9Y2V0	CO041_HUMAN	hypothetical protein LOC84529 isoform 1								protein binding			pancreas(1)	1		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		TTCTCTGTGCTCCCCAAATGTA	0.396													4	2	---	---	---	---	
AP4E1	23431	broad.mit.edu	37	15	51240537	51240538	+	Intron	DEL	TT	-	-	rs71729261		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51240537_51240538delTT	uc001zyx.1	+							NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		AGGAGATGGCTTTTTTTTTTTT	0.366													4	2	---	---	---	---	
PRTG	283659	broad.mit.edu	37	15	55917654	55917654	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55917654delT	uc002adg.2	-							NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin precursor						multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		TTGTGttttcttttttttttt	0.169													1	5	---	---	---	---	
CGNL1	84952	broad.mit.edu	37	15	57752058	57752058	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57752058delA	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		aattctcttgaaattgtaatc	0.000													4	2	---	---	---	---	
RNF111	54778	broad.mit.edu	37	15	59353851	59353851	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59353851delC	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron|RNF111_uc002afw.2_Intron	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		TCCTTCCTTTCCCTTCCAGTT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	60708843	60708843	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60708843delG								ANXA2 (18658 upstream) : NARG2 (2966 downstream)																							gtcctcacatggtggaagtca	0.000													3	3	---	---	---	---	
ZNF609	23060	broad.mit.edu	37	15	64855072	64855081	+	Intron	DEL	GTGTGTGTGT	-	-	rs72434558		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64855072_64855081delGTGTGTGTGT	uc002ann.2	+							NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609							nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						GTAAGCgtgagtgtgtgtgtgtgtgtgtgt	0.290													3	3	---	---	---	---	
MAP2K5	5607	broad.mit.edu	37	15	68062650	68062650	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68062650delT	uc002aqu.2	+						MAP2K5_uc002aqv.2_Intron|MAP2K5_uc002aqw.2_Intron|MAP2K5_uc002aqx.2_Intron	NM_145160	NP_660143	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2						GCCTTCTGCCTTTTTCCTCCT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70698384	70698384	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70698384delC								TLE3 (308128 upstream) : UACA (248511 downstream)																							tggaatcattcccatacttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	70758218	70758218	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70758218delC								TLE3 (367962 upstream) : UACA (188677 downstream)																							GAGTAGGGTGCCCCCATGGCC	0.483													4	2	---	---	---	---	
CSPG4	1464	broad.mit.edu	37	15	75976812	75976812	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75976812delA	uc002baw.2	-							NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor						angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3						GCCACAGAAGAAGGAACAGCA	0.463													4	2	---	---	---	---	
RASGRF1	5923	broad.mit.edu	37	15	79324036	79324037	+	Intron	DEL	GA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79324036_79324037delGA	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc010blm.1_Intron|RASGRF1_uc002ber.3_Intron	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine						activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						gggaaagggggagagagagaga	0.262													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	82044288	82044289	+	IGR	INS	-	A	A	rs139414597	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82044288_82044289insA								TMC3 (377870 upstream) : MEX3B (289839 downstream)																							CACCTAAGGGGAAAAAAAATCC	0.411													4	2	---	---	---	---	
ALPK3	57538	broad.mit.edu	37	15	85377188	85377189	+	Intron	INS	-	TG	TG	rs111934164		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85377188_85377189insTG	uc002ble.2	+							NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3						heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGATTCtgtgttgtgtgtgtgt	0.401													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85721202	85721202	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85721202delT								PDE8A (38832 upstream) : AKAP13 (202669 downstream)																							TTAAAGTGACTTTTTTTTGGT	0.174													4	2	---	---	---	---	
AKAP13	11214	broad.mit.edu	37	15	86251033	86251033	+	Intron	DEL	A	-	-	rs112571964		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86251033delA	uc002blv.1	+						AKAP13_uc002blu.1_Intron|AKAP13_uc010bnf.1_Intron|AKAP13_uc002blw.1_Intron|AKAP13_uc002blx.1_Intron	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						ACAAACACCGAAAAAAAAAAA	0.428													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89316727	89316727	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89316727delG								ISG20 (117848 upstream) : ACAN (29947 downstream)																							gctgtgggatgggaaaggaag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	89948218	89948218	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89948218delT								LOC254559 (6500 upstream) : RHCG (66420 downstream)																							gtgaggtgGGTGGGAGATCCT	0.254													4	2	---	---	---	---	
ZNF710	374655	broad.mit.edu	37	15	90615794	90615794	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90615794delA	uc002bov.1	+							NM_198526	NP_940928	Q8N1W2	ZN710_HUMAN	zinc finger protein 710						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			ggtctgaaccaaaaaggCCAC	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92292862	92292867	+	IGR	DEL	TGGAGA	-	-	rs145621440		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92292862_92292867delTGGAGA								SV2B (454214 upstream) : SLCO3A1 (104071 downstream)																							gtggaggtggtggagatggagatgga	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	92836670	92836670	+	IGR	DEL	G	-	-	rs36081257		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92836670delG								SLCO3A1 (121005 upstream) : ST8SIA2 (100470 downstream)																							GAATGGATCAGAATTTTATAA	0.169													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94594605	94594606	+	IGR	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94594605_94594606delAC								RGMA (962172 upstream) : MCTP2 (180195 downstream)																							CCAAATacatacacacacacac	0.040													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97495948	97495949	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97495948_97495949insA								SPATA8 (167104 upstream) : LOC91948 (789897 downstream)																							AGCGCTGACCCAAAAACGCTGA	0.450													4	2	---	---	---	---	
BAIAP3	8938	broad.mit.edu	37	16	1393820	1393820	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1393820delC	uc002clk.1	+						BAIAP3_uc002clj.2_Intron|BAIAP3_uc010uuz.1_Intron|BAIAP3_uc010uva.1_Intron|BAIAP3_uc010uvc.1_Intron	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3						G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)				GGGGCACAGGCCCTACGTGAG	0.687													4	2	---	---	---	---	
RPL3L	6123	broad.mit.edu	37	16	2002712	2002713	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2002712_2002713delAC	uc002cnh.2	-							NM_005061	NP_005052	Q92901	RL3L_HUMAN	ribosomal protein L3-like						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	RNA binding|structural constituent of ribosome				0						CAACcacacaacacacacacac	0.228													4	3	---	---	---	---	
MGRN1	23295	broad.mit.edu	37	16	4728288	4728289	+	Intron	INS	-	GG	GG	rs140430497	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4728288_4728289insGG	uc002cwz.2	+						MGRN1_uc002cxa.2_Intron|MGRN1_uc010btx.2_Intron|MGRN1_uc010btw.2_Intron|MGRN1_uc002cxb.2_Intron|MGRN1_uc010uxo.1_Intron|MGRN1_uc010uxp.1_Intron|MGRN1_uc010uxq.1_Intron	NM_001142290	NP_001135762	O60291	MGRN1_HUMAN	mahogunin, ring finger 1 isoform 3						endosome to lysosome transport|negative regulation of cAMP-mediated signaling|negative regulation of G-protein coupled receptor protein signaling pathway|protein monoubiquitination	cytosol|early endosome|nucleus|plasma membrane|plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2						CAGCAACACAAGGGAGGTGGAA	0.426													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5666686	5666686	+	IGR	DEL	C	-	-	rs112022358		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5666686delC								FAM86A (518897 upstream) : A2BP1 (402446 downstream)																							CCTTTATCTTCCGCCCCCTGA	0.184													0	7	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	6155999	6155999	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6155999delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		tgctttagtcttttttttttc	0.000													4	2	---	---	---	---	
SHISA9	729993	broad.mit.edu	37	16	13272700	13272705	+	Intron	DEL	TTGTTG	-	-	rs113819568		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13272700_13272705delTTGTTG	uc010uyy.1	+							NM_001145204	NP_001138676	B4DS77	SHSA9_HUMAN	shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0						GGCCAGgtttttgttgttgttgttgt	0.335													4	2	---	---	---	---	
PDXDC1	23042	broad.mit.edu	37	16	15198324	15198325	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15198324_15198325delAC	uc002ddc.2	+						uc010bve.1_Intron	NM_015027	NP_055842	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)	GAGTGAGCAGACACACTCGGGA	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21527446	21527446	+	Intron	DEL	A	-	-	rs72342525		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21527446delA	uc002diq.3	+						LOC100271836_uc002dja.2_Intron|LOC100271836_uc002djb.2_Intron					Homo sapiens cDNA FLJ59829 complete cds.																		ATCACTTTCCAAAAAAAAAAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21536332	21536333	+	Intron	INS	-	CA	CA	rs113987115		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21536332_21536333insCA	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																		catgtgtgaactatctgttcca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	21575680	21575681	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21575680_21575681insA	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																		actaaaaatacaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	23832963	23832964	+	IGR	DEL	GG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23832963_23832964delGG								CHP2 (62707 upstream) : PRKCB (14336 downstream)																							CAGGTACACTGGGGGGATGTGG	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26374123	26374124	+	IGR	INS	-	G	G	rs35533138		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26374123_26374124insG								HS3ST4 (225115 upstream) : C16orf82 (704095 downstream)																							aaaaagaaaaaaaaaaaaacac	0.168													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32364541	32364543	+	IGR	DEL	AGA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32364541_32364543delAGA								HERC2P4 (200667 upstream) : TP53TG3B (320298 downstream)																							GCTCCATGGCAGAAGAAGCCTCT	0.493													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32490382	32490382	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32490382delA								HERC2P4 (326508 upstream) : TP53TG3B (194459 downstream)																							ACAAGAGACCAGGGGGATAAG	0.393													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33483840	33483841	+	IGR	INS	-	AA	AA	rs145732322	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33483840_33483841insAA								SLC6A10P (587377 upstream) : MIR1826 (481667 downstream)																							GGAACCACAACAACaaaaaata	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33569432	33569432	+	IGR	DEL	G	-	-	rs113882576		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33569432delG								SLC6A10P (672969 upstream) : MIR1826 (396076 downstream)																							GCCAGCCAGAGGCATCAGATG	0.458													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33978278	33978278	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33978278delG								MIR1826 (12686 upstream) : UBE2MP1 (425524 downstream)																							aacgctttgaggcctattgtg	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	35232701	35232702	+	IGR	DEL	CT	-	-	rs62057488	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35232701_35232702delCT								LOC146481 (517734 upstream) : None (None downstream)																							attgaactcactgagttgaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46465125	46465125	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46465125delC								None (None upstream) : ANKRD26P1 (38124 downstream)																							ACTAAATAATCCTTATTGCTT	0.448													4	2	---	---	---	---	
ZNF423	23090	broad.mit.edu	37	16	49637325	49637325	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49637325delT	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)				actgtctagattttttttttc	0.000													4	2	---	---	---	---	
LPCAT2	54947	broad.mit.edu	37	16	55576019	55576019	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55576019delT	uc002eie.3	+						LPCAT2_uc002eic.2_Intron	NM_017839	NP_060309	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2						cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0						ATAAACTAGCTTTAGTGATAC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58420472	58420472	+	IGR	DEL	A	-	-	rs78166361		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58420472delA								PRSS54 (91521 upstream) : GINS3 (5826 downstream)																							actccatttcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59252070	59252071	+	IGR	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59252070_59252071delCA								GOT2 (483824 upstream) : None (None downstream)																							cttaaaaagtcacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66222178	66222179	+	IGR	INS	-	A	A	rs141865561	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66222178_66222179insA								LOC283867 (611975 upstream) : CDH5 (178346 downstream)																							CCCATTCCAGTAAAAAAAAACC	0.480													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	70479864	70479865	+	IGR	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70479864_70479865delTT								ST3GAL2 (6873 upstream) : FUK (8633 downstream)																							ttcctccttctttttttttttt	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	72763869	72763869	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72763869delA	uc002fcj.1	+											Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100.																		GGTCCAAAACAAAAAAAAAAA	0.343													6	3	---	---	---	---	
ZFHX3	463	broad.mit.edu	37	16	72983982	72983982	+	Intron	DEL	A	-	-	rs142624386		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72983982delA	uc002fck.2	-						ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A						muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				ggagaaatagaaaaaaaaaaa	0.154													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74847109	74847114	+	IGR	DEL	CTGGGC	-	-	rs71789022		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74847109_74847114delCTGGGC								FA2H (38388 upstream) : WDR59 (60357 downstream)																							GACACCTGGGCTGGGCCTGGGCCTGG	0.694													4	3	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78964133	78964133	+	Intron	DEL	T	-	-	rs141441553	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78964133delT	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)		ccttccttccttccttccttc	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79263035	79263035	+	IGR	DEL	C	-	-	rs67999703		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79263035delC								WWOX (16472 upstream) : MAF (364711 downstream)																							caAACATAGACCCCCCCCAAC	0.254													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79497868	79497869	+	IGR	INS	-	A	A	rs142407694		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79497868_79497869insA								WWOX (251305 upstream) : MAF (129877 downstream)																							ctgaggcttgcaaaaaaaaaaa	0.109													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	83834672	83834672	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83834672delA								CDH13 (4475 upstream) : HSBP1 (6921 downstream)																							actctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84084341	84084341	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84084341delC								SLC38A8 (8579 upstream) : MBTPS1 (3030 downstream)																							AGCTGCAAGGCCCGCATGTGC	0.607													4	4	---	---	---	---	
BANP	54971	broad.mit.edu	37	16	88038682	88038684	+	Intron	DEL	TCC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88038682_88038684delTCC	uc002fkr.2	+						BANP_uc002fkp.2_Intron|BANP_uc002fkq.2_Intron|BANP_uc010vow.1_Intron|BANP_uc002fks.3_Intron|BANP_uc002fko.1_Intron|BANP_uc010vov.1_Intron	NM_079837	NP_524576	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein isoform b						cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0				BRCA - Breast invasive adenocarcinoma(80;0.00551)		CTTTGTGGATTCCTCCTCCTCCA	0.522													4	2	---	---	---	---	
ABR	29	broad.mit.edu	37	17	956676	956677	+	Intron	INS	-	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:956676_956677insG	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CGGAAGGAGCTGGGGACGGCTC	0.475													4	2	---	---	---	---	
SPATA22	84690	broad.mit.edu	37	17	3397332	3397332	+	Intron	DEL	T	-	-	rs112809093		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3397332delT	uc010vrg.1	-						ASPA_uc010ckg.2_Intron|ASPA_uc002fvq.2_Intron	NM_032598	NP_115987	Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22												0						TTTTTCCAGAttttttttttt	0.134													2	4	---	---	---	---	
SPNS2	124976	broad.mit.edu	37	17	4434641	4434641	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4434641delC	uc002fxx.2	+							NM_001124758	NP_001118230	Q8IVW8	SPNS2_HUMAN	spinster homolog 2						lipid transport|transmembrane transport	integral to membrane					0						GCCCTCGGGGCCCCCAGGCTG	0.597													4	2	---	---	---	---	
C17orf68	80169	broad.mit.edu	37	17	8145168	8145168	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8145168delA	uc002gkq.3	-						C17orf68_uc010cnv.2_Intron	NM_025099	NP_079375	Q2NKJ3	CTC1_HUMAN	alpha accessory factor 132						positive regulation of DNA replication|telomere maintenance	Stn1-Ten1 complex	protein binding|single-stranded DNA binding				0						accctgtctcaaaaaaaaaaa	0.000													3	3	---	---	---	---	
HS3ST3A1	9955	broad.mit.edu	37	17	13464706	13464706	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13464706delT	uc002gob.1	-							NM_006042	NP_006033	Q9Y663	HS3SA_HUMAN	heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity			ovary(1)|central_nervous_system(1)	2		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CAGATCAttcttttttttttt	0.224													4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21204581	21204584	+	Intron	DEL	TGTG	-	-	rs34743272		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21204581_21204584delTGTG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CAGTTCTGTCTGTGTGACCATTCG	0.417													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21236092	21236093	+	IGR	INS	-	GGTTACTA	GGTTACTA	rs77031677		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21236092_21236093insGGTTACTA								MAP2K3 (17543 upstream) : KCNJ12 (43606 downstream)																							cctaaaaatgcggttaaagggt	0.134													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21245238	21245239	+	IGR	INS	-	T	T	rs147043183		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21245238_21245239insT								MAP2K3 (26689 upstream) : KCNJ12 (34460 downstream)																							gattgcccagatcacacaatga	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21250573	21250573	+	IGR	DEL	T	-	-	rs67219302		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21250573delT								MAP2K3 (32024 upstream) : KCNJ12 (29126 downstream)																							CCTCCAGGGGTCCTGGCTCCA	0.597													7	4	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21320854	21320854	+	3'UTR	DEL	A	-	-	rs67230821		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21320854delA	uc002gyv.1	+	3						NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	GCCTCCGCCCAATTCCACAGT	0.617										Prostate(3;0.18)			3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21524274	21524275	+	IGR	DEL	TT	-	-	rs149328063		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21524274_21524275delTT								C17orf51 (46543 upstream) : FAM27L (301095 downstream)																							GGTCACTGGATTTTTTTTTTTT	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21539329	21539329	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21539329delA								C17orf51 (61598 upstream) : FAM27L (286041 downstream)																							GATATCAGATAAATAAGTACC	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21541903	21541904	+	IGR	INS	-	G	G	rs146783355		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21541903_21541904insG								C17orf51 (64172 upstream) : FAM27L (283466 downstream)																							ttagtagagatgggttttacca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21547444	21547445	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21547444_21547445insT								C17orf51 (69713 upstream) : FAM27L (277925 downstream)																							tttttaaaatgtttttttgctt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21563911	21563911	+	IGR	DEL	T	-	-	rs112625646		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21563911delT								C17orf51 (86180 upstream) : FAM27L (261459 downstream)																							ctcttatggatttttttctgt	0.000													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25263408	25263409	+	IGR	INS	-	ATGGAATGGT	ATGGAATGGT	rs78119388		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25263408_25263409insATGGAATGGT								None (None upstream) : WSB1 (357697 downstream)																							agtggaatggcgaaatgaaatg	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27581571	27581571	+	IGR	DEL	T	-	-	rs111316904		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27581571delT								CRYBA1 (71 upstream) : NUFIP2 (1284 downstream)																							TGGATGAGAAttttttttttt	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	29103592	29103592	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29103592delT								SUZ12P (6525 upstream) : CRLF3 (6111 downstream)																							GTATCATTCCttttttttttt	0.159													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31931368	31931368	+	Intron	DEL	A	-	-	rs56169311		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31931368delA	uc002hhu.2	-							NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	TGGAGTGGACATGGAGAGCAG	0.488													2	5	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	32130841	32130842	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32130841_32130842insT	uc002hhu.2	-							NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	TGTAACTGGCATTTTTTTTTAT	0.411													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	32755037	32755040	+	IGR	DEL	CCTC	-	-	rs111859202		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32755037_32755040delCCTC								CCL1 (64785 upstream) : C17orf102 (146102 downstream)																							CTCCAcctctcctccctccctccc	0.466													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33167198	33167198	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33167198delA								TMEM132E (200862 upstream) : CCT6B (87742 downstream)																							actctgtctcaaaaaaaaaaa	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35004602	35004602	+	IGR	DEL	T	-	-	rs112219099		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35004602delT								MRM1 (39196 upstream) : LHX1 (289897 downstream)																							CGCAAGCTGAttttttttttt	0.254													4	3	---	---	---	---	
SYNRG	11276	broad.mit.edu	37	17	35952487	35952487	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35952487delT	uc002hoa.2	-						SYNRG_uc010wde.1_Intron|SYNRG_uc010wdf.1_Intron|SYNRG_uc002hoc.2_Intron|SYNRG_uc002hoe.2_Intron|SYNRG_uc002hod.2_Intron|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Intron|SYNRG_uc002hog.1_Intron|SYNRG_uc010wdh.1_Intron	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1						endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2						tggaaaaaagtttggcagcat	0.000													4	2	---	---	---	---	
HNF1B	6928	broad.mit.edu	37	17	36106472	36106472	+	5'Flank	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36106472delG	uc002hok.3	-						HNF1B_uc010wdi.1_5'Flank	NM_000458	NP_000449	P35680	HNF1B_HUMAN	hepatocyte nuclear factor 1-beta isoform 1						endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			acctttttttgggggttgtgt	0.159									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
MSL1	339287	broad.mit.edu	37	17	38277933	38277934	+	5'Flank	INS	-	TC	TC	rs139649796	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38277933_38277934insTC	uc002hub.2	+						MSL1_uc002hua.3_5'Flank	NM_001012241	NP_001012241	Q68DK7	MSL1_HUMAN	hampin						histone H4-K16 acetylation	MSL complex					0						TCTCTCGCGCTTTTTTCCCGGG	0.361													4	4	---	---	---	---	
KRT31	3881	broad.mit.edu	37	17	39553802	39553802	+	5'UTR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39553802delG	uc002hwn.2	-	1					KRT31_uc010cxn.2_5'UTR	NM_002277	NP_002268	Q15323	K1H1_HUMAN	keratin 31						epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000496)				AGTGCTGGGAGGGAGGGAGGG	0.617													13	8	---	---	---	---	
KLHL10	317719	broad.mit.edu	37	17	39997527	39997527	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39997527delG	uc010cxr.2	+						KLHL10_uc010wfv.1_Intron|KLHL10_uc010wfw.1_Intron	NM_152467	NP_689680	Q6JEL2	KLH10_HUMAN	kelch-like 10							cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)				ataaatgcctgggaaaataag	0.015													4	2	---	---	---	---	
EZH1	2145	broad.mit.edu	37	17	40858291	40858291	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40858291delT	uc002iaz.2	-						EZH1_uc002iba.2_Intron|EZH1_uc010wgt.1_Intron|EZH1_uc010wgu.1_Intron|EZH1_uc010wgv.1_Intron|EZH1_uc010wgw.1_Intron|EZH1_uc010cyp.2_Intron|EZH1_uc010cyq.2_Intron|EZH1_uc010cyo.1_Intron	NM_001991	NP_001982	Q92800	EZH1_HUMAN	enhancer of zeste homolog 1						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	chromatin binding|DNA binding			ovary(3)	3		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)		AAGAAGTAAATTTTTTGTGTT	0.403													19	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	41379540	41379540	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41379540delT	uc002ido.2	-						uc010wia.1_5'Flank					Homo sapiens cDNA clone IMAGE:5169062, partial cds.																		AAGtttttaattttttttttg	0.015													3	3	---	---	---	---	
HDAC5	10014	broad.mit.edu	37	17	42162695	42162695	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42162695delT	uc002ifd.1	-						HDAC5_uc002ife.1_Intron|HDAC5_uc002iff.1_Intron|HDAC5_uc010czp.1_Intron|HDAC5_uc002ifg.1_5'UTR|HDAC5_uc002ifh.2_Intron	NM_005474	NP_005465	Q9UQL6	HDAC5_HUMAN	histone deacetylase 5 isoform 1						B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		CCTCTCCAGCttttttttttt	0.323													4	6	---	---	---	---	
SLC4A1	6521	broad.mit.edu	37	17	42333605	42333605	+	Intron	DEL	G	-	-	rs111880434		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42333605delG	uc002igf.3	-							NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member						bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CAATTGACATGGAAACAGAGG	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	42864824	42864824	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42864824delT								ADAM11 (5612 upstream) : GJC1 (10993 downstream)																							GCTCCCAAGCTCCCAGCTTGC	0.587													4	2	---	---	---	---	
NSF	4905	broad.mit.edu	37	17	44713143	44713144	+	Intron	INS	-	TGTG	TGTG			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44713143_44713144insTGTG	uc002iku.2	+						NSF_uc010wke.1_Intron|NSF_uc010wkf.1_Intron|NSF_uc010wkg.1_Intron	NM_006178	NP_006169	P46459	NSF_HUMAN	vesicle-fusing ATPase						protein transport|synaptic transmission	cytosol	ATP binding|metal ion binding			ovary(1)	1		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		GGGAAAATAAAtgtgtgtgtgt	0.208													3	3	---	---	---	---	
CDC27	996	broad.mit.edu	37	17	45237368	45237368	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45237368delT	uc002ild.3	-						CDC27_uc002ile.3_Intron|CDC27_uc002ilf.3_Intron|CDC27_uc010wkp.1_Intron|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|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|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						CCTCTGCTTCTTTTTTTTTTT	0.522													4	2	---	---	---	---	
NPEPPS	9520	broad.mit.edu	37	17	45649408	45649409	+	Intron	INS	-	A	A	rs146404865	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45649408_45649409insA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010dba.1_Intron	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						AGTGAGCGGGCAGCCACTCTCT	0.480													4	4	---	---	---	---	
TTLL6	284076	broad.mit.edu	37	17	46848299	46848299	+	Intron	DEL	A	-	-	rs66852497		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46848299delA	uc010wlo.1	-						TTLL6_uc002iob.2_Intron|TTLL6_uc010dbi.2_Intron|TTLL6_uc002ioc.2_Intron|TTLL6_uc002iod.2_Intron	NM_001130918	NP_001124390	Q8N841	TTLL6_HUMAN	tubulin tyrosine ligase-like family, member 6							cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity				0						acaaagaaacaaaaaaaaaca	0.154													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	47150296	47150296	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47150296delT								IGF2BP1 (16791 upstream) : B4GALNT2 (59526 downstream)																							CAGTAGCTGCttttttttttt	0.040													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51201366	51201366	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51201366delA								CA10 (963989 upstream) : KIF2B (698873 downstream)																							caacacttggaaaaaaaaaag	0.000													4	2	---	---	---	---	
CUEDC1	404093	broad.mit.edu	37	17	55997776	55997777	+	Intron	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55997776_55997777delCA	uc002ive.1	-							NM_017949	NP_060419	Q9NWM3	CUED1_HUMAN	CUE domain-containing 1											skin(2)	2						TTTCTCCATGCACACACACACA	0.312													6	3	---	---	---	---	
MTMR4	9110	broad.mit.edu	37	17	56571107	56571107	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56571107delA	uc002iwj.2	-							NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4							cytoplasm|membrane	metal ion binding|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ggccttttacaaaaaaaaaaa	0.169													4	2	---	---	---	---	
USP32	84669	broad.mit.edu	37	17	58471048	58471049	+	5'Flank	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58471048_58471049insT	uc002iyo.1	-						USP32_uc010wov.1_5'Flank	NM_032582	NP_115971	Q8NFA0	UBP32_HUMAN	ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			CTGTGtttttcttttttttttt	0.183													4	3	---	---	---	---	
DCAF7	10238	broad.mit.edu	37	17	61634865	61634866	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61634865_61634866insA	uc002jbc.2	+						DCAF7_uc002jbb.2_Intron|DCAF7_uc010wpn.1_Intron	NM_005828	NP_005819	P61962	DCAF7_HUMAN	WD-repeat protein						multicellular organismal development	CUL4 RING ubiquitin ligase complex|cytoplasm|nucleus	protein binding			ovary(1)	1						gtgagactgtcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	61992327	61992328	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61992327_61992328insA								CSHL1 (3709 upstream) : GH1 (2236 downstream)																							tcaagaaaaacaaaaaaaaaCT	0.035													4	2	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	63952528	63952529	+	Intron	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63952528_63952529delAC	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			atacatacatacacacacacac	0.000													5	3	---	---	---	---	
CACNG1	786	broad.mit.edu	37	17	65039851	65039852	+	5'Flank	INS	-	AC	AC	rs150316959	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65039851_65039852insAC	uc002jfu.2	+							NM_000727	NP_000718	Q06432	CCG1_HUMAN	voltage-dependent calcium channel gamma-1						muscle contraction	voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(12;1.04e-10)|Breast(2;1.45e-16)|all_epithelial(3;4.81e-12)				Amlodipine(DB00381)|Diltiazem(DB00343)|Ibutilide(DB00308)|Lercanidipine(DB00528)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Nitrendipine(DB01054)|Verapamil(DB00661)	GGCAAAACCAAACAGTGCCCTG	0.287													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	65815716	65815717	+	IGR	DEL	AA	-	-	rs10562488		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65815716_65815717delAA								NOL11 (75450 upstream) : BPTF (6063 downstream)																							actccgtctcaaaaaaaaaaaa	0.183													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	65983924	65983925	+	IGR	DEL	GA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65983924_65983925delGA								BPTF (3431 upstream) : C17orf58 (3293 downstream)																							tcggtaggctgaggcaggagaa	0.000													4	2	---	---	---	---	
ARSG	22901	broad.mit.edu	37	17	66376394	66376394	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66376394delT	uc002jhc.2	+						ARSG_uc002jhb.1_Intron	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			ttctttactcttttttttttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68213861	68213864	+	IGR	DEL	TTTC	-	-	rs72029209		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68213861_68213864delTTTC								KCNJ2 (37680 upstream) : None (None downstream)																							ctttcttccttttctttctttcct	0.132													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68587569	68587569	+	IGR	DEL	T	-	-	rs143770316		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68587569delT								KCNJ2 (411388 upstream) : None (None downstream)																							AAAGTCCACAttttttttttt	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68883235	68883236	+	IGR	INS	-	T	T	rs139160180	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68883235_68883236insT								KCNJ2 (707054 upstream) : None (None downstream)																							TAATCCATATATTTTTTCTTTT	0.406													4	4	---	---	---	---	
SOX9	6662	broad.mit.edu	37	17	70122037	70122038	+	3'UTR	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70122037_70122038delTG	uc002jiw.2	+	3						NM_000346	NP_000337	P48436	SOX9_HUMAN	transcription factor SOX9						cAMP-mediated signaling|negative regulation of transcription, DNA-dependent|positive regulation of branching involved in ureteric bud morphogenesis|protein complex assembly|renal vesicle induction	nucleus|protein complex	core promoter sequence-specific DNA binding|enhancer binding|protein kinase A catalytic subunit binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription				0		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			TGCCTTATATtgtgtgtgtgtg	0.337													4	2	---	---	---	---	
FAM104A	84923	broad.mit.edu	37	17	71223063	71223063	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71223063delT	uc002jji.3	-						FAM104A_uc002jjj.3_Intron	NM_032837	NP_116226	Q969W3	F104A_HUMAN	hypothetical protein LOC84923 isoform 2												0			LUSC - Lung squamous cell carcinoma(166;0.197)			AGCCACGAAATTTCTAACAAA	0.378													4	2	---	---	---	---	
RNF157	114804	broad.mit.edu	37	17	74177043	74177043	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74177043delC	uc002jqz.2	-						RNF157_uc002jra.2_Intron	NM_052916	NP_443148	Q96PX1	RN157_HUMAN	ring finger protein 157								zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)			GTCCAACATGCCGGAGAAATA	0.343													4	2	---	---	---	---	
RNF157	114804	broad.mit.edu	37	17	74183269	74183270	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74183269_74183270insT	uc002jqz.2	-						RNF157_uc002jra.2_Intron	NM_052916	NP_443148	Q96PX1	RN157_HUMAN	ring finger protein 157								zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)			ttttcttcttcttttttttttc	0.163													4	2	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75480683	75480684	+	Intron	INS	-	TGGTGGTGA	TGGTGGTGA	rs141454198	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75480683_75480684insTGGTGGTGA	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc010wtl.1_Intron|SEPT9_uc002jty.3_Intron|SEPT9_uc010wtm.1_Intron|SEPT9_uc010wtn.1_Intron|SEPT9_uc010dhd.2_Intron	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			aattgtgatggtggtggtgatg	0.000													5	4	---	---	---	---	
SEPT9	10801	broad.mit.edu	37	17	75491262	75491263	+	Intron	DEL	AA	-	-	rs35597398		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75491262_75491263delAA	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc010wtl.1_Intron|SEPT9_uc002jty.3_Intron|SEPT9_uc010wtm.1_Intron|SEPT9_uc010wtn.1_Intron|SEPT9_uc010dhd.2_Intron	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)			GGAAATGCACAAGAGAGAGGTC	0.604											OREG0024771	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77657104	77657104	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77657104delA								HRNBP3 (178424 upstream) : ENPP7 (47778 downstream)																							caacaacaacaaaaGGCTGGG	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77904656	77904657	+	IGR	INS	-	C	C	rs72055514		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77904656_77904657insC								CBX4 (91443 upstream) : TBC1D16 (9164 downstream)																							GGAGCTGGCAGCCCCCCCACAC	0.579													3	5	---	---	---	---	
FLJ90757	440465	broad.mit.edu	37	17	79005225	79005226	+	3'UTR	INS	-	TCT	TCT	rs140551922	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79005225_79005226insTCT	uc002jyy.2	-	2						NR_026857				Homo sapiens cDNA FLJ14444 fis, clone HEMBB1001153.												0						GCCAGGCAGAAGGTGGGAGGGG	0.520													2	7	---	---	---	---	
HGS	9146	broad.mit.edu	37	17	79663194	79663203	+	Intron	DEL	TGCCCTGCCC	-	-	rs145540708		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79663194_79663203delTGCCCTGCCC	uc002kbg.2	+							NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	metal ion binding|protein domain specific binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			GTGATGACCAtgccctgccctgccctgccc	0.510													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	80179467	80179468	+	IGR	INS	-	AAC	AAC	rs143230826	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80179467_80179468insAAC								CCDC57 (8778 upstream) : SLC16A3 (6825 downstream)																							gaatgaaactaaacaacaacaa	0.000													3	7	---	---	---	---	
NARF	26502	broad.mit.edu	37	17	80426240	80426240	+	Intron	DEL	G	-	-	rs72250182		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80426240delG	uc002kfg.3	+						NARF_uc002kff.3_Intron|NARF_uc010wvo.1_Intron|NARF_uc010wvp.1_Intron|NARF_uc010dit.2_Intron|NARF_uc002kfj.3_Intron|NARF_uc002kfi.3_Intron|NARF_uc002kfh.3_Intron|NARF_uc002kfk.2_Intron	NM_012336	NP_036468	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor isoform a							lamin filament	lamin binding			skin(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ttttttttttgagacagagta	0.075													4	2	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80802627	80802628	+	Intron	DEL	CT	-	-	rs79729191		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80802627_80802628delCT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GTTCAACCCCCTGTGTTACTCA	0.208													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	1565067	1565067	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1565067delT								C18orf2 (157886 upstream) : METTL4 (972458 downstream)																							tctctcgctctgtgatgcccc	0.000													4	2	---	---	---	---	
MYOM1	8736	broad.mit.edu	37	18	3134953	3134954	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3134953_3134954insT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						TTATTTTACGAttttttttttt	0.168													9	4	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3779765	3779765	+	Intron	DEL	T	-	-	rs35140880		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3779765delT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|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)				CAGTGCACCCTTTTTTTTTTT	0.204													3	3	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	4400076	4400076	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4400076delC	uc010wyz.1	-							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)				ACCACATGTTCCCCCACCCCC	0.562													1	5	---	---	---	---	
L3MBTL4	91133	broad.mit.edu	37	18	6139495	6139496	+	Intron	DEL	CA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6139495_6139496delCA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				Aacacacatgcacacacacaca	0.347													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10121941	10121941	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10121941delT								VAPA (161924 upstream) : APCDD1 (332684 downstream)																							CTTTATTAGGTTTACCCAGAC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15175440	15175441	+	IGR	DEL	TA	-	-	rs142369866		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15175440_15175441delTA								ANKRD30B (322703 upstream) : LOC644669 (138114 downstream)																							aataaagttttatttcttcctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15243447	15243447	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15243447delT								ANKRD30B (390710 upstream) : LOC644669 (70108 downstream)																							agaacaatgctacgatggtct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15307686	15307687	+	IGR	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15307686_15307687delTT								ANKRD30B (454949 upstream) : LOC644669 (5868 downstream)																							TTTGTAGCTGTTTTTTTGTAGG	0.366													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15404673	15404674	+	IGR	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15404673_15404674delTG								LOC644669 (78755 upstream) : None (None downstream)																							ttcaaaacactgtttttgtagt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	29725353	29725353	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29725353delC								RNF138 (13830 upstream) : MEP1B (44634 downstream)																							ATGAGGCCTTCCTGTAACGCC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	37720455	37720455	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37720455delA								LOC647946 (340173 upstream) : None (None downstream)																							gcagaattgtaacagagctcc	0.000													4	2	---	---	---	---	
WDR7	23335	broad.mit.edu	37	18	54584428	54584428	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54584428delA	uc002lgk.1	+						WDR7_uc002lgl.1_Intron	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		attccgtctcaaaaaaaaaaa	0.199													4	2	---	---	---	---	
NEDD4L	23327	broad.mit.edu	37	18	55895496	55895497	+	Intron	INS	-	TACT	TACT	rs142445869	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55895496_55895497insTACT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc010dpl.1_Intron|NEDD4L_uc002lhg.2_Intron	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						aacaactgcgctacTGATAGGC	0.277													2	4	---	---	---	---	
CCBE1	147372	broad.mit.edu	37	18	57141085	57141086	+	Intron	DEL	CT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57141085_57141086delCT	uc002lib.2	-							NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)				ccactatttcctcccccGACTA	0.030													4	3	---	---	---	---	
CDH20	28316	broad.mit.edu	37	18	59062189	59062189	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59062189delC	uc002lif.2	+							NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)				cgaagaggaacctgtgttccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71740383	71740384	+	IGR	DEL	AC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71740383_71740384delAC								None (None upstream) : FBXO15 (204 downstream)																							acacacacatacacacacacac	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	71887448	71887449	+	IGR	INS	-	T	T	rs150994836	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71887448_71887449insT								C18orf55 (61244 upstream) : CYB5A (33079 downstream)																							CAGAGTTATTCTCCCCTAGAAC	0.495													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	73120940	73120940	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73120940delC								TSHZ1 (119040 upstream) : C18orf62 (887 downstream)																							CAAACACTCTCCCAGCTGTGA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	74504731	74504731	+	IGR	DEL	G	-	-	rs5826478		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74504731delG								LOC284276 (232948 upstream) : ZNF236 (31385 downstream)																							TTGGGATGGTGGGGGGAGAGC	0.602													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	74507737	74507740	+	IGR	DEL	GAAA	-	-	rs117680664	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74507737_74507740delGAAA								LOC284276 (235954 upstream) : ZNF236 (28376 downstream)																							ggaaaggaaggaaaggaaggaagg	0.034													4	4	---	---	---	---	
MBP	4155	broad.mit.edu	37	18	74813536	74813536	+	Intron	DEL	G	-	-	rs5826494		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74813536delG	uc010xfd.1	-						MBP_uc002lmr.2_Intron	NM_001025101	NP_001020272	P02686	MBP_HUMAN	Golli-mbp isoform 1						central nervous system development|immune response|synaptic transmission	plasma membrane	structural constituent of myelin sheath			haematopoietic_and_lymphoid_tissue(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)		AACTGGCCCAGGAAGGTGGCT	0.522													0	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	74882376	74882378	+	IGR	DEL	CTC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74882376_74882378delCTC								MBP (37602 upstream) : GALR1 (79630 downstream)																							ctgtatccttctccgtgtgtgtg	0.182													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75886068	75886071	+	IGR	DEL	TGTT	-	-	rs55709857		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75886068_75886071delTGTT								GALR1 (903974 upstream) : SALL3 (854204 downstream)																							TGTCCCTGAGTGTTTGCACATATG	0.078													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75973415	75973415	+	IGR	DEL	T	-	-	rs111428250		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75973415delT								GALR1 (991321 upstream) : SALL3 (766860 downstream)																							tacccacatcttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76539566	76539567	+	IGR	INS	-	GGCA	GGCA	rs10646920		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76539566_76539567insGGCA								None (None upstream) : SALL3 (200708 downstream)																							ttctggtccagggctatttgta	0.000													1	7	---	---	---	---	
NFATC1	4772	broad.mit.edu	37	18	77281548	77281548	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77281548delT	uc010xfg.1	+						NFATC1_uc002lnd.2_Intron|NFATC1_uc002lne.2_Intron|NFATC1_uc010xfh.1_Intron|NFATC1_uc010xfj.1_Intron|NFATC1_uc002lnf.2_Intron|NFATC1_uc002lng.2_Intron|NFATC1_uc010xfk.1_Intron	NM_006162	NP_006153	O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytosolic						intracellular signal transduction|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	FK506 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)		tatgtgtgtgtgggggggcat	0.060													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	481398	481398	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:481398delG								ODF3L2 (6415 upstream) : MADCAM1 (15092 downstream)																							gaaggatgatggggaaggatg	0.005													4	2	---	---	---	---	
TCF3	6929	broad.mit.edu	37	19	1646277	1646277	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1646277delC	uc002ltr.2	-						TCF3_uc002ltt.3_Intron|TCF3_uc002ltq.2_Intron	NM_003200	NP_003191	P15923	TFE2_HUMAN	transcription factor 3 isoform E12						B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus|protein complex|transcription factor complex	bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding			lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1)	7		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCCCAGCCTCCCTCGCCCGC	0.657			T	PBX1|HLF|TFPT	pre B-ALL								4	2	---	---	---	---	
SPPL2B	56928	broad.mit.edu	37	19	2348517	2348518	+	Intron	DEL	TC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2348517_2348518delTC	uc002lvs.2	+						SPPL2B_uc002lvr.2_Intron	NM_152988	NP_694533	Q8TCT7	PSL1_HUMAN	signal peptide peptidase-like 2B isoform 2							Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTGATTCCGTTCTCTCTCCCTC	0.505													6	6	---	---	---	---	
PTPRS	5802	broad.mit.edu	37	19	5287899	5287899	+	Intron	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5287899delG	uc002mbv.2	-						PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.1_5'Flank|PTPRS_uc002mbw.2_Intron|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron|PTPRS_uc002mbz.1_5'Flank	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,						cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		CCGACACACAGTCAGACTGCA	0.448													4	2	---	---	---	---	
TMEM146	257062	broad.mit.edu	37	19	5772064	5772064	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5772064delT	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3						tccttttttcttttttttttt	0.015													4	2	---	---	---	---	
ZNF44	51710	broad.mit.edu	37	19	12381853	12381855	+	Intron	DEL	TGA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12381853_12381855delTGA	uc002mtl.2	-						ZNF44_uc010dyr.1_Intron|ZNF44_uc010xmi.1_Intron|ZNF44_uc002mtn.3_Intron			P15621	ZNF44_HUMAN	Homo sapiens GIOT-2 mRNA for gonadotropin inducible transcription repressor-2, complete cds.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		CCTCTACAAGtgatgatgatgat	0.158													4	2	---	---	---	---	
ZNF709	163051	broad.mit.edu	37	19	12621532	12621532	+	Intron	DEL	C	-	-	rs143398551		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12621532delC	uc002mtx.3	-						ZNF709_uc002mtw.3_Intron	NM_001145647	NP_001139119	Q8N972	ZN709_HUMAN	zinc finger protein 709 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						tagatgatgtccctgtctacc	0.000													4	2	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13105127	13105128	+	5'Flank	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13105127_13105128delGT	uc002mwd.2	+							NM_002501	NP_002492	Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			GGGCAACCCAgtgtgtgtgtgt	0.431													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15172349	15172350	+	IGR	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15172349_15172350delGT								CASP14 (5449 upstream) : OR1I1 (25527 downstream)																							Ctgtgcgtgcgtgtgtgtgtgt	0.084													4	2	---	---	---	---	
CYP4F22	126410	broad.mit.edu	37	19	15654670	15654670	+	Intron	DEL	A	-	-	rs35656737		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15654670delA	uc002nbh.3	+							NM_173483	NP_775754	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F,							endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen			ovary(1)|pancreas(1)	2						tccatctcagaaaaaaaaaaa	0.244													5	3	---	---	---	---	
CHERP	10523	broad.mit.edu	37	19	16633474	16633474	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16633474delC	uc002nei.1	-						MED26_uc002nee.2_Intron|CHERP_uc010xpg.1_Intron	NM_006387	NP_006378	Q8IWX8	CHERP_HUMAN	calcium homeostasis endoplasmic reticulum						cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding			ovary(2)	2						CCACCCCCCTCCCTGTGTGCT	0.632													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	27764488	27764489	+	IGR	INS	-	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27764488_27764489insC								None (None upstream) : LOC148189 (516913 downstream)																							aacactcttttgtagaatctgc	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30056936	30056937	+	IGR	INS	-	AGTC	AGTC	rs148563107	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30056936_30056937insAGTC								VSTM2B (1710 upstream) : POP4 (40233 downstream)																							CAAACACAGGTAGTCAGGTCCC	0.495													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30848134	30848134	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30848134delG								C19orf2 (341523 upstream) : ZNF536 (15194 downstream)																							aggaagggacgctggtagcta	0.000													1	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31252320	31252320	+	IGR	DEL	T	-	-	rs74860492		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31252320delT								ZNF536 (203355 upstream) : DKFZp566F0947 (388463 downstream)																							tttctccagattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31315874	31315876	+	IGR	DEL	GAT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31315874_31315876delGAT								ZNF536 (266909 upstream) : DKFZp566F0947 (324907 downstream)																							gtgatggtaagatgatgatgatg	0.000													4	2	---	---	---	---	
ANKRD27	84079	broad.mit.edu	37	19	33098911	33098912	+	Intron	INS	-	T	T	rs145160419		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33098911_33098912insT	uc002ntn.1	-							NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)						early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)					AAACAACTTCCttttttttttt	0.252													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	34492000	34492000	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34492000delA								KCTD15 (185335 upstream) : LSM14A (171352 downstream)																							ctccgtctccaaaaaaaaaaa	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35297551	35297552	+	IGR	INS	-	ACTC	ACTC	rs137993281	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35297551_35297552insACTC								ZNF599 (33417 upstream) : ZNF30 (120255 downstream)																							agaatagacttatcagatgagt	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	35712155	35712155	+	IGR	DEL	T	-	-	rs112691380		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35712155delT								FXYD5 (51370 upstream) : FAM187B (3549 downstream)																							GCCAAGACAAttttttttttt	0.095													1	7	---	---	---	---	
LSR	51599	broad.mit.edu	37	19	35747629	35747636	+	Intron	DEL	GAATGAAA	-	-	rs71167530		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35747629_35747636delGAATGAAA	uc002nyl.2	+						LSR_uc002nym.2_Intron|LSR_uc002nyn.2_Intron|LSR_uc002nyo.2_Intron|LSR_uc010xsr.1_Intron|LSR_uc002nyp.2_Intron	NM_205834	NP_991403	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor						embryo development|liver development	chylomicron|integral to membrane|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle	receptor activity				0	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			atgaatgaatgaatgaaagaaagaaaga	0.207													5	4	---	---	---	---	
COX6B1	1340	broad.mit.edu	37	19	36145785	36145786	+	Intron	INS	-	C	C			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36145785_36145786insC	uc002oav.2	+							NM_001863	NP_001854	P14854	CX6B1_HUMAN	cytochrome c oxidase subunit VIb polypeptide 1						respiratory electron transport chain	mitochondrial inner membrane|mitochondrial intermembrane space	cytochrome-c oxidase activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CAGCTGAGGCGACCAGGGTGCT	0.550													0	7	---	---	---	---	
MLL4	9757	broad.mit.edu	37	19	36221973	36221973	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36221973delC	uc010eei.2	+							NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4						chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGGAGAGCGGCACGCTGCCTA	0.582													4	2	---	---	---	---	
ZNF420	147923	broad.mit.edu	37	19	37581270	37581285	+	Intron	DEL	GTACTGTGAGTGGCAC	-	-	rs56015738		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37581270_37581285delGTACTGTGAGTGGCAC	uc002ofl.2	+							NM_144689	NP_653290	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			acagtggcatgtactgtgagtggcacgtactgtggt	0.000													4	3	---	---	---	---	
CAPN12	147968	broad.mit.edu	37	19	39227605	39227612	+	Intron	DEL	CTCCTCCC	-	-	rs62120077		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39227605_39227612delCTCCTCCC	uc002ojd.1	-						CAPN12_uc010egd.1_5'Flank|CAPN12_uc002ojc.1_5'Flank	NM_144691	NP_653292	Q6ZSI9	CAN12_HUMAN	calpain 12						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			tgctcctccactcctcccctcctccccg	0.096													6	4	---	---	---	---	
LTBP4	8425	broad.mit.edu	37	19	41130144	41130145	+	Intron	INS	-	CTGT	CTGT	rs139135841	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41130144_41130145insCTGT	uc002ooh.1	+						LTBP4_uc002oog.1_Intron|LTBP4_uc002ooi.1_Intron|LTBP4_uc002ooj.1_Intron|LTBP4_uc002ook.1_Intron|LTBP4_uc002ool.1_Intron|LTBP4_uc010xvp.1_Intron	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding						growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TCTCTGTCCCACTGTCTGTCTC	0.520													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	41136787	41136787	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41136787delG								LTBP4 (1062 upstream) : NUMBL (35027 downstream)																							GGGCCAAGCTGGGAAAAAAAA	0.299													0	6	---	---	---	---	
EGLN2	112398	broad.mit.edu	37	19	41297551	41297552	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41297551_41297552insT	uc010ehd.2	+						RAB4B_uc002opc.1_Intron|RAB4B_uc002opd.1_Intron|RAB4B_uc002ope.1_Intron|RAB4B_uc002opf.1_Intron	NM_080732	NP_542770	Q96KS0	EGLN2_HUMAN	EGL nine (C.elegans) homolog 2						cell redox homeostasis|estrogen receptor signaling pathway|positive regulation of protein catabolic process|regulation of cell growth|response to hypoxia	cytoplasm|nucleus	ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|oxygen sensor activity			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	CCAAACttttgtttttttttga	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	41318431	41318431	+	5'Flank	DEL	T	-	-	rs11395532		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41318431delT	uc002opk.1	-											Homo sapiens cDNA FLJ35459 fis, clone SMINT2004872.																		ACCACttctgttttttttttt	0.244													4	2	---	---	---	---	
CYP2F1	1572	broad.mit.edu	37	19	41862757	41862757	+	Intron	DEL	A	-	-	rs66960437		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41862757delA	uc010xvw.1	+						TGFB1_uc002oqh.1_5'Flank|TMEM91_uc002oqi.2_Intron|B9D2_uc002oqj.2_Intron			P24903	CP2F1_HUMAN	SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0						ctctgtctccaaaaaaaaaaa	0.259													8	4	---	---	---	---	
ATP5SL	55101	broad.mit.edu	37	19	41945431	41945431	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41945431delC	uc002oqw.1	-						CYP2F1_uc010xvw.1_Intron|ATP5SL_uc002oqu.1_5'Flank|ATP5SL_uc002oqv.2_5'UTR|ATP5SL_uc010xwa.1_5'UTR|ATP5SL_uc002oqx.1_Intron|ATP5SL_uc002oqy.1_Intron|ATP5SL_uc002oqz.1_Intron|ATP5SL_uc002ora.1_5'Flank|ATP5SL_uc010xwb.1_5'UTR	NM_018035	NP_060505	Q9NW81	AT5SL_HUMAN	ATP5S-like											large_intestine(1)|breast(1)	2						ACAATCCCTTCCAAGCTCTCT	0.483													4	2	---	---	---	---	
GRIK5	2901	broad.mit.edu	37	19	42564394	42564395	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42564394_42564395insA	uc002osj.1	-						GRIK5_uc010eib.1_Intron	NM_002088	NP_002079	Q16478	GRIK5_HUMAN	glutamate receptor KA2 precursor							cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity				0		Prostate(69;0.059)			L-Glutamic Acid(DB00142)	gccatctctttaaaaaaaaaaa	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42784094	42784100	+	IGR	DEL	CTGGCGG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42784094_42784100delCTGGCGG								ERF (24785 upstream) : CIC (4717 downstream)																							AGGCTGCCTCCTGGCGGCAGGCGGCGG	0.676											OREG0012509|OREG0025500	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)|type=TRANSCRIPTION FACTOR BINDING SITE|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip); Conservation found by scanning with a motif model	2	6	---	---	---	---	
CNFN	84518	broad.mit.edu	37	19	42892147	42892148	+	Intron	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42892147_42892148insA	uc002otp.3	-						CNFN_uc002otq.3_Intron	NM_032488	NP_115877	Q9BYD5	CNFN_HUMAN	cornifelin						keratinization	cornified envelope|cytoplasm					0		Prostate(69;0.00899)				aaacaaaaaacaaaacaaaaaa	0.030													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42986615	42986616	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42986615_42986616insT	uc010eif.1	+						uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron					Homo sapiens cDNA FLJ39530 fis, clone PUAEN2004400.																		taaccagctaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	43947442	43947442	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43947442delC								TEX101 (24676 upstream) : LYPD3 (17504 downstream)																							aactctgtctcaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	44503671	44503672	+	Intron	DEL	TA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44503671_44503672delTA	uc010ejc.1	-						uc002oya.1_Intron					Homo sapiens cDNA FLJ33234 fis, clone ASTRO2002064.																		TTGTGTTCACTATGTGTTAAAT	0.337													3	8	---	---	---	---	
TOMM40	10452	broad.mit.edu	37	19	45392673	45392673	+	5'Flank	DEL	T	-	-	rs111300402		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45392673delT	uc002ozx.3	+						TOMM40_uc002ozy.3_5'Flank|TOMM40_uc002paa.3_5'Flank|TOMM40_uc002ozz.2_5'Flank	NM_006114	NP_006105	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40						protein targeting to mitochondrion	integral to membrane of membrane fraction|integral to mitochondrial outer membrane|mitochondrial outer membrane translocase complex|pore complex	porin activity|protein transmembrane transporter activity|voltage-gated anion channel activity				0	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		AAAAACAAAAttttttttttt	0.154													4	2	---	---	---	---	
VRK3	51231	broad.mit.edu	37	19	50480005	50480006	+	3'UTR	DEL	TT	-	-	rs35937899		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50480005_50480006delTT	uc002prg.2	-	15					VRK3_uc002prh.1_3'UTR|VRK3_uc002pri.1_3'UTR	NM_016440	NP_057524	Q8IV63	VRK3_HUMAN	vaccinia related kinase 3 isoform 1							nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)		CATTACTTCATTTTTTTTTTTC	0.327													2	4	---	---	---	---	
NAPSB	256236	broad.mit.edu	37	19	50846226	50846226	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50846226delT	uc002prw.2	-						NR1H2_uc002prv.3_Intron	NR_002798				Homo sapiens napsin B pseudogene, mRNA sequence.											central_nervous_system(1)	1						ACTGGACttcttttttttttg	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	52056246	52056247	+	IGR	INS	-	A	A	rs141110407	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52056246_52056247insA								SIGLEC6 (21182 upstream) : ZNF175 (18284 downstream)																							ggaagaggagggggggaggaga	0.079													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1418029	1418030	+	IGR	INS	-	AAC	AAC	rs140467683	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1418029_1418030insAAC								FKBP1A (44213 upstream) : NSFL1C (4783 downstream)																							aacaacaacaaaacaacaacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	2353759	2353760	+	IGR	INS	-	A	A	rs137931132	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2353759_2353760insA								TGM3 (32035 upstream) : TGM6 (7794 downstream)																							tccatccaaccagaaatttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	16839136	16839137	+	IGR	INS	-	A	A	rs72536697		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16839136_16839137insA								OTOR (106328 upstream) : PCSK2 (367615 downstream)																							TTGTACAGGGGTTcctgaaaag	0.218													6	3	---	---	---	---	
BFSP1	631	broad.mit.edu	37	20	17509709	17509710	+	Intron	INS	-	GT	GT	rs146802847	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17509709_17509710insGT	uc002wpo.2	-						BFSP1_uc002wpp.2_Intron|BFSP1_uc010zrn.1_Intron|BFSP1_uc010zro.1_Intron	NM_001195	NP_001186	Q12934	BFSP1_HUMAN	filensin isoform 1							cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1						TGGTTAAATAAgtgtgtgtgtg	0.168													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19082569	19082570	+	IGR	INS	-	CA	CA	rs143699136	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19082569_19082570insCA								C20orf79 (287536 upstream) : SLC24A3 (110720 downstream)																							cacacaaacaccacacacacac	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19825290	19825291	+	IGR	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19825290_19825291delTT								SLC24A3 (121750 upstream) : RIN2 (44919 downstream)																							cttcttcttcttcttcttcttc	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19857224	19857224	+	IGR	DEL	A	-	-	rs5840861		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19857224delA								SLC24A3 (153684 upstream) : RIN2 (12986 downstream)																							CGAAATGGGGATATGTGAGTA	0.308													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	20832155	20832156	+	IGR	DEL	TC	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20832155_20832156delTC								RALGAPA2 (138889 upstream) : PLK1S1 (274468 downstream)																							ATATTTTTTTTCTGGACCACTT	0.351													4	2	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25829595	25829596	+	Intron	INS	-	GAA	GAA	rs143279219	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25829595_25829596insGAA	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						ctagaaggaaggaagacaagac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26074950	26074951	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26074950_26074951insA								FAM182A (7398 upstream) : C20orf191 (9102 downstream)																							agtcttgactcaaaaaacaaaa	0.099													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26078131	26078131	+	IGR	DEL	G	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26078131delG								FAM182A (10579 upstream) : C20orf191 (5922 downstream)																							ATGCTCAGCAGCTCTGGGACC	0.373													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29552848	29552850	+	IGR	DEL	CAA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29552848_29552850delCAA								None (None upstream) : FRG1B (59029 downstream)																							acacacacaccaacaccacacac	0.374													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29593423	29593424	+	IGR	DEL	AT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29593423_29593424delAT								None (None upstream) : FRG1B (18455 downstream)																							ACAAATAGAAATAGAGAGATGG	0.312													11	5	---	---	---	---	
COX4I2	84701	broad.mit.edu	37	20	30227362	30227362	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30227362delT	uc002wwj.1	+						COX4I2_uc002wwi.2_Intron	NM_032609	NP_115998	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2						cellular respiration		cytochrome-c oxidase activity			ovary(1)	1	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			ATAAACCTCCttttttttttt	0.134													4	2	---	---	---	---	
LOC647979	647979	broad.mit.edu	37	20	34634933	34634933	+	3'UTR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34634933delT	uc002xet.2	-	1						NR_027451				Homo sapiens cDNA FLJ33322 fis, clone BNGH42008510.												0						CATTGTGCACttttttttttg	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36060760	36060761	+	IGR	INS	-	GT	GT	rs140432969	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36060760_36060761insGT								SRC (26941 upstream) : BLCAP (85059 downstream)																							AGTGCATCATCgtgtgtgtgtg	0.446													3	3	---	---	---	---	
KIAA0406	9675	broad.mit.edu	37	20	36626302	36626303	+	Intron	DEL	TT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36626302_36626303delTT	uc002xhl.2	-						KIAA0406_uc002xhm.2_Intron	NM_014657	NP_055472	O43156	TTI1_HUMAN	hypothetical protein LOC9675								binding				0		Myeloproliferative disorder(115;0.00874)				CTGGATAAGATTTAGCAATACC	0.252													4	2	---	---	---	---	
RALGAPB	57148	broad.mit.edu	37	20	37111069	37111070	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37111069_37111070insT	uc002xiw.2	+						RALGAPB_uc010zvz.1_Intron|RALGAPB_uc002xix.2_Intron	NM_020336	NP_065069	Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2						GTATGtttatcttttttttttt	0.089													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37231052	37231053	+	IGR	INS	-	AT	AT	rs146453991		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37231052_37231053insAT								ADIG (13948 upstream) : SLC32A1 (122052 downstream)																							TCTGGGTGTAGAGTCTTAGGGG	0.564													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	40731706	40731706	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40731706delC	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)				CTGGCATTTGCCCACTGACTT	0.478													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41739026	41739026	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41739026delT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				ccacatgggatttggtagaga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48517539	48517539	+	IGR	DEL	A	-	-	rs73625446		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48517539delA								SLC9A8 (8767 upstream) : SPATA2 (2392 downstream)																							cgtctcaaagaaaaaaaaaaa	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	48595402	48595402	+	IGR	DEL	A	-	-	rs145350714		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48595402delA								RNF114 (24982 upstream) : SNAI1 (4125 downstream)																							ACACTGGTTTAAAAAAAAAAA	0.303													4	3	---	---	---	---	
KCNG1	3755	broad.mit.edu	37	20	49622410	49622411	+	Intron	DEL	GG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49622410_49622411delGG	uc002xwa.3	-							NM_002237	NP_002228	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G,							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2						TCTGTCTCTAGGAATATGTTAG	0.525													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55658474	55658475	+	IGR	DEL	TG	-	-	rs72046343		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55658474_55658475delTG								TFAP2C (444138 upstream) : BMP7 (85334 downstream)																							cgtgtgtgcatgtgtgtacgtg	0.000													3	3	---	---	---	---	
CTCFL	140690	broad.mit.edu	37	20	56079340	56079341	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56079340_56079341insT	uc010gix.1	-						CTCFL_uc010giw.1_Intron|CTCFL_uc002xym.2_Intron|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Intron|CTCFL_uc010gjb.1_Intron|CTCFL_uc010gjc.1_Intron|CTCFL_uc010gjd.1_Intron|CTCFL_uc010gje.2_Intron|CTCFL_uc010gjf.2_Intron|CTCFL_uc010gjg.2_Intron|CTCFL_uc010giu.2_Intron|CTCFL_uc010giv.2_Intron	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein						cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			ccCCCGTCTCCttttttttttt	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9829296	9829297	+	IGR	DEL	AG	-	-	rs79571350	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9829296_9829297delAG								None (None upstream) : None (None downstream)																							acacacacacagacactctcac	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9834353	9834354	+	IGR	INS	-	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9834353_9834354insG								None (None upstream) : None (None downstream)																							GATCTGTGATTAAAAAAAATGC	0.262													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9851541	9851541	+	IGR	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9851541delC								None (None upstream) : None (None downstream)																							aaataccagacctttgaatca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10834177	10834181	+	IGR	DEL	GAATG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10834177_10834181delGAATG								None (None upstream) : TPTE (72562 downstream)																							aaatagattagaatggaatggaatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10839945	10839946	+	IGR	INS	-	GAATG	GAATG	rs138986237	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10839945_10839946insGAATG								None (None upstream) : TPTE (66797 downstream)																							ggaatggactcgaatggaatgg	0.000													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11035978	11035979	+	Intron	INS	-	G	G	rs141469297		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11035978_11035979insG	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CAAATGGTTTACAATTATCTGC	0.307													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088487	11088488	+	Intron	DEL	TG	-	-	rs59973390	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088487_11088488delTG	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tttgtttttttgttgttgttgt	0.114													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11112605	11112606	+	IGR	DEL	AT	-	-	rs141194664		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11112605_11112606delAT								BAGE (13668 upstream) : None (None downstream)																							CTATTCTACCATATGTGTTGAA	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14356250	14356251	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14356250_14356251insT								None (None upstream) : C21orf99 (54236 downstream)																							cttctttctagtttttatgtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14360934	14360934	+	IGR	DEL	G	-	-	rs113186537		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14360934delG								None (None upstream) : C21orf99 (49553 downstream)																							ttctaccataggtcgcaaagc	0.000													4	4	---	---	---	---	
C21orf81	391267	broad.mit.edu	37	21	15347257	15347258	+	Intron	INS	-	A	A	rs80199214		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15347257_15347258insA	uc002yji.2	-							NR_027270				Homo sapiens C21orf81 protein (C21orf81) mRNA, complete cds.												0						ACCCTGCACAGAAAAAAAGTTG	0.307													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20316671	20316672	+	IGR	INS	-	CA	CA	rs149105971	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20316671_20316672insCA								TMPRSS15 (540701 upstream) : None (None downstream)																							ATTTTGTTTCTcacacacacac	0.203													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	20680060	20680063	+	IGR	DEL	ATGG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20680060_20680063delATGG								TMPRSS15 (904090 upstream) : None (None downstream)																							TAAAGACCTAATGGATGGATGGAT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	23605003	23605003	+	IGR	DEL	A	-	-	rs66463347		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23605003delA								NCAM2 (693789 upstream) : None (None downstream)																							ggaaggaaggaaaagaaggaa	0.169													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	25406061	25406061	+	IGR	DEL	A	-	-	rs67671662		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25406061delA								None (None upstream) : None (None downstream)																							CCAAGCCTACAAAACCTCAGT	0.303													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	26555324	26555327	+	IGR	DEL	GTGT	-	-	rs72284829		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26555324_26555327delGTGT								None (None upstream) : NCRNA00158 (202807 downstream)																							ACTGAATATAgtgtgtgtgtgtgt	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	29546596	29546597	+	Intron	INS	-	TTCCTTCC	TTCCTTCC	rs143733666	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29546596_29546597insTTCCTTCC	uc002yml.2	-											Homo sapiens cDNA clone IMAGE:5541115, partial cds.																		ccttccgttctttccttccttc	0.124													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	31630915	31630916	+	IGR	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31630915_31630916delGT								CLDN8 (42597 upstream) : KRTAP24-1 (22713 downstream)																							CATtgtgtgcgtgtgtgtgtgc	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	32949381	32949382	+	IGR	INS	-	A	A			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32949381_32949382insA								TIAM1 (17091 upstream) : SOD1 (82553 downstream)																							AACAAACAAACAAAAAAAACAC	0.248													3	3	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36288872	36288872	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36288872delC	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						tctgaaagggctgaggaggga	0.000			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	37520836	37520836	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37520836delT	uc002yvc.1	-						uc002yvd.1_Intron|uc002yvf.1_Intron					Homo sapiens mRNA expressed in placenta, clone IMAGE:139776.																		TCTTTCATAAttttttttttt	0.025													4	2	---	---	---	---	
HLCS	3141	broad.mit.edu	37	21	38206719	38206719	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38206719delT	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)	GCATTGAAAGTAGCCAGGTGG	0.582													4	2	---	---	---	---	
ERG	2078	broad.mit.edu	37	21	39776679	39776679	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39776679delA	uc010gnw.2	-						ERG_uc002yxa.2_Intron|ERG_uc011aek.1_Intron|ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc011aem.1_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gny.1_5'Flank	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)				CTTAGGGGTCAGGCATGCCAG	0.323													4	2	---	---	---	---	
ABCG1	9619	broad.mit.edu	37	21	43621170	43621170	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43621170delT	uc002zan.2	+						ABCG1_uc002zam.2_Intron	NM_207627	NP_997510	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1						amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|recycling endosome	ADP binding|ATP binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)|central_nervous_system(1)	3					Adenosine triphosphate(DB00171)	catattgtgcttttttttttc	0.000													4	2	---	---	---	---	
RSPH1	89765	broad.mit.edu	37	21	43913095	43913095	+	Frame_Shift_Del	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43913095delA	uc002zbg.2	-	2	254	c.149delT	c.(148-150)TTCfs	p.F50fs		NM_080860	NP_543136	Q8WYR4	RSPH1_HUMAN	testis-specific gene A2	50	MORN 2.				meiosis	cytosol|nucleus				ovary(1)	1						TCTTTTACCGAATTCGTAGCT	0.502													83	49	---	---	---	---	
AGPAT3	56894	broad.mit.edu	37	21	45340089	45340090	+	Intron	DEL	TG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45340089_45340090delTG	uc002zdv.2	+							NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		TCTTCAGCCCtgtgtgtgtgtg	0.282													4	2	---	---	---	---	
TRAPPC10	7109	broad.mit.edu	37	21	45489778	45489778	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45489778delT	uc002zea.2	+						TRAPPC10_uc010gpo.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						gaaggcatacttttttttttt	0.000													4	2	---	---	---	---	
C21orf56	84221	broad.mit.edu	37	21	47590592	47590592	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47590592delT	uc011afu.1	-						C21orf56_uc002zii.2_Intron	NM_001142854	NP_001136326	Q9H0A9	CU056_HUMAN	hypothetical protein LOC84221 isoform 1								protein binding			skin(1)	1	Breast(49;0.214)			Colorectal(79;0.241)		GGGAGGAGCCTCCCTGCTCTG	0.592													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16919714	16919715	+	IGR	INS	-	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16919714_16919715insG								OR11H1 (469910 upstream) : CCT8L2 (151933 downstream)																							AGGGAAAATTTGGGGGAAATTA	0.337													4	2	---	---	---	---	
TUBA8	51807	broad.mit.edu	37	22	18570618	18570618	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18570618delA	uc002znr.2	+						PEX26_uc002znp.3_Intron|PEX26_uc002znq.3_Intron|PEX26_uc002znt.2_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						ccctgtctctaaaaaaaacaa	0.239													9	8	---	---	---	---	
GGT3P	2679	broad.mit.edu	37	22	18795006	18795009	+	5'Flank	DEL	CAAA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18795006_18795009delCAAA	uc002zob.1	-											Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0						AAAAGGTCCCCAAACAAAGAATCC	0.314													5	3	---	---	---	---	
LOC96610	96610	broad.mit.edu	37	22	22905748	22905749	+	Intron	INS	-	A	A	rs141423086	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22905748_22905749insA	uc011aim.1	+						LOC648691_uc011ais.1_Intron					Parts of antibodies, mostly variable regions.												0						TGACAAGAGATACTTTAAGACT	0.431													4	2	---	---	---	---	
SGSM1	129049	broad.mit.edu	37	22	25285927	25285927	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25285927delT	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						cTTAAATGGAttttttttttt	0.010													4	3	---	---	---	---	
SEZ6L	23544	broad.mit.edu	37	22	26723375	26723376	+	Intron	INS	-	CA	CA	rs139127644	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26723375_26723376insCA	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Intron|SEZ6L_uc010gvc.1_Intron	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6						cacatacacaccacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	31710690	31710690	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31710690delA								PIK3IP1 (22170 upstream) : PATZ1 (11101 downstream)																							tctgtgcagcaaaccaccatg	0.050													4	2	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	33951392	33951392	+	Intron	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33951392delA	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				agtcctcttgaaaaaaaaaat	0.174													4	2	---	---	---	---	
IFT27	11020	broad.mit.edu	37	22	37167092	37167093	+	Intron	DEL	GT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37167092_37167093delGT	uc003apv.1	-						IFT27_uc003apu.1_Intron|IFT27_uc003apw.1_Intron|IFT27_uc010gwy.1_Intron	NM_006860	NP_006851	Q9BW83	IFT27_HUMAN	RAB, member of RAS oncogene family-like 4						small GTPase mediated signal transduction	intraflagellar transport particle B|microtubule-based flagellum	GTP binding				0						ctgtcttggggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
MGAT3	4248	broad.mit.edu	37	22	39871638	39871638	+	Intron	DEL	C	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39871638delC	uc003axv.3	+							NM_002409	NP_002400	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity				0	Melanoma(58;0.04)					AGGCTTGGCGCCCTGGGATGC	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	40384712	40384713	+	IGR	INS	-	G	G	rs145273362	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40384712_40384713insG								GRAP2 (4356 upstream) : FAM83F (6240 downstream)																							AAGGGAGGAGTGGGGAGTGGCA	0.396													6	3	---	---	---	---	
TNRC6B	23112	broad.mit.edu	37	22	40446832	40446833	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40446832_40446833insT	uc003aym.2	+							NM_001024843	NP_001020014	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 3						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						ttgtttttgggttttttttttt	0.109													4	3	---	---	---	---	
EFCAB6	64800	broad.mit.edu	37	22	44139870	44139881	+	Intron	DEL	AATGGATGAATG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44139870_44139881delAATGGATGAATG	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				tagataggtaaatggatgaatgaatggatgaa	0.000													4	2	---	---	---	---	
PARVB	29780	broad.mit.edu	37	22	44545506	44545506	+	Intron	DEL	G	-	-	rs9626116	by1000genomes	TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44545506delG	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_Intron	NM_013327	NP_037459	Q9HBI1	PARVB_HUMAN	parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)				TGGTCTTAACGGGGGTCCGCA	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	47774748	47774750	+	IGR	DEL	GAG	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47774748_47774750delGAG								TBC1D22A (205026 upstream) : None (None downstream)																							ggaggaagaagagaagaaggaag	0.099													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49153040	49153042	+	IGR	DEL	AGA	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49153040_49153042delAGA								FAM19A5 (5298 upstream) : C22orf34 (655134 downstream)																							AAggaggaggagaagggaggagg	0.069													7	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	432601	432601	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:432601delT								PPP2R3B (84974 upstream) : SHOX (152478 downstream)																							TGGATATGTATTTTTTTTTTT	0.433													4	2	---	---	---	---	
CDKL5	6792	broad.mit.edu	37	X	18626213	18626214	+	Intron	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18626213_18626214insT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)					AAAATGCTGTGTTTTTTCCCCT	0.386													4	2	---	---	---	---	
RPS6KA3	6197	broad.mit.edu	37	X	20206603	20206603	+	Intron	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20206603delT	uc004czu.2	-						RPS6KA3_uc011mjk.1_Intron|RPS6KA3_uc004czv.2_Intron|RPS6KA3_uc011mjl.1_Intron|RPS6KA3_uc011mjm.1_Intron	NM_004586	NP_004577	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1)	8						AAAACGAGGATTTTTTTTTTA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	56860923	56860923	+	IGR	DEL	A	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56860923delA								LOC550643 (16921 upstream) : SPIN3 (141882 downstream)																							tccaattctgaaagcctgaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61691992	61691993	+	IGR	DEL	AT	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61691992_61691993delAT								None (None upstream) : SPIN4 (875115 downstream)																							agcagtccaaatctccatttgc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61710637	61710637	+	IGR	DEL	A	-	-	rs141330468		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61710637delA								None (None upstream) : SPIN4 (856471 downstream)																							atgtgaagatatttccttttc	0.000													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	61815648	61815648	+	IGR	DEL	T	-	-			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61815648delT								None (None upstream) : SPIN4 (751460 downstream)																							cagaaactactttgtgatgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13270122	13270122	+	IGR	DEL	T	-	-	rs75692746		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13270122delT								None (None upstream) : None (None downstream)																							atttcttttctttttcttttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13433429	13433430	+	IGR	INS	-	G	G			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13433429_13433430insG								None (None upstream) : None (None downstream)																							tgtcttaaaaaaaaaagaaaaa	0.119													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13444778	13444779	+	IGR	INS	-	T	T			TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13444778_13444779insT								None (None upstream) : None (None downstream)																							CTCAAAGGTAATTTTTTCTTTA	0.327													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59016025	59016026	+	IGR	INS	-	A	A	rs7067360		TCGA-66-2795-01A-02D-0983-08	TCGA-66-2795-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59016025_59016026insA								None (None upstream) : None (None downstream)																							cgtctaaaaagaaaaaaaaaTT	0.144													11	5	---	---	---	---	
