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
SPEN	23013	broad.mit.edu	37	1	16255505	16255505	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16255505C>T	uc001axk.1	+	11	2974	c.2770C>T	c.(2770-2772)CCT>TCT	p.P924S	SPEN_uc010obp.1_Missense_Mutation_p.P883S	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	924					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)		TCAGACGGAGCCTGCAAAATC	0.453													17	72	---	---	---	---	PASS
CLCNKB	1188	broad.mit.edu	37	1	16383574	16383574	+	3'UTR	SNP	A	T	T	rs1057841		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16383574A>T	uc001axw.3	+	20					FAM131C_uc010obz.1_Intron|CLCNKB_uc001axx.3_3'UTR|CLCNKB_uc001axy.3_3'UTR	NM_000085	NP_000076	P51801	CLCKB_HUMAN	chloride channel Kb isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			skin(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		AGGATGGCTCATCCTGGGTGG	0.542													3	45	---	---	---	---	PASS
GBP1	2633	broad.mit.edu	37	1	89521767	89521767	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89521767G>A	uc001dmx.2	-	8	1520	c.1300C>T	c.(1300-1302)CGT>TGT	p.R434C		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	434					interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		ACAAAGAGACGATAGCCCCCT	0.428													8	372	---	---	---	---	PASS
CDC7	8317	broad.mit.edu	37	1	91978791	91978791	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91978791C>T	uc001doe.2	+	7	914	c.749C>T	c.(748-750)TCC>TTC	p.S250F	CDC7_uc001dof.2_Missense_Mutation_p.S250F|CDC7_uc010osw.1_Missense_Mutation_p.S222F|CDC7_uc009wdc.2_Missense_Mutation_p.S250F|CDC7_uc009wdd.2_5'Flank	NM_003503	NP_003494	O00311	CDC7_HUMAN	cell division cycle 7	250	Protein kinase.				cell cycle checkpoint|cell division|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|positive regulation of cell proliferation|regulation of S phase	cytoplasm|nucleoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	5		all_lung(203;0.0165)|Lung NSC(277;0.0562)		all cancers(265;0.00108)|Epithelial(280;0.0184)|KIRC - Kidney renal clear cell carcinoma(1967;0.124)		GATCAGCAGTCCACCACAAAA	0.408													78	226	---	---	---	---	PASS
SPAG17	200162	broad.mit.edu	37	1	118509258	118509258	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118509258T>C	uc001ehk.2	-	47	6574	c.6506A>G	c.(6505-6507)GAG>GGG	p.E2169G		NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	2169						cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GAACAGAACCTCATGCTCTGT	0.408													6	304	---	---	---	---	PASS
LOC200030	200030	broad.mit.edu	37	1	148251814	148251814	+	Intron	SNP	T	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148251814T>A	uc001eqe.2	-						LOC200030_uc001eqf.2_Intron|LOC200030_uc001eqg.2_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc009wkf.1_Intron|uc010pah.1_3'UTR|uc010pai.1_3'UTR|uc001eqz.2_3'UTR|uc001erb.2_3'UTR|uc001erd.3_3'UTR|uc001erc.3_RNA|uc010paj.1_3'UTR			Q86T75	NBPFB_HUMAN	SubName: Full=cDNA FLJ78770;							cytoplasm					0						TTCATTCAAATCTTCACGTGC	0.488													5	54	---	---	---	---	PASS
LOC728855	728855	broad.mit.edu	37	1	149648794	149648794	+	Intron	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149648794T>C	uc009wlc.2	+						LOC728855_uc009wld.2_Intron|uc001eso.1_RNA					Homo sapiens mRNA, chromosome 1 specific transcript KIAA0493.												0						TGTTGAATGCTTCCAGCCAAC	0.428													8	490	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152327955	152327955	+	Silent	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152327955G>A	uc001ezw.3	-	3	2380	c.2307C>T	c.(2305-2307)AGC>AGT	p.S769S	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	769	Ser-rich.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTTGGCCATAGCTAGACTGAC	0.517													4	167	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158609713	158609713	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158609713G>A	uc001fst.1	-	34	5021	c.4822C>T	c.(4822-4824)CGT>TGT	p.R1608C		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1608	Spectrin 16.				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)					CTCTGTTGACGACTGGCCTCA	0.463													129	429	---	---	---	---	PASS
DCAF6	55827	broad.mit.edu	37	1	167960476	167960476	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167960476C>A	uc001gew.2	+	6	829	c.587C>A	c.(586-588)TCT>TAT	p.S196Y	DCAF6_uc001gev.2_Missense_Mutation_p.S196Y|DCAF6_uc001gex.2_Missense_Mutation_p.S196Y|DCAF6_uc010plk.1_Missense_Mutation_p.S165Y|DCAF6_uc001gey.2_Missense_Mutation_p.S49Y	NM_001017977	NP_001017977	Q58WW2	DCAF6_HUMAN	IQ motif and WD repeats 1 isoform b	196	WD 4.				positive regulation of transcription from RNA polymerase II promoter	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						GCTGCCACGTCTGTTGCTATT	0.373													19	324	---	---	---	---	PASS
C1orf112	55732	broad.mit.edu	37	1	169798656	169798656	+	Intron	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169798656A>G	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc010plu.1_3'UTR|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN	hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGAAATTGTGATTCATATACA	0.338													5	173	---	---	---	---	PASS
C1orf129	80133	broad.mit.edu	37	1	170914714	170914714	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170914714C>T	uc001ghg.2	+	2	147	c.17C>T	c.(16-18)CCA>CTA	p.P6L	C1orf129_uc009wvy.2_5'UTR|C1orf129_uc010plz.1_Missense_Mutation_p.P6L	NM_025063	NP_079339	Q5TGP6	CA129_HUMAN	hypothetical protein LOC80133 isoform 2	6							binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ACAAGGAATCCAAAAACAAGT	0.338													95	344	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	185985179	185985179	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185985179G>T	uc001grq.1	+	32	5228	c.4999G>T	c.(4999-5001)GGA>TGA	p.G1667*		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	1667	Ig-like C2-type 14.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						CAAAGCTGCTGGAAACCCTTC	0.448													48	170	---	---	---	---	PASS
KIF21B	23046	broad.mit.edu	37	1	200943295	200943295	+	Silent	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200943295G>A	uc001gvs.1	-	35	5159	c.4842C>T	c.(4840-4842)TAC>TAT	p.Y1614Y	KIF21B_uc001gvr.1_Silent_p.Y1601Y|KIF21B_uc009wzl.1_Intron|KIF21B_uc010ppn.1_Intron	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1614	WD 7.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						GTCCAGGGACGTAATTCCACA	0.313													24	82	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201021722	201021722	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201021722A>G	uc001gvv.2	-	32	4143	c.3916T>C	c.(3916-3918)TTC>CTC	p.F1306L		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1306	Extracellular (Potential).|IV.				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	AAGGTCTGGAAGTTGTTGTTC	0.547													7	236	---	---	---	---	PASS
NENF	29937	broad.mit.edu	37	1	212619210	212619210	+	Silent	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212619210G>A	uc001hjd.2	+	4	438	c.381G>A	c.(379-381)GAG>GAA	p.E127E	NENF_uc010ptf.1_RNA	NM_013349	NP_037481	Q9UMX5	NENF_HUMAN	neuron derived neurotrophic factor precursor	127	Cytochrome b5 heme-binding.					extracellular space	heme binding				0				all cancers(67;0.00967)|OV - Ovarian serous cystadenocarcinoma(81;0.0108)|GBM - Glioblastoma multiforme(131;0.0325)|Epithelial(68;0.132)		CCCTGGATGAGGTCTTCACCA	0.537													26	69	---	---	---	---	PASS
DNAH14	127602	broad.mit.edu	37	1	225288430	225288430	+	Silent	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225288430A>G	uc001how.2	+	23	3926	c.3711A>G	c.(3709-3711)GAA>GAG	p.E1237E		NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform	Error:Variant_position_missing_in_Q0VDD8_after_alignment					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						TCCCAGCAGAAACAGAACTTT	0.323													4	89	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237982384	237982384	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237982384G>A	uc001hyl.1	+	101	14602	c.14482G>A	c.(14482-14484)GGG>AGG	p.G4828R	RYR2_uc010pyb.1_Missense_Mutation_p.G261R	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4828					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)			AGGAGGGATCGGGGATGAAAT	0.408													7	498	---	---	---	---	PASS
PPPDE1	51029	broad.mit.edu	37	1	244868992	244868992	+	Silent	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244868992A>G	uc001iao.2	+	5	750	c.486A>G	c.(484-486)GAA>GAG	p.E162E	PPPDE1_uc001iap.2_Silent_p.E129E|PPPDE1_uc001iaq.1_RNA	NM_016076	NP_057160	Q9BSY9	PPDE1_HUMAN	PPPDE peptidase domain containing 1	162										breast(3)	3						TCAGCCAAGAACTCCAGGATG	0.572													13	44	---	---	---	---	PASS
OR6F1	343169	broad.mit.edu	37	1	247875599	247875599	+	Missense_Mutation	SNP	G	T	T	rs144440883	byFrequency	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247875599G>T	uc001idj.1	-	1	459	c.459C>A	c.(457-459)TTC>TTA	p.F153L		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	153	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			CAATGGCCACGAAACCACACA	0.587													8	23	---	---	---	---	PASS
YIPF4	84272	broad.mit.edu	37	2	32517399	32517399	+	Silent	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32517399A>G	uc002rok.2	+	3	654	c.387A>G	c.(385-387)TCA>TCG	p.S129S		NM_032312	NP_115688	Q9BSR8	YIPF4_HUMAN	Yip1 domain family, member 4	129	Helical; (Potential).					endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)					CCATGATATCATTATATGGAC	0.299													106	326	---	---	---	---	PASS
TMEM150A	129303	broad.mit.edu	37	2	85828190	85828190	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85828190C>T	uc002spw.1	-	3	875	c.154G>A	c.(154-156)GGG>AGG	p.G52R	USP39_uc002sqb.2_5'Flank|TMEM150A_uc002spx.1_5'UTR|TMEM150A_uc002spz.1_Silent_p.K21K|TMEM150A_uc002sqa.1_5'UTR|TMEM150A_uc002spy.1_Missense_Mutation_p.G52R	NM_001031738	NP_001026908	Q86TG1	T150A_HUMAN	transmembrane protein 150A isoform 1	52	Extracellular (Potential).					integral to membrane|plasma membrane					0						TTGGGACCCCCTTGCTCAGCA	0.642													9	19	---	---	---	---	PASS
RGPD4	285190	broad.mit.edu	37	2	108507242	108507242	+	3'UTR	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108507242C>A	uc010ywk.1	+	23					RGPD4_uc002tdu.2_3'UTR|RGPD4_uc010ywl.1_RNA	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4						intracellular transport		binding			skin(2)	2						GTTTGGACTTCGATAGGTTGA	0.313													147	525	---	---	---	---	PASS
SLC35F5	80255	broad.mit.edu	37	2	114503891	114503891	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114503891G>A	uc002tku.1	-	5	867	c.443C>T	c.(442-444)GCT>GTT	p.A148V	SLC35F5_uc002tkt.2_RNA|SLC35F5_uc002tkv.2_Missense_Mutation_p.A142V|SLC35F5_uc002tkw.2_Missense_Mutation_p.A148V	NM_025181	NP_079457	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	148					transport	integral to membrane					0						TGTGCAAGCAGCAAAGTAACC	0.373													4	304	---	---	---	---	PASS
ERCC3	2071	broad.mit.edu	37	2	128036918	128036918	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128036918C>A	uc002toh.1	-	10	1656	c.1561G>T	c.(1561-1563)GAA>TAA	p.E521*	ERCC3_uc002toe.1_Nonsense_Mutation_p.E276*|ERCC3_uc002tof.1_Nonsense_Mutation_p.E457*|ERCC3_uc002tog.1_Nonsense_Mutation_p.E457*	NM_000122	NP_000113	P19447	ERCC3_HUMAN	excision repair cross-complementing rodent	521					cell cycle checkpoint|DNA topological change|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA duplex unwinding|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein localization|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	3'-5' DNA helicase activity|ATP binding|damaged DNA binding|protein C-terminus binding|protein N-terminus binding|transcription factor binding			ovary(2)|lung(2)|breast(2)|kidney(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GCCACATATTCCCGGTAAAAT	0.388			Mis|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				48	163	---	---	---	---	PASS
GPD2	2820	broad.mit.edu	37	2	157426664	157426664	+	Silent	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157426664G>A	uc002tzf.3	+	12	1902	c.1542G>A	c.(1540-1542)GTG>GTA	p.V514V	GPD2_uc010zch.1_Silent_p.V287V|GPD2_uc002tzd.3_Silent_p.V514V|GPD2_uc002tze.1_RNA	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,	514					cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						TGGCAAGTGTGACTGGCAAAA	0.463													19	253	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179447134	179447134	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179447134C>A	uc010zfg.1	-	263	58569	c.58345G>T	c.(58345-58347)GTG>TTG	p.V19449L	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V13144L|TTN_uc010zfi.1_Missense_Mutation_p.V13077L|TTN_uc010zfj.1_Missense_Mutation_p.V12952L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20376							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)			AGTTTCTCCACGCTGCAGCTG	0.463													7	156	---	---	---	---	PASS
C2orf67	151050	broad.mit.edu	37	2	210889861	210889861	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210889861C>T	uc002vds.2	-	13	2739	c.2531G>A	c.(2530-2532)TGG>TAG	p.W844*	C2orf67_uc002vdt.2_Nonsense_Mutation_p.W802*	NM_152519	NP_689732	A0AUZ9	CB067_HUMAN	hypothetical protein LOC151050	844										ovary(3)	3		Renal(323;0.202)		Epithelial(149;0.00435)|Lung(261;0.0529)|LUSC - Lung squamous cell carcinoma(261;0.0551)|all cancers(144;0.0696)		GCTTTGCTCCCATAGTGACCA	0.398													119	377	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216274775	216274775	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216274775G>C	uc002vfa.2	-	14	2270	c.2004C>G	c.(2002-2004)ATC>ATG	p.I668M	FN1_uc002vfb.2_Missense_Mutation_p.I668M|FN1_uc002vfc.2_Missense_Mutation_p.I668M|FN1_uc002vfd.2_Missense_Mutation_p.I668M|FN1_uc002vfe.2_Missense_Mutation_p.I668M|FN1_uc002vff.2_Missense_Mutation_p.I668M|FN1_uc002vfg.2_Missense_Mutation_p.I668M|FN1_uc002vfh.2_Missense_Mutation_p.I668M|FN1_uc002vfi.2_Missense_Mutation_p.I668M|FN1_uc002vfj.2_Missense_Mutation_p.I668M	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	668	Fibronectin type-III 1.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TCAGGCCTTTGATGGTGTAGG	0.433													76	215	---	---	---	---	PASS
TMEM169	92691	broad.mit.edu	37	2	216960587	216960587	+	5'UTR	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216960587G>A	uc010zjr.1	+	3					TMEM169_uc010zjs.1_5'UTR|TMEM169_uc002vfw.2_5'UTR|TMEM169_uc002vfv.3_5'UTR	NM_001142310	NP_001135782	Q96HH4	TM169_HUMAN	transmembrane protein 169							integral to membrane				ovary(1)	1		Renal(323;0.0651)		Epithelial(149;6.44e-06)|all cancers(144;0.000398)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGACATCTTTGCATAGCCCCA	0.448													9	14	---	---	---	---	PASS
TNS1	7145	broad.mit.edu	37	2	218669158	218669158	+	3'UTR	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218669158C>A	uc002vgt.2	-	33					TNS1_uc002vgr.2_3'UTR|TNS1_uc002vgs.2_3'UTR|TNS1_uc002vgq.2_3'UTR	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		CCCCATGGCACTGGCCCTGGG	0.582													6	23	---	---	---	---	PASS
UGT1A3	54659	broad.mit.edu	37	2	234638169	234638169	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234638169C>T	uc002vuy.2	+	1	397	c.397C>T	c.(397-399)CAT>TAT	p.H133Y	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A5_uc002vuw.2_Intron|UGT1A4_uc010zna.1_Intron|UGT1A4_uc002vux.2_Intron|UGT1A3_uc010znb.1_Missense_Mutation_p.H133Y	NM_019093	NP_061966	P35503	UD13_HUMAN	UDP glycosyltransferase 1 family, polypeptide A3	133					flavonoid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding			ovary(1)	1		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599)		GGAGCTACTACATAATGAGGC	0.428													6	255	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47079269	47079269	+	Splice_Site	SNP	T	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47079269T>A	uc003cqs.2	-	18	7292	c.7239_splice	c.e18-1	p.R2413_splice	SETD2_uc003cqv.2_Splice_Site_p.R2480_splice|SETD2_uc003cqr.2_Splice_Site_p.L12_splice	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TGAGTCTGCCTAGAAAGAGAC	0.448			N|F|S|Mis		clear cell renal carcinoma								20	63	---	---	---	---	PASS
NEK4	6787	broad.mit.edu	37	3	52775495	52775495	+	Silent	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52775495A>G	uc003dfq.3	-	13	2214	c.2025T>C	c.(2023-2025)TGT>TGC	p.C675C	NEK4_uc011bej.1_Silent_p.C586C|NEK4_uc003dfr.2_Silent_p.C629C	NM_003157	NP_003148	P51957	NEK4_HUMAN	NIMA-related kinase 4	675					cell division|mitosis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		CCTCAGACAGACAATGAATCT	0.363													8	310	---	---	---	---	PASS
MYH15	22989	broad.mit.edu	37	3	108149721	108149721	+	Silent	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108149721T>C	uc003dxa.1	-	27	3387	c.3330A>G	c.(3328-3330)AAA>AAG	p.K1110K		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1110	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7						CTACCAGGCCTTTCTCATTCT	0.328													6	438	---	---	---	---	PASS
STXBP5L	9515	broad.mit.edu	37	3	120973846	120973846	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120973846G>A	uc003eec.3	+	16	1686	c.1546G>A	c.(1546-1548)GCC>ACC	p.A516T	STXBP5L_uc011bji.1_Missense_Mutation_p.A516T	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	516					exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		AGACCCATTTGCCATTCAGAT	0.363													5	281	---	---	---	---	PASS
TRIM59	286827	broad.mit.edu	37	3	160156796	160156796	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160156796C>T	uc003fdm.2	-	3	371	c.176G>A	c.(175-177)TGC>TAC	p.C59Y	IFT80_uc003fda.2_RNA	NM_173084	NP_775107	Q8IWR1	TRI59_HUMAN	tripartite motif-containing 59	59	RING-type.					integral to membrane|intracellular	zinc ion binding				0			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AATACTTCTGCAATTAGGGCA	0.358													5	377	---	---	---	---	PASS
PIGG	54872	broad.mit.edu	37	4	533277	533277	+	3'UTR	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:533277G>A	uc003gak.3	+	13					PIGG_uc003gaj.3_3'UTR|PIGG_uc011bux.1_RNA|PIGG_uc010ibf.2_3'UTR|PIGG_uc003gal.3_3'UTR	NM_001127178	NP_001120650	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			central_nervous_system(2)|ovary(1)|skin(1)	4						CCTGAATTTAGACTAAGCAGT	0.284													5	18	---	---	---	---	PASS
JAKMIP1	152789	broad.mit.edu	37	4	6055538	6055538	+	3'UTR	SNP	A	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6055538A>T	uc003giu.3	-	13					JAKMIP1_uc010idb.1_Intron|JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Intron|JAKMIP1_uc011bwc.1_3'UTR|JAKMIP1_uc003giv.3_3'UTR|JAKMIP1_uc010ide.2_3'UTR	NM_144720	NP_653321	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein						protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						CAATAAATATATTAGCTCTGG	0.299													9	18	---	---	---	---	PASS
POLR2B	5431	broad.mit.edu	37	4	57896551	57896551	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57896551C>T	uc003hcl.1	+	24	3464	c.3421C>T	c.(3421-3423)CGC>TGC	p.R1141C	POLR2B_uc011cae.1_Missense_Mutation_p.R1134C|POLR2B_uc011caf.1_Missense_Mutation_p.R1066C|POLR2B_uc003hcm.1_Missense_Mutation_p.R634C	NM_000938	NP_000929	P30876	RPB2_HUMAN	DNA directed RNA polymerase II polypeptide B	1141					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)					CAGGGGCTGCCGCAATAAAAC	0.433													4	105	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79420893	79420893	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79420893A>C	uc003hlb.2	+	61	9574	c.9134A>C	c.(9133-9135)GAA>GCA	p.E3045A	FRAS1_uc003hlc.1_Missense_Mutation_p.E47A	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3040	Calx-beta 5.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						ATTGAGTTTGAAGAAGCTGCA	0.483													40	124	---	---	---	---	PASS
ADAD1	132612	broad.mit.edu	37	4	123333824	123333824	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123333824T>C	uc003ieo.2	+	10	1341	c.1109T>C	c.(1108-1110)GTT>GCT	p.V370A	ADAD1_uc003iep.2_Missense_Mutation_p.V359A|ADAD1_uc003ieq.2_Missense_Mutation_p.V352A	NM_139243	NP_640336	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1	370	A to I editase.				multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0						TATCTGACTGTTTACTGTCCT	0.408													7	344	---	---	---	---	PASS
SPATA5	166378	broad.mit.edu	37	4	124177248	124177248	+	Silent	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124177248T>C	uc003iez.3	+	15	2491	c.2418T>C	c.(2416-2418)TTT>TTC	p.F806F		NM_145207	NP_660208	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	806					cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0						GGGAAATATTTAAGCTGCAGT	0.433													6	350	---	---	---	---	PASS
ANXA10	11199	broad.mit.edu	37	4	169085402	169085402	+	Silent	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169085402T>C	uc003irm.2	+	5	508	c.363T>C	c.(361-363)AAT>AAC	p.N121N	ANXA10_uc003irn.2_5'Flank	NM_007193	NP_009124	Q9UJ72	ANX10_HUMAN	annexin A10	121	Annexin 2.						calcium ion binding|calcium-dependent phospholipid binding				0		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		CAAGAACAAATGGAGAAATTT	0.313													52	300	---	---	---	---	PASS
MAP3K1	4214	broad.mit.edu	37	5	56167860	56167860	+	Splice_Site	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56167860T>C	uc003jqw.3	+	7	1924	c.1423_splice	c.e7+2	p.W475_splice		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase						cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TGTCAATTTGTATGTGGCTCT	0.438													4	208	---	---	---	---	PASS
ERAP2	64167	broad.mit.edu	37	5	96253275	96253275	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96253275C>T	uc003kmq.2	+	19	3559	c.2849C>T	c.(2848-2850)CCG>CTG	p.P950L	uc003kmo.1_Intron|ERAP2_uc003kmt.2_Missense_Mutation_p.P950L|ERAP2_uc003kmr.2_RNA|ERAP2_uc003kms.2_Missense_Mutation_p.P899L|ERAP2_uc003kmu.2_RNA	NM_022350	NP_071745	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	950	Lumenal (Potential).				antigen processing and presentation of endogenous peptide antigen via MHC class I|proteolysis|regulation of blood pressure	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding				0		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		AAGAATCTTCCGACTCTGAGG	0.264													5	347	---	---	---	---	PASS
CSNK1G3	1456	broad.mit.edu	37	5	122923847	122923847	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122923847G>T	uc003ktm.2	+	7	1478	c.759G>T	c.(757-759)AAG>AAT	p.K253N	CSNK1G3_uc003ktl.2_Missense_Mutation_p.K253N|CSNK1G3_uc003ktn.2_Missense_Mutation_p.K253N|CSNK1G3_uc003kto.2_Missense_Mutation_p.K253N|CSNK1G3_uc011cwr.1_Missense_Mutation_p.K178N|CSNK1G3_uc011cws.1_Missense_Mutation_p.K140N|CSNK1G3_uc010jda.2_Missense_Mutation_p.K253N	NM_004384	NP_004375	Q9Y6M4	KC1G3_HUMAN	casein kinase 1, gamma 3 isoform 1	253	Protein kinase.				Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)		AAGGCTTAAAGGTAATTGTTT	0.284													124	570	---	---	---	---	PASS
CATSPER3	347732	broad.mit.edu	37	5	134303651	134303651	+	5'UTR	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134303651A>G	uc003lag.2	+	1					PCBD2_uc011cxw.1_3'UTR	NM_178019	NP_821138	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGGATGCTAAAAGCAAGGAAT	0.453													32	132	---	---	---	---	PASS
PCDHB5	26167	broad.mit.edu	37	5	140517263	140517263	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140517263C>A	uc003liq.2	+	1	2464	c.2247C>A	c.(2245-2247)CAC>CAA	p.H749Q		NM_015669	NP_056484	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5 precursor	749	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGAGCTACCACTACGAGGTGT	0.627													12	70	---	---	---	---	PASS
SLC36A1	206358	broad.mit.edu	37	5	150867814	150867814	+	Nonstop_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150867814A>G	uc003luc.2	+	11	1647	c.1430A>G	c.(1429-1431)TAG>TGG	p.*477W	GM2A_uc011dcs.1_Intron	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1	477					cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)	GCCTTCATATAGGGATCTGGG	0.562													5	72	---	---	---	---	PASS
GABRG2	2566	broad.mit.edu	37	5	161569238	161569238	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161569238T>A	uc003lyz.3	+	7	1196	c.838T>A	c.(838-840)TAT>AAT	p.Y280N	GABRG2_uc010jjc.2_Missense_Mutation_p.Y320N|GABRG2_uc003lyy.3_Missense_Mutation_p.Y280N|GABRG2_uc011dej.1_Missense_Mutation_p.Y185N	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	280	Helical; (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)		CATCCAGACCTATATCCCCTG	0.443													33	513	---	---	---	---	PASS
HTR1E	3354	broad.mit.edu	37	6	87725923	87725923	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87725923C>T	uc003pli.2	+	2	1574	c.871C>T	c.(871-873)CGC>TGC	p.R291C		NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E	291	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity			ovary(2)|skin(1)	3		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Eletriptan(DB00216)	GAAGGCAGCACGCATCCTGGG	0.517													34	90	---	---	---	---	PASS
RFX6	222546	broad.mit.edu	37	6	117201735	117201735	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117201735G>A	uc003pxm.2	+	3	472	c.409G>A	c.(409-411)GGA>AGA	p.G137R		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	137	RFX-type winged-helix.				glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	protein binding|transcription regulatory region DNA binding			ovary(1)|pancreas(1)|skin(1)	3						TGTATGTGAAGGAGTTTGCTT	0.358													8	368	---	---	---	---	PASS
SERINC1	57515	broad.mit.edu	37	6	122777761	122777761	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122777761A>G	uc003pyy.1	-	3	306	c.236T>C	c.(235-237)GTC>GCC	p.V79A		NM_020755	NP_065806	Q9NRX5	SERC1_HUMAN	serine incorporator 1	79	Lumenal (Potential).				phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	L-serine transmembrane transporter activity|protein binding	p.V79L(1)		ovary(1)	1				GBM - Glioblastoma multiforme(226;0.126)		GTTACAAGGGACAACACCTTT	0.308													7	528	---	---	---	---	PASS
EPM2A	7957	broad.mit.edu	37	6	145948647	145948647	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145948647G>T	uc003qkw.2	-	4	1258	c.901C>A	c.(901-903)CCG>ACG	p.P301T	EPM2A_uc003qkv.2_Missense_Mutation_p.P301T|EPM2A_uc010khr.2_Missense_Mutation_p.A220D|EPM2A_uc003qkx.2_Missense_Mutation_p.P163T|EPM2A_uc003qku.2_Missense_Mutation_p.P147T	NM_005670	NP_005661	O95278	EPM2A_HUMAN	laforin isoform a	301	Tyrosine-protein phosphatase.		P -> L (in EPM2; loss of phosphatase activity; affects glycogen binding; disrupts the interaction with PPP1R5).		glycogen metabolic process	cytosol|endoplasmic reticulum|nucleus|plasma membrane|polysome	carbohydrate binding|identical protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		TAGACAGCCGGCCTCTTGGCC	0.567													7	32	---	---	---	---	PASS
ETV1	2115	broad.mit.edu	37	7	13935479	13935479	+	3'UTR	SNP	C	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13935479C>G	uc011jxq.1	-	14					ETV1_uc011jxn.1_3'UTR|ETV1_uc011jxo.1_3'UTR|ETV1_uc011jxp.1_3'UTR|ETV1_uc003ssw.3_3'UTR|ETV1_uc003ssx.2_RNA|ETV1_uc011jxr.1_3'UTR|ETV1_uc011jxs.1_3'UTR	NM_004956	NP_004947	P50549	ETV1_HUMAN	ets variant gene 1 isoform a						transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		TMPRSS2/ETV1(24)|EWSR1/ETV1(7)	prostate(24)|soft_tissue(4)|bone(3)|lung(2)|central_nervous_system(1)|ovary(1)	35						CCCTGCTTGACTGTCACTTGT	0.418			T	EWSR1|TMPRSS2|SLC45A3|C15orf21|HNRNPA2B1. ACSL3	Ewing sarcoma|prostate								21	71	---	---	---	---	PASS
TYW1	55253	broad.mit.edu	37	7	66582492	66582492	+	Silent	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66582492C>T	uc003tvn.2	+	13	1734	c.1585C>T	c.(1585-1587)CTG>TTG	p.L529L	TYW1_uc010lai.2_RNA|TYW1_uc011kef.1_Silent_p.L143L	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	529					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)				GGTTACTCAGCTGTATGTCAG	0.398													93	165	---	---	---	---	PASS
SPDYE7P	441251	broad.mit.edu	37	7	72338316	72338316	+	RNA	SNP	T	A	A	rs142786145	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72338316T>A	uc010lal.1	-	1		c.1340A>T				NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0						TGATTAGAGATCAGATGTCAG	0.532													9	242	---	---	---	---	PASS
MCM7	4176	broad.mit.edu	37	7	99695276	99695276	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99695276C>T	uc003usw.1	-	9	1588	c.1078G>A	c.(1078-1080)GGG>AGG	p.G360R	MCM7_uc003usv.1_Missense_Mutation_p.G184R|MCM7_uc003usx.1_Missense_Mutation_p.G184R	NM_005916	NP_005907	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	360	MCM.				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|regulation of phosphorylation|response to DNA damage stimulus|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				Atorvastatin(DB01076)	TCCACACCCCCGACTAGCAGG	0.507													129	222	---	---	---	---	PASS
ING3	54556	broad.mit.edu	37	7	120613183	120613183	+	Intron	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120613183C>T	uc003vjn.2	+						ING3_uc003vjo.2_Intron|ING3_uc003vjp.2_3'UTR|ING3_uc011kns.1_Intron	NM_019071	NP_061944	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3 isoform 1						histone H2A acetylation|histone H4 acetylation|positive regulation of apoptosis|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Piccolo NuA4 histone acetyltransferase complex	zinc ion binding			ovary(1)	1	all_neural(327;0.117)					CCAGCAGTATCATACATAAAC	0.308													5	388	---	---	---	---	PASS
CHRM2	1129	broad.mit.edu	37	7	136701169	136701169	+	3'UTR	SNP	C	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136701169C>G	uc003vtf.1	+	4					CHRM2_uc003vtg.1_3'UTR|CHRM2_uc003vtj.1_3'UTR|CHRM2_uc003vtk.1_3'UTR|CHRM2_uc003vtl.1_3'UTR|CHRM2_uc003vtm.1_3'UTR|CHRM2_uc003vti.1_3'UTR|CHRM2_uc003vto.1_3'UTR|CHRM2_uc003vtn.1_3'UTR|uc003vtp.1_Intron	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2						activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)	CTTATCACGCCTAGGCTCCAG	0.393													4	12	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	136848967	136848967	+	RNA	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136848967C>T	uc003vtp.1	-	1		c.122G>A								Homo sapiens clone N1 NTera2D1 teratocarcinoma mRNA.																		TCGCACCAACCGACCACCTCT	0.517													4	23	---	---	---	---	PASS
DENND2A	27147	broad.mit.edu	37	7	140301430	140301430	+	Silent	SNP	A	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140301430A>C	uc010lnj.2	-	1	913	c.768T>G	c.(766-768)GGT>GGG	p.G256G	DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Silent_p.G256G|DENND2A_uc003vvw.2_Silent_p.G256G|DENND2A_uc003vvx.2_Silent_p.G256G	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	256										ovary(3)|breast(1)	4	Melanoma(164;0.00956)					TTGTGGGGGAACCCTCCGAGC	0.587													7	18	---	---	---	---	PASS
CHMP7	91782	broad.mit.edu	37	8	23116262	23116262	+	Silent	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23116262G>A	uc003xdc.2	+	8	1626	c.978G>A	c.(976-978)CAG>CAA	p.Q326Q	CHMP7_uc011kzs.1_RNA|CHMP7_uc003xdd.2_Silent_p.Q216Q|CHMP7_uc003xde.2_Silent_p.Q184Q	NM_152272	NP_689485	Q8WUX9	CHMP7_HUMAN	CHMP family, member 7	326					cellular membrane organization|late endosome to vacuole transport	cytosol|ESCRT III complex	protein transporter activity				0		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		ACGCCTACCAGGCTGGGGTAG	0.468													41	108	---	---	---	---	PASS
WRN	7486	broad.mit.edu	37	8	30945246	30945246	+	Intron	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30945246G>A	uc003xio.3	+						WRN_uc011lbe.1_Intron|WRN_uc010lvk.2_5'UTR	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		AAAAAGATACGACACTGTCAG	0.363			Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				50	126	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113651000	113651000	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113651000C>T	uc003ynu.2	-	21	3610	c.3451G>A	c.(3451-3453)GGA>AGA	p.G1151R	CSMD3_uc003yns.2_Missense_Mutation_p.G423R|CSMD3_uc003ynt.2_Missense_Mutation_p.G1111R|CSMD3_uc011lhx.1_Missense_Mutation_p.G1047R	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1151	Extracellular (Potential).|CUB 6.					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						CTGAAATTTCCATAGAGACCA	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			5	285	---	---	---	---	PASS
KIAA1432	57589	broad.mit.edu	37	9	5720258	5720258	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5720258A>G	uc003zji.2	+	4	373	c.280A>G	c.(280-282)ACA>GCA	p.T94A	KIAA1432_uc003zjh.2_Missense_Mutation_p.T94A|KIAA1432_uc003zjl.3_Missense_Mutation_p.T94A|KIAA1432_uc003zjj.1_5'UTR	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a	173						integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		GGAAGGAATGACAAATGGAAG	0.398													7	564	---	---	---	---	PASS
CCL27	10850	broad.mit.edu	37	9	34662409	34662409	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34662409G>T	uc003zvm.1	-	2	134	c.75C>A	c.(73-75)TTC>TTA	p.F25L		NM_006664	NP_006655	Q9Y4X3	CCL27_HUMAN	small inducible cytokine A27 precursor	25					cell-cell signaling|chemotaxis|immune response	extracellular space	chemokine activity				0	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		GTGGCAGTAGGAATGCTAGGG	0.547													21	67	---	---	---	---	PASS
ZCCHC7	84186	broad.mit.edu	37	9	37357188	37357188	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37357188A>G	uc003zzq.2	+	9	1728	c.1555A>G	c.(1555-1557)AAG>GAG	p.K519E	ZCCHC7_uc011lqh.1_Missense_Mutation_p.K229E|ZCCHC7_uc011lqi.1_Missense_Mutation_p.K518E|ZCCHC7_uc010mlt.2_Missense_Mutation_p.K518E	NM_032226	NP_115602	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	519							nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)		GGGCAAGCAGAAGAAAAAGGA	0.433													6	176	---	---	---	---	PASS
TRDMT1	1787	broad.mit.edu	37	10	17195498	17195498	+	Intron	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17195498C>A	uc001iop.2	-						TRDMT1_uc001ioq.2_Intron|TRDMT1_uc001ior.2_Intron|TRDMT1_uc001ios.2_Intron|TRDMT1_uc009xjt.2_Intron|TRDMT1_uc010qcc.1_Intron|TRDMT1_uc010qcd.1_Missense_Mutation_p.W238C	NM_004412	NP_004403	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1 isoform						tRNA processing	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|RNA binding			ovary(1)	1						TGCACGTATCCCACATACCGA	0.378													9	628	---	---	---	---	PASS
KIAA0913	23053	broad.mit.edu	37	10	75545700	75545700	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75545700T>G	uc009xrl.2	+	1	96	c.64T>G	c.(64-66)TTT>GTT	p.F22V	KIAA0913_uc009xrk.1_Missense_Mutation_p.F119C|KIAA0913_uc001jve.2_Missense_Mutation_p.F22V|KIAA0913_uc001jvf.2_Missense_Mutation_p.F22V|uc009xrm.1_5'Flank	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053	22							zinc ion binding			breast(1)	1	Prostate(51;0.0112)					TTCGGACCGTTTTGAGGAGGA	0.478													10	28	---	---	---	---	PASS
CPXM2	119587	broad.mit.edu	37	10	125651046	125651046	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125651046C>T	uc001lhk.1	-	1	455	c.130G>A	c.(130-132)GAG>AAG	p.E44K	CPXM2_uc001lhj.2_Intron	NM_198148	NP_937791	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	44					cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TAGTAGGGCTCCCGGCTCCAG	0.736													3	1	---	---	---	---	PASS
BCCIP	56647	broad.mit.edu	37	10	127520153	127520153	+	Silent	SNP	T	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127520153T>G	uc001ljb.3	+	5	599	c.576T>G	c.(574-576)GCT>GCG	p.A192A	BCCIP_uc001ljd.3_Silent_p.A192A|BCCIP_uc010qui.1_Silent_p.A192A|BCCIP_uc001ljc.3_Silent_p.A192A|BCCIP_uc010quj.1_Silent_p.A162A	NM_078468	NP_510868	Q9P287	BCCIP_HUMAN	BRCA2 and CDKN1A-interacting protein isoform	192	Interaction with CDKN1A.				cell cycle|DNA repair|neuroendocrine cell differentiation|regulation of cyclin-dependent protein kinase activity	nuclear cyclin-dependent protein kinase holoenzyme complex	kinase regulator activity|protein binding			ovary(1)|breast(1)	2		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				CACAGATCGCTCTGCCCATGT	0.388													23	106	---	---	---	---	PASS
LOC650368	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3427845C>T	uc010qxs.1	+	9		c.838C>T			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						CTTCAAGTGGCAGGAGCAGAA	0.587													3	30	---	---	---	---	PASS
MICAL2	9645	broad.mit.edu	37	11	12278355	12278355	+	Silent	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12278355C>T	uc001mjz.2	+	24	3267	c.2979C>T	c.(2977-2979)CCC>CCT	p.P993P	MICAL2_uc010rch.1_Silent_p.P803P|MICAL2_uc001mka.2_Silent_p.P993P|MICAL2_uc010rci.1_Silent_p.P972P|MICAL2_uc001mkb.2_Silent_p.P767P|MICAL2_uc001mkc.2_Silent_p.P746P|MICAL2_uc001mkd.2_Silent_p.P575P|MICAL2_uc010rcj.1_Silent_p.P205P|MICAL2_uc001mkf.2_RNA	NM_014632	NP_055447	O94851	MICA2_HUMAN	microtubule associated monoxygenase, calponin	993						cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)		AGTCATTTCCCCTTAACCTGG	0.522													19	57	---	---	---	---	PASS
ASRGL1	80150	broad.mit.edu	37	11	62124611	62124611	+	Silent	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62124611T>C	uc001nte.3	+	4	770	c.486T>C	c.(484-486)TGT>TGC	p.C162C	ASRGL1_uc001ntf.3_Silent_p.C162C|ASRGL1_uc001ntg.3_Silent_p.C34C|ASRGL1_uc001nth.1_RNA	NM_025080	NP_079356	Q7L266	ASGL1_HUMAN	asparaginase-like 1	162					asparagine catabolic process via L-aspartate|protein maturation	cytoplasm|microtubule cytoskeleton|nucleus	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	AAACAGATTGTCAAAAGTAAG	0.368													8	413	---	---	---	---	PASS
MRPL48	51642	broad.mit.edu	37	11	73555925	73555925	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73555925A>G	uc001ouh.3	+	5	375	c.275A>G	c.(274-276)AAT>AGT	p.N92S	MRPL48_uc009ytt.2_5'UTR|MRPL48_uc010rri.1_Missense_Mutation_p.N74S|MRPL48_uc009ytu.2_5'UTR	NM_016055	NP_057139	Q96GC5	RM48_HUMAN	mitochondrial ribosomal protein L48 precursor	92					translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0						GGGGTTTTAAATATTCATCTG	0.403													80	259	---	---	---	---	PASS
NNMT	4837	broad.mit.edu	37	11	114167217	114167217	+	5'UTR	SNP	T	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114167217T>A	uc001por.1	+	3					NNMT_uc001pos.1_5'UTR	NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase						xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)	GCAGGGTCACTCCCTGGCTTC	0.483													6	21	---	---	---	---	PASS
CSDA	8531	broad.mit.edu	37	12	10865871	10865871	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10865871G>A	uc001qyt.2	-	5	755	c.512C>T	c.(511-513)GCT>GTT	p.A171V	CSDA_uc001qyu.2_Missense_Mutation_p.A171V	NM_003651	NP_003642	P16989	DBPA_HUMAN	cold shock domain protein A isoform a	171					negative regulation of transcription from RNA polymerase II promoter|response to cold	cytoplasm|nucleus	double-stranded DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|lung(1)|large_intestine(1)	4	Glioma(1;0.155)					CCGATCTGCAGCGTAACGACT	0.502													11	20	---	---	---	---	PASS
LRMP	4033	broad.mit.edu	37	12	25232192	25232192	+	Silent	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25232192A>G	uc001rgh.2	+	6	1073	c.39A>G	c.(37-39)GAA>GAG	p.E13E	LRMP_uc001rgg.1_RNA|LRMP_uc010sja.1_Silent_p.E13E|LRMP_uc010sjb.1_5'UTR|LRMP_uc001rgi.2_RNA|LRMP_uc010sjc.1_Silent_p.E13E|LRMP_uc010sjd.1_5'UTR	NM_006152	NP_006143	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein	69	Cytoplasmic (Potential).				vesicle fusion|vesicle targeting	endoplasmic reticulum membrane|integral to plasma membrane				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					ATGGTGTTGAACGCGTGTGTC	0.368													9	732	---	---	---	---	PASS
CCDC91	55297	broad.mit.edu	37	12	28702165	28702165	+	3'UTR	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28702165A>G	uc001riq.2	+	12					CCDC91_uc001rio.2_3'UTR|CCDC91_uc009zjk.2_RNA|CCDC91_uc001rir.2_3'UTR|CCDC91_uc009zjl.2_3'UTR	NM_018318	NP_060788	Q7Z6B0	CCD91_HUMAN	GGA binding partner						protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					TTCAAAATACACACTCTGAAT	0.313													5	106	---	---	---	---	PASS
FGD4	121512	broad.mit.edu	37	12	32760919	32760919	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32760919T>C	uc001rkz.2	+	8	1499	c.1022T>C	c.(1021-1023)TTG>TCG	p.L341S	FGD4_uc001rlc.2_Missense_Mutation_p.L426S|FGD4_uc001rky.2_Missense_Mutation_p.L93S|FGD4_uc001rla.2_5'UTR|FGD4_uc010ske.1_Missense_Mutation_p.L453S|FGD4_uc001rlb.1_RNA	NM_139241	NP_640334	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	341	DH.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					AGCTTAACTTTGCAGCATCAC	0.393													6	319	---	---	---	---	PASS
GXYLT1	283464	broad.mit.edu	37	12	42491343	42491343	+	Silent	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42491343T>C	uc001rms.3	-	7	1287	c.1062A>G	c.(1060-1062)GAA>GAG	p.E354E	GXYLT1_uc001rmt.3_Silent_p.E323E	NM_173601	NP_775872	Q4G148	GXLT1_HUMAN	glycosyltransferase 8 domain containing 3	354	Lumenal (Potential).				O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0						CTTCTTCTGCTTCTTGGCAAT	0.373													6	319	---	---	---	---	PASS
LRIG3	121227	broad.mit.edu	37	12	59266250	59266250	+	3'UTR	SNP	T	A	A	rs11172787	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59266250T>A	uc001sqr.2	-	19					LRIG3_uc009zqh.2_3'UTR|LRIG3_uc010ssh.1_RNA	NM_153377	NP_700356	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like							integral to membrane				skin(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;1.17e-18)			ATTTTTATCCTTTTAAAATTC	0.254													36	53	---	---	---	---	PASS
USP15	9958	broad.mit.edu	37	12	62778003	62778003	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62778003A>G	uc001src.1	+	11	1402	c.1393A>G	c.(1393-1395)ACA>GCA	p.T465A	USP15_uc001srb.1_Missense_Mutation_p.T436A	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	465					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TTGTTACTTGACACTTCCATT	0.353													8	573	---	---	---	---	PASS
NUP107	57122	broad.mit.edu	37	12	69113188	69113188	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69113188A>G	uc001suf.2	+	13	1266	c.1151A>G	c.(1150-1152)TAC>TGC	p.Y384C	NUP107_uc001sug.2_Missense_Mutation_p.Y231C|NUP107_uc010stj.1_Missense_Mutation_p.Y355C	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	384					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TGGAAACTGTACCATGACCCT	0.413													6	409	---	---	---	---	PASS
LTA4H	4048	broad.mit.edu	37	12	96396759	96396759	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96396759T>C	uc001ten.1	-	18	1765	c.1697A>G	c.(1696-1698)AAG>AGG	p.K566R	LTA4H_uc010suy.1_Missense_Mutation_p.K528R|LTA4H_uc010suz.1_3'UTR|LTA4H_uc010sva.1_RNA	NM_000895	NP_000886	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	566	Substrate binding.			K->R: No effect on epoxide hydrolase and aminopeptidase activity.|K->A,M: Strongly reduced affinity for peptide substrates. Reduced epoxide hydrolase and aminopeptidase activity.	hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1						CCGGGTAAACTTCATTCTTCC	0.418													7	694	---	---	---	---	PASS
FAM71C	196472	broad.mit.edu	37	12	100042248	100042248	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100042248G>C	uc001tgn.2	+	1	718	c.296G>C	c.(295-297)AGG>ACG	p.R99T	ANKS1B_uc001tge.1_Intron|ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_153364	NP_699195	Q8NEG0	FA71C_HUMAN	hypothetical protein LOC196472	99											0				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		GACAATGCCAGGTGTGGTCCT	0.537													10	33	---	---	---	---	PASS
NUAK1	9891	broad.mit.edu	37	12	106466600	106466600	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106466600T>C	uc001tlj.1	-	5	1981	c.601A>G	c.(601-603)AAC>GAC	p.N201D		NM_014840	NP_055655	O60285	NUAK1_HUMAN	AMPK-related protein kinase 5	201	Protein kinase.						ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2						TGGTACAGGTTGGAAAGCCCA	0.468													36	99	---	---	---	---	PASS
G2E3	55632	broad.mit.edu	37	14	31074726	31074726	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31074726T>G	uc001wqk.2	+	11	1180	c.1026T>G	c.(1024-1026)TTT>TTG	p.F342L	G2E3_uc010tpe.1_Intron|G2E3_uc010tpf.1_Missense_Mutation_p.F296L	NM_017769	NP_060239	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin ligase	342					apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						GCAGCAAATTTAGAAGAAATG	0.274													10	49	---	---	---	---	PASS
YLPM1	56252	broad.mit.edu	37	14	75248651	75248651	+	Silent	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75248651C>T	uc001xqj.3	+	4	2029	c.1905C>T	c.(1903-1905)CCC>CCT	p.P635P	YLPM1_uc001xql.3_RNA	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	440					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		GAATACCTCCCCCTGGAGTTC	0.557													32	110	---	---	---	---	PASS
C15orf55	256646	broad.mit.edu	37	15	34640274	34640274	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34640274C>T	uc001zif.2	+	2	276	c.121C>T	c.(121-123)CCA>TCA	p.P41S	C15orf55_uc010ucc.1_Missense_Mutation_p.P69S|C15orf55_uc010ucd.1_Missense_Mutation_p.P59S	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	41	Pro-rich.					cytoplasm|nucleus			BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	midline_organs(25)|ovary(2)|lung(2)|skin(1)	30		all_lung(180;2.78e-08)		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)		ACCAGACCACCCACCCAGGGA	0.582			T	BRD3|BRD4	lethal midline carcinoma								4	109	---	---	---	---	PASS
AQR	9716	broad.mit.edu	37	15	35210525	35210525	+	Silent	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35210525A>G	uc001ziv.2	-	15	1457	c.1276T>C	c.(1276-1278)TTG>CTG	p.L426L		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	426						catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GTTGGATACAAAGGCATCTGG	0.368													7	375	---	---	---	---	PASS
SEMA6D	80031	broad.mit.edu	37	15	48060820	48060820	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48060820T>C	uc010bek.2	+	18	2168	c.1808T>C	c.(1807-1809)ATC>ACC	p.I603T	SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvy.2_Missense_Mutation_p.I603T|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor	603	Extracellular (Potential).				axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		ATGGCAAGTATCCCAGAAATC	0.368													6	117	---	---	---	---	PASS
GLDN	342035	broad.mit.edu	37	15	51692438	51692438	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51692438T>A	uc002aba.2	+	7	1036	c.867T>A	c.(865-867)GAT>GAA	p.D289E	GLDN_uc002abb.2_Missense_Mutation_p.D165E	NM_181789	NP_861454	Q6ZMI3	GLDN_HUMAN	gliomedin	289	Extracellular (Potential).				cell differentiation|nervous system development	collagen|integral to membrane|plasma membrane				ovary(2)	2				all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942)		GAAAAGCTGATGAGAAAGCCA	0.418													51	150	---	---	---	---	PASS
CPEB1	64506	broad.mit.edu	37	15	83221251	83221251	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83221251G>C	uc002bit.2	-	8	1511	c.1374C>G	c.(1372-1374)AGC>AGG	p.S458R	CPEB1_uc002biq.2_Missense_Mutation_p.S318R|CPEB1_uc002bir.2_Missense_Mutation_p.S323R|CPEB1_uc002bis.2_Missense_Mutation_p.S318R|CPEB1_uc010uod.1_Missense_Mutation_p.S167R|CPEB1_uc010uoe.1_Missense_Mutation_p.S396R|CPEB1_uc002biu.2_Missense_Mutation_p.S420R|CPEB1_uc010uof.1_Missense_Mutation_p.S318R|CPEB1_uc002biv.2_Missense_Mutation_p.S393R|CPEB1_uc002bip.2_Missense_Mutation_p.S167R	NM_001079533	NP_001073001	Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding	398	RRM 1.|Necessary for stress granule assembly and correct localization in dcp1 bodies.				mRNA processing|regulation of translation	cell junction|cytoplasmic mRNA processing body|dendrite|postsynaptic density|postsynaptic membrane	nucleotide binding|RNA binding			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(143;0.229)			GCATCCTTCGGCTGGACATCT	0.498													17	62	---	---	---	---	PASS
FAM57B	83723	broad.mit.edu	37	16	30036624	30036624	+	Silent	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30036624G>A	uc002dvt.2	-	5	1043	c.705C>T	c.(703-705)AAC>AAT	p.N235N	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|FAM57B_uc002dvu.2_3'UTR	NM_031478	NP_113666	Q71RH2	FA57B_HUMAN	hypothetical protein LOC83723	235	TLC.|Helical; (Potential).					endoplasmic reticulum|integral to membrane					0						CAGCGCCCAGGTTGACGTGGG	0.726													3	3	---	---	---	---	PASS
CDH5	1003	broad.mit.edu	37	16	66426107	66426107	+	Silent	SNP	C	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66426107C>G	uc002eom.3	+	7	1194	c.1038C>G	c.(1036-1038)CTC>CTG	p.L346L	CDH5_uc002eon.1_Silent_p.L346L	NM_001795	NP_001786	P33151	CADH5_HUMAN	cadherin 5, type 2 preproprotein	346	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)		CCATCGACCTCCGATACATGA	0.502													4	74	---	---	---	---	PASS
SLC12A4	6560	broad.mit.edu	37	16	67983803	67983803	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67983803C>G	uc002euz.2	-	13	1789	c.1648G>C	c.(1648-1650)GTG>CTG	p.V550L	SLC12A4_uc010ceu.2_Missense_Mutation_p.V544L|SLC12A4_uc010vkh.1_Missense_Mutation_p.V519L|SLC12A4_uc010vki.1_Missense_Mutation_p.V550L|SLC12A4_uc010vkj.1_Missense_Mutation_p.V552L|SLC12A4_uc002eva.2_Missense_Mutation_p.V550L|SLC12A4_uc010cev.1_5'Flank|SLC12A4_uc002evb.2_RNA	NM_005072	NP_005063	Q9UP95	S12A4_HUMAN	solute carrier family 12, member 4 isoform a	550					cell volume homeostasis|potassium ion transport|sodium ion transport	integral to plasma membrane|membrane fraction	potassium:chloride symporter activity			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	TCACCATTCACCTTCCCGTGG	0.627													19	59	---	---	---	---	PASS
SLC12A4	6560	broad.mit.edu	37	16	67983804	67983804	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67983804C>A	uc002euz.2	-	13	1788	c.1647G>T	c.(1645-1647)AAG>AAT	p.K549N	SLC12A4_uc010ceu.2_Missense_Mutation_p.K543N|SLC12A4_uc010vkh.1_Missense_Mutation_p.K518N|SLC12A4_uc010vki.1_Missense_Mutation_p.K549N|SLC12A4_uc010vkj.1_Missense_Mutation_p.K551N|SLC12A4_uc002eva.2_Missense_Mutation_p.K549N|SLC12A4_uc010cev.1_5'Flank|SLC12A4_uc002evb.2_RNA	NM_005072	NP_005063	Q9UP95	S12A4_HUMAN	solute carrier family 12, member 4 isoform a	549					cell volume homeostasis|potassium ion transport|sodium ion transport	integral to plasma membrane|membrane fraction	potassium:chloride symporter activity			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CACCATTCACCTTCCCGTGGC	0.632													18	59	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76555082	76555082	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76555082T>C	uc002feu.1	+	18	2796	c.2411T>C	c.(2410-2412)CTT>CCT	p.L804P	CNTNAP4_uc002fev.1_Missense_Mutation_p.L668P|CNTNAP4_uc010chb.1_Missense_Mutation_p.L731P|CNTNAP4_uc002fex.1_Missense_Mutation_p.L807P	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	804	Extracellular (Potential).|Laminin G-like 3.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						GCTTCATATCTTCATTTTCCT	0.348													9	771	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11583161	11583161	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11583161G>T	uc002gne.2	+	18	3509	c.3441G>T	c.(3439-3441)GAG>GAT	p.E1147D	DNAH9_uc010coo.2_Missense_Mutation_p.E441D	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1147	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GCTTGGTTGAGATCATGGGAC	0.423													34	139	---	---	---	---	PASS
UNC45B	146862	broad.mit.edu	37	17	33495265	33495265	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33495265T>G	uc002hja.2	+	10	1434	c.1337T>G	c.(1336-1338)ATC>AGC	p.I446S	UNC45B_uc002hjb.2_Missense_Mutation_p.I446S|UNC45B_uc002hjc.2_Missense_Mutation_p.I446S|UNC45B_uc010cto.2_Missense_Mutation_p.I446S	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	446					cell differentiation|muscle organ development	cytosol	binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)				GAGGCCCTCATCCATGCCTCC	0.557													9	32	---	---	---	---	PASS
CCL16	6360	broad.mit.edu	37	17	34308475	34308475	+	5'UTR	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34308475C>T	uc002hkl.2	-	1					CCL16_uc002hkm.2_RNA	NM_004590	NP_004581	O15467	CCL16_HUMAN	small inducible cytokine A16 precursor						cell-cell signaling|immune response|inflammatory response	extracellular space	chemoattractant activity|chemokine activity				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CGAGGCAGTACAGCTTCAGGG	0.557													8	57	---	---	---	---	PASS
ARHGAP23	57636	broad.mit.edu	37	17	36619105	36619105	+	5'UTR	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36619105G>A	uc010wdp.1	+	4						NM_020876	NP_065927	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23						signal transduction	intracellular	GTPase activator activity			lung(1)	1						CCCCGGTACCGCCTGGAGCCC	0.627													7	21	---	---	---	---	PASS
PCGF2	7703	broad.mit.edu	37	17	36892363	36892363	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36892363A>T	uc002hqp.1	-	10	880	c.637T>A	c.(637-639)TAC>AAC	p.Y213N	PCGF2_uc002hqn.1_Missense_Mutation_p.L214Q|PCGF2_uc002hqo.1_Missense_Mutation_p.L214Q|PCGF2_uc010cvo.1_Missense_Mutation_p.Y88N|PCGF2_uc002hqq.1_Missense_Mutation_p.L214Q	NM_007144	NP_009075	P35227	PCGF2_HUMAN	ring finger protein 110	213					negative regulation of transcription from RNA polymerase II promoter	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)|skin(1)	2	Breast(7;9.07e-22)					GGGTAGATGTAGGCGATGTCC	0.642													8	24	---	---	---	---	PASS
CCDC45	90799	broad.mit.edu	37	17	62512882	62512882	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62512882C>A	uc002jem.2	+	5	467	c.409C>A	c.(409-411)CGT>AGT	p.R137S	CCDC45_uc002jen.2_RNA|CCDC45_uc010wqb.1_Intron	NM_138363	NP_612372	Q96GE4	CEP95_HUMAN	coiled-coil domain containing 45	137						centrosome|spindle pole	protein binding				0	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			TCGAGGAGAACGTTTGGAAGA	0.343													66	454	---	---	---	---	PASS
EXOC7	23265	broad.mit.edu	37	17	74093949	74093949	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74093949G>A	uc002jqs.2	-	5	663	c.568C>T	c.(568-570)CAC>TAC	p.H190Y	EXOC7_uc010dgv.1_Missense_Mutation_p.H137Y|EXOC7_uc002jqq.2_Missense_Mutation_p.H190Y|EXOC7_uc010wsw.1_Missense_Mutation_p.H190Y|EXOC7_uc010wsx.1_Missense_Mutation_p.H190Y|EXOC7_uc002jqr.2_Missense_Mutation_p.H190Y|EXOC7_uc010wsv.1_Missense_Mutation_p.H149Y|EXOC7_uc002jqu.2_Missense_Mutation_p.H190Y	NM_001145297	NP_001138769	Q9UPT5	EXOC7_HUMAN	exocyst complex component 7 isoform 4	190					exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)			TCGGGCAGGTGCTCCAGGGTC	0.597													3	22	---	---	---	---	PASS
DNAH17	8632	broad.mit.edu	37	17	76454729	76454729	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76454729C>T	uc010dhp.1	-	7	1117	c.895G>A	c.(895-897)GCG>ACG	p.A299T	DNAH17_uc002jvs.2_RNA					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TTTTCAAACGCTGAGGTTAGG	0.532													4	319	---	---	---	---	PASS
SETBP1	26040	broad.mit.edu	37	18	42530495	42530495	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42530495C>T	uc010dni.2	+	4	1486	c.1190C>T	c.(1189-1191)TCA>TTA	p.S397L		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	397						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GAAAATGACTCAAGTCATGTC	0.473									Schinzel-Giedion_syndrome				11	37	---	---	---	---	PASS
CCDC68	80323	broad.mit.edu	37	18	52602100	52602100	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52602100T>C	uc002lfs.2	-	7	723	c.551A>G	c.(550-552)AAA>AGA	p.K184R	CCDC68_uc002lft.2_Missense_Mutation_p.K184R	NM_001143829	NP_001137301	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	184	Potential.									skin(1)	1				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		TTGACTGTGTTTTTCTTCAAG	0.358													7	766	---	---	---	---	PASS
GPX4	2879	broad.mit.edu	37	19	1106418	1106418	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1106418G>C	uc010xgg.1	+	7	628	c.521G>C	c.(520-522)GGC>GCC	p.G174A	GPX4_uc010xgh.1_Silent_p.R181R|GPX4_uc010xgi.1_Missense_Mutation_p.G211A	NM_002085	NP_002076	P36969	GPX4_HUMAN	glutathione peroxidase 4 isoform A precursor	174					multicellular organismal development|phospholipid metabolic process		glutathione peroxidase activity|phospholipid-hydroperoxide glutathione peroxidase activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;0.000172)|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)	Glutathione(DB00143)	GACAAGAACGGCTGCGTGGTG	0.647													5	23	---	---	---	---	PASS
GPX4	2879	broad.mit.edu	37	19	1106419	1106419	+	Silent	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1106419C>T	uc010xgg.1	+	7	629	c.522C>T	c.(520-522)GGC>GGT	p.G174G	GPX4_uc010xgh.1_Silent_p.L182L|GPX4_uc010xgi.1_Silent_p.G211G	NM_002085	NP_002076	P36969	GPX4_HUMAN	glutathione peroxidase 4 isoform A precursor	174					multicellular organismal development|phospholipid metabolic process		glutathione peroxidase activity|phospholipid-hydroperoxide glutathione peroxidase activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;0.000172)|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)	Glutathione(DB00143)	ACAAGAACGGCTGCGTGGTGA	0.647													5	23	---	---	---	---	PASS
UHRF1	29128	broad.mit.edu	37	19	4950899	4950899	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4950899A>G	uc002mbo.2	+	13	1877	c.1709A>G	c.(1708-1710)AAG>AGG	p.K570R	UHRF1_uc010xik.1_RNA|UHRF1_uc010duf.2_RNA|UHRF1_uc002mbp.2_Missense_Mutation_p.K583R	NM_001048201	NP_001041666	Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains	570	YDG.|Methyl-CpG binding and interaction with HDAC1.				cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		GAGAAGGGGAAGTCCGGGTTT	0.647													26	68	---	---	---	---	PASS
ZNF699	374879	broad.mit.edu	37	19	9407262	9407262	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9407262T>C	uc002mlc.1	-	5	818	c.818A>G	c.(817-819)CAC>CGC	p.H273R		NM_198535	NP_940937	Q32M78	ZN699_HUMAN	zinc finger protein 699	273	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CTTTCCGATGTGAATCTTCAT	0.403													7	394	---	---	---	---	PASS
UNC13A	23025	broad.mit.edu	37	19	17756598	17756598	+	Silent	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17756598G>A	uc002nhd.2	-	19	2505	c.2505C>T	c.(2503-2505)GAC>GAT	p.D835D		NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A	747	C2 2.				exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						ATTTGATGTCGTCATCCTCGT	0.592													15	61	---	---	---	---	PASS
ZNF429	353088	broad.mit.edu	37	19	21720845	21720845	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21720845A>T	uc002nqd.1	+	4	2127	c.1990A>T	c.(1990-1992)ATC>TTC	p.I664F	ZNF429_uc010ecu.1_Intron	NM_001001415	NP_001001415	Q86V71	ZN429_HUMAN	zinc finger protein 429	664					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						aggtgggcggatcacgaggtc	0.080													11	31	---	---	---	---	PASS
TSHZ3	57616	broad.mit.edu	37	19	31768936	31768936	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31768936T>C	uc002nsy.3	-	2	1828	c.1763A>G	c.(1762-1764)AAC>AGC	p.N588S		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	588					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)					CAGGGTCTGGTTTTTCGTCGG	0.542													4	74	---	---	---	---	PASS
RAB4B	53916	broad.mit.edu	37	19	41286335	41286335	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41286335G>A	uc002opd.1	+	3	253	c.143G>A	c.(142-144)CGG>CAG	p.R48Q	MIA_uc010xvt.1_RNA|RAB4B_uc002opc.1_RNA|RAB4B_uc002ope.1_RNA|EGLN2_uc010ehd.2_5'UTR|RAB4B_uc002opf.1_Missense_Mutation_p.R74Q	NM_016154	NP_057238	P61018	RAB4B_HUMAN	ras-related GTP-binding protein 4b	48					protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	intracellular|plasma membrane	GTP binding|GTPase activity			skin(1)	1			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TTTGGATCCCGGGTGGTCAAC	0.592													33	101	---	---	---	---	PASS
RAB4B	53916	broad.mit.edu	37	19	41286350	41286350	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41286350G>T	uc002opd.1	+	3	268	c.158G>T	c.(157-159)GGT>GTT	p.G53V	MIA_uc010xvt.1_RNA|RAB4B_uc002opc.1_RNA|RAB4B_uc002ope.1_RNA|EGLN2_uc010ehd.2_5'UTR|RAB4B_uc002opf.1_Missense_Mutation_p.G79V	NM_016154	NP_057238	P61018	RAB4B_HUMAN	ras-related GTP-binding protein 4b	53					protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	intracellular|plasma membrane	GTP binding|GTPase activity			skin(1)	1			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GTCAACGTGGGTGGGAAGACT	0.582													28	97	---	---	---	---	PASS
PSG5	5673	broad.mit.edu	37	19	43680096	43680096	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43680096G>C	uc002ovu.2	-	3	766	c.635C>G	c.(634-636)ACA>AGA	p.T212R	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovx.2_Missense_Mutation_p.T212R|PSG5_uc002ovv.2_Missense_Mutation_p.T305R|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	212	Ig-like C2-type 1.				female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)				ATAGGGTCCTGTTTCATTTCT	0.507													23	128	---	---	---	---	PASS
A1BG	1	broad.mit.edu	37	19	58863915	58863915	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58863915A>T	uc002qsd.3	-	4	409	c.347T>A	c.(346-348)TTG>TAG	p.L116*	NCRNA00181_uc002qse.2_Intron|A1BG_uc002qsf.1_RNA|NCRNA00181_uc002qsg.2_RNA	NM_130786	NP_570602	P04217	A1BG_HUMAN	alpha 1B-glycoprotein precursor	116	Ig-like V-type 2.					extracellular region					0		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		GGGAGCAGGCAAGGACTCTGT	0.592													3	10	---	---	---	---	PASS
PRNT	149830	broad.mit.edu	37	20	4713404	4713404	+	RNA	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4713404A>G	uc002wlb.2	-	2		c.620T>C			PRNT_uc010zqp.1_RNA|PRNT_uc010zqq.1_RNA	NR_024268				Homo sapiens mRNA for putative M8 protein, isoform 2.												0						agagaatgaaaggagcaagat	0.000													4	77	---	---	---	---	PASS
SUN5	140732	broad.mit.edu	37	20	31572986	31572986	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31572986C>T	uc002wyi.2	-	12	996	c.903G>A	c.(901-903)ATG>ATA	p.M301I		NM_080675	NP_542406	Q8TC36	SUN5_HUMAN	sperm associated antigen 4-like	301	SUN.				spermatogenesis					skin(1)	1						GGGAGCCCTCCATGCCCTGTG	0.498													28	62	---	---	---	---	PASS
ZNF512B	57473	broad.mit.edu	37	20	62596015	62596015	+	Silent	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62596015C>T	uc002yhl.1	-	6	1143	c.1089G>A	c.(1087-1089)GAG>GAA	p.E363E		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	363					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					ACTCCCCATTCTCTGGCCTGG	0.667													3	28	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11014937	11014937	+	Splice_Site	SNP	C	T	T	rs76467559	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11014937C>T	uc002yis.1	-	7		c.1508_splice	c.e7+1					P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						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)		CAGCACAATACCTATCACATT	0.328													4	107	---	---	---	---	PASS
TMPRSS15	5651	broad.mit.edu	37	21	19732177	19732177	+	Silent	SNP	T	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19732177T>C	uc002ykw.2	-	8	808	c.777A>G	c.(775-777)GTA>GTG	p.V259V		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	259	Extracellular (Potential).|CUB 1.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						GTCCTTGGTTTACACTAAATT	0.234													4	144	---	---	---	---	PASS
PKNOX1	5316	broad.mit.edu	37	21	44427621	44427621	+	Silent	SNP	A	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44427621A>G	uc002zcq.1	+	3	260	c.72A>G	c.(70-72)TTA>TTG	p.L24L	PKNOX1_uc002zcp.1_Silent_p.L24L|PKNOX1_uc011aex.1_5'UTR|PKNOX1_uc002zcr.2_Silent_p.L24L	NM_004571	NP_004562	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	24							sequence-specific DNA binding			large_intestine(2)	2						TAACAGAGTTAAAGACAGAAC	0.468													25	100	---	---	---	---	PASS
RRP1B	23076	broad.mit.edu	37	21	45106789	45106789	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45106789G>A	uc002zdk.2	+	12	1228	c.1114G>A	c.(1114-1116)GAG>AAG	p.E372K	RRP1B_uc002zdl.2_5'UTR	NM_015056	NP_055871	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1 homolog B	372					rRNA processing	cytosol|nucleolus|preribosome, small subunit precursor	protein binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.178)		TAAACTTTTAGAGAAAACTAA	0.443													10	247	---	---	---	---	PASS
POTEH	23784	broad.mit.edu	37	22	16278057	16278057	+	Intron	SNP	G	A	A	rs146119771		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16278057G>A	uc010gqp.2	-						POTEH_uc002zlg.1_Intron|POTEH_uc002zlh.1_Intron|POTEH_uc002zlj.1_Intron|uc002zlk.2_RNA	NM_001136213	NP_001129685	Q6S545	POTEH_HUMAN	ANKRD26-like family C, member 3											skin(1)	1						CACCAAGGTTGAAAGGAAGGG	0.368													4	21	---	---	---	---	PASS
TTC28	23331	broad.mit.edu	37	22	28692316	28692316	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28692316C>T	uc003adp.3	-	5	945	c.803G>A	c.(802-804)GGT>GAT	p.G268D		NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	268							binding				0						TGTCTGGTCACCTGGATTGAA	0.373													4	150	---	---	---	---	PASS
L3MBTL2	83746	broad.mit.edu	37	22	41620747	41620747	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41620747C>A	uc003azo.2	+	10	1247	c.1193C>A	c.(1192-1194)GCC>GAC	p.A398D	L3MBTL2_uc010gyi.1_Missense_Mutation_p.A307D|L3MBTL2_uc003azn.2_RNA	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2	398	MBT 3.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3						AGTGACATGGCCCATCACCCC	0.582													7	163	---	---	---	---	PASS
MAGEB10	139422	broad.mit.edu	37	X	27840135	27840135	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27840135C>A	uc004dbw.2	+	3	939	c.712C>A	c.(712-714)CAC>AAC	p.H238N		NM_182506	NP_872312	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	238	MAGE.									lung(1)|breast(1)|central_nervous_system(1)	3						CGGAATTGAGCACTTCATGTT	0.463													34	114	---	---	---	---	PASS
TMEM47	83604	broad.mit.edu	37	X	34648496	34648496	+	Silent	SNP	A	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34648496A>T	uc004ddh.2	-	3	739	c.480T>A	c.(478-480)ACT>ACA	p.T160T	TMEM47_uc010ngs.2_RNA	NM_031442	NP_113630	Q9BQJ4	TMM47_HUMAN	transmembrane protein 47	160	Helical; (Potential).					integral to membrane				lung(1)	1						ACGAAAATATAGTTGCACCCC	0.433													11	528	---	---	---	---	PASS
WAS	7454	broad.mit.edu	37	X	48544489	48544489	+	Silent	SNP	A	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48544489A>T	uc004dkm.3	+	6	582	c.525A>T	c.(523-525)CCA>CCT	p.P175P		NM_000377	NP_000368	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome protein	175					blood coagulation|defense response|epidermis development|immune response|T cell receptor signaling pathway	actin cytoskeleton|cytosol	identical protein binding|small GTPase regulator activity			ovary(1)	1		all_lung(315;1.27e-10)				GAGGGCTCCCACCCCTGCCCC	0.463			Mis|N|F|S			lymphoma			Wiskott-Aldrich_syndrome				22	93	---	---	---	---	PASS
ERCC6L	54821	broad.mit.edu	37	X	71426172	71426172	+	Silent	SNP	T	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71426172T>A	uc004eaq.1	-	2	2542	c.2445A>T	c.(2443-2445)CCA>CCT	p.P815P	PIN4_uc004eao.1_Intron|ERCC6L_uc004eap.1_Silent_p.P692P	NM_017669	NP_060139	Q2NKX8	ERC6L_HUMAN	excision repair protein ERCC6-like	815					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol	ATP binding|DNA binding|helicase activity|protein binding			ovary(3)	3	Renal(35;0.156)					CAAACCCCTTTGGTAAAGTAG	0.383													81	243	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76777788	76777788	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76777788G>T	uc004ecp.3	-	32	7160	c.6928C>A	c.(6928-6930)CCT>ACT	p.P2310T	ATRX_uc004ecq.3_Missense_Mutation_p.P2272T|ATRX_uc004eco.3_Missense_Mutation_p.P2095T	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2310					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	AAATTGAAAGGAATATAAGGA	0.388			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						77	303	---	---	---	---	PASS
MIR766	768218	broad.mit.edu	37	X	118780702	118780702	+	RNA	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118780702C>T	hsa-mir-766|MI0003836	-			c.110C>T			SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Intron|SEPT6_uc004ert.2_Intron|SEPT6_uc004eru.2_Intron|SEPT6_uc004erv.2_Intron|SEPT6_uc004erw.2_Intron|SEPT6_uc011mtv.1_Intron|SEPT6_uc011mtw.1_Intron																	0						TCCAATCCAGCTCCTATGACA	0.517													18	97	---	---	---	---	PASS
GPC3	2719	broad.mit.edu	37	X	132834052	132834052	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132834052C>A	uc004exe.1	-	4	1227	c.1037G>T	c.(1036-1038)GGC>GTC	p.G346V	GPC3_uc004exd.1_Missense_Mutation_p.G218V|GPC3_uc010nrn.1_Missense_Mutation_p.G369V|GPC3_uc011mvh.1_Missense_Mutation_p.G330V|GPC3_uc010nro.1_Missense_Mutation_p.G292V|GPC3_uc010nrp.1_Missense_Mutation_p.G218V	NM_004484	NP_004475	P51654	GPC3_HUMAN	glypican 3 isoform 2 precursor	346						extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)					ACATAACTTGCCAATCTGAAA	0.318			T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				25	164	---	---	---	---	PASS
ZNF75D	7626	broad.mit.edu	37	X	134427883	134427883	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134427883C>T	uc004eyp.2	-	3	2839	c.184G>A	c.(184-186)GGA>AGA	p.G62R	ZNF75D_uc004eym.2_Intron|ZNF75D_uc004eyn.2_5'Flank|ZNF75D_uc004eyo.2_Missense_Mutation_p.G62R	NM_007131	NP_009062	P51815	ZN75D_HUMAN	zinc finger protein 75	62	SCAN box.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TCAAGCGGTCCGGTTGCTTCA	0.473													34	82	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	9400	9400	+	RNA	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:9400G>A	uc011mfi.1	+	1		c.738G>A			uc004cov.3_5'Flank|uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		AACACGAGAAAGCACATACCA	0.443													28	251	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11126	11126	+	RNA	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11126G>A	uc004cov.3	+	1		c.549G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		ATATCTTCTTCGAAACCACAC	0.413													26	215	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11192	11192	+	RNA	SNP	G	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11192G>A	uc004cov.3	+	1		c.615G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		AACGCCTGAACGCAGGCACAT	0.468													62	203	---	---	---	---	PASS
CCNL2	81669	broad.mit.edu	37	1	1330443	1330443	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1330443delA	uc001afi.2	-						CCNL2_uc001aff.1_5'Flank|CCNL2_uc001afg.1_Intron|CCNL2_uc001afh.2_Intron|CCNL2_uc001afj.2_Intron|CCNL2_uc001afk.2_Intron	NM_030937	NP_112199	Q96S94	CCNL2_HUMAN	cyclin L2 isoform A						regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nuclear speck	protein kinase binding			ovary(2)|central_nervous_system(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		actccatctcaaaaaaaaaga	0.104													4	2	---	---	---	---	
KAZ	23254	broad.mit.edu	37	1	15351662	15351662	+	Intron	DEL	A	-	-	rs34741422		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15351662delA	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron|KAZ_uc001avo.2_Intron|KAZ_uc001avp.2_Intron|KAZ_uc001avq.2_Intron|KAZ_uc001avr.2_Intron	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0						ccaggaacttaatatcacagg	0.139													4	7	---	---	---	---	
PLEKHM2	23207	broad.mit.edu	37	1	16056542	16056556	+	Intron	DEL	GGGCGGGGCGGGGCG	-	-	rs12729712		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16056542_16056556delGGGCGGGGCGGGGCG	uc010obo.1	+							NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M						Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TCGCCTACCTgggcggggcggggcggggcggggcg	0.465													5	3	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16944979	16944981	+	RNA	DEL	AAG	-	-	rs142983965		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16944979_16944981delAAG	uc010ocf.1	-	4		c.1176_1178delCTT			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						GGATGGATAAAAGAagagcctct	0.197													8	4	---	---	---	---	
MST1P9	11223	broad.mit.edu	37	1	17090902	17090903	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17090902_17090903insT	uc010ock.1	-						CROCC_uc009voy.1_Intron	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						CTTCCTGTTTATTGCACCGGGC	0.599													3	4	---	---	---	---	
PUM1	9698	broad.mit.edu	37	1	31405847	31405847	+	3'UTR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31405847delA	uc001bsi.1	-	22					PUM1_uc001bsf.1_3'UTR|PUM1_uc001bsg.1_3'UTR|PUM1_uc001bsh.1_3'UTR|PUM1_uc001bsj.1_3'UTR|PUM1_uc010oga.1_3'UTR|PUM1_uc001bsk.1_3'UTR|PUM1_uc010ogb.1_3'UTR	NM_014676	NP_055491	Q14671	PUM1_HUMAN	pumilio 1 isoform 2						cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TTAGTCAATTAAAAAAAATAG	0.353													4	2	---	---	---	---	
TINAGL1	64129	broad.mit.edu	37	1	32044322	32044323	+	Intron	DEL	GT	-	-	rs138914866	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32044322_32044323delGT	uc001bta.2	+						TINAGL1_uc001bsz.2_Intron|TINAGL1_uc010ogi.1_Intron|TINAGL1_uc010ogj.1_Intron|TINAGL1_uc010ogk.1_Intron	NM_022164	NP_071447	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1						endosome transport|immune response|proteolysis	extracellular region	cysteine-type endopeptidase activity|extracellular matrix structural constituent|polysaccharide binding|scavenger receptor activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		GTGAGAGCTGGTGTGTGTGTGT	0.327													4	2	---	---	---	---	
RNF19B	127544	broad.mit.edu	37	1	33415573	33415573	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33415573delT	uc010oho.1	-						RNF19B_uc001bwm.3_Intron|RNF19B_uc010ohp.1_Intron	NM_153341	NP_699172	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B isoform a							integral to membrane	ligase activity|protein binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GAAAGTAAACttttttttttt	0.104													4	2	---	---	---	---	
TRIM62	55223	broad.mit.edu	37	1	33630328	33630328	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33630328delG	uc001bxb.2	-							NM_018207	NP_060677	Q9BVG3	TRI62_HUMAN	tripartite motif-containing 62							intracellular	zinc ion binding				0		Myeloproliferative disorder(586;0.0393)				GGAGGGCTTCGAGGGGACATG	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	35688927	35688928	+	IGR	INS	-	T	T	rs33986753		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35688927_35688928insT								SFPQ (30184 upstream) : ZMYM4 (45640 downstream)																							CTTGGTGCTAAttttttttttt	0.089													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	41824371	41824371	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41824371delG								SCMH1 (116583 upstream) : EDN2 (120078 downstream)																							AGGAATGAAAGGGGAAGCAAG	0.562													4	2	---	---	---	---	
EBNA1BP2	10969	broad.mit.edu	37	1	43733019	43733022	+	Intron	DEL	GGAG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43733019_43733022delGGAG	uc001cio.2	-						TMEM125_uc001cir.2_5'Flank	NM_006824	NP_006815	Q99848	EBP2_HUMAN	EBNA1 binding protein 2 isoform 2						ribosome biogenesis	membrane fraction|nucleolus	protein binding				0	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				cattcctgaaggagggagggaggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48010567	48010567	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48010567delG								FOXD2 (104205 upstream) : SKINTL (556820 downstream)																							ggtcagaggaggcttcctagc	0.000													4	2	---	---	---	---	
OSBPL9	114883	broad.mit.edu	37	1	52074532	52074532	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52074532delA	uc001css.2	+							NM_148905	NP_683703	Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9 isoform a						lipid transport		lipid binding			central_nervous_system(1)	1						TTGCTGGGGGAAAAAAAAAAT	0.428													4	4	---	---	---	---	
GLIS1	148979	broad.mit.edu	37	1	54102114	54102114	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54102114delA	uc001cvr.1	-							NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1						ccccgaaaagaaaaaaaaaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	59464617	59464617	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59464617delA								JUN (214832 upstream) : LOC729467 (132993 downstream)																							caaagactctaagaaactgtt	0.000													4	2	---	---	---	---	
SGIP1	84251	broad.mit.edu	37	1	67198419	67198420	+	Intron	INS	-	T	T	rs150404620	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67198419_67198420insT	uc001dcr.2	+						SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|SGIP1_uc009wat.2_Intron|SGIP1_uc001dcu.2_Intron	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						AATTTTCTCTCTTTTTTTTTTA	0.208													3	3	---	---	---	---	
LRRIQ3	127255	broad.mit.edu	37	1	74545852	74545853	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74545852_74545853insA	uc001dfy.3	-						LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3											ovary(2)	2						ATATCACACACAAAAAAAACCA	0.322													4	2	---	---	---	---	
ST6GALNAC3	256435	broad.mit.edu	37	1	76595410	76595410	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76595410delT	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541	Q8NDV1	SIA7C_HUMAN	sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5						atggcaaagattttttttcca	0.144													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	86001274	86001274	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86001274delT	uc001dlc.2	-							NM_001134445	NP_001127917	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	TCTTTTTCAGTTTTCTGAAAG	0.279													4	2	---	---	---	---	
HS2ST1	9653	broad.mit.edu	37	1	87465374	87465374	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87465374delT	uc010osk.1	+						HS2ST1_uc001dmc.3_Intron|LOC339524_uc001dme.1_Intron	NM_012262	NP_036394	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1 isoform							Golgi membrane|integral to membrane				central_nervous_system(1)	1		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		CAAATTATGCTTTCCCCCCCA	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88247487	88247487	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88247487delG								LMO4 (432884 upstream) : PKN2 (902435 downstream)																							TGCCAAGACTGGAGAAAGCTG	0.423													4	2	---	---	---	---	
GBP1	2633	broad.mit.edu	37	1	89526178	89526178	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89526178delA	uc001dmx.2	-							NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,						interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		CAATGCATGGAAACATTCAGG	0.184													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91296515	91296515	+	RNA	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91296515delA	uc001dnt.1	-	2		c.1575delT			uc001dnu.1_RNA					Homo sapiens cDNA FLJ12836 fis, clone NT2RP2003206.																		TCAAGAGGGGAAAAAAAGTCT	0.383													4	2	---	---	---	---	
TGFBR3	7049	broad.mit.edu	37	1	92268644	92268644	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92268644delC	uc001doh.2	-						TGFBR3_uc009wde.2_Intron|TGFBR3_uc010osy.1_Intron|TGFBR3_uc001doi.2_Intron|TGFBR3_uc001doj.2_Intron	NM_003243	NP_003234	Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III						BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		acttatcactccatctctgct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	95116894	95116894	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95116894delA								F3 (109523 upstream) : SLC44A3 (169007 downstream)																							TCATGTTCTTACCAGTCAAAG	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96306295	96306296	+	IGR	DEL	TA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96306295_96306296delTA								RWDD3 (593522 upstream) : PTBP2 (880879 downstream)																							cttgctcccctatatctggttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	104455658	104455658	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104455658delA								AMY1A (248486 upstream) : None (None downstream)																							CTCTTTTTCTAAAAATAATAT	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	106908965	106908965	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106908965delT								None (None upstream) : PRMT6 (690302 downstream)																							TGAGAACAGGTGTGTAAATAT	0.199													4	2	---	---	---	---	
NTNG1	22854	broad.mit.edu	37	1	107714519	107714519	+	Intron	DEL	T	-	-	rs11306051		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107714519delT	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697	Q9Y2I2	NTNG1_HUMAN	netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		ttttttcccctttttttttgt	0.259													2	4	---	---	---	---	
NTNG1	22854	broad.mit.edu	37	1	107782414	107782414	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107782414delA	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697	Q9Y2I2	NTNG1_HUMAN	netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)		GTGGTTAAATAAAAAAAAAAT	0.353													4	2	---	---	---	---	
HIPK1	204851	broad.mit.edu	37	1	114514340	114514341	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114514340_114514341insT	uc001eem.2	+						HIPK1_uc001eel.2_Intron|HIPK1_uc001een.2_Intron|HIPK1_uc001eeo.2_Intron|HIPK1_uc001eep.2_Intron|HIPK1_uc001eeq.2_Intron	NM_198268	NP_938009	Q86Z02	HIPK1_HUMAN	homeodomain-interacting protein kinase 1 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(4)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAATTGAGACCTTAATGCTTGC	0.361													22	10	---	---	---	---	
GDAP2	54834	broad.mit.edu	37	1	118411745	118411746	+	3'UTR	DEL	TT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118411745_118411746delTT	uc001ehf.2	-	14						NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated											ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		AAGGTTCTGCTTTTTTTTTTCT	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120627425	120627425	+	IGR	DEL	G	-	-	rs111900640		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120627425delG								NOTCH2 (15149 upstream) : FAM72B (211580 downstream)																							GACTGATTCAGGACACAGCAG	0.294													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142686091	142686092	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142686091_142686092insA	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		cctccgtgtggaaaagctacag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143158882	143158882	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143158882delC	uc001eiw.1	+						uc001ejf.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		AGCTAGGCAACCAAGAAACCC	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143181181	143181181	+	Intron	DEL	C	-	-	rs71237956		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143181181delC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																		atgacccaagctgtacctgtg	0.000													4	2	---	---	---	---	
FAM72D	728833	broad.mit.edu	37	1	143911730	143911731	+	Intron	DEL	TT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143911730_143911731delTT	uc002qvn.1	-						FAM72D_uc010evy.1_Intron	NM_207418	NP_997301	Q6L9T8	FA72D_HUMAN	hypothetical protein LOC653573												0						AGAAAACGGATTTTTTTTTTTT	0.322													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144011450	144011450	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144011450delT	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		TTGTCCTCTCTTTTTTTGGCA	0.453													4	2	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145104805	145104805	+	Intron	DEL	A	-	-	rs112695430		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145104805delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						AAAACAAAACAAAAATTCTCT	0.294													4	4	---	---	---	---	
C1orf54	79630	broad.mit.edu	37	1	150249349	150249350	+	Intron	INS	-	A	A	rs146501979	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150249349_150249350insA	uc001eud.2	+						C1orf54_uc001euc.2_Intron|C1orf54_uc001eue.2_Intron|C1orf54_uc001euf.2_Intron|C1orf54_uc001eug.2_Intron	NM_024579	NP_078855	Q8WWF1	CA054_HUMAN	hypothetical protein LOC79630 precursor							extracellular region					0	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGTCCTCAAGGATTTATAAAAT	0.297													2	4	---	---	---	---	
SEMA4A	64218	broad.mit.edu	37	1	156138347	156138347	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156138347delT	uc001fnl.2	+						SEMA4A_uc009wrq.2_Intron|SEMA4A_uc001fnm.2_Intron|SEMA4A_uc001fnn.2_Intron|SEMA4A_uc001fno.2_Intron	NM_022367	NP_071762	Q9H3S1	SEM4A_HUMAN	semaphorin B precursor						axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)					cttcttcttcttttttttttc	0.000													4	2	---	---	---	---	
POU2F1	5451	broad.mit.edu	37	1	167280427	167280427	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167280427delA	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						gatacattataataaaacttt	0.000													4	2	---	---	---	---	
FMO3	2328	broad.mit.edu	37	1	171060642	171060642	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171060642delA	uc001ghi.2	+						FMO3_uc010pma.1_Intron|FMO3_uc001ghh.2_Intron|FMO3_uc010pmb.1_Intron|FMO3_uc010pmc.1_Intron	NM_001002294	NP_001002294	P31513	FMO3_HUMAN	flavin containing monooxygenase 3						xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TCAGGAACAGAAAAAAGTTAG	0.368													4	2	---	---	---	---	
DNM3	26052	broad.mit.edu	37	1	171849194	171849194	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171849194delT	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						ggaaatgaggtttttagtttt	0.025													4	2	---	---	---	---	
TNR	7143	broad.mit.edu	37	1	175360167	175360167	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175360167delA	uc001gkp.1	-						TNR_uc009wwu.1_Intron	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					AGATCAGCATAAATACAATGG	0.368													4	2	---	---	---	---	
RFWD2	64326	broad.mit.edu	37	1	175917410	175917410	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175917410delG	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						GTAGGAAACTGGGCATCTAAA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	176337848	176337848	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176337848delA								RFWD2 (161478 upstream) : PAPPA2 (94459 downstream)																							TTACTTCAGGATCCTGCAGGT	0.308													4	2	---	---	---	---	
RALGPS2	55103	broad.mit.edu	37	1	178787931	178787931	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178787931delT	uc001glz.2	+						RALGPS2_uc001gly.1_Intron|RALGPS2_uc010pnb.1_Intron	NM_152663	NP_689876	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0						aggctgttggttttttttact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	184240589	184240589	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184240589delC								TSEN15 (197248 upstream) : C1orf21 (115561 downstream)																							TTTTAGTTATCCCAGCACTTG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	194131350	194131351	+	IGR	INS	-	T	T	rs149885574	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194131350_194131351insT								CDC73 (907410 upstream) : None (None downstream)																							ttcttcttctctttttttttaa	0.005													4	3	---	---	---	---	
PPFIA4	8497	broad.mit.edu	37	1	203025015	203025016	+	Intron	DEL	AC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203025015_203025016delAC	uc001gyz.2	+						PPFIA4_uc009xaj.2_Intron|PPFIA4_uc010pqf.1_Intron|PPFIA4_uc001gza.2_Intron|PPFIA4_uc001gzb.1_5'Flank	NM_015053	NP_055868	O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f						cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5						ATGAGCCCAGACTGCTTAAGAA	0.510													4	2	---	---	---	---	
LEMD1	93273	broad.mit.edu	37	1	205357901	205357901	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205357901delT	uc001hcj.1	-						LEMD1_uc001hci.1_Intron|LEMD1_uc001hck.1_Intron|LEMD1_uc001hcl.1_Intron|LEMD1_uc001hcm.1_Intron|LEMD1_uc001hcn.1_Intron			Q68G75	LEMD1_HUMAN	RecName: Full=LEM domain-containing protein 1;          Short=LEMP-1; AltName: Full=Cancer/testis antigen 50;          Short=CT50;							integral to membrane|nuclear envelope					0	Breast(84;0.247)		BRCA - Breast invasive adenocarcinoma(75;0.0938)			GGAAGTAACATTTTTAGTCAA	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	209984680	209984680	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209984680delA								IRF6 (5198 upstream) : C1orf107 (16653 downstream)																							AGAGCTCAACAAAAATAATAG	0.308													4	2	---	---	---	---	
USH2A	7399	broad.mit.edu	37	1	216595003	216595003	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216595003delT	uc001hku.1	-						USH2A_uc001hkv.2_Intron	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TATTTTCACATTTTTTTTCAT	0.328										HNSCC(13;0.011)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	221332843	221332844	+	IGR	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221332843_221332844insA								HLX (274445 upstream) : LOC400804 (170426 downstream)																							GGAGGTGTTGGAAAAAAAACAA	0.307													4	2	---	---	---	---	
CNIH3	149111	broad.mit.edu	37	1	224853678	224853678	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224853678delT	uc001hos.1	+							NM_152495	NP_689708	Q8TBE1	CNIH3_HUMAN	cornichon homolog 3						intracellular signal transduction|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic shaft|postsynaptic membrane					0	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)		CACCCTCTGGTTTTGATTTAG	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228897129	228897129	+	IGR	DEL	A	-	-	rs35978424		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228897129delA								RHOU (14720 upstream) : RAB4A (509750 downstream)																							gattacccttaaaaaaaaaag	0.060													2	4	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230271147	230271148	+	Intron	INS	-	T	T	rs150218704	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230271147_230271148insT	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				CATTTTCCAGCTTTCTTCATCT	0.391													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	231255668	231255668	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231255668delA								FAM89A (79673 upstream) : TRIM67 (43006 downstream)																							ggagaccttcaaagaaaatca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	235053997	235053997	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235053997delG								IRF2BP2 (308726 upstream) : TOMM20 (218663 downstream)																							CCTAACAATTGGGAATGTTTT	0.458													4	2	---	---	---	---	
ADSS	159	broad.mit.edu	37	1	244572632	244572633	+	3'UTR	INS	-	A	A	rs140156508	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244572632_244572633insA	uc001iaj.2	-	13						NM_001126	NP_001117	P30520	PURA2_HUMAN	adenylosuccinate synthase						AMP biosynthetic process|immune system process|purine base metabolic process	cytosol|plasma membrane	adenylosuccinate synthase activity|GTP binding|magnesium ion binding|phosphate binding			ovary(2)|kidney(1)	3	all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)	all_cancers(173;0.0896)|all_epithelial(177;0.172)	all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014)		L-Aspartic Acid(DB00128)	ACTAAACATTGAAAAAAAAAAC	0.327													6	4	---	---	---	---	
ALLC	55821	broad.mit.edu	37	2	3721053	3721053	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3721053delT	uc010ewt.2	+							NM_018436	NP_060906	Q8N6M5	ALLC_HUMAN	allantoicase isoform a								allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		cctttcgaactcctgggctgg	0.129										HNSCC(21;0.051)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	4174434	4174434	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4174434delA								ALLC (424176 upstream) : None (None downstream)																							ttccagAGCTAAAAAAAAaaa	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	5643887	5643887	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5643887delT								None (None upstream) : SOX11 (188912 downstream)																							aatctgtctcttgttataggg	0.035													4	2	---	---	---	---	
GREB1	9687	broad.mit.edu	37	2	11776785	11776785	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11776785delC	uc002rbk.1	+						GREB1_uc002rbp.1_Intron	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CTGTGGGAGTCCCCAGGGAAG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13977910	13977911	+	IGR	INS	-	A	A	rs146509848	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13977910_13977911insA								None (None upstream) : FAM84A (794945 downstream)																							atcatgggggcaggtctttcct	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	14514221	14514221	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14514221delT	uc002rby.2	-											Homo sapiens cDNA clone IMAGE:5263003.																		AGAACTAAAATTTTTAGAAAT	0.313													4	2	---	---	---	---	
SMC6	79677	broad.mit.edu	37	2	17975788	17975789	+	Intron	DEL	CA	-	-	rs34731510		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17975788_17975789delCA	uc010exo.2	-							NM_024624	NP_078900	Q96SB8	SMC6_HUMAN	SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					ACAGGGAGCTCAAGGCATCCTT	0.505													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18010659	18010660	+	IGR	INS	-	G	G	rs138881134	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18010659_18010660insG								MSGN1 (12293 upstream) : KCNS3 (48454 downstream)																							GAATGTTCTCAGGGATTGGAAG	0.426													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18582169	18582169	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18582169delT								KCNS3 (467945 upstream) : NT5C1B (153822 downstream)																							caaaagacagttttttttgtt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20672872	20672873	+	IGR	INS	-	C	C	rs149400603	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20672872_20672873insC								RHOB (23672 upstream) : HS1BP3 (144691 downstream)																							ccagcttcccatgaagggtact	0.114													3	3	---	---	---	---	
MFSD2B	388931	broad.mit.edu	37	2	24240100	24240101	+	Intron	DEL	CG	-	-	rs115127918	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24240100_24240101delCG	uc002reo.1	+						MFSD2B_uc010exz.1_Intron	NM_001080473	NP_001073942	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing						transport	integral to membrane				ovary(2)	2						TGGGGGAGGTCGCCCGCTGTCA	0.634													4	2	---	---	---	---	
ITSN2	50618	broad.mit.edu	37	2	24435349	24435350	+	Intron	DEL	CA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24435349_24435350delCA	uc002rfe.2	-						ITSN2_uc002rff.2_Intron	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1						endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTTTCTGTGCACACACACACA	0.545													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	37652415	37652415	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37652415delA								QPCT (51951 upstream) : CDC42EP3 (218328 downstream)																							actccatctcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
PLEKHH2	130271	broad.mit.edu	37	2	43918296	43918297	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43918296_43918297insT	uc010yny.1	+						PLEKHH2_uc002rte.3_Intron|PLEKHH2_uc002rtf.3_Intron	NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H							cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				Ttgatgcaggattttttgcttc	0.183													4	2	---	---	---	---	
CCDC88A	55704	broad.mit.edu	37	2	55536584	55536585	+	Intron	INS	-	T	T	rs150783848	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55536584_55536585insT	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc010fbw.2_5'Flank|CCDC88A_uc002ryu.2_Intron|CCDC88A_uc002rys.2_Intron|CCDC88A_uc002ryw.2_Intron|CCDC88A_uc010fby.1_Intron	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						AAAAATTTACATTTTTTTTTCC	0.243													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58687276	58687276	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58687276delT								FANCL (218761 upstream) : None (None downstream)																							AGACATAACATTTTTTTTACT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	62783827	62783828	+	IGR	DEL	CT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62783827_62783828delCT								TMEM17 (21047 upstream) : EHBP1 (117185 downstream)																							CCATCTCAGGCTCTCTCTCTCT	0.297													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	65447962	65447962	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65447962delA								RAB1A (90527 upstream) : ACTR2 (6867 downstream)																							ggcttcagacaaaaaaaaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	69915663	69915664	+	IGR	DEL	TA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69915663_69915664delTA								AAK1 (44686 upstream) : ANXA4 (53463 downstream)																							ggaatacttttataaagagaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70566902	70566903	+	IGR	DEL	CA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70566902_70566903delCA								FAM136A (37682 upstream) : TGFA (107516 downstream)																							catgtgcatgcacacacacaca	0.248													4	2	---	---	---	---	
LOXL3	84695	broad.mit.edu	37	2	74773432	74773432	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74773432delA	uc002smp.1	-						LOXL3_uc002smo.1_Intron|LOXL3_uc010ffm.1_Intron|LOXL3_uc002smq.1_Intron|LOXL3_uc010ffn.1_Intron|DOK1_uc002smr.2_5'Flank	NM_032603	NP_115992	P58215	LOXL3_HUMAN	lysyl oxidase-like 3 precursor							extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0						agtagtactgaaaaaaaaatg	0.000													2	4	---	---	---	---	
FAM176A	84141	broad.mit.edu	37	2	75728164	75728165	+	Intron	DEL	AG	-	-	rs78473697		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75728164_75728165delAG	uc002sni.2	-						FAM176A_uc002snj.1_Intron|FAM176A_uc002snk.1_Intron	NM_001135032	NP_001128504	Q9H8M9	F176A_HUMAN	family with sequence similarity 176, member A						apoptosis|autophagy	endoplasmic reticulum membrane|integral to membrane|lysosomal membrane|plasma membrane					0						AAAAAAAAAAAGAGGGCACTCA	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	81253348	81253349	+	IGR	INS	-	T	T	rs145988289	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81253348_81253349insT								CTNNA2 (377444 upstream) : None (None downstream)																							gttagtagccattttttttttc	0.000													3	3	---	---	---	---	
POLR1A	25885	broad.mit.edu	37	2	86309664	86309664	+	Intron	DEL	C	-	-	rs113272245		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86309664delC	uc002sqs.2	-						POLR1A_uc002sqv.2_Intron	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3						AACTCCAGTGCTTTTTTTTTT	0.363													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91770005	91770005	+	IGR	DEL	A	-	-	rs71380646		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91770005delA								None (None upstream) : LOC654342 (35187 downstream)																							CCTATTACTTAAAAAAAAGAC	0.219													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91774680	91774680	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91774680delA								None (None upstream) : LOC654342 (30512 downstream)																							gcactttgggaggccaagggg	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92194836	92194837	+	IGR	INS	-	T	T	rs145003390		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92194836_92194837insT								FKSG73 (64342 upstream) : None (None downstream)																							AGAGCAGGCTCTTGCCCACATC	0.495													6	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96180499	96180499	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96180499delT								FAHD2A (101621 upstream) : TRIM43 (77267 downstream)																							GTCCACCGGCTTTTTTTTCCT	0.353													8	4	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97817271	97817271	+	Intron	DEL	T	-	-	rs138016319		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97817271delT	uc010yva.1	+						ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						ATTAATTTACTTTTTTTATTA	0.254													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105606805	105606805	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105606805delA								POU3F3 (133335 upstream) : MRPS9 (47678 downstream)																							taacaacaacaaaaaaacgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106268885	106268885	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106268885delA								FHL2 (213655 upstream) : NCK2 (92469 downstream)																							CAGCTAAGGGAAAAAAAAATT	0.428													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106523941	106523941	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106523941delT								NCK2 (13215 upstream) : C2orf40 (158172 downstream)																							tctgttgttgttttttttttt	0.119													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	108552192	108552193	+	IGR	INS	-	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108552192_108552193insG								RGPD4 (43193 upstream) : SLC5A7 (50802 downstream)																							GGCTGAGCAAAGGGGAAACAGT	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	110494538	110494538	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110494538delA								ANKRD57 (117975 upstream) : RGPD5 (55797 downstream)																							TTTCAAGCTGAAAAAAAAAAA	0.418													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129417041	129417042	+	IGR	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129417041_129417042insA								HS6ST1 (340870 upstream) : None (None downstream)																							acagtcatttcggggtgctgat	0.064													4	2	---	---	---	---	
STAM2	10254	broad.mit.edu	37	2	153006422	153006423	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153006422_153006423insA	uc002tyc.3	-						STAM2_uc010foa.1_Intron|STAM2_uc002tyd.2_Intron	NM_005843	NP_005834	O75886	STAM2_HUMAN	signal transducing adaptor molecule 2						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.22)		gtaagctagagaaaaaaaaatg	0.000													4	2	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160675917	160675917	+	Intron	DEL	T	-	-	rs149173418		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160675917delT	uc002ubc.3	-						LY75_uc002ubb.3_Intron|LY75_uc010fos.2_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)		aagcctttcctTTTTTTTTTG	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	168241334	168241335	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168241334_168241335insT								XIRP2 (125075 upstream) : B3GALT1 (433847 downstream)																							CCTCTCACCTGTTTAAAACCTC	0.411													4	2	---	---	---	---	
LASS6	253782	broad.mit.edu	37	2	169458067	169458067	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169458067delT	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288	Q6ZMG9	CERS6_HUMAN	longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1						TGGCCTTATCttttttttttt	0.209													3	3	---	---	---	---	
LRP2	4036	broad.mit.edu	37	2	170050002	170050002	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170050002delT	uc002ues.2	-							NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TATTTGTGGGTTTTTTTTTTC	0.209													3	3	---	---	---	---	
DCAF17	80067	broad.mit.edu	37	2	172305520	172305520	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172305520delT	uc002ugx.2	+						DCAF17_uc010zdq.1_Intron|DCAF17_uc010fqf.1_Intron|DCAF17_uc010zdr.1_Intron	NM_025000	NP_079276	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17 isoform 1							CUL4 RING ubiquitin ligase complex|integral to membrane|nucleolus					0						ATCAtttgtcttttttttttc	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	180761437	180761437	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180761437delA								ZNF385B (35205 upstream) : CWC22 (48167 downstream)																							tcgtccccacaaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	186744933	186744933	+	IGR	DEL	T	-	-	rs5836961		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186744933delT								ZNF804A (940721 upstream) : ZC3H15 (605952 downstream)																							agggagagcattttttttttt	0.005													2	4	---	---	---	---	
HECW2	57520	broad.mit.edu	37	2	197195655	197195655	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197195655delT	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						CCAGGTCTGATTTTTTTTTTA	0.269													4	2	---	---	---	---	
PLCL1	5334	broad.mit.edu	37	2	198966234	198966234	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198966234delC	uc010fsp.2	+						PLCL1_uc002uuv.3_Intron	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;						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)	TTAAGTTACACTTTAGTCTTT	0.338													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	201014264	201014264	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201014264delG								C2orf47 (185419 upstream) : SPATS2L (156340 downstream)																							GTATCAGGGTGGGGGGACCTT	0.348													4	2	---	---	---	---	
RESP18	389075	broad.mit.edu	37	2	220195258	220195258	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220195258delT	uc002vlc.3	-						RESP18_uc002vlb.2_Intron|RESP18_uc010zle.1_Intron	NM_001007089	NP_001007090	Q5W5W9	RES18_HUMAN	regulated endocrine-specific protein 18							endoplasmic reticulum|extracellular region|Golgi apparatus					0						TTCAGTTTTGTTTTTTTTTTT	0.478													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229233520	229233520	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229233520delA								SPHKAP (187159 upstream) : PID1 (655170 downstream)																							actgagggggaaaaaaagggc	0.000													4	2	---	---	---	---	
HJURP	55355	broad.mit.edu	37	2	234754724	234754724	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234754724delA	uc002vvg.2	-						HJURP_uc010znd.1_Intron|HJURP_uc010zne.1_Intron	NM_018410	NP_060880	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein						cell cycle|CenH3-containing nucleosome assembly at centromere|centromeric core chromatin assembly|chromosome segregation|regulation of DNA binding|regulation of protein complex assembly	condensed chromosome kinetochore|cytoplasm|nucleolus|nucleoplasm	DNA binding|histone binding			ovary(1)	1		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		CTAGACCAGGAAAAAAAAAAT	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240475769	240475770	+	IGR	DEL	GA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240475769_240475770delGA								HDAC4 (152423 upstream) : NDUFA10 (424388 downstream)																							AGCAGCTGTGGAGAGAGAGAGA	0.500													4	2	---	---	---	---	
JAGN1	84522	broad.mit.edu	37	3	9934142	9934143	+	Intron	INS	-	GCCACCAT	GCCACCAT	rs145566429	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9934142_9934143insGCCACCAT	uc003btt.3	+						CIDEC_uc003bto.2_Intron	NM_032492	NP_115881	Q8N5M9	JAGN1_HUMAN	jagunal homolog 1							endoplasmic reticulum membrane|integral to membrane				ovary(1)	1	Medulloblastoma(99;0.227)					tagagttgtgagccCAGCCTCT	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	18064203	18064204	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18064203_18064204insA	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																		ctctccctgccaggttgtaggt	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34396098	34396098	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34396098delG								PDCD6IP (484904 upstream) : None (None downstream)																							cattttaggaggctgatgtgg	0.000													4	2	---	---	---	---	
DHX30	22907	broad.mit.edu	37	3	47852443	47852443	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47852443delT	uc003cru.2	+						DHX30_uc003crr.3_Intron|DHX30_uc003crs.2_Intron|DHX30_uc003crt.2_Intron	NM_138615	NP_619520	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 30							mitochondrial nucleoid	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)	4				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		ATTAAAATCCttttttttttt	0.259													5	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52678410	52678410	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52678410delT	uc003des.2	-						PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_Intron|PBRM1_uc003dew.2_Intron|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Intron|PBRM1_uc003dfb.1_Intron	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGACAttttcttttttttttg	0.149			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								4	2	---	---	---	---	
DNAH12	201625	broad.mit.edu	37	3	57484894	57484894	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57484894delA	uc003dit.2	-						DNAH12_uc003diu.2_Intron	NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2						acaaaaacctaatctatagta	0.000													4	2	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71243413	71243414	+	Intron	DEL	AA	-	-	rs72484295		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71243413_71243414delAA	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		AGGTGGTACCaaaaaaaaaaaa	0.322			T	PAX5	ALL								4	3	---	---	---	---	
CADM2	253559	broad.mit.edu	37	3	85234481	85234481	+	Intron	DEL	A	-	-	rs71669900		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85234481delA	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		ACAAAAAATGAAAAAAAAAAA	0.299													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	86659042	86659042	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86659042delT								CADM2 (541094 upstream) : VGLL3 (328083 downstream)																							CCATGAAAGCTTTTTTTTTTT	0.204													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	88527306	88527306	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88527306delT								C3orf38 (320193 upstream) : EPHA3 (629368 downstream)																							ATATTCCCAATTTTTTTTTGC	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	96031743	96031743	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96031743delA								None (None upstream) : EPHA6 (501682 downstream)																							TCATTGACTGAAAAAAAAAAA	0.388													4	4	---	---	---	---	
DCBLD2	131566	broad.mit.edu	37	3	98534196	98534196	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98534196delA	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron	NM_080927	NP_563615	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3						agtgggggagaaaaataagaa	0.000													4	2	---	---	---	---	
IMPG2	50939	broad.mit.edu	37	3	100951402	100951402	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100951402delT	uc003duq.1	-						IMPG2_uc011bhe.1_Intron|IMPG2_uc010hpj.1_Intron	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2						visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						ATTTAGACAATTTTTTTTTTG	0.209													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103112952	103112952	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103112952delC								ZPLD1 (914267 upstream) : None (None downstream)																							ATTTATTTGACAAAGAAATGA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	103643687	103643688	+	5'Flank	INS	-	A	A	rs113732888		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103643687_103643688insA	uc003dvu.2	+											Homo sapiens cDNA clone IMAGE:6614812, partial cds.																		CGTTTAACTTGAAAAAAAAAAA	0.307													2	4	---	---	---	---	
ALCAM	214	broad.mit.edu	37	3	105155725	105155725	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105155725delA	uc003dvx.2	+						ALCAM_uc003dvv.2_Intron|ALCAM_uc003dvw.1_Intron|ALCAM_uc003dvy.2_Intron|ALCAM_uc011bhh.1_5'Flank	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3						cagaagggtgaatgactgcta	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	106382233	106382233	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106382233delG								CBLB (793967 upstream) : LOC100302640 (173427 downstream)																							aattttttgaggaacaggcac	0.000													4	2	---	---	---	---	
LOC100302640	100302640	broad.mit.edu	37	3	106569178	106569178	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106569178delT	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0						TAATGACTGATTTTTTTTTTC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	112395626	112395626	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112395626delA								CCDC80 (35649 upstream) : CD200R1L (138930 downstream)																							TTTTTCATGCAAAAAAAACCT	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	120074144	120074145	+	IGR	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120074144_120074145insA								LRRC58 (5958 upstream) : FSTL1 (38917 downstream)																							ttcaaaaggttaaaaaaaatag	0.000													4	2	---	---	---	---	
CCDC58	131076	broad.mit.edu	37	3	122082116	122082116	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122082116delA	uc003eey.2	-							NM_001017928	NP_001017928	Q4VC31	CCD58_HUMAN	coiled-coil domain containing 58												0				GBM - Glioblastoma multiforme(114;0.148)		tgagagctttaaaaaaAAAAT	0.144													4	2	---	---	---	---	
CHST13	166012	broad.mit.edu	37	3	126258832	126258833	+	Intron	DEL	AC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126258832_126258833delAC	uc003eja.2	+							NM_152889	NP_690849	Q8NET6	CHSTD_HUMAN	carbohydrate sulfotransferase 13						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.151)		cacacgcatgacacacacacac	0.000													4	3	---	---	---	---	
MCM2	4171	broad.mit.edu	37	3	127338244	127338244	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127338244delA	uc003ejp.2	+						MCM2_uc011bkm.1_Intron|MCM2_uc010hsl.2_Intron|MCM2_uc011bkn.1_Intron	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2						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	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4						GGGAGGCATTAAAAAAAAAAT	0.303													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	144815039	144815039	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144815039delG								None (None upstream) : PLOD2 (972189 downstream)																							AAGTGCAGGTGCATGAAGAGC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	151152978	151152981	+	IGR	DEL	GAGC	-	-	rs71797893		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151152978_151152981delGAGC								MED12L (1169 upstream) : IGSF10 (1497 downstream)																							GAATAAGATGGAGCGAGACCCCAG	0.417													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	157249815	157249815	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157249815delC								VEPH1 (28400 upstream) : C3orf55 (11344 downstream)																							GGATGGATTGCCCCCCCACAC	0.468													4	2	---	---	---	---	
MLF1	4291	broad.mit.edu	37	3	158316193	158316193	+	Intron	DEL	T	-	-	rs34704638		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158316193delT	uc003fcb.2	+						MLF1_uc003fbz.2_Intron|MLF1_uc003fca.2_Intron|MLF1_uc003fbx.2_Intron|MLF1_uc003fcc.2_Intron|MLF1_uc003fby.2_Intron|MLF1_uc010hvx.2_Intron	NM_022443	NP_071888	P58340	MLF1_HUMAN	myeloid leukemia factor 1 isoform 1						cell cycle arrest|myeloid progenitor cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein domain specific binding				0		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			GTTTGTGGCATTTTTTTTGTA	0.453			T	NPM1	AML								4	2	---	---	---	---	
SCHIP1	29970	broad.mit.edu	37	3	159601640	159601640	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159601640delT	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron|SCHIP1_uc010hvz.1_Intron|SCHIP1_uc003fcu.1_Intron|SCHIP1_uc003fcv.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)			CTCCCCCAACTTTTTTTTTTC	0.393													6	3	---	---	---	---	
SERPINI1	5274	broad.mit.edu	37	3	167492951	167492952	+	Intron	INS	-	A	A	rs139260495	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167492951_167492952insA	uc003ffa.3	+						SERPINI1_uc003ffb.3_Intron	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor						central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1						GTGTGTGTTCTAGTAACTTCTC	0.277													0	6	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	171158114	171158115	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171158114_171158115insT	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhq.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			ctctattctaattttttttcaa	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176624346	176624346	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176624346delA								None (None upstream) : TBL1XR1 (114197 downstream)																							actctgttccaaaaacttggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	178017562	178017562	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178017562delA								None (None upstream) : KCNMB2 (236662 downstream)																							TTAATCACATAAATTCCTAAA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181699403	181699403	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181699403delA	uc003fky.2	+											Homo sapiens cDNA clone IMAGE:5296886.																		AACTCAATGGAAAAATCTCAC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	181932265	181932265	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181932265delG								SOX2OT (473262 upstream) : ATP11B (579026 downstream)																							TTCACAGAAAGGGTGCAGGGC	0.343													4	2	---	---	---	---	
POLR2H	5437	broad.mit.edu	37	3	184084881	184084882	+	Intron	DEL	TG	-	-	rs10575340		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184084881_184084882delTG	uc003fok.1	+						POLR2H_uc003foj.1_Intron	NM_006232	NP_006223	P52434	RPAB3_HUMAN	RNA polymerase II, polypeptide H						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase I transcription|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex|nucleolus	DNA-directed RNA polymerase activity|protein binding|zinc ion binding				0	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGTTAGGCTTtgtgtgtgtgtg	0.257													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186819827	186819827	+	IGR	DEL	T	-	-	rs113411247		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186819827delT								ST6GAL1 (23488 upstream) : RPL39L (18914 downstream)																							agcttcactctcaagttctgg	0.000													5	3	---	---	---	---	
ZNF595	152687	broad.mit.edu	37	4	50564	50564	+	5'Flank	DEL	C	-	-	rs112480187		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:50564delC	uc003fzv.1	+						ZNF595_uc003fzu.1_5'Flank|ZNF718_uc003fzt.3_5'Flank|ZNF595_uc010iay.1_5'Flank|ZNF595_uc011bus.1_5'Flank|ZNF595_uc011but.1_5'Flank	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TGacttagagccacttagagc	0.159													2	5	---	---	---	---	
RGS12	6002	broad.mit.edu	37	4	3344470	3344470	+	Intron	DEL	T	-	-	rs112112932		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3344470delT	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_Intron|RGS12_uc003ggy.1_Intron|RGS12_uc003ggx.1_Intron	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GGGATGACTGTTTTTTTTTCA	0.219													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12436719	12436719	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12436719delC								None (None upstream) : HSP90AB2P (898318 downstream)																							gtgtgggattctttttatcaa	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	14819721	14819722	+	Intron	INS	-	T	T	rs145282082	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14819721_14819722insT	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																		gaatcagaatctctaggggtgg	0.069													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	17257995	17257995	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17257995delT								LDB2 (357571 upstream) : QDPR (230025 downstream)																							ccctcTTGACttttttttttt	0.010													4	2	---	---	---	---	
STIM2	57620	broad.mit.edu	37	4	26860027	26860031	+	5'Flank	DEL	AAGGA	-	-	rs147233613		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26860027_26860031delAAGGA	uc003gsh.3	+						STIM2_uc003gsg.3_5'Flank|STIM2_uc010iex.2_5'Flank	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				GGCGACAGGGAAGGAGAGAAAGCTT	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	29861168	29861168	+	IGR	DEL	T	-	-	rs111639351		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29861168delT								None (None upstream) : PCDH7 (860869 downstream)																							tttgagcaaatttttttttct	0.000													0	8	---	---	---	---	
TBC1D1	23216	broad.mit.edu	37	4	38061190	38061191	+	Intron	INS	-	TCT	TCT	rs144646951	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38061190_38061191insTCT	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron|TBC1D1_uc011byf.1_Intron	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1						AGTGCATTCTCTCTTGGTGCTG	0.460													2	4	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39280429	39280429	+	Intron	DEL	T	-	-	rs5857667		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39280429delT	uc003gtv.2	+						WDR19_uc011byi.1_Intron	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						TTTTGATGTATTTTTTTTAAT	0.388													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	42792558	42792558	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42792558delC								ATP8A1 (133436 upstream) : GRXCR1 (102726 downstream)																							gacatattttctacttcaaaa	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43194187	43194187	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43194187delT								GRXCR1 (161514 upstream) : KCTD8 (981735 downstream)																							CTATGGTACATTTGGTTTACC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	45263158	45263158	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45263158delT								GNPDA2 (534546 upstream) : GABRG1 (774631 downstream)																							GCTCCAGGTGTTTTTTTTTAT	0.328													4	2	---	---	---	---	
SLAIN2	57606	broad.mit.edu	37	4	48346871	48346871	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48346871delA	uc003gya.3	+							NM_020846	NP_065897	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2							centrosome					0						ctgtttcattaaaaaaaaatg	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49220204	49220204	+	IGR	DEL	G	-	-	rs73152053	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49220204delG								CWH43 (156111 upstream) : None (None downstream)																							agaacctcttggaaaacctct	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	55457309	55457310	+	IGR	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55457309_55457310insA								PDGFRA (292898 upstream) : KIT (66785 downstream)																							AGTGTAAAACGAAAAAAAAAGA	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	60891330	60891331	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60891330_60891331insT								None (None upstream) : None (None downstream)																							ttgattaactgtttttttgttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	67936245	67936245	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67936245delG								MIR1269 (793599 upstream) : CENPC1 (401744 downstream)																							caatttcttaggacaaggtta	0.000													4	2	---	---	---	---	
CXCL3	2921	broad.mit.edu	37	4	74905533	74905533	+	5'Flank	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74905533delT	uc003hhl.2	-							NM_002090	NP_002081	P19876	CXCL3_HUMAN	chemokine (C-X-C motif) ligand 3						immune response|inflammatory response|neutrophil chemotaxis	extracellular space	chemokine activity			central_nervous_system(1)	1	Breast(15;0.00612)		all cancers(17;0.00273)|Lung(101;0.196)			AACAGGGCACTTTTTTTTCTC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	82006122	82006122	+	IGR	DEL	T	-	-	rs71664828		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82006122delT								BMP3 (27438 upstream) : PRKG2 (3715 downstream)																							tttgtttatattctgtttgtt	0.000													3	5	---	---	---	---	
PRKG2	5593	broad.mit.edu	37	4	82088628	82088628	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82088628delA	uc003hmh.2	-						PRKG2_uc011cch.1_Intron	NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II						platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7						AGACAGGGGGAAAAAAATCAC	0.313													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84123915	84123915	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84123915delT								PLAC8 (88004 upstream) : COQ2 (58774 downstream)																							TTTTGTTTTGTTTTTGAGACA	0.065													4	2	---	---	---	---	
AGPAT9	84803	broad.mit.edu	37	4	84474344	84474344	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84474344delA	uc003how.2	+						AGPAT9_uc003hox.2_Intron|AGPAT9_uc003hoy.2_Intron	NM_032717	NP_116106	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9						phospholipid biosynthetic process|regulation of TOR signaling cascade|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	glycerol-3-phosphate O-acyltransferase activity			skin(1)	1		Hepatocellular(203;0.114)				TGGTTCTGGCAGGAAATGAGA	0.373													4	2	---	---	---	---	
HERC6	55008	broad.mit.edu	37	4	89318273	89318273	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89318273delT	uc011cdi.1	+						HERC6_uc003hrp.1_Intron|HERC6_uc011cdj.1_Intron|HERC6_uc011cdk.1_Intron|HERC6_uc011cdl.1_Intron	NM_017912	NP_060382	Q8IVU3	HERC6_HUMAN	hect domain and RLD 6 isoform 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytosol	ubiquitin-protein ligase activity			lung(3)|ovary(1)|kidney(1)	5		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		tatttatttatttttttttga	0.159													11	5	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91534074	91534074	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91534074delA	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						CAGGGAAGTTAAAAAAAGTCA	0.393													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91843108	91843108	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91843108delT	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						GATAAATACATTTTTTTCTCA	0.299													4	2	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	92124800	92124801	+	Intron	INS	-	A	A	rs147183441	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92124800_92124801insA	uc003hsv.3	+							NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						TATACTATGTTAAAAAAAAACA	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	100581323	100581325	+	IGR	DEL	AAA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100581323_100581325delAAA								MTTP (36170 upstream) : DAPP1 (156656 downstream)																							ttatgatagcaaaaaaaaaaaag	0.089													4	2	---	---	---	---	
LEF1	51176	broad.mit.edu	37	4	109013611	109013613	+	Intron	DEL	CAT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109013611_109013613delCAT	uc003hyt.1	-						LEF1_uc011cfj.1_Intron|LEF1_uc011cfk.1_Intron|LEF1_uc003hyu.1_Intron|LEF1_uc003hyv.1_Intron|LEF1_uc010imb.1_Intron	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1						canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		ATATGTGGCACATCATCATCACA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	109128012	109128012	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109128012delA								LEF1 (38434 upstream) : LOC285456 (331334 downstream)																							tccagGAAAGAAAAAAAGTGG	0.139													4	2	---	---	---	---	
COL25A1	84570	broad.mit.edu	37	4	109981023	109981024	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109981023_109981024insT	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzh.1_Intron	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		aatggatgACCTTTTTTTTTAA	0.109													4	2	---	---	---	---	
ARSJ	79642	broad.mit.edu	37	4	114900260	114900261	+	5'UTR	INS	-	AA	AA	rs146140248	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114900260_114900261insAA	uc003ibq.1	-	1					ARSJ_uc010imu.1_5'Flank|ARSJ_uc010imv.1_Intron	NM_024590	NP_078866	Q5FYB0	ARSJ_HUMAN	arylsulfatase J precursor							extracellular region	arylsulfatase activity|metal ion binding			ovary(1)	1		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		TTCCACCAAGGAAAAAAAAAAG	0.460													4	2	---	---	---	---	
PRDM5	11107	broad.mit.edu	37	4	121828999	121828999	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121828999delA	uc003idn.2	-						PRDM5_uc003ido.2_Intron|PRDM5_uc010ine.2_Intron|PRDM5_uc010inf.2_Intron|PRDM5_uc003idp.1_Intron	NM_018699	NP_061169	Q9NQX1	PRDM5_HUMAN	PR domain containing 5						histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2						CATATGTTTCAATCCTCTTCA	0.398													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	135812600	135812600	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135812600delA								PABPC4L (689697 upstream) : None (None downstream)																							gaacgagcctaaaagtcaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	142675027	142675028	+	IGR	DEL	AG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142675027_142675028delAG								IL15 (20416 upstream) : INPP4B (274156 downstream)																							TGCCAATACAAGTTGACTGTTT	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	142675030	142675031	+	IGR	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142675030_142675031delTG								IL15 (20419 upstream) : INPP4B (274153 downstream)																							CAATACAAGTTGACTGTTTACT	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	145300238	145300238	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145300238delA								GYPA (238334 upstream) : HHIP (266935 downstream)																							ATCCTTTCCTATTGCAGAAGA	0.299													4	2	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148675772	148675773	+	Intron	DEL	TT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148675772_148675773delTT	uc003ilf.2	+						ARHGAP10_uc003ile.1_Intron	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TTGTATTCAATTTTTTTTTTTG	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	150416706	150416707	+	Intron	DEL	AC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150416706_150416707delAC	uc003ill.2	-											Homo sapiens cDNA clone IMAGE:5295442.																		GCACACATATACACACACTAAA	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	150681175	150681176	+	Intron	INS	-	A	A	rs142645861	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150681175_150681176insA	uc003ill.2	-											Homo sapiens cDNA clone IMAGE:5295442.																		aggaaggaaggaagggaaggga	0.193													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	165119006	165119007	+	Intron	INS	-	AT	AT	rs140822955	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165119006_165119007insAT	uc003iqs.1	-						ANP32C_uc011cjk.1_5'Flank	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CAAATATTATAATAAAGGGACT	0.401													7	4	---	---	---	---	
KLHL2	11275	broad.mit.edu	37	4	166218560	166218561	+	Intron	DEL	AA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166218560_166218561delAA	uc003irb.2	+						KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1						intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		TTGGGTAAATAAAAAAAAAAAG	0.302													4	2	---	---	---	---	
DDX60L	91351	broad.mit.edu	37	4	169378595	169378596	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169378595_169378596insA	uc003irq.3	-						DDX60L_uc003irr.1_Intron|DDX60L_uc003irs.1_5'Flank	NM_001012967	NP_001012985	Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TTGAGCATCAGAAAAAAAAAAA	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	172138511	172138512	+	IGR	INS	-	T	T	rs138236690	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172138511_172138512insT								None (None upstream) : GALNTL6 (596063 downstream)																							AGTTTTGTTTGTTTTTTCCCGC	0.302													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180372698	180372698	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180372698delT								None (None upstream) : None (None downstream)																							TTGACTATGCTTTTTTGTTTC	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	180755521	180755522	+	IGR	INS	-	T	T	rs146926540	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180755521_180755522insT								None (None upstream) : None (None downstream)																							ctctcctccacttcagtaccaa	0.000													3	4	---	---	---	---	
IRF2	3660	broad.mit.edu	37	4	185379004	185379004	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185379004delA	uc003iwf.3	-							NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2						blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AAAACCTTCCAAAAAAAAAAG	0.448													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188927993	188927993	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188927993delC								ZFP42 (1794 upstream) : TRIML2 (84434 downstream)																							TTAGTTAAATCCTGACTGAGG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189959648	189959648	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189959648delC								TRIML1 (890999 upstream) : FRG1 (902326 downstream)																							ATTTTCACATCTCACCTTTCC	0.438													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190629928	190629929	+	IGR	DEL	AT	-	-	rs146357307		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190629928_190629929delAT								None (None upstream) : FRG1 (232045 downstream)																							ATATTTACAAATATTTTTTTGA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190842430	190842431	+	Intron	INS	-	GA	GA	rs77290568		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190842430_190842431insGA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																		tcaagtagaagaaaaaaacagt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	5384772	5384783	+	IGR	DEL	CATCTATGTGGG	-	-	rs36228019		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5384772_5384783delCATCTATGTGGG								ADAMTS16 (64361 upstream) : KIAA0947 (38024 downstream)																							CCCCAAGGGAcatctatgtgggcatctatgtg	0.481													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7242582	7242582	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7242582delA								PAPD7 (485421 upstream) : ADCY2 (153761 downstream)																							CCGCTTAAAGAAAAAAAAAAA	0.438													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8715021	8715021	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8715021delT								MTRR (813788 upstream) : SEMA5A (320117 downstream)																							TAACTTGTCATTTTTCCTGAC	0.313													4	2	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10405429	10405429	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10405429delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						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						CCAATGAATGTTTTTTTTTTC	0.358													4	2	---	---	---	---	
ZNF622	90441	broad.mit.edu	37	5	16456476	16456477	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16456476_16456477insA	uc003jfq.2	-							NM_033414	NP_219482	Q969S3	ZN622_HUMAN	zinc finger protein 622							cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1						GAAGGAAACCCAAAAAAACCTT	0.401											OREG0016527	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	5	17353804	17353805	+	5'Flank	DEL	TT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17353804_17353805delTT	uc003jfz.2	+											full-length cDNA clone CS0DK001YG07 of HeLa cells Cot 25-normalized of Homo sapiens (human).																		ATCTCTTCACTTTTTTTTTTTT	0.337													6	3	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19481720	19481720	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19481720delA	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TTACACTCCTAAAACAAAACT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	40477938	40477938	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40477938delA								None (None upstream) : PTGER4 (202094 downstream)																							GAACTCCTAGAAAAAAAAACA	0.363													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	52509990	52509993	+	IGR	DEL	TTTG	-	-	rs66703856		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52509990_52509993delTTTG								MOCS2 (104392 upstream) : FST (266602 downstream)																							AGAGTAGCTTtttgtttgtttgtt	0.230													1	5	---	---	---	---	
CDC20B	166979	broad.mit.edu	37	5	54433832	54433833	+	Intron	DEL	AC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54433832_54433833delAC	uc003jpo.1	-						CDC20B_uc003jpn.1_Intron|CDC20B_uc010ivu.1_Intron|CDC20B_uc010ivv.1_Intron|CDC20B_uc003jpp.2_Intron	NM_152623	NP_689836	Q86Y33	CD20B_HUMAN	CDC20 cell division cycle 20 homolog B isoform												0		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			tcccacacatacacacacaccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56359660	56359660	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56359660delT								MIER3 (92159 upstream) : GPBP1 (110115 downstream)																							ggggtgtacatttgtatttca	0.149													4	2	---	---	---	---	
NDUFAF2	91942	broad.mit.edu	37	5	60274925	60274925	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60274925delC	uc003jsp.3	+						NDUFAF2_uc003jso.3_Intron	NM_174889	NP_777549	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha							membrane|mitochondrion	electron carrier activity|NADH dehydrogenase (ubiquinone) activity				0		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				aatacctggtccctgcaggat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	63151624	63151624	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63151624delA								None (None upstream) : HTR1A (104655 downstream)																							TGAGGCATGCAAACACATATA	0.308													4	2	---	---	---	---	
NLN	57486	broad.mit.edu	37	5	65055829	65055829	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65055829delT	uc003juf.2	+						NLN_uc003jue.2_Intron	NM_020726	NP_065777	Q9BYT8	NEUL_HUMAN	neurolysin precursor						proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		GACAGACAACTTTGGCTGTGT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	65173033	65173033	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65173033delT								NLN (53646 upstream) : ERBB2IP (49351 downstream)																							cctcttcttcttttttttttg	0.025													4	2	---	---	---	---	
PIK3R1	5295	broad.mit.edu	37	5	67519199	67519199	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67519199delT	uc003jva.2	+							NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding			endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)	ACTGCTCTCCTTTTTTTTTTT	0.468			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			2	5	---	---	---	---	
UTP15	84135	broad.mit.edu	37	5	72865103	72865104	+	Intron	INS	-	T	T	rs138866794	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72865103_72865104insT	uc003kcw.1	+						UTP15_uc011cso.1_Intron|UTP15_uc011csp.1_Intron|UTP15_uc010ize.1_Intron	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,						rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		CTATCCTTTAATTTTTTTTAAC	0.277													3	3	---	---	---	---	
AP3B1	8546	broad.mit.edu	37	5	77458454	77458455	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77458454_77458455insA	uc003kfj.2	-							NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		CCTATTTTACTAAAAAAAAAAG	0.297									Hermansky-Pudlak_syndrome				11	6	---	---	---	---	
SSBP2	23635	broad.mit.edu	37	5	80733496	80733496	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80733496delT	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		TTCCCAATCGTTTTTTTTTTA	0.289													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	82264880	82264880	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82264880delA								ATP6AP1L (650734 upstream) : TMEM167A (83787 downstream)																							TACCAAGGGGAAAAAAAAAAC	0.358													3	4	---	---	---	---	
TMEM161B	153396	broad.mit.edu	37	5	87491918	87491918	+	3'UTR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87491918delT	uc003kjc.2	-	12					TMEM161B_uc011cty.1_3'UTR|TMEM161B_uc010jax.2_RNA|TMEM161B_uc011ctx.1_3'UTR	NM_153354	NP_699185	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		TTCTGATATGTTTTTTTTTTC	0.284													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	96532857	96532857	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96532857delT								RIOK2 (13852 upstream) : None (None downstream)																							tcatttttccttttagcaaca	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	97957201	97957201	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97957201delT								None (None upstream) : RGMB (147798 downstream)																							tgcttttacatttttttaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	105649080	105649081	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105649080_105649081insT								None (None upstream) : None (None downstream)																							cacacctcttctgtcttaaaac	0.079													4	2	---	---	---	---	
MAN2A1	4124	broad.mit.edu	37	5	109175636	109175636	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109175636delT	uc003kou.1	+							NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		ATTTACATTCTTTTTTTTTTT	0.308													5	3	---	---	---	---	
TMEM232	642987	broad.mit.edu	37	5	109820664	109820665	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109820664_109820665insA	uc011cvh.1	-						TMEM232_uc003kow.1_Intron|TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;							integral to membrane					0						atagccttaataaaaaaaaaat	0.000													4	2	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112727421	112727421	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112727421delA	uc003kql.3	-							NM_001085377	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		gtctctggggaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	122955009	122955009	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122955009delA								CSNK1G3 (2547 upstream) : None (None downstream)																							tgctgccatcaaaccgctatg	0.000													4	2	---	---	---	---	
CHSY3	337876	broad.mit.edu	37	5	129397007	129397007	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129397007delG	uc003kvd.2	+							NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3							Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		agtggggaaaggacaccttat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	136274628	136274629	+	IGR	INS	-	A	A	rs148444887	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136274628_136274629insA								TRPC7 (581555 upstream) : SPOCK1 (36359 downstream)																							caAGTGTTAAGAAAAAATAACA	0.233													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139132061	139132061	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139132061delG								CXXC5 (69381 upstream) : PSD2 (43345 downstream)																							acatgggcacgaggacagcca	0.219													4	2	---	---	---	---	
ARHGAP26	23092	broad.mit.edu	37	5	142410480	142410480	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142410480delA	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)			TCACAGAATCACACATATCAG	0.413													4	2	---	---	---	---	
SH3TC2	79628	broad.mit.edu	37	5	148138267	148138267	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148138267delT	uc003lpp.1	-							NM_024577		Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			gtctattgaatttttttagtg	0.000													4	2	---	---	---	---	
CSNK1A1	1452	broad.mit.edu	37	5	148927418	148927419	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148927418_148927419insT	uc003lqx.1	-						CSNK1A1_uc011dcc.1_Intron|CSNK1A1_uc003lqv.1_Intron|CSNK1A1_uc003lqw.1_Intron|CSNK1A1_uc003lqy.1_Intron|CSNK1A1_uc010jha.1_Intron	NM_001892	NP_001883	P48729	KC1A_HUMAN	casein kinase 1, alpha 1 isoform 2						cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		TTGGAACTTTGTtttttttttt	0.158													4	2	---	---	---	---	
GALNT10	55568	broad.mit.edu	37	5	153714701	153714702	+	Intron	INS	-	C	C	rs145443744	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153714701_153714702insC	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron|GALNT10_uc010jid.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)			GGGTTCTTTCGCCTTTTTGAGT	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157680211	157680212	+	IGR	DEL	TG	-	-	rs10539598		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157680211_157680212delTG								CLINT1 (394043 upstream) : EBF1 (442712 downstream)																							gtgaggattatgtgtgtgtgtg	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163352967	163352968	+	IGR	INS	-	AA	AA	rs148526135	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163352967_163352968insAA								MAT2B (406634 upstream) : None (None downstream)																							cagtactgaataactcaaatcc	0.025													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163704589	163704589	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163704589delT								MAT2B (758256 upstream) : None (None downstream)																							ccttccgtccTTTTTTTTTCC	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173437104	173437104	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173437104delT								C5orf47 (3962 upstream) : HMP19 (35620 downstream)																							tataatgcccttttttgtctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	179369756	179369757	+	IGR	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179369756_179369757delTG								TBC1D9B (34900 upstream) : RNF130 (12717 downstream)																							ACTTCAAATATGTGATGTTTTC	0.381													4	2	---	---	---	---	
BPHL	670	broad.mit.edu	37	6	3146560	3146560	+	Intron	DEL	C	-	-	rs111270975		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3146560delC	uc003mva.2	+						BPHL_uc003muz.2_Intron|BPHL_uc011dht.1_Intron|BPHL_uc003muy.2_Intron	NM_004332	NP_004323	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like precursor						cellular amino acid metabolic process|response to toxin	mitochondrion	hydrolase activity				0	Ovarian(93;0.0386)	all_hematologic(90;0.108)				tggttcgggtcagagtgctgg	0.050													4	2	---	---	---	---	
SLC22A23	63027	broad.mit.edu	37	6	3437487	3437487	+	Intron	DEL	A	-	-	rs78457551		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3437487delA	uc003mvm.3	-						SLC22A23_uc003mvn.3_Intron|SLC22A23_uc003mvo.3_Intron|SLC22A23_uc003mvp.1_Intron|SLC22A23_uc010jnn.2_Intron|SLC22A23_uc010jno.2_Intron	NM_015482	NP_056297	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				ACATAAAACCAAAAAAAAACC	0.333													4	2	---	---	---	---	
F13A1	2162	broad.mit.edu	37	6	6305237	6305237	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6305237delT	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	CATGCTAAGATTTACAAACAT	0.249													4	2	---	---	---	---	
RIOK1	83732	broad.mit.edu	37	6	7404379	7404381	+	Intron	DEL	TAG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7404379_7404381delTAG	uc003mxn.2	+						RIOK1_uc003mxo.2_Intron	NM_031480	NP_113668	Q9BRS2	RIOK1_HUMAN	RIO kinase 1 isoform 1								ATP binding|protein serine/threonine kinase activity			ovary(2)|stomach(1)|skin(1)	4	Ovarian(93;0.0418)					CCCACTATATTAGTGAATAAGTG	0.315													50	25	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	11989905	11989905	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11989905delT								C6orf105 (210625 upstream) : HIVEP1 (22819 downstream)																							cagtacttccttttttcttgc	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	13982805	13982806	+	IGR	DEL	GA	-	-	rs141366165		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13982805_13982806delGA								RNF182 (2572 upstream) : CD83 (135059 downstream)																							agagaggactgagaggctgagc	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14019219	14019219	+	IGR	DEL	G	-	-	rs57251187		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14019219delG								RNF182 (38986 upstream) : CD83 (98646 downstream)																							catagaaaaagaaaaaactct	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14194633	14194633	+	IGR	DEL	C	-	-	rs853393	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14194633delC								CD83 (57487 upstream) : None (None downstream)																							AAAAAAAAAACCAAAATGTTT	0.318													4	2	---	---	---	---	
GMPR	2766	broad.mit.edu	37	6	16239046	16239046	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16239046delT	uc003nbs.2	+							NM_006877	NP_006868	P36959	GMPR1_HUMAN	guanosine monophosphate reductase						nucleotide metabolic process|purine base metabolic process|purine-containing compound salvage|response to cold	cytosol	GMP reductase activity|metal ion binding			ovary(1)	1	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				TGGGGTGGGATTTTTTTTTCC	0.637													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16825192	16825192	+	IGR	DEL	A	-	-	rs35423385		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16825192delA								ATXN1 (63471 upstream) : RBM24 (456617 downstream)																							CTTAGTGAGGAAAAAAAAAAG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16837179	16837180	+	IGR	DEL	TT	-	-	rs75300165	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16837179_16837180delTT								ATXN1 (75458 upstream) : RBM24 (444629 downstream)																							TTGGTTTTGGTTTTTTTTTTTC	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19235771	19235772	+	IGR	INS	-	T	T	rs78634830		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19235771_19235772insT								MIR548A1 (663660 upstream) : ID4 (601845 downstream)																							attcaaactgatttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27293740	27293740	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27293740delA								FKSG83 (1 upstream) : ZNF204P (31862 downstream)																							accctgtctgaaaaaaaaaaa	0.080													10	5	---	---	---	---	
C6orf134	79969	broad.mit.edu	37	6	30602033	30602033	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30602033delT	uc003nqu.2	+						C6orf134_uc003nqr.3_Intron|C6orf134_uc003rdc.2_Intron|C6orf134_uc003nqs.3_Intron|C6orf134_uc003rdd.2_Intron|C6orf134_uc003nqt.2_Intron|C6orf134_uc011dmm.1_Intron|C6orf134_uc003nqv.2_Intron	NM_024909	NP_079185	Q5SQI0	ATAT_HUMAN	hypothetical protein LOC79969 isoform 2								tubulin N-acetyltransferase activity				0						GTTAGGGTCAttttttttttc	0.119													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32105709	32105709	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32105709delA								FKBPL (7642 upstream) : PRRT1 (10432 downstream)																							ccacatcagtaaaaaatagaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	32450379	32450381	+	IGR	DEL	CTT	-	-	rs145836346		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32450379_32450381delCTT								HLA-DRA (37558 upstream) : HLA-DRB1 (34782 downstream)																							tggcctgtgacttcttctttttt	0.000													3	3	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32521955	32521956	+	Intron	INS	-	T	T	rs141382595		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32521955_32521956insT	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obm.1_Intron|HLA-DRB6_uc003obn.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CATCAAACTCATTCAAATATTA	0.248													4	3	---	---	---	---	
DAAM2	23500	broad.mit.edu	37	6	39766648	39766648	+	Intron	DEL	C	-	-	rs35202369		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39766648delC	uc003oow.2	+						DAAM2_uc010jxc.2_Intron|DAAM2_uc003oox.2_Intron|DAAM2_uc003oov.3_Intron	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					TCTGTCATCACATTGAACACA	0.393													2	5	---	---	---	---	
DAAM2	23500	broad.mit.edu	37	6	39780394	39780396	+	Intron	DEL	TTC	-	-	rs34070868		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39780394_39780396delTTC	uc003oow.2	+						DAAM2_uc010jxc.2_Intron|DAAM2_uc003oox.2_Intron|DAAM2_uc003oov.3_Intron	NM_015345	NP_056160	Q86T65	DAAM2_HUMAN	dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)					CAGCCTTCTATTCTTAGTGTGGA	0.493													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	41761501	41761502	+	5'Flank	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41761501_41761502insA	uc003orh.1	-											Homo sapiens cDNA FLJ13620 fis, clone PLACE1010947.																		TAGATTGAGGTAAAAAAAAATC	0.450													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	46467831	46467831	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46467831delA	uc003oye.2	+											Homo sapiens cDNA clone IMAGE:4821026.																		ATACTCATTGAAAAAAATAAG	0.308													4	2	---	---	---	---	
GPR115	221393	broad.mit.edu	37	6	47678849	47678850	+	Intron	DEL	AA	-	-	rs138891164		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47678849_47678850delAA	uc003oza.1	+						GPR115_uc003oyz.1_Intron|GPR115_uc003ozb.1_Intron	NM_153838	NP_722580	Q8IZF3	GP115_HUMAN	G-protein coupled receptor 115 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8						AACTTTTCTCAAAAAAAAAAAA	0.347													4	3	---	---	---	---	
OPN5	221391	broad.mit.edu	37	6	47776414	47776414	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47776414delG	uc003ozc.2	+						OPN5_uc003ozd.2_Intron	NM_181744	NP_859528	Q6U736	OPN5_HUMAN	opsin 5 isoform 1						phototransduction|protein-chromophore linkage|visual perception	integral to membrane	G-protein coupled receptor activity|photoreceptor activity			ovary(1)	1						ATTTATGCATGGCTCGTACAT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	50970268	50970268	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50970268delT								TFAP2B (154943 upstream) : PKHD1 (509877 downstream)																							TTTTGATGTGTTTTTATTTCC	0.358													4	2	---	---	---	---	
PKHD1	5314	broad.mit.edu	37	6	51663957	51663958	+	Intron	INS	-	CA	CA	rs139311898	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51663957_51663958insCA	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)					aaAATTAacaccacacacacac	0.094													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57515229	57515233	+	IGR	DEL	TTTGA	-	-	rs67538111		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57515229_57515233delTTTGA								PRIM2 (1854 upstream) : GUSBL2 (730926 downstream)																							TCTTGACAATTTTGATTTGTTTTCT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57537951	57537953	+	IGR	DEL	TGT	-	-	rs67143578		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57537951_57537953delTGT								PRIM2 (24576 upstream) : GUSBL2 (708206 downstream)																							TATGTAAATATGTTTTTTATACA	0.291													4	2	---	---	---	---	
KHDRBS2	202559	broad.mit.edu	37	6	62705671	62705671	+	Intron	DEL	A	-	-	rs113809871		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62705671delA	uc003peg.2	-							NM_152688	NP_689901	Q5VWX1	KHDR2_HUMAN	KH domain-containing, RNA-binding, signal						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)		TGTTTCAGAGAAAAAAAAATC	0.259													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	64664095	64664095	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64664095delT	uc011dxu.1	-						EYS_uc011dxt.1_Intron	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						tatttccttctttccttttcc	0.000													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	64837502	64837502	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64837502delA	uc011dxu.1	-						EYS_uc011dxt.1_Intron	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						GATGTAAAGTAATTGCTTCTA	0.244													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65707793	65707793	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65707793delA	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						TATTTAACTTAAAAAAAAAAC	0.239													4	2	---	---	---	---	
SNAP91	9892	broad.mit.edu	37	6	84392651	84392651	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84392651delG	uc011dze.1	-						SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron|SNAP91_uc011dzf.1_Intron	NM_014841	NP_055656	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		CTCAAGACTTGGGACATCATT	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	86401723	86401723	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86401723delG								SNHG5 (13272 upstream) : None (None downstream)																							cgggcagtctggagtgcccat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	106089610	106089610	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106089610delG								PREP (238641 upstream) : PRDM1 (444585 downstream)																							ATGGCCAGCTGGGGAGTTGTA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	109649160	109649160	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109649160delT								C6orf182 (164047 upstream) : CD164 (38558 downstream)																							ACCCCTTTAAttttttttttt	0.214													6	5	---	---	---	---	
REV3L	5980	broad.mit.edu	37	6	111714389	111714389	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111714389delT	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		gcgcagcaaattttttttgta	0.000								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
FYN	2534	broad.mit.edu	37	6	112192098	112192098	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112192098delG	uc003pvk.2	-							NM_002037	NP_002028	P06241	FYN_HUMAN	protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	TTTCCTTCCTGGGTCTGGCAT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	115541707	115541707	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115541707delA								HS3ST5 (878167 upstream) : FRK (720986 downstream)																							GATTTTAAAGAAAAAAATACA	0.363													3	3	---	---	---	---	
HBS1L	10767	broad.mit.edu	37	6	135303873	135303873	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135303873delT	uc003qez.2	-						HBS1L_uc003qey.2_Intron|HBS1L_uc011ecy.1_Intron|HBS1L_uc011ecz.1_Intron|HBS1L_uc011eda.1_Intron	NM_006620	NP_006611	Q9Y450	HBS1L_HUMAN	Hsp70 subfamily B suppressor 1-like protein						signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CACACTTTACTTTTTTTTTTT	0.184													15	7	---	---	---	---	
NHSL1	57224	broad.mit.edu	37	6	138754911	138754911	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138754911delT	uc003qhx.2	-						NHSL1_uc011edp.1_Intron	NM_020464	NP_065197	Q5SYE7	NHSL1_HUMAN	NHS-like 1 isoform 1												0						TTTAAAAAAATTTTTCTATTT	0.328													4	2	---	---	---	---	
HECA	51696	broad.mit.edu	37	6	139491024	139491024	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139491024delT	uc003qin.2	+							NM_016217	NP_057301	Q9UBI9	HDC_HUMAN	headcase						respiratory tube development						0				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		aatactctgctttttgatgga	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	141141982	141141982	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141141982delC								None (None upstream) : None (None downstream)																							tgtgatattgccggccaaaac	0.005													4	2	---	---	---	---	
STXBP5	134957	broad.mit.edu	37	6	147701782	147701782	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147701782delA	uc003qlz.2	+						STXBP5_uc010khz.1_Intron|STXBP5_uc003qlx.2_Intron|STXBP5_uc003qly.2_Intron	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b						exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		caaccaaaggaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148480109	148480109	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148480109delT								SAMD5 (588952 upstream) : SASH1 (183620 downstream)																							GGGTGatttattgatttatgc	0.219													4	2	---	---	---	---	
ARID1B	57492	broad.mit.edu	37	6	157150706	157150706	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157150706delT	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)						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)		ACAGGTATAATTTTTTTTTTC	0.373													4	2	---	---	---	---	
WDR27	253769	broad.mit.edu	37	6	170021366	170021367	+	Intron	DEL	AC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170021366_170021367delAC	uc003qwx.2	-						WDR27_uc003qwv.1_Intron|WDR27_uc010kkw.1_Intron|WDR27_uc003qwy.2_Intron			A2RRH5	WDR27_HUMAN	RecName: Full=WD repeat-containing protein 27;											pancreas(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		attcatgcatacacacacacac	0.059													4	2	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	2221908	2221909	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2221908_2221909insA	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		atgcagtcattaaaaaaaaaaa	0.020													4	2	---	---	---	---	
AMZ1	155185	broad.mit.edu	37	7	2753275	2753276	+	3'UTR	INS	-	CA	CA			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2753275_2753276insCA	uc003smr.1	+	7					AMZ1_uc003sms.1_3'UTR|AMZ1_uc011jwa.1_3'UTR	NM_133463	NP_597720	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1								metallopeptidase activity|zinc ion binding				0		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		TCAACCACATGCACACACACAC	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	5182819	5182819	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5182819delC	uc011jwf.1	-											SubName: Full=cDNA FLJ60262, weakly similar to Zinc finger protein 81;																		AACCATAGTACCAGTTTCATT	0.378													4	2	---	---	---	---	
RNF216	54476	broad.mit.edu	37	7	5800759	5800759	+	5'UTR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5800759delT	uc003soy.1	-	2					RNF216_uc010ksz.1_5'UTR|RNF216_uc010kta.1_5'UTR|RNF216_uc011jwj.1_5'UTR|RNF216_uc003sox.1_5'UTR	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)		TGACCATCTGTTTCAAAAGAA	0.388													305	151	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	5831752	5831755	+	IGR	DEL	TGAC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5831752_5831755delTGAC								RNF216 (10460 upstream) : ZNF815 (31036 downstream)																							cttgagagaatgactgactgacaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	10185000	10185000	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10185000delA								PER4 (509553 upstream) : NDUFA4 (787815 downstream)																							tgcaaagcagaaaaaaaaaaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	21011778	21011779	+	IGR	INS	-	GT	GT	rs72369350		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21011778_21011779insGT								RPL23P8 (144339 upstream) : SP4 (455910 downstream)																							AAAAAAAgtgcgtgtgtgtgtg	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	21410887	21410887	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21410887delA								RPL23P8 (543448 upstream) : SP4 (56802 downstream)																							TGAGCTTTCCAAAAAAAACAT	0.333													4	2	---	---	---	---	
GPNMB	10457	broad.mit.edu	37	7	23300645	23300646	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23300645_23300646insT	uc003swc.2	+						GPNMB_uc003swb.2_Intron|GPNMB_uc011jyy.1_Intron|GPNMB_uc011jyz.1_Intron	NM_001005340	NP_001005340	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb isoform a						negative regulation of cell proliferation	melanosome				ovary(3)|breast(2)	5			GBM - Glioblastoma multiforme(13;0.154)			TGACCCTCCTCATTTGCACTGG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24155530	24155530	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24155530delA								STK31 (211165 upstream) : NPY (168279 downstream)																							CAGGGAATATAAATCAAATAA	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24167685	24167685	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24167685delA								STK31 (223320 upstream) : NPY (156124 downstream)																							ATTTCCCCTGAAAAAAAAGAC	0.274													4	2	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	32588197	32588198	+	Intron	INS	-	AA	AA	rs151060193	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32588197_32588198insAA	uc003tcv.1	+						AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_Intron	NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						ACATAAAGTATTTTccatgaga	0.223													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	40904266	40904266	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40904266delA								C7orf10 (3909 upstream) : INHBA (824337 downstream)																							AAACAAGTACAAAAAAGGAGA	0.413													4	2	---	---	---	---	
INHBA	3624	broad.mit.edu	37	7	41738090	41738090	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41738090delA	uc003thq.2	-						LOC285954_uc003tht.3_Intron|INHBA_uc003thr.2_Intron|LOC285954_uc003ths.2_Intron	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor						cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity			lung(5)|ovary(1)	6						AAAAGTTGAGAAAAAAAAATG	0.383										TSP Lung(11;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	42499758	42499758	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42499758delC								GLI3 (223140 upstream) : C7orf25 (449116 downstream)																							CGGGGGCTTACCCTTGTCCTC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	43135439	43135440	+	IGR	DEL	AG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43135439_43135440delAG								MRPL32 (157988 upstream) : HECW1 (16758 downstream)																							agagagagaaagagagagagag	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53292974	53292974	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53292974delT								POM121L12 (188357 upstream) : HPVC1 (975943 downstream)																							AAAAGTGTGATGTCCCTTTAG	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	54489254	54489255	+	IGR	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54489254_54489255delTG								HPVC1 (219140 upstream) : VSTM2A (120764 downstream)																							TATGCGGGTCTGTGTGTGATAT	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57628416	57628417	+	IGR	INS	-	A	A	rs150287172	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57628416_57628417insA								ZNF716 (95151 upstream) : None (None downstream)																							AAAACAAAAACAAAAAGAAGTC	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61064901	61064901	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61064901delG								None (None upstream) : None (None downstream)																							ACAGTGAGAAGATTGGATGCG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68034427	68034427	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68034427delA								None (None upstream) : None (None downstream)																							AATGAGTCCTAGTGGATAAGA	0.418													4	2	---	---	---	---	
BCL7B	9275	broad.mit.edu	37	7	72952651	72952651	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72952651delT	uc003tyf.1	-						BCL7B_uc010lbf.1_Intron|BCL7B_uc003tye.1_Intron|BCL7B_uc003tyg.1_Intron	NM_001707	NP_001698	Q9BQE9	BCL7B_HUMAN	B-cell CLL/lymphoma 7B								actin binding			ovary(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTTCTGagagttgctatgagg	0.259													4	2	---	---	---	---	
STAG3L2	442582	broad.mit.edu	37	7	74300557	74300564	+	Frame_Shift_Del	DEL	AGAGCTCC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74300557_74300564delAGAGCTCC	uc003ubj.3	-	5	625_632	c.243_250delGGAGCTCT	c.(241-252)CTGGAGCTCTTCfs	p.L81fs	STAG3L2_uc011kfj.1_RNA	NM_001025202	NP_001020373	P0CL84	ST3L2_HUMAN	STAG3-like	81_84	SCD.					nucleus	binding				0						CGGCCAGTGAAGAGCTCCAGGCGTGCGG	0.572													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	75488376	75488377	+	IGR	DEL	CT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75488376_75488377delCT								CCL24 (45343 upstream) : RHBDD2 (19940 downstream)																							tatttgaatcctctctctctct	0.000													4	2	---	---	---	---	
ZP3	7784	broad.mit.edu	37	7	76054009	76054010	+	5'Flank	INS	-	A	A	rs76164389		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76054009_76054010insA	uc003ufd.3	+						ZP3_uc003ufc.3_Intron	NM_001110354	NP_001103824	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 isoform 1						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0						ACACACACAGCAAAAAAaaact	0.064													4	2	---	---	---	---	
PMS2L11	441263	broad.mit.edu	37	7	76626477	76626478	+	Intron	INS	-	GT	GT	rs141618293	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76626477_76626478insGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0						AAGTGTgtggggtgtgaggtgg	0.015													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	77595202	77595202	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77595202delT								PHTF2 (8384 upstream) : MAGI2 (51173 downstream)																							ATTTTTCATGTCAGTTGACTA	0.383													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	77934552	77934552	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77934552delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TCTGTCTTTCAAAAAGCCTAC	0.453													4	2	---	---	---	---	
MAGI2	9863	broad.mit.edu	37	7	78021626	78021626	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78021626delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TGAAGAAGGCAAAAAATAGAA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81248404	81248404	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81248404delT	uc003uhk.1	-											Homo sapiens mRNA sequence.																		GGGTAAATGATTTTTTTTCTC	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84596482	84596482	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84596482delT								SEMA3A (772265 upstream) : SEMA3D (28392 downstream)																							tattgtatacttgaaattgct	0.000													4	2	---	---	---	---	
RUNDC3B	154661	broad.mit.edu	37	7	87399736	87399736	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87399736delT	uc003ujb.2	+						RUNDC3B_uc011khd.1_Intron|RUNDC3B_uc011khe.1_Intron|RUNDC3B_uc003ujc.2_Intron|RUNDC3B_uc003ujd.2_Intron	NM_138290	NP_612147	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B isoform a											skin(1)	1	Esophageal squamous(14;0.00164)					TAACTTGCCATTTTTTTTTCA	0.323													4	2	---	---	---	---	
SLC25A40	55972	broad.mit.edu	37	7	87478871	87478871	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87478871delG	uc003uje.2	-							NM_018843	NP_061331	Q8TBP6	S2540_HUMAN	mitochondrial carrier family protein						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			haematopoietic_and_lymphoid_tissue(1)	1	Esophageal squamous(14;0.00202)					actgatagaaggataagcaca	0.000													4	2	---	---	---	---	
ADAM22	53616	broad.mit.edu	37	7	87607053	87607053	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87607053delT	uc003ujn.2	+						ADAM22_uc003uji.1_Intron|ADAM22_uc003ujj.1_Intron|ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			AAATAGTGAATTTTTTTTTTC	0.338													3	3	---	---	---	---	
GNG11	2791	broad.mit.edu	37	7	93549638	93549638	+	5'Flank	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93549638delT	uc003und.2	+							NM_004126	NP_004117	P61952	GBG11_HUMAN	guanine nucleotide binding protein gamma 11						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway	heterotrimeric G-protein complex	GTPase activity|signal transducer activity			kidney(1)	1	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			TCCCTGCTTATTTACAAGTAA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	97260380	97260380	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97260380delG								ACN9 (449307 upstream) : TAC1 (100891 downstream)																							CTATGTCAAAGAAAACATCAG	0.348													4	2	---	---	---	---	
TRRAP	8295	broad.mit.edu	37	7	98588855	98588855	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98588855delA	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated						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)			GAAACGGCGGAAGCGTGGCTA	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	108704604	108704615	+	IGR	DEL	AAAAAAAAAAAA	-	-	rs66733037		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108704604_108704615delAAAAAAAAAAAA								C7orf66 (179967 upstream) : EIF3IP1 (894669 downstream)																							acttcgtctcaaaaaaaaaaaaaaaaaaaaaa	0.000													3	3	---	---	---	---	
FOXP2	93986	broad.mit.edu	37	7	114279584	114279585	+	Intron	DEL	AA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114279584_114279585delAA	uc003vhb.2	+						FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgz.2_Intron|FOXP2_uc003vha.2_Intron|FOXP2_uc011kmu.1_Intron|FOXP2_uc011kmv.1_Intron|FOXP2_uc010ljz.1_Intron|FOXP2_uc003vgx.2_Intron|FOXP2_uc003vhd.2_Intron|FOXP2_uc003vhc.2_Intron	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						acatgattttaaaaaaaaagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	119893572	119893572	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119893572delT								None (None upstream) : KCND2 (20150 downstream)																							TCTTTTACCCTTTTATCATAG	0.313													4	2	---	---	---	---	
C7orf58	79974	broad.mit.edu	37	7	120647609	120647609	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120647609delT	uc003vjq.3	+						C7orf58_uc003vjr.1_Intron|C7orf58_uc003vjs.3_Intron	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)					TTATCATTAATTAATTTCTAG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	123010158	123010158	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123010158delT								SLC13A1 (170133 upstream) : IQUB (82080 downstream)																							CTCAGACTCATTTTTTTAAGC	0.418													4	2	---	---	---	---	
DGKI	9162	broad.mit.edu	37	7	137348118	137348118	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137348118delA	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota						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						CTGAACCAGTAAAAAGGGTCT	0.418													4	2	---	---	---	---	
UBN2	254048	broad.mit.edu	37	7	138969521	138969521	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138969521delT	uc011kqr.1	+							NM_173569	NP_775840	Q6ZU65	UBN2_HUMAN	ubinuclein 2											ovary(1)|skin(1)	2						GGGATATGGATTTTTTTTTTT	0.388													4	4	---	---	---	---	
MGAM	8972	broad.mit.edu	37	7	141786962	141786963	+	Intron	DEL	TT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141786962_141786963delTT	uc003vwy.2	+							NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase						polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTGGTGTATCTTTTTTTTTTCC	0.381													4	2	---	---	---	---	
KEL	3792	broad.mit.edu	37	7	142654701	142654701	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142654701delT	uc003wcb.2	-							NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase						proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)					CCAGGCCTACTTCTGTCTTCC	0.299													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149031906	149031906	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149031906delC								ZNF212 (79225 upstream) : ZNF777 (96555 downstream)																							AGATGACTGACCAGGAGGCTA	0.348													4	2	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151504031	151504031	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151504031delA	uc003wkj.2	-						PRKAG2_uc003wkk.2_Intron|PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron|uc003wkn.2_Frame_Shift_Del_p.E17fs	NM_001040633	NP_001035723	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		cagcctgggGAAAAAAAAAAG	0.214													4	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151891933	151891933	+	Intron	DEL	A	-	-	rs111444313		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151891933delA	uc003wla.2	-						MLL3_uc003wkz.2_Intron	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		AACTCCTGCCAAAAAAAAAAA	0.274			N		medulloblastoma								3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153227975	153227976	+	IGR	DEL	AC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153227975_153227976delAC								ACTR3B (675512 upstream) : DPP6 (356443 downstream)																							acaacatacaacacacacacac	0.302													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157940288	157940289	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157940288_157940289insT	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)		GTCTTTCCCCCTCAATGACACC	0.589													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	1205623	1205624	+	IGR	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1205623_1205624delTG								ERICH1 (524397 upstream) : DLGAP2 (243945 downstream)																							GCCTGGGTGCTGTGTGTGTGTG	0.604													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9358674	9358676	+	IGR	DEL	AAC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9358674_9358676delAAC								PPP1R3B (349590 upstream) : TNKS (54769 downstream)																							GAAATGTAAAAACAACAACAACA	0.443													4	2	---	---	---	---	
FGL1	2267	broad.mit.edu	37	8	17738053	17738053	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17738053delT	uc003wxx.2	-						FGL1_uc003wxy.2_Intron|FGL1_uc003wxz.2_Intron|FGL1_uc003wya.2_Intron|FGL1_uc003wyb.2_Intron|FGL1_uc003wyc.2_Intron|FGL1_uc003wyd.2_Intron|FGL1_uc003wye.2_Intron|FGL1_uc003wyf.2_Intron	NM_201553	NP_963847	Q08830	FGL1_HUMAN	fibrinogen-like 1 precursor						signal transduction	fibrinogen complex	receptor binding				0				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		ATGAACTACCTTCCTTTCATT	0.219													4	2	---	---	---	---	
PCM1	5108	broad.mit.edu	37	8	17812057	17812057	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17812057delT	uc003wyi.3	+						PCM1_uc011kyh.1_Intron|PCM1_uc003wyj.3_Intron|PCM1_uc003wyh.2_Intron|PCM1_uc010lta.1_Intron	NM_006197	NP_006188	Q15154	PCM1_HUMAN	pericentriolar material 1						centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2)	36				Colorectal(111;0.0789)		TTAAAGCCTATTTTTTTCCTC	0.413			T	RET|JAK2	papillary thyroid|CML|MPD								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	21032451	21032451	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21032451delT								LZTS1 (919648 upstream) : GFRA2 (517079 downstream)																							GTTTCTTTTCTTTTTTTTCTT	0.184													4	2	---	---	---	---	
PPP3CC	5533	broad.mit.edu	37	8	22346552	22346552	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22346552delT	uc003xbs.2	+						PPP3CC_uc003xbr.1_Intron|PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron	NM_005605	NP_005596	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		attggaggaattttttttttt	0.000													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	26101786	26101786	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26101786delG	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		CCAACTGCTAGGGCCTTTCTG	0.463													4	2	---	---	---	---	
INTS9	55756	broad.mit.edu	37	8	28628716	28628716	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28628716delT	uc003xha.2	-						INTS9_uc011lav.1_Intron|INTS9_uc011law.1_Intron|INTS9_uc011lax.1_Intron|INTS9_uc010lvc.2_Intron	NM_018250	NP_060720	Q9NV88	INT9_HUMAN	integrator complex subunit 9 isoform 1						snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		AGGTAAACAAttttttttttt	0.323													10	5	---	---	---	---	
FUT10	84750	broad.mit.edu	37	8	33269672	33269672	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33269672delC	uc003xje.2	-						FUT10_uc003xjc.2_Intron|FUT10_uc003xjd.2_Intron|FUT10_uc011lbi.1_Intron|FUT10_uc003xjf.2_Intron|FUT10_uc003xjg.2_Intron|FUT10_uc003xjh.2_Intron	NM_032664	NP_116053	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10						embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		AGAACTGGGACGGAAAATCCT	0.338													4	2	---	---	---	---	
MAK16	84549	broad.mit.edu	37	8	33352867	33352867	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33352867delA	uc003xjj.2	+						C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898	Q9BXY0	MAK16_HUMAN	MAK16 homolog							nucleolus				ovary(1)	1						TTCAAAATGGAAATGTTCCCA	0.318													16	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	33879439	33879439	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33879439delT								DUSP26 (422000 upstream) : None (None downstream)																							gtgaatgtacttttttcacag	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	34961680	34961680	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34961680delA								None (None upstream) : UNC5D (131295 downstream)																							ACAGAGGTTTAAAAAAAAAGA	0.308													4	2	---	---	---	---	
UNC5D	137970	broad.mit.edu	37	8	35179856	35179856	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35179856delT	uc003xjr.1	+							NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor						apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		TTCTCCCCCCTTTTTTTTTTC	0.313													4	2	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40394424	40394424	+	Intron	DEL	A	-	-	rs33947310		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40394424delA	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)			GGGTTTGgagaaaaaaaaaaa	0.333													4	2	---	---	---	---	
POLB	5423	broad.mit.edu	37	8	42219887	42219887	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42219887delA	uc003xoz.1	+						POLB_uc003xpa.1_Intron|POLB_uc011lcs.1_Intron	NM_002690	NP_002681	P06746	DPOLB_HUMAN	DNA-directed DNA polymerase beta						DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	ATTCCCTGCCAAAAAAAAAAA	0.164								DNA_polymerases_(catalytic_subunits)					4	2	---	---	---	---	
POTEA	340441	broad.mit.edu	37	8	43154188	43154189	+	Intron	DEL	TC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43154188_43154189delTC	uc003xpz.1	+						POTEA_uc003xqa.1_Intron	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2											ovary(1)	1						ctttcttctttctttctttttt	0.119													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49442380	49442380	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49442380delT								UBE2V2 (467928 upstream) : EFCAB1 (180971 downstream)																							AAAAGTCCCCTTTTCTAGAAT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55351772	55351772	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55351772delT								MRPL15 (290698 upstream) : SOX17 (18723 downstream)																							ccctcaacgcttttttttatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	56000654	56000654	+	IGR	DEL	T	-	-	rs113106761		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56000654delT								RP1 (318123 upstream) : XKR4 (14363 downstream)																							GGTTTGAGGATTTTTTTTTTT	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	56455365	56455365	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56455365delT								XKR4 (16657 upstream) : TMEM68 (195955 downstream)																							TCAAAAGTACTTTTTAAAAAG	0.109													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	64698000	64698000	+	RNA	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64698000delC	uc003xvc.2	+	3		c.3654delC								Homo sapiens hypothetical protein LOC286184, mRNA (cDNA clone IMAGE:5265748).																		GCAAGTGAATCCACCTTGCAT	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65186579	65186579	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65186579delA								None (None upstream) : MIR124-2 (105127 downstream)																							TGTTACTTATAATGAAAATTT	0.343													4	2	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68374282	68374282	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68374282delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			GTTTAAAATATTTTTTTGAAT	0.333													4	2	---	---	---	---	
CPA6	57094	broad.mit.edu	37	8	68482335	68482335	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68482335delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			AAACAAGAACTTTTTTTTTTC	0.313													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	69002479	69002480	+	Intron	INS	-	TTA	TTA			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69002479_69002480insTTA	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						TATGTTTCTGGTCTTCTCATTT	0.287													1	8	---	---	---	---	
PEX2	5828	broad.mit.edu	37	8	77899678	77899678	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77899678delG	uc003yax.2	-						PEX2_uc003yay.2_Intron|PEX2_uc003yaz.2_Intron	NM_000318	NP_000309	P28328	PEX2_HUMAN	peroxin 2						peroxisome organization	integral to peroxisomal membrane	protein binding|zinc ion binding			ovary(1)	1						agataaggctggaaagaagca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	78523865	78523865	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78523865delA								PEX2 (611341 upstream) : PKIA (904471 downstream)																							TAATTTATATAAAAGGTAAAA	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79421857	79421857	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79421857delA								None (None upstream) : PKIA (6479 downstream)																							caaagaaagtaaactttcagt	0.080													4	2	---	---	---	---	
PAG1	55824	broad.mit.edu	37	8	81989860	81989861	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81989860_81989861insT	uc003ybz.2	-							NM_018440	NP_060910	Q9NWQ8	PAG1_HUMAN	phosphoprotein associated with glycosphingolipid						epidermal growth factor receptor signaling pathway|intracellular signal transduction|T cell receptor signaling pathway	integral to membrane|intracellular|membrane raft|plasma membrane	SH2 domain binding|SH3/SH2 adaptor activity				0	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			CCACAACTAAGTTTTTTTTTCG	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	83902210	83902211	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83902210_83902211insT								None (None upstream) : None (None downstream)																							agaaagctagatttttttttgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	84189730	84189731	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84189730_84189731insT								None (None upstream) : RALYL (905722 downstream)																							aattctgtgggtttttttgaca	0.000													4	2	---	---	---	---	
CA3	761	broad.mit.edu	37	8	86356598	86356599	+	Intron	DEL	GT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86356598_86356599delGT	uc003ydj.2	+						CA3_uc011lfv.1_Intron	NM_005181	NP_005172	P07451	CAH3_HUMAN	carbonic anhydrase III						one-carbon metabolic process	cytoplasm	carbonate dehydratase activity|zinc ion binding				0						GATGTGGGAGGTGTGTGTGTGT	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96435612	96435612	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96435612delT								C8orf37 (154175 upstream) : GDF6 (718948 downstream)																							TCTTTGTCTATTTTTTTTTTT	0.443													3	3	---	---	---	---	
VPS13B	157680	broad.mit.edu	37	8	100356943	100356944	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100356943_100356944insT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yix.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)			AGATGTTcctctttttttttcc	0.035													4	6	---	---	---	---	
RAD21	5885	broad.mit.edu	37	8	117883270	117883270	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117883270delA	uc003yod.2	-							NM_006265	NP_006256	O60216	RAD21_HUMAN	RAD21 homolog						apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding			lung(1)|skin(1)	2	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					GAGTGATGCTAAAATTAATGT	0.438													4	2	---	---	---	---	
EXT1	2131	broad.mit.edu	37	8	119074295	119074295	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119074295delA	uc003yok.1	-							NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			CAGCTTCATTAAAAAAAAACA	0.353			Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				4	2	---	---	---	---	
ASAP1	50807	broad.mit.edu	37	8	131146794	131146795	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131146794_131146795insA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						tatttttacagaaaaaaaaact	0.099													6	3	---	---	---	---	
EFR3A	23167	broad.mit.edu	37	8	133013651	133013651	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133013651delT	uc003yte.2	+							NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A							plasma membrane	binding			ovary(3)|breast(1)|central_nervous_system(1)	5	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			CAGAGCATTGTTTACTTACAA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	1744021	1744021	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1744021delT								DMRT2 (686468 upstream) : SMARCA2 (271321 downstream)																							ATCATCCTCATTACAGTTTTC	0.388													4	2	---	---	---	---	
SMARCA2	6595	broad.mit.edu	37	9	2192379	2192380	+	Intron	INS	-	T	T	rs138154668	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2192379_2192380insT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron|SMARCA2_uc011llw.1_Intron|SMARCA2_uc003zhf.2_Intron|SMARCA2_uc011llx.1_Intron|SMARCA2_uc003zhe.2_Intron|SMARCA2_uc003zhg.2_Intron|SMARCA2_uc010mhb.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		AATGCAGGGTATTTTTTTTTCT	0.347													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	4479604	4479604	+	IGR	DEL	C	-	-	rs5896075		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4479604delC								GLIS3 (179569 upstream) : SLC1A1 (10840 downstream)																							CAAGTCAGCACCCCTGCCTCC	0.527													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	7844293	7844293	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7844293delA								C9orf123 (44494 upstream) : PTPRD (469954 downstream)																							gatttttcataaaaatctgga	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	19155130	19155131	+	IGR	DEL	TC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19155130_19155131delTC								PLIN2 (27557 upstream) : DENND4C (135571 downstream)																							TGTGGACTTGTCTCTCTCTCAA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	20275330	20275331	+	IGR	INS	-	CA	CA			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20275330_20275331insCA								SLC24A2 (486522 upstream) : MLLT3 (69637 downstream)																							GCAAGAAAAATCACACACTCCT	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22426423	22426423	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22426423delA								CDKN2BAS (305332 upstream) : DMRTA1 (20417 downstream)																							TCATAACAAGAAAAATCAACC	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	28937788	28937788	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28937788delT								MIR873 (48835 upstream) : None (None downstream)																							ATCATTTTTCtttttttttcc	0.259													4	2	---	---	---	---	
DNAI1	27019	broad.mit.edu	37	9	34464910	34464912	+	Intron	DEL	AGA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34464910_34464912delAGA	uc003zum.2	+						DNAI1_uc011lom.1_Intron	NM_012144	NP_036276	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1						cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		aggtttggatagaagaagaagag	0.172									Kartagener_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38306380	38306380	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38306380delT								SHB (237170 upstream) : ALDH1B1 (86322 downstream)																							cttcagtttgtttttttttaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	47202619	47202619	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:47202619delA								KGFLP1 (454234 upstream) : None (None downstream)																							AAACTTCTCCAAAAAAAAAGT	0.443													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66477526	66477527	+	IGR	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66477526_66477527insA								FAM74A4 (983140 upstream) : LOC442421 (18943 downstream)																							tgtgtacatttaaaaaatctat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66479112	66479113	+	IGR	INS	-	T	T	rs71293617		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66479112_66479113insT								FAM74A4 (984726 upstream) : LOC442421 (17357 downstream)																							ttttgatggtgtttttttcttg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68420783	68420783	+	IGR	DEL	C	-	-	rs67820203		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68420783delC								FAM27B (626594 upstream) : MIR1299 (581456 downstream)																							CACACACACACAAACTTGTAT	0.383													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68688108	68688109	+	IGR	DEL	AG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68688108_68688109delAG								FAM27B (893919 upstream) : MIR1299 (314130 downstream)																							CAACAAAAAAAGAAAACTGAAC	0.252													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70126408	70126408	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70126408delA								LOC100133920 (461459 upstream) : FOXD4L5 (49301 downstream)																							ggtcttacgcaaaaaaatctt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	75053269	75053269	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75053269delA								ZFAND5 (73106 upstream) : TMC1 (83448 downstream)																							TGCGTTTGTCAAAAAAAGTTC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	76929899	76929899	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76929899delC								None (None upstream) : RORB (182353 downstream)																							tgaaaagtgtccattgggttt	0.065													4	2	---	---	---	---	
ZCCHC6	79670	broad.mit.edu	37	9	88919513	88919513	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88919513delA	uc004aoq.2	-						ZCCHC6_uc010mqe.2_Intron|ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2						AGATAACCAGAAAAAAAAAAG	0.418													3	3	---	---	---	---	
DAPK1	1612	broad.mit.edu	37	9	90188395	90188395	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90188395delA	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2						GCAGAGAGGGAGGGAGGGGTG	0.512									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				4	2	---	---	---	---	
NR4A3	8013	broad.mit.edu	37	9	102626287	102626287	+	3'UTR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102626287delT	uc004baf.1	+	8					NR4A3_uc004bag.1_3'UTR|NR4A3_uc004bai.2_3'UTR	NM_006981	NP_008912	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding		EWSR1/NR4A3(140)|TAF15/NR4A3(33)	bone(173)	173		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				AAAGACTTTCTTTTTTTTCTG	0.438			T	EWSR1	extraskeletal myxoid chondrosarcoma								4	2	---	---	---	---	
LPPR1	54886	broad.mit.edu	37	9	104039432	104039432	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104039432delT	uc004bbb.2	+						LPPR1_uc011lvi.1_Intron|LPPR1_uc004bbc.2_Intron|LPPR1_uc010mtc.2_Intron	NM_207299	NP_997182	Q8TBJ4	LPPR1_HUMAN	plasticity related gene 3							integral to membrane	catalytic activity				0						CATTTCTGCCTTCTTGGAGAT	0.388													4	2	---	---	---	---	
GRIN3A	116443	broad.mit.edu	37	9	104450524	104450524	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104450524delA	uc004bbp.1	-						GRIN3A_uc004bbq.1_Intron	NM_133445	NP_597702	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic,						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)	CCTACGTACCAAAAAATGTGT	0.353													4	2	---	---	---	---	
EPB41L4B	54566	broad.mit.edu	37	9	112033065	112033066	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112033065_112033066insT	uc004bdz.1	-						EPB41L4B_uc004bea.2_Intron	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3						TCTCATCTTTAGCCAAGTCCAA	0.292													4	2	---	---	---	---	
ROD1	9991	broad.mit.edu	37	9	114994246	114994247	+	Intron	DEL	AG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114994246_114994247delAG	uc004bfw.2	-						ROD1_uc004bfv.2_Intron|ROD1_uc004bfx.2_Intron|ROD1_uc011lwu.1_Intron|ROD1_uc004bfy.2_Intron|ROD1_uc004bfz.2_Intron	NM_005156	NP_005147	O95758	ROD1_HUMAN	ROD1 regulator of differentiation 1 isoform 1						anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1						agagaagagaagagagaagaga	0.045													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	116894149	116894149	+	IGR	DEL	G	-	-	rs6478068		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116894149delG								KIF12 (32642 upstream) : COL27A1 (24082 downstream)																							TGGTTAAAAAGAAAAAAGCCA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	118734559	118734560	+	IGR	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118734559_118734560delTG								C9orf27 (47182 upstream) : PAPPA (181511 downstream)																							ATGGGCAGATtgtgtgtgtgtg	0.327													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	120222805	120222805	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120222805delT								ASTN2 (45488 upstream) : TLR4 (243655 downstream)																							GAGAGCTGCCTTTTGATATTA	0.363													4	2	---	---	---	---	
GOLGA1	2800	broad.mit.edu	37	9	127647851	127647853	+	Intron	DEL	GGA	-	-	rs71987630		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127647851_127647853delGGA	uc004bpc.2	-						GOLGA1_uc010mws.2_Intron	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97							Golgi cisterna membrane				ovary(1)	1						gcatggtgagggagggtggggtt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	130899804	130899805	+	IGR	INS	-	A	A	rs112519485		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130899804_130899805insA								LOC389791 (6893 upstream) : LCN2 (11927 downstream)																							GGACCACAGGGCCCCTTATGCA	0.446													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132338718	132338723	+	Intron	DEL	CACACT	-	-	rs72072909		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132338718_132338723delCACACT	uc004bya.1	+											Homo sapiens cDNA clone IMAGE:4812570.																		gcactcctcacacactcacacactct	0.170													4	3	---	---	---	---	
ASS1	445	broad.mit.edu	37	9	133364631	133364632	+	Intron	DEL	TA	-	-	rs543048	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133364631_133364632delTA	uc004bzm.2	+						ASS1_uc004bzn.2_Intron|ASS1_uc010mza.2_Intron|ASS1_uc004bzo.2_Intron|ASS1_uc010mzb.2_Intron|ASS1_uc004bzp.2_Intron|ASS1_uc010mzc.2_Intron	NM_000050	NP_000041	P00966	ASSY_HUMAN	argininosuccinate synthetase 1						arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	ttattattattatttttttttt	0.441													8	4	---	---	---	---	
VAV2	7410	broad.mit.edu	37	9	136664901	136664901	+	Intron	DEL	A	-	-	rs59232037	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136664901delA	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)		TTCCCCTTTTAAAAAAAAATG	0.413													4	2	---	---	---	---	
AKR1C1	1645	broad.mit.edu	37	10	4995169	4995169	+	5'UTR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4995169delT	uc001iho.2	+	5					AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron	NM_001353	NP_001344	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1						bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)	ACACACTTCCTTACATTAGAA	0.299													4	2	---	---	---	---	
CAMK1D	57118	broad.mit.edu	37	10	12475405	12475405	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12475405delT	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)		AAGGGTTTGATTTTTTTTTTT	0.363													4	2	---	---	---	---	
FRMD4A	55691	broad.mit.edu	37	10	14374771	14374771	+	5'Flank	DEL	T	-	-	rs72130207		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14374771delT	uc001ims.2	-						FRMD4A_uc009xjf.1_5'Flank|FRMD4A_uc001imv.2_Intron|FRMD4A_uc001imw.1_Intron	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3						TTACCATTTCTTTTTTTTGTA	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30430375	30430376	+	IGR	INS	-	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30430375_30430376insC								KIAA1462 (25955 upstream) : MTPAP (168355 downstream)																							tgACTTACTAGCCCCAAAACCT	0.243													4	2	---	---	---	---	
CCDC7	221016	broad.mit.edu	37	10	32766675	32766675	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32766675delT	uc001iwj.2	+						CCDC7_uc009xlu.1_Intron|CCDC7_uc001iwk.2_Intron|CCDC7_uc009xlv.2_Intron|CCDC7_uc009xlw.1_Intron|CCDC7_uc009xlx.1_Intron|CCDC7_uc009xly.1_Intron	NM_145023	NP_659460	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7												0		Breast(68;0.000207)|Prostate(175;0.0107)				ttactttagcttttagtaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38595613	38595613	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38595613delT								LOC100129055 (92341 upstream) : HSD17B7P2 (49695 downstream)																							CTTTGTCAGGTtttttttgtt	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42627717	42627717	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42627717delT								None (None upstream) : LOC441666 (199598 downstream)																							ACAAATAACATTTAAACTTTA	0.294													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	46675329	46675329	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46675329delA	uc001jdv.2	-						uc009xmy.1_Intron	NM_001042524	NP_001035989			FERM and PDZ domain containing 2 like 1 isoform																		AATGGAAGAGAAAAAAAAAAC	0.428													4	2	---	---	---	---	
SYT15	83849	broad.mit.edu	37	10	46964697	46964697	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46964697delG	uc001jea.2	-						SYT15_uc001jdz.2_Intron|SYT15_uc001jeb.2_Intron|SYT15_uc010qfp.1_Intron	NM_031912	NP_114118	Q9BQS2	SYT15_HUMAN	synaptotagmin XV isoform a							integral to membrane|plasma membrane					0						ggtggaggcaggcaggacagt	0.184													5	3	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47028001	47028002	+	Intron	INS	-	CT	CT	rs149264405		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47028001_47028002insCT	uc001jed.3	-									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						TCGTTTGCGTGCTCTCTCTCTC	0.455													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	51008456	51008456	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51008456delT								OGDHL (38031 upstream) : PARG (17871 downstream)																							TCCCATAAACTTTTTTTTTCC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64482821	64482821	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64482821delT								ZNF365 (51050 upstream) : ADO (81695 downstream)																							TTCCTGGCCATTTTTTTTCTC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	64541530	64541533	+	IGR	DEL	CTAT	-	-	rs71472224		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64541530_64541533delCTAT								ZNF365 (109759 upstream) : ADO (22983 downstream)																							TAAAATAAAACTATCTATCACTTA	0.353													3	3	---	---	---	---	
JMJD1C	221037	broad.mit.edu	37	10	65185220	65185221	+	Intron	INS	-	AT	AT	rs141621218	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65185220_65185221insAT	uc001jmn.2	-						JMJD1C_uc001jmr.1_Intron	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					gtccaaactgcatatcacatga	0.000													4	2	---	---	---	---	
CDH23	64072	broad.mit.edu	37	10	73563299	73563299	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73563299delA	uc001jrx.3	+						CDH23_uc001jsg.3_Intron|CDH23_uc001jsh.3_Intron|CDH23_uc001jsi.3_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						TAGCTCCAGGaaaaaaaaaac	0.299													4	4	---	---	---	---	
CBARA1	10367	broad.mit.edu	37	10	74145943	74145943	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74145943delT	uc001jtb.1	-						CBARA1_uc010qjw.1_Intron|CBARA1_uc010qjx.1_Intron|CBARA1_uc009xqo.1_Intron	NM_006077	NP_006068	Q9BPX6	MICU1_HUMAN	calcium binding atopy-related autoantigen 1						calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1						TGGGAATGTCttttttttttg	0.085													4	2	---	---	---	---	
NRG3	10718	broad.mit.edu	37	10	84652040	84652040	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84652040delA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron|NRG3_uc001kcr.2_Intron	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		CAGTGTAGCCAAAAAAAAAGG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	87351592	87351592	+	Intron	DEL	A	-	-	rs76657297		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87351592delA	uc001kdk.1	+											Homo sapiens cDNA FLJ40336 fis, clone TESTI2031986.																		gtgttgaattaaaaaaaaaaa	0.000													2	4	---	---	---	---	
LIPJ	142910	broad.mit.edu	37	10	90350888	90350889	+	Intron	INS	-	GTTT	GTTT	rs149992085	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90350888_90350889insGTTT	uc001kff.2	+							NM_001010939	NP_001010939	Q5W064	LIPJ_HUMAN	lipase, family member J						lipid catabolic process		hydrolase activity			ovary(1)	1		all_cancers(4;2.79e-10)|Prostate(4;1.68e-15)|all_epithelial(4;1.43e-09)|Colorectal(252;0.0381)|Breast(4;0.141)|Melanoma(5;0.2)|all_hematologic(4;0.222)		Colorectal(12;1.02e-05)|COAD - Colon adenocarcinoma(12;1.54e-05)		tgagggtaggggtttgtttgtt	0.109													2	5	---	---	---	---	
LOC100188947	100188947	broad.mit.edu	37	10	93350373	93350373	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93350373delG	uc010qnl.1	-							NR_024467				Homo sapiens, clone IMAGE:6063621, mRNA.												0						AGGAAGAAATGGGGGAAAGAA	0.468													4	2	---	---	---	---	
EXOC6	54536	broad.mit.edu	37	10	94760497	94760497	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94760497delA	uc001kig.2	+						EXOC6_uc010qnr.1_Intron|EXOC6_uc001kie.2_Intron|EXOC6_uc009xub.2_Intron|EXOC6_uc009xuc.2_Intron|EXOC6_uc001kih.2_Intron|EXOC6_uc001kii.2_Intron	NM_019053	NP_061926	Q8TAG9	EXOC6_HUMAN	SEC15-like 1 isoform a						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)				CTGATGGGACAAAAAAAATTG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	94890541	94890541	+	IGR	DEL	C	-	-	rs141435454	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94890541delC								CYP26A1 (52900 upstream) : MYOF (175646 downstream)																							ctataaaagtcctgcacgccc	0.015													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95137468	95137468	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95137468delA	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a						blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						taaaaggcagaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	96134633	96134634	+	IGR	INS	-	AA	AA			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96134633_96134634insAA								NOC3L (11950 upstream) : TBC1D12 (27552 downstream)																							ctgtctcaaagaaaaaaaaaga	0.173													4	2	---	---	---	---	
SORBS1	10580	broad.mit.edu	37	10	97163836	97163836	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97163836delT	uc001kkp.2	-						SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GCTGGAGGCCTTTTTTATCTA	0.279													4	2	---	---	---	---	
SCD	6319	broad.mit.edu	37	10	102111105	102111105	+	Intron	DEL	C	-	-	rs77607180		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102111105delC	uc001kqy.2	+							NM_005063	NP_005054	O00767	ACOD_HUMAN	stearoyl-CoA desaturase 1						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity				0		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		GAGAGCGTTGCCCGGTGAGAG	0.547													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107093446	107093446	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107093446delA								SORCS3 (68453 upstream) : None (None downstream)																							ACAAACAAACAAAACAACAAC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	109477755	109477755	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109477755delA								SORCS1 (553463 upstream) : None (None downstream)																							gataatttttatagcagcctt	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113645491	113645491	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113645491delT								ADRA2A (804831 upstream) : GPAM (264131 downstream)																							TAAGCTCCAATTTTTTTTTCA	0.224													4	2	---	---	---	---	
NHLRC2	374354	broad.mit.edu	37	10	115632306	115632306	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115632306delA	uc001lax.1	+							NM_198514	NP_940916	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2						cell redox homeostasis					ovary(1)	1				Epithelial(162;0.017)|all cancers(201;0.0187)		aggaataatgaaaaaaaaaca	0.000													4	2	---	---	---	---	
VWA2	340706	broad.mit.edu	37	10	116019639	116019639	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116019639delC	uc001lbl.1	+						VWA2_uc001lbk.1_Intron|VWA2_uc009xyf.1_Intron	NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)		GCTTAAGGTGCCCAACAGCTC	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	122533594	122533595	+	Intron	DEL	GA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122533594_122533595delGA	uc001lfa.1	-						uc001lfb.1_Intron					Homo sapiens cDNA FLJ37330 fis, clone BRAMY2019509.																		GATGAGGCATgagagagagaga	0.277													4	2	---	---	---	---	
WDR11	55717	broad.mit.edu	37	10	122631007	122631007	+	Intron	DEL	A	-	-	rs145936030		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122631007delA	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2							integral to membrane					0						CCTGGAACTTAAAAAAAAAAA	0.348													5	7	---	---	---	---	
WDR11	55717	broad.mit.edu	37	10	122639011	122639011	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122639011delA	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2							integral to membrane					0						TCATTGACTTAAAAAAAAGAA	0.373													4	4	---	---	---	---	
DHX32	55760	broad.mit.edu	37	10	127581186	127581186	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127581186delG	uc001ljg.1	-							NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GGAAGCACCTGGTCATTTCCT	0.478													4	2	---	---	---	---	
C10orf90	118611	broad.mit.edu	37	10	128273412	128273413	+	Intron	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128273412_128273413delTG	uc010qum.1	-						C10orf90_uc009yao.2_Intron	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		CACTATATGATGTGTGTGTGTG	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134824470	134824471	+	IGR	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134824470_134824471delTG								C10orf93 (68406 upstream) : GPR123 (59962 downstream)																							gcttgtgtgatgtgtTTTAGCA	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	135464251	135464252	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135464251_135464252insT								FRG2B (23952 upstream) : LOC653544 (26027 downstream)																							caggttcattcttttacatgtg	0.000													4	3	---	---	---	---	
SYT9	143425	broad.mit.edu	37	11	7439588	7439588	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7439588delT	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		CCCGTTCTCATTTTTTTTCCT	0.488													5	3	---	---	---	---	
SPON1	10418	broad.mit.edu	37	11	14147795	14147795	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14147795delA	uc001mle.2	+							NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)		atataaaattaaccatcacTC	0.179													4	2	---	---	---	---	
PSMA1	5682	broad.mit.edu	37	11	14662123	14662123	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14662123delA	uc001mll.2	-							NM_148976	NP_683877	P25786	PSA1_HUMAN	proteasome alpha 1 subunit isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2						gaaAAGAACTAAAAGAATGAG	0.214													4	2	---	---	---	---	
NAV2	89797	broad.mit.edu	37	11	19495104	19495104	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19495104delA	uc001mpp.2	+							NM_001111018	NP_001104488	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 3							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						ccttccctttaaggtacaacc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	28616914	28616914	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28616914delT								METT5D1 (261860 upstream) : None (None downstream)																							tttCTCTCTCTTTTTTTGGGA	0.229													4	2	---	---	---	---	
API5	8539	broad.mit.edu	37	11	43354539	43354539	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43354539delC	uc010rfh.1	+						API5_uc010rfg.1_Intron|API5_uc001mxf.2_Intron|API5_uc010rfi.1_Intron|API5_uc001mxg.2_Intron	NM_001142930	NP_001136402	Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5 isoform a						anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3						ttgtctttcacctttattgct	0.000													4	2	---	---	---	---	
F2	2147	broad.mit.edu	37	11	46742602	46742602	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46742602delT	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497	P00734	THRB_HUMAN	coagulation factor II preproprotein						activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)	tgaattaatgttttttttttt	0.164													4	2	---	---	---	---	
OR4A15	81328	broad.mit.edu	37	11	55132453	55132453	+	5'Flank	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55132453delA	uc010rif.1	+							NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						CATTCACATCACCATGTGAAA	0.189													4	2	---	---	---	---	
OR9Q1	219956	broad.mit.edu	37	11	57938925	57938925	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57938925delC	uc001nmj.2	+							NM_001005212	NP_001005212	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.222)				ATCAGCAAGGCCATCTAAACA	0.433													4	2	---	---	---	---	
GAL	51083	broad.mit.edu	37	11	68458593	68458593	+	3'UTR	DEL	T	-	-	rs75147512		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68458593delT	uc001oob.2	+	6						NM_015973	NP_057057	P22466	GALA_HUMAN	galanin preproprotein						growth hormone secretion|insulin secretion|neuropeptide signaling pathway|smooth muscle contraction	extracellular region	neuropeptide hormone activity				0	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)		TCATTTAAGATTTTTTTTTTT	0.358													7	4	---	---	---	---	
PPME1	51400	broad.mit.edu	37	11	73910105	73910105	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73910105delG	uc001ouw.2	+							NM_016147	NP_057231	Q9Y570	PPME1_HUMAN	protein phosphatase methylesterase 1						protein demethylation		carboxylesterase activity|protein C-terminal methylesterase activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity				0	Breast(11;3.29e-05)					TTTTGTTGTTGTTTGTTTTCA	0.284													4	2	---	---	---	---	
GDPD4	220032	broad.mit.edu	37	11	76940921	76940921	+	Intron	DEL	C	-	-	rs149475629		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76940921delC	uc001oyf.2	-							NM_182833	NP_878253	Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process	integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding			skin(1)	1						TCTTCTGGGTCCTCTCATTGA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79280649	79280649	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79280649delG								ODZ4 (128954 upstream) : None (None downstream)																							ttggacttttgggggtgatta	0.055													4	2	---	---	---	---	
CCDC67	159989	broad.mit.edu	37	11	93097693	93097694	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93097693_93097694insA	uc001pdq.2	+						CCDC67_uc001pdo.1_Intron|CCDC67_uc001pdp.2_Intron	NM_181645	NP_857596	Q05D60	CCD67_HUMAN	coiled-coil domain containing 67											ovary(1)	1		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				TTTGGGAGATTAAAAAAAAAAG	0.332													6	3	---	---	---	---	
KIAA1731	85459	broad.mit.edu	37	11	93408523	93408523	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93408523delC	uc009ywb.1	+							NM_033395	NP_203753	Q9C0D2	K1731_HUMAN	hypothetical protein LOC85459							centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GTTAGCGACACCTTGAAGATG	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	97263532	97263533	+	IGR	INS	-	A	A	rs145238205	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97263532_97263533insA								None (None upstream) : None (None downstream)																							gttaaactgataAAAAAAAATT	0.005													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99628829	99628829	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99628829delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		GTATAATAACTTTGCTTTAGC	0.338													4	2	---	---	---	---	
ARHGAP42	143872	broad.mit.edu	37	11	100830963	100830964	+	Intron	INS	-	T	T	rs35888487		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100830963_100830964insT	uc001pge.2	+						ARHGAP42_uc001pgc.2_Intron	NM_152432	NP_689645	A6NI28	RHG42_HUMAN	Rho-type GTPase-activating protein FLJ32810						filopodium assembly|signal transduction	intracellular	cytoskeletal adaptor activity|GTPase activator activity|SH3 domain binding				0						CACCTCTTTGATTTTTTTTTTT	0.351													4	2	---	---	---	---	
MMP20	9313	broad.mit.edu	37	11	102449511	102449512	+	Intron	INS	-	AC	AC	rs10670953		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102449511_102449512insAC	uc001phc.2	-							NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein						proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)		caaaaaacaaaacacacacaca	0.089													8	7	---	---	---	---	
GRIA4	2893	broad.mit.edu	37	11	105836404	105836405	+	Intron	INS	-	A	A	rs139321638	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105836404_105836405insA	uc001pix.2	+						GRIA4_uc001piw.2_Intron|GRIA4_uc010rvm.1_Intron|GRIA4_uc009yxl.1_Intron	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	ACTGTTTTGCCAAAAAAAATCC	0.312													2	4	---	---	---	---	
DDX10	1662	broad.mit.edu	37	11	108548785	108548785	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108548785delT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		CATTTGATTATTTTTTTTTCT	0.353			T	NUP98	AML*								4	2	---	---	---	---	
NNMT	4837	broad.mit.edu	37	11	114148271	114148271	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114148271delG	uc001por.1	+							NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase						xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)	ggatatttgagggtaagccac	0.119													4	2	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117653811	117653812	+	Intron	DEL	CA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117653811_117653812delCA	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)		cacacaggtgcacacacacata	0.361													4	2	---	---	---	---	
GRIK4	2900	broad.mit.edu	37	11	120464670	120464671	+	Intron	DEL	TC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120464670_120464671delTC	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)	tttatacccttctctctctcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127766482	127766482	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127766482delT								KIRREL3 (893127 upstream) : ETS1 (562174 downstream)																							CACAAGGGAATTTTTTTTATT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128146789	128146789	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128146789delG								None (None upstream) : ETS1 (181867 downstream)																							actatgttttggcttgcatta	0.000													4	2	---	---	---	---	
FLI1	2313	broad.mit.edu	37	11	128678621	128678621	+	Intron	DEL	T	-	-	rs35474388		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128678621delT	uc010sbu.1	+						FLI1_uc010sbt.1_Intron|FLI1_uc010sbv.1_Intron|FLI1_uc009zci.2_Intron	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1						hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		tcatgctACATTTAAAAAAAA	0.174			T	EWSR1	Ewing sarcoma								3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	133710506	133710506	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133710506delC								OPCML (308103 upstream) : SPATA19 (11 downstream)																							TGGCACAGCACCCCAACCAGC	0.522													4	2	---	---	---	---	
C12orf4	57102	broad.mit.edu	37	12	4639391	4639391	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4639391delA	uc001qms.2	-						C12orf4_uc001qmt.2_Intron	NM_020374	NP_065107	Q9NQ89	CL004_HUMAN	hypothetical protein LOC57102												0			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		CTAAGCACAGAAAAAAAAAAT	0.348													11	5	---	---	---	---	
ETV6	2120	broad.mit.edu	37	12	12061975	12061975	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12061975delG	uc001raa.1	+							NM_001987	NP_001978	P41212	ETV6_HUMAN	ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				actgacatatggccagaatag	0.149			T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	17539585	17539586	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17539585_17539586insT								LMO3 (776827 upstream) : RERGL (694218 downstream)																							TTTGTCTATTCTTTTTTTTAAC	0.198													4	2	---	---	---	---	
PLEKHA5	54477	broad.mit.edu	37	12	19416357	19416357	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19416357delT	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron	NM_019012	NP_061885	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TAATCACGAGTTTTTGCCCCC	0.239													4	2	---	---	---	---	
KRAS	3845	broad.mit.edu	37	12	25382070	25382071	+	Intron	INS	-	T	T	rs7137630	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25382070_25382071insT	uc001rgp.1	-						KRAS_uc001rgq.1_Intron	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor						activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding			large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			acaaaaaaaaaTTTTTTAAAGG	0.144		119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30576086	30576086	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30576086delA								TMTC1 (638394 upstream) : IPO8 (205837 downstream)																							ctctcagagtaaaagcttaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31399399	31399399	+	IGR	DEL	T	-	-	rs113637821		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31399399delT								DDX11 (141674 upstream) : FAM60A (34128 downstream)																							ctacaactacttttttttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	34423365	34423365	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34423365delC								ALG10 (242131 upstream) : None (None downstream)																							tcaagctcttcccccgcaagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	40565513	40565514	+	IGR	INS	-	T	T	rs139985420	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40565513_40565514insT								SLC2A13 (65852 upstream) : LRRK2 (53299 downstream)																							AGGACTTGTGGTTTTTTTTTAA	0.366													4	2	---	---	---	---	
CNTN1	1272	broad.mit.edu	37	12	41294241	41294242	+	Intron	DEL	GT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41294241_41294242delGT	uc001rmm.1	+						CNTN1_uc009zjy.1_Intron|CNTN1_uc001rmn.1_Intron|CNTN1_uc001rmo.2_Intron	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				CATTTTGGGAGTGTGTGTGTGT	0.421													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	47447378	47447378	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47447378delA								SLC38A4 (227598 upstream) : AMIGO2 (22113 downstream)																							ctctcctctgaaaaaaaaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48412446	48412447	+	IGR	DEL	TC	-	-	rs71893725		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48412446_48412447delTC								COL2A1 (14161 upstream) : SENP1 (24311 downstream)																							TTCTTTTTGTtctctctctctc	0.312													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48814489	48814489	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48814489delT								ZNF641 (69468 upstream) : ANP32D (51959 downstream)																							acgtactccattaaccaacct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48907454	48907454	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48907454delT								C12orf54 (17289 upstream) : OR8S1 (11961 downstream)																							aaatcttgggttttTTTCACT	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54527921	54527922	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54527921_54527922insT								LOC400043 (1302 upstream) : SMUG1 (45861 downstream)																							CTCCTGGCCCCTTTGTCCTCAC	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	56227468	56227468	+	3'UTR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56227468delA	uc001shz.1	+	1										Homo sapiens cDNA FLJ34386 fis, clone HCHON1000166.																		CAGGGCACTGAAAAAAAAAGT	0.468													4	2	---	---	---	---	
SDR9C7	121214	broad.mit.edu	37	12	57321482	57321482	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57321482delC	uc010sqw.1	-							NM_148897	NP_683695	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C,							cytoplasm	binding|oxidoreductase activity			central_nervous_system(1)	1						ctcctattttcccagcagacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	63654867	63654867	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63654867delA								AVPR1A (108277 upstream) : DPY19L2 (297826 downstream)																							ACAAACAAACAAAAAAACTCT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	64989991	64989991	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64989991delT								TBK1 (94100 upstream) : RASSF3 (14302 downstream)																							aaaatggacattttcccctgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	65983415	65983415	+	IGR	DEL	A	-	-	rs113146545		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65983415delA								MSRB3 (122735 upstream) : RPSAP52 (168388 downstream)																							AAACCTGATTAAAAAAAAAAA	0.358													3	4	---	---	---	---	
MDM2	4193	broad.mit.edu	37	12	69233935	69233935	+	3'UTR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69233935delT	uc001sui.2	+	11					MDM2_uc009zri.2_3'UTR|MDM2_uc009zqx.2_3'UTR|MDM2_uc009zqw.2_3'UTR|MDM2_uc001suk.2_3'UTR|MDM2_uc001sun.3_3'UTR|MDM2_uc009zqz.2_3'UTR|MDM2_uc009zra.2_3'UTR|MDM2_uc009zrd.2_3'UTR|MDM2_uc009zrc.2_3'UTR|MDM2_uc009zre.2_3'UTR|MDM2_uc009zrf.2_3'UTR|MDM2_uc001suo.2_3'UTR|MDM2_uc009zrg.2_3'UTR|MDM2_uc009zrh.2_3'UTR	NM_002392	NP_002383	Q00987	MDM2_HUMAN	mouse double minute 2 homolog isoform MDM2						cellular response to hypoxia|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|establishment of protein localization|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein complex assembly|protein destabilization|protein localization to nucleus|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to antibiotic|synaptic transmission	cytosol|endocytic vesicle membrane|insoluble fraction|nucleolus|nucleoplasm|plasma membrane|protein complex	enzyme binding|identical protein binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|central_nervous_system(1)	3	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TAACTTATTAttttttttgag	0.104			A		sarcoma|glioma|colorectal|other								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	69594715	69594716	+	IGR	INS	-	GAGG	GAGG			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69594715_69594716insGAGG								CPM (237695 upstream) : CPSF6 (38601 downstream)																							gaggaagagataggagatgagg	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	74669120	74669120	+	Intron	DEL	T	-	-	rs113849001		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74669120delT	uc009zrx.1	-						uc001sxc.2_Intron					Homo sapiens cDNA clone IMAGE:3926153, partial cds.																		TTTTTTGGGGTTTTTTTTTTT	0.303													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77671473	77671474	+	IGR	INS	-	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77671473_77671474insG								E2F7 (212113 upstream) : NAV3 (553595 downstream)																							gaccaaatttaggggaaatggg	0.000													4	2	---	---	---	---	
C12orf26	84190	broad.mit.edu	37	12	82868266	82868266	+	Intron	DEL	T	-	-	rs113316962		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82868266delT	uc001szq.2	+							NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190												0						tGCGTTGTTATTTTTTTTTTC	0.224													4	2	---	---	---	---	
TMTC2	160335	broad.mit.edu	37	12	83342403	83342403	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83342403delT	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2						AATTTATTGCTTTAACAGCAG	0.358													4	2	---	---	---	---	
CCDC41	51134	broad.mit.edu	37	12	94702283	94702283	+	3'UTR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94702283delA	uc001tdd.2	-	17					CCDC41_uc001tde.2_3'UTR	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen												0						TCAAAATGCCAAAAAAAAAAA	0.284													6	3	---	---	---	---	
CCDC41	51134	broad.mit.edu	37	12	94820245	94820245	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94820245delA	uc001tdd.2	-						CCDC41_uc001tde.2_Intron|CCDC41_uc009zsw.1_Intron|CCDC41_uc001tdf.2_Intron	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen												0						cccaacacctaaaaaaccaca	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	98381263	98381263	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98381263delT								RMST (422470 upstream) : LOC100128191 (525490 downstream)																							AACAATAGAATTTTTTTTTTT	0.323													4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99945726	99945727	+	Intron	DEL	CA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99945726_99945727delCA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		ctccccccaccacacacacaca	0.035													4	2	---	---	---	---	
DRAM1	55332	broad.mit.edu	37	12	102271549	102271551	+	5'UTR	DEL	CGG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102271549_102271551delCGG	uc001tix.2	+	1					DRAM1_uc010svv.1_5'UTR	NM_018370	NP_060840	Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1						apoptosis|autophagy	integral to membrane|lysosomal membrane				ovary(1)	1						AGCACTCCGTCGGCGGCGGCGGC	0.714													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	103904873	103904873	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103904873delA								C12orf42 (15124 upstream) : STAB2 (76196 downstream)																							AACCTCCAAGAAAAAATGGAG	0.378													4	2	---	---	---	---	
ACACB	32	broad.mit.edu	37	12	109553203	109553203	+	5'Flank	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109553203delT	uc001tob.2	+							NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	AGCCTAAGAATTTTTTTCAAT	0.254													4	2	---	---	---	---	
ATXN2	6311	broad.mit.edu	37	12	111924888	111924888	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111924888delT	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsg.2_Intron	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2						CAAAAAATACttttttttttt	0.154													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	114944070	114944071	+	IGR	INS	-	ACA	ACA			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114944070_114944071insACA								TBX5 (97823 upstream) : TBX3 (163988 downstream)																							ccaccatcaccatcaccaccat	0.168													4	2	---	---	---	---	
GCN1L1	10985	broad.mit.edu	37	12	120570110	120570111	+	Intron	DEL	TG	-	-	rs142859275		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120570110_120570111delTG	uc001txo.2	-							NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					Cagtaataactgtatttacata	0.213													2	4	---	---	---	---	
RILPL2	196383	broad.mit.edu	37	12	123900707	123900707	+	Intron	DEL	A	-	-	rs35289744		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123900707delA	uc001uey.1	-							NM_145058	NP_659495	Q969X0	RIPL2_HUMAN	Rab interacting lysosomal protein-like 2							cytosol|plasma membrane	identical protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)		ccccatctctaaaaaaaaaaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	124562078	124562078	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124562078delT								ZNF664 (62111 upstream) : FAM101A (211632 downstream)																							TTCCAGAGCATTTGGGGACTG	0.473													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	130358683	130358683	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130358683delA	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		gaaattcactaagaaagtaaa	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130751291	130751292	+	IGR	INS	-	TCAT	TCAT	rs148209624	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130751291_130751292insTCAT								FZD10 (101007 upstream) : PIWIL1 (71322 downstream)																							TGACAATGGACtcattcattca	0.153													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131374275	131374275	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131374275delT								RAN (13451 upstream) : GPR133 (64177 downstream)																							gggcatgtactttttttcccc	0.000													4	2	---	---	---	---	
MTUS2	23281	broad.mit.edu	37	13	30027903	30027903	+	Intron	DEL	A	-	-	rs11353192		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30027903delA	uc001usl.3	+						MTUS2_uc001usm.3_Intron|MTUS2_uc010aau.2_Intron	NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						ATCTCTAAGCAGGAGGAGTAG	0.403													4	4	---	---	---	---	
SLC7A1	6541	broad.mit.edu	37	13	30148222	30148223	+	Intron	INS	-	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30148222_30148223insG	uc001uso.2	-							NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid						cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity				0		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GAGACACCACAGGGGGTGAGGA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	32270340	32270340	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32270340delA								B3GALTL (363931 upstream) : RXFP2 (43339 downstream)																							aaacagtcagaaaaaaaatat	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	32307021	32307021	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32307021delA								B3GALTL (400612 upstream) : RXFP2 (6658 downstream)																							CCCAAGAATTAAAAAAAAAAA	0.343													6	3	---	---	---	---	
NBEA	26960	broad.mit.edu	37	13	35933069	35933069	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35933069delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		aaaagaaatattacaaagact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	37242959	37242959	+	IGR	DEL	C	-	-	rs682593	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37242959delC								CCNA1 (225941 upstream) : C13orf36 (5090 downstream)																							taaacaacaacaaaaaaggaa	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	47847088	47847088	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47847088delC								HTR2A (376038 upstream) : SUCLA2 (669704 downstream)																							ATTTTTTTTTCTCGCACTATT	0.348													4	2	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	48942412	48942412	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48942412delA	uc001vcb.2	+						RB1_uc010act.1_Intron	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TTTCACTTTTAAAAAAAGACT	0.299		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	51872358	51872359	+	IGR	INS	-	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51872358_51872359insG								FAM124A (16742 upstream) : SERPINE3 (42809 downstream)																							TGGAGTAGGACGGCGGGGAAAA	0.455													4	2	---	---	---	---	
VPS36	51028	broad.mit.edu	37	13	52992422	52992423	+	Intron	INS	-	A	A	rs137939288	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52992422_52992423insA	uc001vgs.2	-						VPS36_uc001vgq.2_Intron	NM_016075	NP_057159	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36						cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|late endosome|membrane|nucleus	lipid binding			skin(1)	1		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		attaaaaaaataaaaagaggcc	0.050													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	55841546	55841546	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55841546delT								MIR1297 (955363 upstream) : None (None downstream)																							CTCATTCTTCTTTTTTACATA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	57083338	57083338	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57083338delT								None (None upstream) : PRR20C (631714 downstream)																							aagatagtgcttttttttttc	0.000													4	3	---	---	---	---	
TDRD3	81550	broad.mit.edu	37	13	61013243	61013244	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61013243_61013244insA	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		AGACAATGCGTAAAAAAAACTG	0.322													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66457069	66457069	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66457069delT								None (None upstream) : PCDH9 (419898 downstream)																							aagctgagcctttttttcaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68299752	68299752	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68299752delT								PCDH9 (495284 upstream) : None (None downstream)																							tgtagtattctttttttttga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	68874395	68874396	+	IGR	INS	-	A	A	rs140513759	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68874395_68874396insA								None (None upstream) : None (None downstream)																							TAACAGGAAGGAAAAAAAAAAC	0.342													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71685682	71685682	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71685682delT								ATXN8OS (971797 upstream) : DACH1 (326416 downstream)																							TCAAAAGACATTTTGGGTCTT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	71921995	71921995	+	IGR	DEL	T	-	-	rs75006868	byFrequency	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71921995delT								None (None upstream) : DACH1 (90103 downstream)																							atccatgctgttttttttgtc	0.000													6	3	---	---	---	---	
C13orf37	440145	broad.mit.edu	37	13	73297370	73297370	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73297370delT	uc001viu.2	-							NM_001071775	NP_001065243	Q08AG7	MZT1_HUMAN	hypothetical protein LOC440145						gamma-tubulin complex localization	centrosome|gamma-tubulin ring complex|spindle	protein binding				0						TGCTGTTTTCTTAGTCCATCT	0.363													4	2	---	---	---	---	
PIBF1	10464	broad.mit.edu	37	13	73472510	73472510	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73472510delA	uc001vjc.2	+						PIBF1_uc010aeo.1_Intron|PIBF1_uc001vjb.2_Intron|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337	Q8WXW3	PIBF1_HUMAN	progesterone-induced blocking factor 1							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)		gaaagagcacaaacagacaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78383037	78383037	+	IGR	DEL	T	-	-	rs111800868		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78383037delT								SLAIN1 (44660 upstream) : EDNRB (86579 downstream)																							AATTTTAAGGTTTTTTTTTTC	0.363													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	91101512	91101512	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91101512delA								MIR622 (217981 upstream) : LOC144776 (441696 downstream)																							agaaacaaacaaaaaaaactt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	91972800	91972800	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91972800delT								LOC144776 (393949 upstream) : MIR17HG (27274 downstream)																							AATTTTGCTATTTTTTTTTCA	0.403													3	3	---	---	---	---	
UGGT2	55757	broad.mit.edu	37	13	96485564	96485564	+	Intron	DEL	A	-	-	rs11329248		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96485564delA	uc001vmt.2	-						UGGT2_uc001vms.2_Intron	NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3						TAAGTCTGTCAAAAAAAAATT	0.274													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102885479	102885480	+	Intron	INS	-	TTG	TTG			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102885479_102885480insTTG	uc001vpf.2	-							NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					atatgccatttttgttgttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19090397	19090398	+	IGR	DEL	GT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19090397_19090398delGT								None (None upstream) : OR11H12 (287196 downstream)																							CTTATAGTGAGTGTGTGTGTGT	0.356													4	2	---	---	---	---	
THTPA	79178	broad.mit.edu	37	14	23982602	23982603	+	Intron	DEL	GT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23982602_23982603delGT	uc001wkb.3	+						uc001wkc.1_RNA			Q9BU02	THTPA_HUMAN	Homo sapiens thiamine triphosphatase mRNA, complete cds.						dephosphorylation|generation of precursor metabolites and energy|thiamine metabolic process	cytosol|nucleolus|soluble fraction	thiamin-triphosphatase activity				0	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)	Thiamine(DB00152)	TCATGGGGCCgtgtgtgtgtgt	0.545													4	3	---	---	---	---	
STXBP6	29091	broad.mit.edu	37	14	25478943	25478944	+	Intron	DEL	CA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25478943_25478944delCA	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)		AAAACAACATCACACACACACA	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	34604947	34604947	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34604947delG								EGLN3 (184660 upstream) : C14orf147 (297198 downstream)																							cgatttctgtggtatgcaaac	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	43996783	43996783	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43996783delG								None (None upstream) : FSCB (976572 downstream)																							tgctgctgatggaagtataat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	49673609	49673609	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49673609delA								None (None upstream) : SDCCAG1 (359418 downstream)																							TTTTGGAGTCAAAAAAAAAAA	0.413													6	3	---	---	---	---	
SDCCAG1	9147	broad.mit.edu	37	14	50117790	50117791	+	Intron	DEL	AA	-	-	rs10572392		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50117790_50117791delAA	uc010anj.1	-						POLE2_uc010ann.2_Intron|POLE2_uc001wwu.2_Intron|POLE2_uc001wwv.2_Intron|POLE2_uc010ano.2_Intron	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		TCTGTCCTCTAAAGGACATACA	0.203													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51757017	51757019	+	IGR	DEL	ATG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51757017_51757019delATG								TMX1 (32647 upstream) : FRMD6 (198836 downstream)																							gataatgataatgatgatgatgg	0.177													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54183644	54183654	+	IGR	DEL	TTGATGTAGCT	-	-	rs150006546	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54183644_54183654delTTGATGTAGCT								DDHD1 (563598 upstream) : BMP4 (232803 downstream)																							TTCATTTCAGTTGATGTAGCTTTGACTTGGA	0.412													3	3	---	---	---	---	
WDHD1	11169	broad.mit.edu	37	14	55462099	55462100	+	Intron	INS	-	TTCT	TTCT	rs139485649	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55462099_55462100insTTCT	uc001xbm.1	-						WDHD1_uc001xbn.1_Intron	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1							cytoplasm|nucleoplasm	DNA binding			skin(1)	1						tatttccttccatttgcttggg	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	59016171	59016171	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59016171delT								KIAA0586 (623 upstream) : DACT1 (84615 downstream)																							TGCCTGGGGATTTTTTTTCTC	0.313													4	2	---	---	---	---	
SPTB	6710	broad.mit.edu	37	14	65307384	65307385	+	Intron	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65307384_65307385delTG	uc001xhs.2	-						SPTB_uc001xhu.2_Intron	NM_001024858	NP_001020029	P11277	SPTB1_HUMAN	spectrin beta isoform a						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)		CTGGCTGAGCTGTGACCCACAG	0.505													4	2	---	---	---	---	
MAX	4149	broad.mit.edu	37	14	65543066	65543066	+	3'UTR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65543066delA	uc001xif.1	-	5					MAX_uc001xic.1_Intron|MAX_uc001xie.1_3'UTR|MAX_uc010aql.1_3'UTR|MAX_uc001xig.1_3'UTR|MAX_uc001xih.1_RNA	NM_002382	NP_002373	P61244	MAX_HUMAN	MAX protein isoform a						transcription from RNA polymerase II promoter	cytoplasm|MLL1 complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(1)	1				all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999)		ataaaaatttaaaaaaaaaaG	0.383													4	2	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67631635	67631635	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67631635delA	uc001xiy.2	+						GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		CACTGGCAAGAAAAAAAAAAA	0.323			T	MLL	AL								4	4	---	---	---	---	
GPHN	10243	broad.mit.edu	37	14	67632166	67632187	+	Intron	DEL	TATCAAAGCACATTCCAAATCC	-	-	rs3830996		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67632166_67632187delTATCAAAGCACATTCCAAATCC	uc001xiy.2	+						GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		agataatatatatcaaagcacattccaaatcctatcaaagca	0.153			T	MLL	AL								9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	72296894	72296894	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72296894delA								SIPA1L1 (90776 upstream) : RGS6 (102262 downstream)																							gcaaacacctaaaactctgag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	88482022	88482022	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88482022delT								GPR65 (3608 upstream) : KCNK10 (164432 downstream)																							tgtcttcccctttttggttta	0.040													4	2	---	---	---	---	
C14orf102	55051	broad.mit.edu	37	14	90784178	90784178	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90784178delA	uc001xyi.1	-						C14orf102_uc001xyj.1_Intron	NM_017970	NP_060440	Q9H7Z3	CN102_HUMAN	hypothetical protein LOC55051 isoform 1								protein binding			ovary(2)|lung(1)	3		all_cancers(154;0.118)		COAD - Colon adenocarcinoma(157;0.218)		CAAAGCAAAGAAAAAAAAAAG	0.353													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99118366	99118366	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99118366delA								C14orf64 (673905 upstream) : C14orf177 (59584 downstream)																							GCAGAACATTAAAAAAAAAAC	0.259													4	2	---	---	---	---	
BCL11B	64919	broad.mit.edu	37	14	99707814	99707814	+	Intron	DEL	A	-	-	rs112147952		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99707814delA	uc001yga.2	-						BCL11B_uc001ygb.2_Intron	NM_138576	NP_612808	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B isoform 1							nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)|lung(1)	10		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		AAAGAAAAAGAAAAAAAAAAA	0.468			T	TLX3	T-ALL								2	5	---	---	---	---	
CCDC85C	317762	broad.mit.edu	37	14	100044514	100044515	+	Intron	DEL	GT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100044514_100044515delGT	uc010avr.2	-							NM_001144995	NP_001138467	A6NKD9	CC85C_HUMAN	coiled-coil domain containing 85C												0						TCCCCCATCAgtgtgtgtgtgt	0.416													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107234830	107234830	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107234830delT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						GAAAAGTGACTCCATGACAAT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20107044	20107044	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20107044delA								None (None upstream) : GOLGA6L6 (630050 downstream)																							GCCAATAAGGAAAAAAAAAGC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20447061	20447062	+	IGR	INS	-	CCCTAGG	CCCTAGG	rs146140470	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20447061_20447062insCCCTAGG								None (None upstream) : GOLGA6L6 (290032 downstream)																							ttgagaccagcctaggcaacat	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20454213	20454214	+	IGR	INS	-	T	T	rs144687403		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20454213_20454214insT								None (None upstream) : GOLGA6L6 (282880 downstream)																							GACCCTCAAGCtttttttttct	0.267													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20527370	20527372	+	IGR	DEL	ATC	-	-	rs148807711		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20527370_20527372delATC								None (None upstream) : GOLGA6L6 (209722 downstream)																							TATCCATATTATCACTACCAAGT	0.315													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	22482640	22482642	+	IGR	DEL	TGT	-	-	rs140253182		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22482640_22482642delTGT								OR4N3P (68255 upstream) : MIR1268 (30587 downstream)																							ACAGAATAAATGTTGTATGAAAA	0.128													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	25788855	25788855	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25788855delT								UBE3A (104727 upstream) : ATP10A (135007 downstream)																							AGTCACCCTGtttttccctgt	0.249													4	2	---	---	---	---	
GABRG3	2567	broad.mit.edu	37	15	27472086	27472086	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27472086delA	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		TCTGCCTCCTAAAGCAGTACT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	30782699	30782699	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30782699delA								CHRFAM7A (96835 upstream) : FAM7A2 (82059 downstream)																							ATATCTGTCTAAATGATTTTA	0.318													4	2	---	---	---	---	
GREM1	26585	broad.mit.edu	37	15	33008938	33008938	+	5'Flank	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33008938delA	uc001zhe.1	+						GREM1_uc001zhd.1_5'Flank|GREM1_uc010uby.1_5'Flank	NM_013372	NP_037504	O60565	GREM1_HUMAN	gremlin-1 precursor						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)		GACTAAAGAGAAAAAAAAAAT	0.348													4	2	---	---	---	---	
INO80	54617	broad.mit.edu	37	15	41351852	41351852	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41351852delA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						accttgtctcaaaaaaaaaGA	0.164													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	58151361	58151361	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58151361delC								GCOM1 (141609 upstream) : ALDH1A2 (94267 downstream)																							AAAAAAAAAACCCAACAGTGT	0.378													4	2	---	---	---	---	
CORO2B	10391	broad.mit.edu	37	15	69001680	69001681	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69001680_69001681insT	uc002arj.3	+						CORO2B_uc010bic.2_Intron	NM_006091	NP_006082	Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6						ggctctttttatttttttttgg	0.005													4	2	---	---	---	---	
CSPG4	1464	broad.mit.edu	37	15	76004115	76004119	+	Intron	DEL	GCCCT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76004115_76004119delGCCCT	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						TGATGGATGGGCCCTAAGGCCACAG	0.522													4	2	---	---	---	---	
NRG4	145957	broad.mit.edu	37	15	76249100	76249100	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76249100delA	uc002bbo.2	-						NRG4_uc010bkm.1_Intron|NRG4_uc002bbn.2_Intron|NRG4_uc010bkn.2_Intron|NRG4_uc010bko.2_Intron	NM_138573	NP_612640	Q8WWG1	NRG4_HUMAN	neuregulin 4							extracellular region|integral to membrane|plasma membrane	growth factor activity				0						ACTAAAGTTCAAAAGGACCTC	0.368													4	2	---	---	---	---	
CIB2	10518	broad.mit.edu	37	15	78408344	78408345	+	Intron	INS	-	A	A	rs138647133	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78408344_78408345insA	uc002bdb.1	-						CIB2_uc002bdc.1_Intron|CIB2_uc010ums.1_Intron	NM_006383	NP_006374	O75838	CIB2_HUMAN	DNA-dependent protein kinase catalytic								calcium ion binding				0						aaaatatttggaaaaaaaaaat	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87788552	87788552	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87788552delT								AGBL1 (216269 upstream) : NCRNA00052 (331608 downstream)																							GGGTTTCACATTTTTTTTTCT	0.468													4	2	---	---	---	---	
NTRK3	4916	broad.mit.edu	37	15	88610462	88610462	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88610462delT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_Intron|NTRK3_uc002bmg.2_Intron	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)			CCACACGCCATTTTTTTTCAC	0.428			T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	88808730	88808732	+	IGR	DEL	TGA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88808730_88808732delTGA								NTRK3 (9069 upstream) : MRPL46 (193976 downstream)																							AGAATGATGGTGATGATGATGat	0.286													4	2	---	---	---	---	
IQGAP1	8826	broad.mit.edu	37	15	91009836	91009836	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91009836delC	uc002bpl.1	+							NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AAATATCCTTCCCCCCCCCCT	0.368													5	3	---	---	---	---	
FAM174B	400451	broad.mit.edu	37	15	93214184	93214184	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93214184delC	uc002bsl.3	-									Q3ZCQ3	F174B_HUMAN	Homo sapiens cDNA PSEC0264 fis, clone NT2RP3002337.							integral to membrane					0						CCTGGCCTGTCCCCAAGTTCC	0.468													4	2	---	---	---	---	
MCTP2	55784	broad.mit.edu	37	15	94953431	94953432	+	Intron	DEL	AC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94953431_94953432delAC	uc002btj.2	+						MCTP2_uc010boj.2_Intron|MCTP2_uc010bok.2_Intron|MCTP2_uc002btl.2_Intron	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CCTCGCTAAAACACACACACAC	0.411													4	2	---	---	---	---	
CHTF18	63922	broad.mit.edu	37	16	843084	843085	+	Intron	INS	-	GGGTG	GGGTG	rs139806285	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:843084_843085insGGGTG	uc002cke.3	+						CHTF18_uc010bre.1_Intron|CHTF18_uc002ckf.3_Intron|CHTF18_uc010brf.2_Intron|CHTF18_uc002ckg.3_Intron	NM_022092	NP_071375	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor						cell cycle|DNA replication	nucleus	ATP binding|DNA binding|nucleoside-triphosphatase activity			kidney(1)	1		Hepatocellular(780;0.00335)				CGGCAGGCACCGGGTGGGGTGG	0.678													16	8	---	---	---	---	
BAIAP3	8938	broad.mit.edu	37	16	1385463	1385464	+	Intron	INS	-	G	G	rs147345623	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1385463_1385464insG	uc002clk.1	+						BAIAP3_uc002clj.2_Intron|BAIAP3_uc010uuz.1_Intron|BAIAP3_uc010uva.1_Intron|BAIAP3_uc010uvb.1_Intron|BAIAP3_uc010uvc.1_5'Flank	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)				ACGGGAAAGACGGGGGGTCCCC	0.609													2	4	---	---	---	---	
ADCY9	115	broad.mit.edu	37	16	4074026	4074026	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4074026delT	uc002cvx.2	-							NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6						Attttttaacttttttttttt	0.169													4	2	---	---	---	---	
HMOX2	3163	broad.mit.edu	37	16	4540918	4540919	+	Intron	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4540918_4540919delTG	uc010bts.2	+						HMOX2_uc002cwr.3_Intron|HMOX2_uc002cwq.3_Intron|HMOX2_uc002cws.3_Intron	NM_001127206	NP_001120678	P30519	HMOX2_HUMAN	heme oxygenase (decyclizing) 2						cellular iron ion homeostasis|heme catabolic process|heme oxidation|response to hypoxia|transmembrane transport	endoplasmic reticulum membrane|microsome|plasma membrane	electron carrier activity|heme oxygenase (decyclizing) activity|metal ion binding|protein binding				0					NADH(DB00157)	tggtggggtatgtgtgtgtgtg	0.089													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7065778	7065778	+	Intron	DEL	T	-	-	rs116952084	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7065778delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	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)		TTCTTAAAGATTTTTTTTTTC	0.239													4	2	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7355121	7355122	+	Intron	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7355121_7355122delTG	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	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)		TTAGGGTGTTTGTGTGTGTGTG	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9304923	9304923	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9304923delT								C16orf72 (91378 upstream) : GRIN2A (542344 downstream)																							ggcatattgcttttcagaacc	0.194													4	2	---	---	---	---	
BFAR	51283	broad.mit.edu	37	16	14731783	14731783	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14731783delT	uc002dco.2	+						BFAR_uc002dcm.2_Intron|BFAR_uc002dcn.2_Intron|BFAR_uc002dcp.2_Intron	NM_016561	NP_057645	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator						anti-apoptosis|apoptosis	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	structural molecule activity|zinc ion binding			ovary(1)|skin(1)	2						CTCTCTTTGATTTTTTTTTTC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	20296154	20296154	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20296154delG								GPR139 (211054 upstream) : GP2 (25658 downstream)																							ggatgtaaccgggggggaaga	0.000													4	2	---	---	---	---	
ANKS4B	257629	broad.mit.edu	37	16	21246159	21246160	+	Intron	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21246159_21246160delTG	uc010bwp.1	+							NM_145865	NP_665872	Q8N8V4	ANS4B_HUMAN	harmonin-interacting ankyrin-repeat containing											ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0565)		ctaTGATATTTGTGTGTGTGTG	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	23028714	23028714	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23028714delT								HS3ST2 (101057 upstream) : USP31 (44015 downstream)																							TTGATACTTAttttttttttg	0.184													5	4	---	---	---	---	
HS3ST4	9951	broad.mit.edu	37	16	26055946	26055947	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26055946_26055947insA	uc002dof.2	+							NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)		aaatgtaagttaaAAAAAAATA	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	28513069	28513070	+	Intron	DEL	CT	-	-	rs497094		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28513069_28513070delCT	uc010vct.1	-						IL27_uc002dqc.2_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		cactcacacactctcacagtca	0.000													2	5	---	---	---	---	
MVP	9961	broad.mit.edu	37	16	29847914	29847914	+	Intron	DEL	C	-	-	rs72332338		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29847914delC	uc002dui.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MVP_uc010bzh.1_Intron|MVP_uc010vdz.1_Intron|MVP_uc002duj.2_Intron|MVP_uc010vea.1_Intron	NM_005115	NP_005106	Q14764	MVP_HUMAN	major vault protein						mRNA transport|protein transport|response to drug|transmembrane transport	cytoplasm|nuclear pore|ribonucleoprotein complex	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4						aaaaaaaaaacaaTCCCTGGA	0.264													5	3	---	---	---	---	
ZNF267	10308	broad.mit.edu	37	16	31928043	31928044	+	3'UTR	INS	-	TT	TT			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31928043_31928044insTT	uc002ecs.3	+	4						NM_003414	NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)|skin(1)	4						TAGAGAAACACTATAGATGTAA	0.287													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32830850	32830850	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32830850delG								TP53TG3B (141972 upstream) : SLC6A10P (57947 downstream)																							caatccatatgcttgttgact	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33543022	33543023	+	IGR	INS	-	ATT	ATT	rs138472598	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33543022_33543023insATT								SLC6A10P (646559 upstream) : MIR1826 (422485 downstream)																							ACACAATGACAATTACACTTTA	0.356													6	4	---	---	---	---	
ITFG1	81533	broad.mit.edu	37	16	47246728	47246728	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47246728delT	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				ctcctctctctttttttttgg	0.000													4	2	---	---	---	---	
N4BP1	9683	broad.mit.edu	37	16	48620375	48620375	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48620375delT	uc002efp.2	-							NM_153029	NP_694574	O75113	N4BP1_HUMAN	Nedd4 binding protein 1						negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)				attactctgatttttttttca	0.164													4	2	---	---	---	---	
NKD1	85407	broad.mit.edu	37	16	50599980	50599980	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50599980delT	uc002egg.1	+							NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1						Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		AAAGCTGGAGTTTTTCCTTCT	0.512													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	60105942	60105942	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60105942delT								None (None upstream) : None (None downstream)																							CCCTTTTCTGTTTGCAGACAA	0.323													4	2	---	---	---	---	
PDPR	55066	broad.mit.edu	37	16	70175439	70175441	+	Intron	DEL	GAA	-	-	rs72232114		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70175439_70175441delGAA	uc002eyf.1	+						CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron|PDPR_uc002eyg.1_Intron	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory						glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		CAGGCACAATGAAGAATCGAATG	0.414													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	71370826	71370827	+	IGR	INS	-	T	T	rs138039609	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71370826_71370827insT								FTSJD1 (47313 upstream) : CALB2 (21799 downstream)																							ATTAGGTTCGCTGTTTCACATT	0.332													2	4	---	---	---	---	
WDR59	79726	broad.mit.edu	37	16	75012648	75012648	+	Intron	DEL	T	-	-	rs111946957		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75012648delT	uc002fdh.1	-						WDR59_uc002fdi.2_Intron|WDR59_uc002fdj.2_Intron	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59											ovary(1)|breast(1)	2						TAAACCTGGATTTTTTTTTTT	0.224													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	77121446	77121446	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77121446delA								CNTNAP4 (528311 upstream) : MON1B (103390 downstream)																							CAAAAACACTAACACTTTATA	0.174													4	2	---	---	---	---	
WWOX	51741	broad.mit.edu	37	16	78302364	78302364	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78302364delC	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron|WWOX_uc002ffj.1_Intron	NM_016373	NP_057457	Q9NZC7	WWOX_HUMAN	WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		AGAGTCACTACCTGCATTTGC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79422987	79422987	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79422987delG								WWOX (176424 upstream) : MAF (204759 downstream)																							TCTGGTTGTAGGGGGCTGGAC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	79699322	79699322	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79699322delT								MAF (64700 upstream) : DYNLRB2 (875532 downstream)																							cactgctggcttttttttttc	0.000													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	83335385	83335385	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83335385delT	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TTTCCTGTAATTTTTTTTTCT	0.338													4	2	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89469959	89469960	+	Intron	DEL	AA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89469959_89469960delAA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		ACAGTAGCTTAAAAAAAAAAAG	0.505													3	3	---	---	---	---	
SHPK	23729	broad.mit.edu	37	17	3522329	3522330	+	Intron	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3522329_3522330insT	uc002fvz.1	-							NM_013276	NP_037408	Q9UHJ6	SHPK_HUMAN	carbohydrate kinase-like						carbohydrate metabolic process	cytoplasm	ATP binding|sedoheptulokinase activity			ovary(1)	1				COAD - Colon adenocarcinoma(5;0.0828)		caTGTTCTCACTTTTTTTTTTT	0.109													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	6753230	6753230	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6753230delC								TEKT1 (18170 upstream) : ALOX12P2 (3665 downstream)																							CTTCTTGGATCCCCATCCATT	0.358													4	2	---	---	---	---	
POLR2A	5430	broad.mit.edu	37	17	7394486	7394486	+	Intron	DEL	T	-	-	rs67389240		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7394486delT	uc002ghf.3	+						POLR2A_uc002ghe.2_Intron	NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)				TAATCTGttcttttttttttt	0.090													8	4	---	---	---	---	
NDEL1	81565	broad.mit.edu	37	17	8355096	8355096	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8355096delT	uc002glj.2	+						NDEL1_uc002gli.2_Intron	NM_030808	NP_110435	Q9GZM8	NDEL1_HUMAN	nudE nuclear distribution gene E homolog (A.						chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|microtubule|spindle					0						CCCCCCTTGCTTTTTTTTTCC	0.363													3	3	---	---	---	---	
MYH10	4628	broad.mit.edu	37	17	8505134	8505134	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8505134delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2						aatccAATTTAAAAAAAATTA	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	14477611	14477612	+	IGR	INS	-	A	A	rs34078250		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14477611_14477612insA								HS3ST3B1 (228119 upstream) : PMP22 (655485 downstream)																							cttttttttttaaatctccaga	0.119													4	2	---	---	---	---	
TRIM16	10626	broad.mit.edu	37	17	15496417	15496417	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15496417delA	uc002gor.1	-						CDRT1_uc010vvy.1_Intron|CDRT1_uc010vvz.1_Intron|CDRT1_uc002gov.3_Intron			O95361	TRI16_HUMAN	SubName: Full=Putative uncharacterized protein; Flags: Fragment;						histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		actatgtctcaaaaaaaaaaa	0.194													5	4	---	---	---	---	
PIGL	9487	broad.mit.edu	37	17	16221408	16221408	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16221408delT	uc002gpv.2	+							NM_004278	NP_004269	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		GACTTTAGCCttttttttcta	0.239													4	2	---	---	---	---	
LLGL1	3996	broad.mit.edu	37	17	18141525	18141526	+	Frame_Shift_Ins	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18141525_18141526insA	uc002gsp.2	+	15	2110_2111	c.2049_2050insA	c.(2047-2052)AGCAAGfs	p.S683fs		NM_004140	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1	683_684					cortical actin cytoskeleton organization|exocytosis|protein complex assembly	cortical actin cytoskeleton	protein kinase binding|structural molecule activity			breast(2)|skin(2)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)	6	all_neural(463;0.228)					ATGCCAGCAGCAAGGTGAGCTG	0.624													20	9	---	---	---	---	
CYTSB	92521	broad.mit.edu	37	17	20037783	20037784	+	Intron	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20037783_20037784insA	uc002gwq.2	+						CYTSB_uc010cqx.2_Intron|CYTSB_uc002gwr.2_Intron|CYTSB_uc002gws.2_Intron	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0						CCTGGGAAGGGAAAAAAAATTG	0.446													4	2	---	---	---	---	
FLJ36000	284124	broad.mit.edu	37	17	21904405	21904408	+	Intron	DEL	TCTC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21904405_21904408delTCTC	uc002gza.2	+							NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						CATTCTCCCTTCTCTCTCTGTCTC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25274265	25274265	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25274265delA								None (None upstream) : WSB1 (346841 downstream)																							ataaacaaataggcattgtaa	0.090													6	3	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31659471	31659472	+	Intron	DEL	GT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31659471_31659472delGT	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)	tggcgatctggtgtgtgtgttg	0.000													4	2	---	---	---	---	
AP2B1	163	broad.mit.edu	37	17	33974751	33974751	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33974751delT	uc002hjr.2	+						AP2B1_uc002hjq.2_Intron|AP2B1_uc010wci.1_Intron|AP2B1_uc002hjs.2_Intron|AP2B1_uc002hjt.2_Intron|AP2B1_uc010ctv.2_Intron|AP2B1_uc010wcj.1_Intron	NM_001282	NP_001273	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		aacatcagggtaactactgct	0.000													4	2	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35731737	35731737	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35731737delC	uc002hno.2	-						ACACA_uc002hnn.2_Intron|ACACA_uc002hnq.2_Intron|C17orf78_uc010cva.1_5'Flank|C17orf78_uc002hns.2_5'Flank	NM_198834	NP_942131	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 1						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGAATGTTGTCCACCAATACT	0.418													4	2	---	---	---	---	
SOCS7	30837	broad.mit.edu	37	17	36530467	36530467	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36530467delA	uc002hqa.2	+						SOCS7_uc010cvl.2_Intron|SOCS7_uc002hqb.2_Intron	NM_014598	NP_055413	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7						intracellular signal transduction|negative regulation of signal transduction|regulation of growth	cytoplasm|nucleus|plasma membrane	protein binding|SH3 domain binding			skin(1)	1	Breast(7;3.47e-17)					gagatatggcaaaaaaagaag	0.000													4	2	---	---	---	---	
IKZF3	22806	broad.mit.edu	37	17	37995877	37995877	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37995877delC	uc002hsu.2	-						IKZF3_uc002htd.2_Intron|IKZF3_uc010cwd.2_Intron|IKZF3_uc002hsv.2_Intron|IKZF3_uc010cwe.2_Intron|IKZF3_uc010cwf.2_Intron|IKZF3_uc010cwg.2_Intron|IKZF3_uc002hsw.2_Intron|IKZF3_uc002hsx.2_Intron|IKZF3_uc002hsy.2_Intron|IKZF3_uc002hsz.2_Intron|IKZF3_uc002hta.2_Intron|IKZF3_uc002htb.2_Intron|IKZF3_uc010cwh.2_Intron|IKZF3_uc002htc.2_Intron	NM_012481	NP_036613	Q9UKT9	IKZF3_HUMAN	aiolos isoform 1						B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			gactctgttgcccaggctgga	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	39544651	39544652	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39544651_39544652insT								KRT34 (6015 upstream) : KRT31 (5327 downstream)																							ttttgtttttgtttttttttGC	0.183													4	2	---	---	---	---	
LOC100128977	100128977	broad.mit.edu	37	17	43942634	43942634	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43942634delG	uc010wjz.1	-							NR_024559				Homo sapiens cDNA clone IMAGE:4819956.												0						GAACCACATAGGGGTATTTCT	0.398													2	4	---	---	---	---	
ABCC3	8714	broad.mit.edu	37	17	48768172	48768172	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48768172delC	uc002isl.2	+						ABCC3_uc002isn.2_Intron	NM_003786	NP_003777	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C, member 3						bile acid metabolic process	integral to plasma membrane|membrane fraction	ATP binding|bile acid-exporting ATPase activity|organic anion transmembrane transporter activity			skin(3)|central_nervous_system(1)	4			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Glibenclamide(DB01016)	AGTCCTGTGACCCCGGCAAGG	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	58511030	58511030	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58511030delT								C17orf64 (2244 upstream) : APPBP2 (9490 downstream)																							ttTCTTTTTCTTTTTTTTTCA	0.184													5	3	---	---	---	---	
PRKAR1A	5573	broad.mit.edu	37	17	66518016	66518019	+	Intron	DEL	TTAC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66518016_66518019delTTAC	uc002jhg.2	+						PRKAR1A_uc002jhh.2_Intron|PRKAR1A_uc002jhi.2_Intron|PRKAR1A_uc002jhj.2_Intron|PRKAR1A_uc002jhk.2_Intron|PRKAR1A_uc002jhl.2_Intron|PRKAR1A_uc002jhm.2_Intron	NM_212471	NP_997636	P10644	KAP0_HUMAN	cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding			adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1)	12	Breast(10;1.64e-13)					TTTTTCCCTTTTACTTCAGGCACA	0.275			T|Mis|N|F|S	RET	papillary thyroid	myxoma|endocrine|papillary thyroid			Carney_Complex|Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial|Cardiac_Myxomas_Familial_Clustering_of				1	6	---	---	---	---	
ABCA6	23460	broad.mit.edu	37	17	67099747	67099747	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67099747delC	uc002jhw.1	-							NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6						transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)					CTAGAGCACACCAGAGCAAGC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	67886604	67886605	+	IGR	INS	-	G	G	rs141485419	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67886604_67886605insG								MAP2K6 (348142 upstream) : KCNJ16 (184821 downstream)																							CCTTCTAAAAAATCTGATTGCA	0.327													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70064468	70064468	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70064468delT								None (None upstream) : SOX9 (52693 downstream)																							GCACtttttcttttttttttt	0.219													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	71108790	71108790	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71108790delA								SLC39A11 (19937 upstream) : SSTR2 (52370 downstream)																							ATATAAGGGGAAAAAAGATAC	0.234													4	2	---	---	---	---	
EIF4A3	9775	broad.mit.edu	37	17	78123210	78123210	+	5'Flank	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78123210delA	uc010wuc.1	-						EIF4A3_uc002jxs.2_5'Flank	NM_014740	NP_055555	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A,						mRNA transport|negative regulation of translation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation|rRNA processing	catalytic step 2 spliceosome|cytoplasm|exon-exon junction complex|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|poly(A) RNA binding|protein binding			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			catctctactaaaaaaaaaat	0.000													4	3	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78589562	78589562	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78589562delT	uc002jyt.1	+						RPTOR_uc002jys.2_Intron|RPTOR_uc010wuf.1_Intron|RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						TCCTCCATTCTTTTTCTTCCC	0.453													4	2	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80875667	80875668	+	Intron	DEL	CC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80875667_80875668delCC	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kgb.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)			ctcccgttctCCTGCTAGCTGG	0.337											OREG0024830	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	18	4581867	4581867	+	IGR	DEL	T	-	-	rs79227071		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4581867delT								DLGAP1 (126601 upstream) : LOC642597 (561805 downstream)																							AGAAAATGACTTTTTTTTTGG	0.269													2	4	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	7768332	7768332	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7768332delA	uc002knn.3	+						PTPRM_uc010dkv.2_Intron	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)				ctatcaaaggaaaaaaaaatt	0.000													4	2	---	---	---	---	
NDUFV2	4729	broad.mit.edu	37	18	9119825	9119825	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9119825delT	uc002knu.2	+							NM_021074	NP_066552	P19404	NDUV2_HUMAN	NADH dehydrogenase ubiquinone flavoprotein 2						cardiac muscle tissue development|mitochondrial electron transport, NADH to ubiquinone|nervous system development|transport	mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|electron carrier activity|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity			ovary(1)	1					NADH(DB00157)	AGGGTATGTGTTTTTTTTTTT	0.299													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15173524	15173528	+	IGR	DEL	GCTCG	-	-	rs74972396	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15173524_15173528delGCTCG								ANKRD30B (320787 upstream) : LOC644669 (140027 downstream)																							ccattgatcagctcgttcaacttcc	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15379584	15379584	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15379584delC								LOC644669 (53666 upstream) : None (None downstream)																							taaagttattcttttacggtt	0.025													3	4	---	---	---	---	
SS18	6760	broad.mit.edu	37	18	23605671	23605671	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23605671delA	uc002kvm.2	-						SS18_uc002kvn.2_Intron|SS18_uc010xbf.1_Intron|SS18_uc010xbg.1_Intron|SS18_uc010xbh.1_Intron|SS18_uc010xbi.1_Intron	NM_001007559	NP_001007560	Q15532	SSXT_HUMAN	synovial sarcoma translocation, chromosome 18						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	ligand-dependent nuclear receptor transcription coactivator activity|protein binding		SS18/SSX1(1169)|SS18/SSX2(702)|SS18/SSX4(12)	soft_tissue(1883)|ovary(1)	1884	all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124)					aatttctcacaaaaaaaacta	0.000			T	SSX1| SSX2	synovial sarcoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	30495208	30495208	+	IGR	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30495208delG								KLHL14 (142234 upstream) : C18orf34 (22158 downstream)																							CTTCTCTCCTGGGGTTAAATT	0.423													4	2	---	---	---	---	
MAPRE2	10982	broad.mit.edu	37	18	32612654	32612654	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32612654delT	uc010xcc.1	+						MAPRE2_uc010xcb.1_Intron	NM_001143827	NP_001137299	Q15555	MARE2_HUMAN	microtubule-associated protein, RP/EB family,						cell division|cell proliferation|mitosis|signal transduction	cytoplasm|microtubule	microtubule binding			ovary(1)	1						TTTTGTTTTGTTTTTTTGTTT	0.418													4	2	---	---	---	---	
SLC14A1	6563	broad.mit.edu	37	18	43308076	43308076	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43308076delT	uc010xcn.1	+						SLC14A1_uc010dnk.2_Intron|SLC14A1_uc002lbf.3_Intron|SLC14A1_uc002lbg.3_Intron|SLC14A1_uc010xco.1_Intron|SLC14A1_uc002lbh.3_Intron|SLC14A1_uc002lbi.3_Intron|SLC14A1_uc002lbj.3_Intron|SLC14A1_uc002lbk.3_5'Flank	NM_001146036	NP_001139508	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter),							integral to plasma membrane	urea transmembrane transporter activity			central_nervous_system(1)|pancreas(1)	2						GCAATAAGTCTTCTATATGTT	0.458													4	2	---	---	---	---	
PIAS2	9063	broad.mit.edu	37	18	44395658	44395658	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44395658delA	uc002lck.2	-						PIAS2_uc010dnp.2_Intron	NM_004671	NP_004662	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT X isoform						androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|PML body	androgen receptor binding|DNA binding|protein binding|SUMO ligase activity|transcription coactivator activity|zinc ion binding			ovary(2)|breast(1)|skin(1)	4						TGAACCATCTAAAAAAAAAAA	0.318													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49378831	49378831	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49378831delT								MEX3C (655141 upstream) : DCC (487740 downstream)																							TAGGAAGCTGTTGACAGAAGC	0.502													4	2	---	---	---	---	
CCBE1	147372	broad.mit.edu	37	18	57177658	57177659	+	Intron	INS	-	T	T	rs35277466		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57177658_57177659insT	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)				gcaaattgaacttttttttttt	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	58922522	58922522	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58922522delA								MC4R (882521 upstream) : CDH20 (78466 downstream)																							ATTATAAAACAACTAACAAAA	0.299													4	2	---	---	---	---	
KDSR	2531	broad.mit.edu	37	18	61037027	61037027	+	5'Flank	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61037027delG	uc010dpw.2	-						KDSR_uc010xem.1_5'Flank	NM_002035	NP_002026	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase precursor						3-keto-sphinganine metabolic process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding			skin(1)	1						GACATTTGGAGGAGCCAGTGT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62141896	62141896	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62141896delA								C18orf20 (325636 upstream) : None (None downstream)																							TTGACAAGTTAAAGTTATTTT	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62223941	62223942	+	IGR	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62223941_62223942insA								C18orf20 (407681 upstream) : None (None downstream)																							GAATAAGAACTAAAAAAACAGA	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	69935589	69935592	+	IGR	DEL	TCTC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69935589_69935592delTCTC								None (None upstream) : CBLN2 (268323 downstream)																							GCTTTCTTGTtctctctctctctc	0.314													4	2	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7513558	7513558	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7513558delA	uc002mgi.2	+						ARHGEF18_uc010xjm.1_Intron|ARHGEF18_uc002mgh.2_Intron|ARHGEF18_uc002mgj.1_Intron	NM_001130955	NP_001124427	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				aaaaaaatacaaaaaaaaaaa	0.244													7	5	---	---	---	---	
EVI5L	115704	broad.mit.edu	37	19	7920699	7920699	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7920699delT	uc002min.2	+						EVI5L_uc010xjz.1_Intron|EVI5L_uc002mio.1_Intron	NM_145245	NP_660288	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like isoform							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						TAAAACTTTATTTTTTTGTAA	0.483													4	2	---	---	---	---	
PPAN-P2RY11	692312	broad.mit.edu	37	19	10217863	10217863	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10217863delA	uc002mna.2	+						PPAN-P2RY11_uc010xla.1_Intron|PPAN_uc002mmz.1_Intron|PPAN_uc002mnb.1_Intron|SNORD105_uc010dwy.1_5'Flank|SNORD105B_uc010dwz.1_5'Flank	NM_001040664	NP_001035754	Q9NQ55	SSF1_HUMAN	PPAN-P2RY11 protein						RNA splicing	nucleolus	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			accgtgttagaaaaaaaaaga	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	15924225	15924226	+	IGR	DEL	AG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15924225_15924226delAG								OR10H1 (5289 upstream) : UCA1 (15531 downstream)																							TAGGTAAAACagagagagagaa	0.248													4	2	---	---	---	---	
KLHL26	55295	broad.mit.edu	37	19	18745939	18745940	+	5'Flank	DEL	GT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18745939_18745940delGT	uc002njz.1	+							NM_018316	NP_060786	Q53HC5	KLH26_HUMAN	kelch-like 26											ovary(1)	1						GCAGGCAAGGGTGTGTGTGTGT	0.545													4	2	---	---	---	---	
ANKRD27	84079	broad.mit.edu	37	19	33142705	33142705	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33142705delC	uc002ntn.1	-						ANKRD27_uc002nto.1_Intron	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)					TTcactgcatccccactgtca	0.383													4	2	---	---	---	---	
GPATCH1	55094	broad.mit.edu	37	19	33592114	33592116	+	Intron	DEL	CTT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33592114_33592116delCTT	uc002nug.1	+							NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					CCCTAAGGTACTTCTTCTAAAAA	0.483													3	4	---	---	---	---	
KIAA0355	9710	broad.mit.edu	37	19	34764810	34764810	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34764810delA	uc002nvd.3	+						KIAA0355_uc010edk.1_Intron	NM_014686	NP_055501	O15063	K0355_HUMAN	hypothetical protein LOC9710											ovary(1)	1	Esophageal squamous(110;0.162)					gaaaattgggaagggtaatgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	34995137	34995138	+	IGR	INS	-	AG	AG	rs150734670	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34995137_34995138insAG								WTIP (3053 upstream) : LOC643719 (72501 downstream)																							ggataagctgcagagagagagg	0.228													3	3	---	---	---	---	
FXYD5	53827	broad.mit.edu	37	19	35654308	35654309	+	Intron	INS	-	T	T	rs147706080		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35654308_35654309insT	uc002nyg.1	+						FXYD5_uc010xsq.1_Intron|FXYD5_uc002nyh.1_Intron|FXYD5_uc002nyi.1_5'Flank	NM_014164	NP_054883	Q96DB9	FXYD5_HUMAN	FXYD domain-containing ion transport regulator 5						microvillus assembly|negative regulation of calcium-dependent cell-cell adhesion	integral to membrane	actin binding|cadherin binding|ion channel activity				0	all_lung(56;9.4e-09)|Lung NSC(56;1.4e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.75e-22)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;7.07e-19)|LUSC - Lung squamous cell carcinoma(66;0.0221)			GGAGGTACTGATTTTTTTTTTT	0.327													2	4	---	---	---	---	
SPTBN4	57731	broad.mit.edu	37	19	41071881	41071883	+	Intron	DEL	ATG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41071881_41071883delATG	uc002ony.2	+						SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGAAGGAGGAATGGGAGTCAGAA	0.557													5	3	---	---	---	---	
C19orf61	56006	broad.mit.edu	37	19	44238870	44238870	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44238870delT	uc002oxj.2	-						C19orf61_uc002oxk.2_Intron	NM_019108	NP_061981	Q9H0W8	SMG9_HUMAN	SMG9 protein						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	intracellular	protein binding				0		Prostate(69;0.0352)				GTTTACTGTATTTTTttttta	0.045													6	3	---	---	---	---	
GRLF1	2909	broad.mit.edu	37	19	47458847	47458847	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47458847delT	uc010ekv.2	+							NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1						axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)		tcatacgatgttttttgtttt	0.149													4	2	---	---	---	---	
SSC5D	284297	broad.mit.edu	37	19	56001100	56001100	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56001100delC	uc002qlg.3	+							NM_001144950	NP_001138422	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine-rich glycoprotein							extracellular region|membrane	scavenger receptor activity				0						AAGTCCTTAGCCCCAGCAAGT	0.612													4	2	---	---	---	---	
NLRP11	204801	broad.mit.edu	37	19	56318493	56318493	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56318493delC	uc010ygf.1	-						NLRP11_uc002qlz.2_Intron|NLRP11_uc002qmb.2_Intron|NLRP11_uc002qmc.2_Intron|NLRP11_uc010ete.1_Intron	NM_145007	NP_659444	P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11								ATP binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		tgtcttttttccccccattga	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4452579	4452579	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4452579delC								ADRA1D (222920 upstream) : PRNP (214218 downstream)																							CCTCAGGAgtccccttgccct	0.279													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6988818	6988819	+	IGR	DEL	AA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6988818_6988819delAA								BMP2 (227908 upstream) : HAO1 (874812 downstream)																							aattctttttaaacattgttga	0.000													4	2	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8665965	8665966	+	Intron	DEL	CA	-	-	rs75405686		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8665965_8665966delCA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						AAAATGCAACCACGGCTGACAT	0.441													4	2	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8797057	8797057	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8797057delT	uc002wnb.2	+						PLCB1_uc002wna.2_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						cactcacaaattgaaagtcag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	11330620	11330620	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11330620delT								JAG1 (675926 upstream) : BTBD3 (540857 downstream)																							ttaagaaacatttttttttga	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12029887	12029887	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12029887delA								BTBD3 (122645 upstream) : SPTLC3 (959740 downstream)																							gttgttatgcaaaaaaatcac	0.010													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15419911	15419911	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15419911delT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				ACCTGTTTGCTTTGGAGTTAC	0.468													4	2	---	---	---	---	
DTD1	92675	broad.mit.edu	37	20	18653092	18653092	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18653092delT	uc002wrf.3	+							NM_080820	NP_543010	Q8TEA8	DTD1_HUMAN	D-tyrosyl-tRNA deacylase 1						D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2						CTTTTTTCAGTTTTTTTTTTT	0.328													6	3	---	---	---	---	
RALGAPA2	57186	broad.mit.edu	37	20	20448207	20448210	+	Intron	DEL	ATTG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20448207_20448210delATTG	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						tgcaagagccattgattgattgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	22683078	22683078	+	IGR	DEL	C	-	-	rs73304730	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22683078delC								FOXA2 (116977 upstream) : SSTR4 (332979 downstream)																							CTGCCGCTCACCCCAGCATCA	0.443													4	2	---	---	---	---	
FAM182B	728882	broad.mit.edu	37	20	25829628	25829629	+	Intron	INS	-	AA	AA	rs141949476	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25829628_25829629insAA	uc002wvd.1	-						FAM182B_uc002wve.2_Intron					Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						ctgcaattgacagaggtagtgg	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25901275	25901276	+	IGR	INS	-	AT	AT			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25901275_25901276insAT								FAM182B (52489 upstream) : LOC100134868 (89159 downstream)																							CATGCACACACGTGTGTGCACA	0.223													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26254890	26254892	+	IGR	DEL	ATC	-	-	rs112198153		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26254890_26254892delATC								MIR663 (65976 upstream) : None (None downstream)																							CATAGCAATAATCTTTTAAGACT	0.325													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29423140	29423140	+	IGR	DEL	A	-	-	rs111708884		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29423140delA								None (None upstream) : FRG1B (188739 downstream)																							AGGTCTACTTAAAAAAAAGAA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29584721	29584725	+	IGR	DEL	TGCTG	-	-	rs148627987	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29584721_29584725delTGCTG								None (None upstream) : FRG1B (27154 downstream)																							TGTTCATTAATGCTGTTTCTAATTT	0.351													4	2	---	---	---	---	
DEFB121	245934	broad.mit.edu	37	20	29994597	29994597	+	5'Flank	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29994597delT	uc002wvv.1	-							NM_001011878	NP_001011878	Q5J5C9	DB121_HUMAN	defensin, beta 121 precursor						defense response to bacterium	extracellular region					0	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TGTTGTGGTCTtttttttatt	0.179													4	2	---	---	---	---	
MYLK2	85366	broad.mit.edu	37	20	30414026	30414026	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30414026delG	uc002wwq.2	+						MYLK2_uc002wws.2_5'Flank	NM_033118	NP_149109	Q9H1R3	MYLK2_HUMAN	skeletal myosin light chain kinase						cardiac muscle tissue morphogenesis|regulation of muscle filament sliding		ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			lung(2)|skin(2)|ovary(1)|central_nervous_system(1)	6			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			tggagatattggagtctagaa	0.000													4	2	---	---	---	---	
TOMM34	10953	broad.mit.edu	37	20	43580921	43580921	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43580921delA	uc002xmy.2	-						PABPC1L_uc002xmx.2_Intron|TOMM34_uc002xmz.2_Intron	NM_006809	NP_006800	Q15785	TOM34_HUMAN	translocase of outer mitochondrial membrane 34						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane	heat shock protein binding|signal sequence binding				0		Myeloproliferative disorder(115;0.0122)				ACCATGATCCAAAAAGACTAT	0.343													3	3	---	---	---	---	
EYA2	2139	broad.mit.edu	37	20	45700426	45700426	+	Intron	DEL	G	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45700426delG	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235	O00167	EYA2_HUMAN	eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				GACCCCACCTGGCCATGGTAC	0.403													4	2	---	---	---	---	
ZMYND8	23613	broad.mit.edu	37	20	45918356	45918357	+	Intron	INS	-	A	A	rs112205773		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45918356_45918357insA	uc002xta.1	-						ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xtg.2_Intron|ZMYND8_uc010ghs.1_Intron	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			ttgatcgaatgaaaaaaaaaaa	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46650870	46650870	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46650870delA								SULF2 (235510 upstream) : LOC284749 (337784 downstream)																							TGTTTGACTTACCTGCTTGGT	0.289													4	2	---	---	---	---	
ARFGEF2	10564	broad.mit.edu	37	20	47610513	47610513	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47610513delA	uc002xtx.3	+						ARFGEF2_uc010zyf.1_Intron	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine						exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			aagcactaagaaaaaaaaagt	0.000													4	2	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51664266	51664266	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51664266delA	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			ATTTTGGAGCAAAAAAAAACC	0.299													4	2	---	---	---	---	
PHACTR3	116154	broad.mit.edu	37	20	58197123	58197124	+	Intron	DEL	AT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58197123_58197124delAT	uc002yau.2	+						PHACTR3_uc002yat.2_Intron	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			gtgtttgtgcatatatatatgt	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59151453	59151453	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59151453delC	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																		ATTTTTAGGTCCCATTTGAAG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9830196	9830196	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9830196delC								None (None upstream) : None (None downstream)																							CACAACTTTACTTTTCCCTTT	0.463													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9850105	9850105	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9850105delC								None (None upstream) : None (None downstream)																							gcaggcatttccccagacctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9856378	9856380	+	IGR	DEL	CTC	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9856378_9856380delCTC								None (None upstream) : None (None downstream)																							CCTCTGCCTTCTCCTCCAGGGCA	0.581													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10086432	10086433	+	IGR	INS	-	T	T	rs150934414	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10086432_10086433insT								None (None upstream) : TPTE (820310 downstream)																							gtgttccagcctttttttgaca	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10462609	10462609	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10462609delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		TGATAATGAATTTTTTTTAAT	0.244													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10498497	10498497	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10498497delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		cagagaactgaaaaaaaattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10703449	10703450	+	IGR	DEL	AC	-	-	rs147280456		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10703449_10703450delAC								None (None upstream) : TPTE (203293 downstream)																							cagtttggaaacagtctttttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10705685	10705685	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10705685delC								None (None upstream) : TPTE (201058 downstream)																							cacaaaaaaactagacagaag	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10856088	10856092	+	IGR	DEL	GAATT	-	-	rs59507187		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10856088_10856092delGAATT								None (None upstream) : TPTE (50651 downstream)																							gaatggaatggaattgaatggaatg	0.000													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088831	11088831	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088831delT	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TATGTCTGTATTTTTTTTCTA	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	14368427	14368427	+	IGR	DEL	A	-	-	rs147842587	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14368427delA								None (None upstream) : C21orf99 (42060 downstream)																							tatttcctttaccaccatagg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	15979588	15979588	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15979588delA								SAMSN1 (23865 upstream) : NRIP1 (353968 downstream)																							ATTAACAGCTAAAAAGGAGTG	0.234													4	2	---	---	---	---	
DOPEY2	9980	broad.mit.edu	37	21	37571740	37571741	+	Intron	INS	-	T	T	rs66909424		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37571740_37571741insT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2						TGCTTTCtttcttttttttttt	0.243													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	39675354	39675354	+	IGR	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39675354delC								KCNJ15 (1610 upstream) : ERG (76598 downstream)																							AATCAGTGTGCCCCACAAGCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40310173	40310174	+	IGR	DEL	CT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40310173_40310174delCT								ETS2 (113297 upstream) : PSMG1 (237216 downstream)																							tgtttttctcctctctctctct	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17235341	17235341	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17235341delT								psiTPTE22 (55820 upstream) : XKR3 (28972 downstream)																							aatgtttgtatatagagtgaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17237155	17237155	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17237155delT								psiTPTE22 (57634 upstream) : XKR3 (27158 downstream)																							TAGTTACTTATTTTTATGACt	0.030													4	2	---	---	---	---	
SNAP29	9342	broad.mit.edu	37	22	21217602	21217603	+	Intron	INS	-	CCT	CCT	rs141661964	by1000genomes	TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21217602_21217603insCCT	uc011ahw.1	+							NM_004782	NP_004773	O95721	SNP29_HUMAN	synaptosomal-associated protein 29						cellular membrane fusion|exocytosis|protein transport|vesicle targeting	cell junction|cytoplasm|nucleus|synapse|synaptosome	SNAP receptor activity				0	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			CAACTTAGGTGCCTGGTTACCC	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	24185192	24185193	+	IGR	INS	-	C	C			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24185192_24185193insC								DERL3 (3877 upstream) : SLC2A11 (13866 downstream)																							GCCATCCTCAGCCCCCAAGCCT	0.450													4	2	---	---	---	---	
SYN3	8224	broad.mit.edu	37	22	33023686	33023686	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33023686delC	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1						AACTCCAAGACCCCCATACTT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	37340460	37340460	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37340460delA								CSF2RB (3983 upstream) : C22orf33 (46701 downstream)																							tttgctgcttaaaaaaaataa	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41050748	41050748	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41050748delA								MKL1 (18058 upstream) : MCHR1 (24434 downstream)																							AGGTTGTCTCAAAAAAATAAA	0.144											OREG0026584	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	X	3451938	3451938	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3451938delA								MXRA5 (187254 upstream) : PRKX (70475 downstream)																							ACAGTCTCCCAAAAGTAAATT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	4217512	4217512	+	IGR	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4217512delT								PRKX (585851 upstream) : None (None downstream)																							ACTTTGCCCATTTTTTTACTG	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6515078	6515078	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6515078delA								VCX3A (61919 upstream) : HDHD1A (451883 downstream)																							AATAAATGGCAAAAAAAAATC	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	7863015	7863015	+	IGR	DEL	A	-	-	rs144038046		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7863015delA								VCX (50832 upstream) : PNPLA4 (3789 downstream)																							TATAATATGCAACCAAAATGT	0.323													1	5	---	---	---	---	
TBL1X	6907	broad.mit.edu	37	X	9528924	9528924	+	Intron	DEL	C	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9528924delC	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_Intron	NM_001139466	NP_001132938	O60907	TBL1X_HUMAN	transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)				CCTTCCACCACCCAAAGTGAA	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	14328116	14328119	+	IGR	DEL	CTTT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14328116_14328119delCTTT								GEMIN8 (280081 upstream) : GLRA2 (219301 downstream)																							ccatcctatgcttttttttttttt	0.000													4	2	---	---	---	---	
PPEF1	5475	broad.mit.edu	37	X	18836489	18836490	+	Intron	DEL	TT	-	-	rs35346016		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18836489_18836490delTT	uc004cyq.2	+						PPEF1_uc004cyp.2_Intron|PPEF1_uc004cyr.2_Intron|PPEF1_uc004cys.2_Intron|PPEF1_uc011mja.1_Intron|PPEF1_uc011mjb.1_Intron	NM_006240	NP_006231	O14829	PPE1_HUMAN	protein phosphatase with EF hand calcium-binding						detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)					TGAATTAAACtttttttttttt	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	20505226	20505226	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20505226delA								RPS6KA3 (219703 upstream) : CNKSR2 (887754 downstream)																							TACCTGCCTGAAAAAAAGTGA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	23436604	23436604	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23436604delA								PTCHD1 (21687 upstream) : PRDX4 (249041 downstream)																							CTGAAGAGTGAAAAAAATCAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	24235113	24235114	+	IGR	INS	-	GAG	GAG	rs112426126		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24235113_24235114insGAG								ZFX (2486 upstream) : FAM48B2 (93866 downstream)																							GAAAAGGGGGAGAGTTCCCTTA	0.475													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	27327237	27327237	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27327237delA	uc004dbt.2	-											Homo sapiens cDNA clone IMAGE:4824334.																		atccattggcaaagggcagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	39633331	39633332	+	IGR	INS	-	T	T			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39633331_39633332insT								MID1IP1 (967550 upstream) : BCOR (277169 downstream)																							tttttgcttcgttttttttcca	0.035													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	42279008	42279009	+	IGR	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42279008_42279009delTG								CASK (496721 upstream) : PPP1R2P9 (357610 downstream)																							CAAGCGTGTATGTGTGTGTGTG	0.480													4	2	---	---	---	---	
SUV39H1	6839	broad.mit.edu	37	X	48559163	48559164	+	Intron	DEL	GT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48559163_48559164delGT	uc004dkn.2	+						SUV39H1_uc011mmf.1_Intron|SUV39H1_uc011mmg.1_Intron	NM_003173	NP_003164	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1						cell cycle|cell differentiation|chromatin silencing at rDNA|interspecies interaction between organisms|rRNA processing|transcription, DNA-dependent	chromatin silencing complex|chromosome, centromeric region|condensed nuclear chromosome|rDNA heterochromatin	chromatin binding|histone methyltransferase activity (H3-K9 specific)|protein N-terminus binding|zinc ion binding				0						ATGGGACCCGGTGTGTGTGTGC	0.599													4	2	---	---	---	---	
CLCN5	1184	broad.mit.edu	37	X	49849025	49849025	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49849025delT	uc004dos.1	+						CLCN5_uc004dor.1_Intron|CLCN5_uc004doq.1_Intron|CLCN5_uc004dot.1_Intron	NM_000084	NP_000075	P51795	CLCN5_HUMAN	chloride channel 5 isoform b						excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)					TTTGAATTGGTTttttttgtt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	56740799	56740800	+	IGR	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56740799_56740800insA								UBQLN2 (147430 upstream) : LOC550643 (14918 downstream)																							CATGTGTTAGTAAAAAAAAAAA	0.213													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	58099120	58099120	+	IGR	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:58099120delA								ZXDA (162053 upstream) : None (None downstream)																							tagattctacaaaaagagatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	63074591	63074592	+	IGR	DEL	GA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63074591_63074592delGA								MIR1468 (68624 upstream) : FAM123B (330406 downstream)																							CATTGTATCCgagagagagaga	0.074													4	3	---	---	---	---	
KLHL4	56062	broad.mit.edu	37	X	86879998	86879998	+	Intron	DEL	A	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86879998delA	uc004efb.2	+						KLHL4_uc004efa.2_Intron	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1							cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						CAAATCCGCCAAAAAGATTGC	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	101197882	101197883	+	IGR	DEL	TA	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101197882_101197883delTA								ZMAT1 (10882 upstream) : TCEAL2 (182777 downstream)																							tggaggtaggtatatatatata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	102102558	102102559	+	Intron	INS	-	T	T	rs150622799		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102102558_102102559insT	uc004ejq.1	+						uc004ejr.2_Intron					Homo sapiens cDNA clone IMAGE:5576940.																		tttttacagtgttttttttttt	0.000													4	2	---	---	---	---	
IL1RAPL2	26280	broad.mit.edu	37	X	104967516	104967516	+	Intron	DEL	T	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104967516delT	uc004elz.1	+							NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2						central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3						ccattccacattttttggtat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	123311486	123311487	+	IGR	DEL	TG	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123311486_123311487delTG								STAG2 (74983 upstream) : SH2D1A (168661 downstream)																							TTTCTTCCTCTGTTCTTCCTCT	0.193													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	142326641	142326644	+	IGR	DEL	CACA	-	-	rs72263985		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142326641_142326644delCACA								SPANXN4 (204576 upstream) : SPANXN3 (269921 downstream)																							catacaggcgcacacacacacaca	0.314													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	150259476	150259477	+	IGR	INS	-	G	G			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150259476_150259477insG								HMGB3 (100230 upstream) : GPR50 (85582 downstream)																							ccagtgctttagggggagtcat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	155028612	155028613	+	IGR	INS	-	A	A			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155028612_155028613insA								SPRY3 (16495 upstream) : VAMP7 (82334 downstream)																							CCAGGTTCTCTAGGAGTCAGAA	0.282													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13415841	13415844	+	IGR	DEL	CAAT	-	-			TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13415841_13415844delCAAT								None (None upstream) : None (None downstream)																							aggtacatcccaatcagtttcctt	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59019360	59019361	+	IGR	DEL	AT	-	-	rs138718736		TCGA-A3-3358-01A-01D-1534-10	TCGA-A3-3358-11A-01D-1534-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59019360_59019361delAT								None (None upstream) : None (None downstream)																							aaaaaataaaataaaaacaaaG	0.114													5	4	---	---	---	---	
