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	16257631	16257631	+	Silent	SNP	A	G	G			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16257631A>G	uc001axk.1	+	11	5100	c.4896A>G	c.(4894-4896)AAA>AAG	p.K1632K	SPEN_uc010obp.1_Silent_p.K1591K	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1632					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)		CAGAACTGAAAACTCCACCTT	0.473													5	96	---	---	---	---	PASS
TRIM45	80263	broad.mit.edu	37	1	117661045	117661045	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117661045C>T	uc001egz.2	-	2	1421	c.833G>A	c.(832-834)CGG>CAG	p.R278Q	TRIM45_uc009whe.2_Missense_Mutation_p.R278Q|TRIM45_uc001eha.2_Missense_Mutation_p.R174Q	NM_025188	NP_079464	Q9H8W5	TRI45_HUMAN	tripartite motif-containing 45 isoform 1	278						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)	1	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		CGAGAATGTCCGGACATCAGC	0.572													3	30	---	---	---	---	PASS
TDRD5	163589	broad.mit.edu	37	1	179638437	179638437	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179638437C>T	uc001gnf.1	+	16	2846	c.2596C>T	c.(2596-2598)CCC>TCC	p.P866S	TDRD5_uc010pnp.1_Missense_Mutation_p.P920S|TDRD5_uc001gnh.1_Missense_Mutation_p.P421S	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	866					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						CCAGTCTGAACCCAACAACAG	0.488													11	188	---	---	---	---	PASS
LYST	1130	broad.mit.edu	37	1	235971939	235971939	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235971939G>A	uc001hxj.2	-	5	2354	c.2179C>T	c.(2179-2181)CAG>TAG	p.Q727*	LYST_uc009xgb.1_RNA|LYST_uc010pxs.1_RNA|LYST_uc001hxl.1_Nonsense_Mutation_p.Q727*	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	727					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AATTTCCACTGAACAACTATA	0.328									Chediak-Higashi_syndrome				32	175	---	---	---	---	PASS
CEP170	9859	broad.mit.edu	37	1	243362432	243362432	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243362432C>A	uc001hzs.2	-	7	969	c.561G>T	c.(559-561)GAG>GAT	p.E187D	CEP170_uc001hzt.2_Missense_Mutation_p.E187D|CEP170_uc001hzu.2_Missense_Mutation_p.E187D	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha	187						centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TTTCATCCACCTCATCATCCC	0.423													164	383	---	---	---	---	PASS
NT5C1B	93034	broad.mit.edu	37	2	18765441	18765441	+	Silent	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18765441C>T	uc002rcz.2	-	6	1088	c.984G>A	c.(982-984)GAG>GAA	p.E328E	NT5C1B_uc002rcy.2_Silent_p.E328E|NT5C1B_uc010exr.2_Silent_p.E270E|NT5C1B_uc010yju.1_Silent_p.E268E|NT5C1B_uc002rda.2_Silent_p.E268E|NT5C1B_uc010yjv.1_Silent_p.E345E|NT5C1B_uc010yjw.1_Silent_p.E311E|NT5C1B_uc010exs.2_Silent_p.E330E|NT5C1B_uc002rdb.1_Silent_p.E120E	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	328					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			skin(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)				GACCCTCTTGCTCGTAGATTT	0.552													18	99	---	---	---	---	PASS
LYG2	254773	broad.mit.edu	37	2	99870749	99870749	+	Splice_Site	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99870749C>T	uc002szw.1	-	2	89	c.-24_splice	c.e2-1		MRPL30_uc002szl.1_Intron|LYG2_uc010fip.1_Splice_Site|LYG2_uc002szx.1_Splice_Site	NM_175735	NP_783862	Q86SG7	LYG2_HUMAN	lysozyme G-like 2 precursor						cell wall macromolecule catabolic process|peptidoglycan catabolic process	extracellular region	lysozyme activity			ovary(1)	1						CTTCCAGGACCTGCTCTGATT	0.353													4	251	---	---	---	---	PASS
IL1RL2	8808	broad.mit.edu	37	2	102855726	102855726	+	3'UTR	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102855726C>T	uc002tbs.2	+	12					IL1RL2_uc002tbt.2_3'UTR	NM_003854	NP_003845	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2 precursor						cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2						ACACCTATGGCTGGAAGATGA	0.463													4	184	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109368085	109368085	+	Silent	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109368085G>A	uc002tem.3	+	11	1683	c.1557G>A	c.(1555-1557)GTG>GTA	p.V519V		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	519					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						CCCTTCCTGTGTGTAAACAGC	0.393													7	224	---	---	---	---	PASS
STAT1	6772	broad.mit.edu	37	2	191865873	191865873	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191865873A>G	uc002usj.2	-	6	777	c.389T>C	c.(388-390)ATT>ACT	p.I130T	STAT1_uc010fse.1_Missense_Mutation_p.I130T|STAT1_uc002usk.2_Missense_Mutation_p.I130T|STAT1_uc002usl.2_Missense_Mutation_p.I132T|STAT1_uc010fsf.1_5'UTR	NM_007315	NP_009330	P42224	STAT1_HUMAN	signal transducer and activator of transcription	130					activation of caspase activity|I-kappaB kinase/NF-kappaB cascade|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway|tyrosine phosphorylation of STAT protein	cytosol|nucleolus|nucleoplasm	calcium ion binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity|signal transducer activity			lung(3)|breast(3)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)		Fludarabine(DB01073)	TGTGCTCTGAATATTCCCCGA	0.428													8	602	---	---	---	---	PASS
EEF1B2	1933	broad.mit.edu	37	2	207025366	207025366	+	Silent	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207025366G>A	uc002vbf.1	+	3	293	c.135G>A	c.(133-135)CCG>CCA	p.P45P	NDUFS1_uc010ziq.1_5'Flank|NDUFS1_uc002vbe.2_5'Flank|NDUFS1_uc010zir.1_5'Flank|NDUFS1_uc010zis.1_5'Flank|NDUFS1_uc010zit.1_5'Flank|NDUFS1_uc010ziu.1_5'Flank|EEF1B2_uc002vbg.1_Silent_p.P45P|EEF1B2_uc002vbh.1_Silent_p.P45P|SNORD51_uc002vbi.1_5'Flank|SNORA41_uc002vbj.2_5'Flank	NM_001037663	NP_001032752	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta	45	GST C-terminal.					cytosol|eukaryotic translation elongation factor 1 complex	protein binding|translation elongation factor activity				0						CCAGCCCACCGCCTGCCGACT	0.448													5	134	---	---	---	---	PASS
C2orf57	165100	broad.mit.edu	37	2	232458055	232458055	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232458055A>C	uc002vrz.2	+	1	444	c.393A>C	c.(391-393)AAA>AAC	p.K131N		NM_152614	NP_689827	Q53QW1	CB057_HUMAN	hypothetical protein LOC165100	131										ovary(1)	1		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)		TCCTGGGTAAAGACAAGATGT	0.552													22	134	---	---	---	---	PASS
C3orf63	23272	broad.mit.edu	37	3	56667432	56667432	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56667432G>T	uc003did.3	-	17	3305	c.3204C>A	c.(3202-3204)AAC>AAA	p.N1068K	C3orf63_uc003dib.3_Missense_Mutation_p.N187K|C3orf63_uc003dic.3_Missense_Mutation_p.N692K|C3orf63_uc003die.3_Missense_Mutation_p.N1129K	NM_015224	NP_056039	Q9UK61	CC063_HUMAN	retinoblastoma-associated protein 140 isoform b	1129				N -> S (in Ref. 1; AAD55098).						ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)		GATGTTTATTGTTGAAGTCAC	0.438													39	149	---	---	---	---	PASS
DRD5	1816	broad.mit.edu	37	4	9783962	9783962	+	Silent	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9783962G>T	uc003gmb.3	+	1	705	c.309G>T	c.(307-309)GTG>GTT	p.V103V		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	103	Helical; Name=2; (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)	TCGCCGAGGTGGCCGGTTACT	0.612													3	33	---	---	---	---	PASS
C4orf26	152816	broad.mit.edu	37	4	76489700	76489700	+	3'UTR	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76489700G>T	uc003hip.1	+	2					C4orf26_uc011cbn.1_RNA|C4orf26_uc011cbo.1_Missense_Mutation_p.R163I	NM_178497	NP_848592	Q17RF5	CD026_HUMAN	hypothetical protein LOC152816 precursor							extracellular region					0			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CTATCCTTCAGAAAAAAGCAA	0.363													12	58	---	---	---	---	PASS
MOCS2	4338	broad.mit.edu	37	5	52404436	52404436	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52404436G>A	uc011cqf.1	-	2	95	c.56C>T	c.(55-57)ACA>ATA	p.T19I	MOCS2_uc003joz.2_5'UTR|uc003jpb.1_5'Flank	NM_176806	NP_789776	O96033	MOC2A_HUMAN	molybdopterin synthase small subunit MOCS2A	19					Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex	nucleotide binding				0		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				ACGAACTCCTGTTATTTCAGC	0.363													97	453	---	---	---	---	PASS
WDR41	55255	broad.mit.edu	37	5	76728962	76728962	+	Nonstop_Mutation	SNP	A	G	G			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76728962A>G	uc003kff.1	-	13	1665	c.1378T>C	c.(1378-1380)TAG>CAG	p.*460Q	WDR41_uc011csy.1_Nonstop_Mutation_p.*402Q|WDR41_uc011csz.1_Nonstop_Mutation_p.*405Q	NM_018268	NP_060738	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	460											0		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		TCCTTAAACTAGACAGCAAGG	0.318													6	310	---	---	---	---	PASS
UBE2B	7320	broad.mit.edu	37	5	133710127	133710127	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133710127T>C	uc003kzh.2	+	2	515	c.98T>C	c.(97-99)ATC>ACC	p.I33T		NM_003337	NP_003328	P63146	UBE2B_HUMAN	ubiquitin-conjugating enzyme E2B	33					canonical Wnt receptor signaling pathway|histone H2A ubiquitination|negative regulation of cAMP-mediated signaling|postreplication repair|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein stabilization|response to drug|response to UV	cytoplasm|plasma membrane|replication fork	ATP binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity			lung(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GAAAACAACATCATGCAGTGG	0.393								Direct_reversal_of_damage|Rad6_pathway					7	347	---	---	---	---	PASS
PCDHGA5	56110	broad.mit.edu	37	5	140745027	140745027	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140745027G>A	uc003lju.1	+	1	1130	c.1130G>A	c.(1129-1131)GGA>GAA	p.G377E	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc011das.1_Missense_Mutation_p.G377E	NM_018918	NP_061741	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5 isoform 1	377	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGATTCTGGAGAAAATGGT	0.443													37	200	---	---	---	---	PASS
GALNT10	55568	broad.mit.edu	37	5	153760081	153760081	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153760081C>G	uc003lvh.2	+	6	960	c.828C>G	c.(826-828)TAC>TAG	p.Y276*	GALNT10_uc003lvg.1_Nonsense_Mutation_p.Y276*|GALNT10_uc010jic.2_RNA|GALNT10_uc010jid.2_Nonsense_Mutation_p.Y117*	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a	276	Lumenal (Potential).					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)			ACTTTCGGTACGAGACACAGG	0.547													5	100	---	---	---	---	PASS
FAM71B	153745	broad.mit.edu	37	5	156592756	156592756	+	Silent	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156592756G>A	uc003lwn.2	-	1	524	c.424C>T	c.(424-426)CTG>TTG	p.L142L		NM_130899	NP_570969	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	142						nucleus				ovary(4)|pancreas(1)|skin(1)	6	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCGAGTTTCAGGCGCAGCTGC	0.493													50	92	---	---	---	---	PASS
FAM71B	153745	broad.mit.edu	37	5	156592758	156592758	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156592758C>T	uc003lwn.2	-	1	522	c.422G>A	c.(421-423)CGC>CAC	p.R141H		NM_130899	NP_570969	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	141						nucleus				ovary(4)|pancreas(1)|skin(1)	6	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GAGTTTCAGGCGCAGCTGCTG	0.498													48	91	---	---	---	---	PASS
HLA-G	3135	broad.mit.edu	37	6	29896268	29896268	+	Intron	SNP	T	C	C	rs113454222		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29896268T>C	uc011dmb.1	+						HCG4P6_uc003nog.1_RNA|HCG4P6_uc003noh.1_5'Flank|uc003noi.2_RNA	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						CCATCGTGGGTATCGTTGCTG	0.562													5	10	---	---	---	---	PASS
HLA-G	3135	broad.mit.edu	37	6	29896275	29896275	+	Intron	SNP	G	A	A	rs116811069	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29896275G>A	uc011dmb.1	+						HCG4P6_uc003nog.1_RNA|HCG4P6_uc003noh.1_5'Flank|uc003noi.2_RNA	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						GGGTATCGTTGCTGGCCTGGT	0.572													5	11	---	---	---	---	PASS
BTBD9	114781	broad.mit.edu	37	6	38160335	38160335	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38160335G>T	uc003ooa.3	-	11	2177	c.1601C>A	c.(1600-1602)TCC>TAC	p.S534Y	BTBD9_uc003ony.3_Missense_Mutation_p.S466Y|BTBD9_uc010jwv.2_Missense_Mutation_p.S495Y|BTBD9_uc010jww.2_RNA|BTBD9_uc010jwx.2_Missense_Mutation_p.S534Y	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a	534					cell adhesion						0						ACGGATGAAGGAGGCAGGCTG	0.473													60	279	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129371227	129371227	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129371227C>A	uc003qbn.2	+	2	382	c.277C>A	c.(277-279)CCA>ACA	p.P93T	LAMA2_uc003qbo.2_Missense_Mutation_p.P93T	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	93	Laminin N-terminal.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CAGCAGCAATCCAAACCGTAT	0.438													59	224	---	---	---	---	PASS
KIAA0415	9907	broad.mit.edu	37	7	4830337	4830337	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4830337T>C	uc003sne.2	+	16	2055	c.1972T>C	c.(1972-1974)TAC>CAC	p.Y658H	KIAA0415_uc010ksp.2_RNA|KIAA0415_uc003snf.2_Missense_Mutation_p.Y135H	NM_014855	NP_055670	O43299	K0415_HUMAN	hypothetical protein LOC9907	658					cell death|double-strand break repair via homologous recombination	cytoplasm|nucleus	protein binding			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.091)|OV - Ovarian serous cystadenocarcinoma(56;8.35e-15)		GTCGGTGACCTACGATCGGAG	0.657													9	24	---	---	---	---	PASS
SNX13	23161	broad.mit.edu	37	7	17915293	17915293	+	Silent	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17915293T>C	uc003stw.1	-	6	774	c.561A>G	c.(559-561)AAA>AAG	p.K187K	SNX13_uc003stv.2_Silent_p.K187K|SNX13_uc010kuc.2_5'UTR|SNX13_uc003stx.1_Silent_p.K107K			Q9Y5W8	SNX13_HUMAN	SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;	187	PXA.				cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)					AGATATTACCTTTCACTTGAT	0.313													9	829	---	---	---	---	PASS
PI15	51050	broad.mit.edu	37	8	75756222	75756222	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75756222G>T	uc003yal.2	+	3	459	c.280G>T	c.(280-282)GAT>TAT	p.D94Y	uc003yak.1_Intron|PI15_uc003yam.2_Missense_Mutation_p.D94Y	NM_015886	NP_056970	O43692	PI15_HUMAN	protease inhibitor 15 preproprotein	94						extracellular region	peptidase inhibitor activity			central_nervous_system(2)|ovary(1)	3	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)			ACAGGTTTGGGATGAAAATCT	0.393													34	177	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32631847	32631847	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32631847C>T	uc003zrg.1	-	1	3821	c.3731G>A	c.(3730-3732)CGG>CAG	p.R1244Q	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1244					male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTGAATCCTCCGCCGTTCTTT	0.458													8	276	---	---	---	---	PASS
ALDH1A1	216	broad.mit.edu	37	9	75555088	75555088	+	Silent	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75555088G>A	uc004ajd.2	-	2	200	c.147C>T	c.(145-147)CTC>CTT	p.L49L	ALDH1A1_uc011lsh.1_5'UTR	NM_000689	NP_000680	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1A1	49					cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity			ovary(3)|lung(1)	4					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	CTACCTGGCAGAGCTCCTCCT	0.408													86	339	---	---	---	---	PASS
WDFY4	57705	broad.mit.edu	37	10	49988080	49988080	+	Silent	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49988080C>T	uc001jha.3	+	19	3569	c.3492C>T	c.(3490-3492)CAC>CAT	p.H1164H		NM_020945	NP_065996	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1164						integral to membrane	binding				0						AGTGGCATCACTTGGCTGTGG	0.537													25	137	---	---	---	---	PASS
C10orf76	79591	broad.mit.edu	37	10	103769151	103769151	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103769151A>G	uc009xwy.1	-	13	1036	c.934T>C	c.(934-936)TTC>CTC	p.F312L		NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591	312						integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		ACTGTGATGAAGTTGCGATTT	0.368													8	506	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32996944	32996944	+	Intron	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32996944C>T	uc001mty.2	+						QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_Silent_p.L1213L	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1											ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					TAAGGAGACTCTAGCCATAGT	0.284													9	134	---	---	---	---	PASS
HEPHL1	341208	broad.mit.edu	37	11	93836116	93836116	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93836116G>T	uc001pep.2	+	15	2769	c.2612G>T	c.(2611-2613)AGA>ATA	p.R871I	uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	871	Plastocyanin-like 5.|Extracellular (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				ATCCCTAAAAGATCCGGTCCA	0.343													72	370	---	---	---	---	PASS
PANX3	116337	broad.mit.edu	37	11	124489482	124489482	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124489482T>C	uc001qah.2	+	4	830	c.830T>C	c.(829-831)GTA>GCA	p.V277A		NM_052959	NP_443191	Q96QZ0	PANX3_HUMAN	pannexin 3	277	Helical; (Potential).				protein hexamerization	gap junction|integral to membrane	gap junction hemi-channel activity|ion channel activity				0	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		CTCTCCAGTGTAGCAATATAC	0.458													5	199	---	---	---	---	PASS
PLEKHG7	440107	broad.mit.edu	37	12	93135280	93135280	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93135280T>C	uc001tcj.2	+	4	343	c.113T>C	c.(112-114)TTT>TCT	p.F38S		NM_001004330	NP_001004330	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G	38	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1						AGCCTTGGTTTTGTGAACAGT	0.398													6	388	---	---	---	---	PASS
NAA25	80018	broad.mit.edu	37	12	112499165	112499165	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112499165G>C	uc001ttm.2	-	12	1197	c.1177C>G	c.(1177-1179)CCT>GCT	p.P393A	NAA25_uc001ttn.3_RNA|NAA25_uc009zvz.1_Missense_Mutation_p.P365A|NAA25_uc009zwa.1_Missense_Mutation_p.P393A	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20	393						cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3						GTCGACAAAGGAACAACTCCA	0.443													6	193	---	---	---	---	PASS
PIWIL1	9271	broad.mit.edu	37	12	130847615	130847615	+	Silent	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130847615C>T	uc001uik.2	+	18	2211	c.2121C>T	c.(2119-2121)GGC>GGT	p.G707G	PIWIL1_uc001uij.1_Silent_p.G707G	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	707	Piwi.				gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		TAGGAGACGGCCAGCTGAAAA	0.478													7	123	---	---	---	---	PASS
SKA3	221150	broad.mit.edu	37	13	21742500	21742500	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21742500A>G	uc001unt.2	-	4	464	c.370T>C	c.(370-372)TCT>CCT	p.S124P	SKA3_uc001unv.2_Missense_Mutation_p.S42P|SKA3_uc001unu.2_Missense_Mutation_p.S124P	NM_145061	NP_659498	Q8IX90	SKA3_HUMAN	SKA3	124					cell division|chromosome segregation|mitosis|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytoplasm|spindle microtubule	protein binding				0						TCACAATTAGACAACTCTGGG	0.383													5	168	---	---	---	---	PASS
BRCA2	675	broad.mit.edu	37	13	32893430	32893430	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32893430T>A	uc001uub.1	+	3	511	c.284T>A	c.(283-285)GTA>GAA	p.V95E	BRCA2_uc001uua.1_5'UTR	NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	95					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		CAATCTCCTGTAAAAGAATTA	0.249			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			4	131	---	---	---	---	PASS
RALGAPA1	253959	broad.mit.edu	37	14	36143766	36143766	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36143766G>A	uc001wti.2	-	22	3647	c.3256C>T	c.(3256-3258)CAA>TAA	p.Q1086*	RALGAPA1_uc010amp.2_5'Flank|RALGAPA1_uc001wtj.2_Nonsense_Mutation_p.Q1086*|RALGAPA1_uc010tpv.1_Nonsense_Mutation_p.Q1099*|RALGAPA1_uc010tpw.1_Nonsense_Mutation_p.Q1133*	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1	1086					activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						TCAAAAACTTGAGCATGTATT	0.353													11	63	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64689952	64689952	+	Silent	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64689952T>C	uc001xgm.2	+	112	20397	c.20167T>C	c.(20167-20169)TTA>CTA	p.L6723L	SYNE2_uc001xgl.2_Silent_p.L6746L|SYNE2_uc010apy.2_Silent_p.L3108L|SYNE2_uc001xgn.2_Silent_p.L1685L|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_Silent_p.L693L|SYNE2_uc001xgq.2_Silent_p.L1102L|SYNE2_uc001xgr.2_Silent_p.L506L|SYNE2_uc010tsi.1_Silent_p.L380L|SYNE2_uc001xgs.2_Silent_p.L394L|SYNE2_uc001xgt.2_Silent_p.L268L	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6723	Potential.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGTGGACATGTTACAGGAGAT	0.423													5	149	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107099545	107099545	+	RNA	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107099545C>T	uc010tyt.1	-	95		c.4319G>A								Parts of antibodies, mostly variable regions.												0						TGAATCACCTCTTAAAATAGC	0.463													4	123	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107099577	107099577	+	RNA	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107099577C>T	uc010tyt.1	-	95		c.4287G>A								Parts of antibodies, mostly variable regions.												0						CCCAGCTCAGCCCAAACTCCA	0.498													4	113	---	---	---	---	PASS
PGBD4	161779	broad.mit.edu	37	15	34394999	34394999	+	Silent	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34394999C>T	uc001zho.2	+	1	726	c.267C>T	c.(265-267)ACC>ACT	p.T89T	C15orf24_uc001zhm.2_5'Flank|C15orf24_uc001zhn.2_5'Flank	NM_152595	NP_689808	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	89											0		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)		ATGACTTTACCGGCACACCTG	0.418													4	104	---	---	---	---	PASS
KIAA1199	57214	broad.mit.edu	37	15	81199027	81199027	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81199027G>C	uc002bfw.1	+	12	1695	c.1435G>C	c.(1435-1437)GGG>CGG	p.G479R	KIAA1199_uc010unn.1_Missense_Mutation_p.G479R	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor	479										upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						CCTGCACATCGGGGAGGAGAT	0.582													7	148	---	---	---	---	PASS
IQGAP1	8826	broad.mit.edu	37	15	91020913	91020913	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91020913A>C	uc002bpl.1	+	26	3222	c.3121A>C	c.(3121-3123)ATT>CTT	p.I1041L		NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1041	Ras-GAP.|C1.				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)			GGTAGATCAGATTCAAGAGAT	0.413													27	141	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9858545	9858545	+	Silent	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9858545T>C	uc002czo.3	-	13	3404	c.2856A>G	c.(2854-2856)AAA>AAG	p.K952K	GRIN2A_uc010uym.1_Silent_p.K952K|GRIN2A_uc010uyn.1_Silent_p.K795K|GRIN2A_uc002czr.3_Silent_p.K952K	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	952	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	AAATGCTCTCTTTCCCCTGAA	0.443													7	267	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													4	40	---	---	---	---	PASS
SPAG7	9552	broad.mit.edu	37	17	4864088	4864088	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4864088C>T	uc002gae.2	-	2	179	c.146G>A	c.(145-147)CGT>CAT	p.R49H	SPAG7_uc002gad.2_5'UTR|SPAG7_uc002gaf.2_Missense_Mutation_p.R49H	NM_004890	NP_004881	O75391	SPAG7_HUMAN	sperm associated antigen 7	49	R3H.|Nuclear localization signal (Potential).					nucleus	nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)	2						CACCCTTTTACGAAACTCCAC	0.463													5	345	---	---	---	---	PASS
GPATCH8	23131	broad.mit.edu	37	17	42476146	42476146	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42476146C>A	uc002igw.1	-	8	3363	c.3299G>T	c.(3298-3300)AGG>ATG	p.R1100M	GPATCH8_uc002igv.1_Missense_Mutation_p.R1022M|GPATCH8_uc010wiz.1_Missense_Mutation_p.R1022M	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1100						intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		CTCCACTTTCCTTGACTGGAT	0.532													43	178	---	---	---	---	PASS
ABCA9	10350	broad.mit.edu	37	17	66985190	66985190	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66985190T>C	uc002jhu.2	-	31	4168	c.4025A>G	c.(4024-4026)GAC>GGC	p.D1342G	ABCA9_uc010dez.2_Missense_Mutation_p.D1304G	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	1342	ABC transporter 2.				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					TGGTTTTGTGTCTCCAGTTAT	0.373													9	776	---	---	---	---	PASS
SMCHD1	23347	broad.mit.edu	37	18	2738518	2738518	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2738518T>C	uc002klm.3	+	26	3589	c.3400T>C	c.(3400-3402)TCT>CCT	p.S1134P	SMCHD1_uc002klk.3_RNA|SMCHD1_uc002kll.3_RNA	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible	1134					chromosome organization		ATP binding				0						TGATCATGTGTCTTTGGAAAG	0.398													8	567	---	---	---	---	PASS
NPC1	4864	broad.mit.edu	37	18	21137135	21137135	+	Missense_Mutation	SNP	C	T	T	rs150154006		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21137135C>T	uc002kum.3	-	7	1175	c.901G>A	c.(901-903)GAG>AAG	p.E301K	NPC1_uc010xaz.1_Missense_Mutation_p.E85K|NPC1_uc010xba.1_Missense_Mutation_p.E146K	NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor	301					autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GGAGTGTACTCGGAGACAAAA	0.388													8	349	---	---	---	---	PASS
C3	718	broad.mit.edu	37	19	6712358	6712358	+	Silent	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6712358G>A	uc002mfm.2	-	11	1241	c.1179C>T	c.(1177-1179)GGC>GGT	p.G393G		NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	393					complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		CAGTGTCCTCGCCCTGGACTG	0.617													11	94	---	---	---	---	PASS
COL5A3	50509	broad.mit.edu	37	19	10084447	10084447	+	Silent	SNP	G	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10084447G>A	uc002mmq.1	-	49	3683	c.3597C>T	c.(3595-3597)GGC>GGT	p.G1199G		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1199	Triple-helical region.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)			CACCCACGGCGCCTGGCTGAC	0.592													5	125	---	---	---	---	PASS
LIPE	3991	broad.mit.edu	37	19	42912472	42912472	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42912472G>C	uc002otr.2	-	3	1699	c.1422C>G	c.(1420-1422)TTC>TTG	p.F474L	uc010eif.1_Intron|LIPE_uc002ots.1_Missense_Mutation_p.F219L	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	474					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)				TGGCAGGCGTGAACTGTGGAG	0.602													11	52	---	---	---	---	PASS
PSG3	5671	broad.mit.edu	37	19	43234081	43234081	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43234081G>C	uc002oue.2	-	4	969	c.837C>G	c.(835-837)AGC>AGG	p.S279R	PSG3_uc002ouf.2_RNA|PSG1_uc002oug.1_Intron|PSG3_uc010eil.2_Missense_Mutation_p.S301R	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	279	Ig-like C2-type 2.				defense response|female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)				TGACCGGGAGGCTCTGACCAT	0.463													32	196	---	---	---	---	PASS
PLAUR	5329	broad.mit.edu	37	19	44153294	44153294	+	Silent	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44153294T>C	uc002oxf.1	-	7	986	c.756A>G	c.(754-756)GAA>GAG	p.E252E	PLAUR_uc002oxd.1_Intron|PLAUR_uc002oxe.1_Silent_p.E247E|PLAUR_uc002oxg.1_Silent_p.E207E	NM_002659	NP_002650	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	252	UPAR/Ly6 3.			E -> G (in Ref. 12; AAF71751).	attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis	anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane	enzyme binding|U-plasminogen activator receptor activity			ovary(1)	1		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013)	GGTTTTTCGGTTCTGAGGAAA	0.537													4	60	---	---	---	---	PASS
CPT1C	126129	broad.mit.edu	37	19	50213761	50213761	+	Intron	SNP	C	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50213761C>A	uc002ppj.2	+						CPT1C_uc002ppl.3_Missense_Mutation_p.P550Q|CPT1C_uc002ppi.2_Intron|CPT1C_uc002ppk.2_Intron|CPT1C_uc010eng.2_Intron|CPT1C_uc010enh.2_Intron|CPT1C_uc010ybc.1_Missense_Mutation_p.P455Q|CPT1C_uc010eni.1_Intron	NM_152359	NP_689572	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C isoform 2						fatty acid metabolic process	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		GTTCCCCATCCACAGCCCCCG	0.602													12	37	---	---	---	---	PASS
PTOV1	53635	broad.mit.edu	37	19	50358311	50358311	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50358311T>A	uc002pqf.1	+	5	705	c.535T>A	c.(535-537)TGC>AGC	p.C179S	PTOV1_uc010ybf.1_Missense_Mutation_p.C147S|PTOV1_uc002ppz.3_RNA|PTOV1_uc002pqb.3_Missense_Mutation_p.C147S|PTOV1_uc002pqa.2_RNA|PTOV1_uc002pqc.1_RNA|PTOV1_uc002pqd.2_RNA|PTOV1_uc002pqe.1_RNA	NM_017432	NP_059128	Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	179					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|plasma membrane					0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		CAAGGGGCTCTGCCGCATCAT	0.632													9	26	---	---	---	---	PASS
ZNF160	90338	broad.mit.edu	37	19	53577475	53577475	+	Silent	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53577475C>T	uc010eqk.2	-	6	605	c.189G>A	c.(187-189)GGG>GGA	p.G63G	ZNF160_uc002qaq.3_Silent_p.G63G|ZNF160_uc002qar.3_Silent_p.G63G|ZNF160_uc002qas.3_Silent_p.G63G	NM_001102603	NP_001096073	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	63	KRAB.				hemopoiesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(134;0.02)		AGGGCTCTTTCCCTTCCTCCA	0.458													65	260	---	---	---	---	PASS
NLRP8	126205	broad.mit.edu	37	19	56467043	56467043	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56467043G>T	uc002qmh.2	+	3	1690	c.1619G>T	c.(1618-1620)CGC>CTC	p.R540L	NLRP8_uc010etg.2_Missense_Mutation_p.R540L	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	540						cytoplasm	ATP binding			ovary(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|kidney(1)	13		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AATATCCAGCGCCTGATAGCG	0.463													40	202	---	---	---	---	PASS
ZNF543	125919	broad.mit.edu	37	19	57838032	57838032	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57838032C>G	uc002qoi.1	+	3	522	c.177C>G	c.(175-177)TAC>TAG	p.Y59*		NM_213598	NP_998763	Q08ER8	ZN543_HUMAN	zinc finger protein 543	59	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)|pancreas(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AGCTGATCTACCAGTTGGATC	0.498													16	88	---	---	---	---	PASS
RRBP1	6238	broad.mit.edu	37	20	17641024	17641024	+	Silent	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17641024G>T	uc010zrq.1	-	3	483	c.129C>A	c.(127-129)GCC>GCA	p.A43A	RRBP1_uc002wpu.2_5'Flank|RRBP1_uc002wpv.1_Silent_p.A43A|RRBP1_uc002wpw.1_Silent_p.A43A|RRBP1_uc010gcl.1_Intron|RRBP1_uc010zrr.1_Silent_p.A43A			Q9P2E9	RRBP1_HUMAN	SubName: Full=RRBP1 protein; Flags: Fragment;	43	Cytoplasmic (Potential).				protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1						TGCGCTGGTTGGCTAGGGCTT	0.358													46	223	---	---	---	---	PASS
HM13	81502	broad.mit.edu	37	20	30135489	30135489	+	Intron	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30135489C>T	uc002wwe.2	+						HM13_uc002wwc.2_Intron|HM13_uc002wwd.2_Intron|HM13_uc002wwf.2_5'UTR|HM13_uc010gdu.2_5'UTR|PSIMCT-1_uc010gdt.2_RNA	NM_030789	NP_110416	Q8TCT9	HM13_HUMAN	minor histocompatibility antigen 13 isoform 1						membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			ATACAGAAATCCTTACCGTAA	0.403													4	53	---	---	---	---	PASS
C20orf107	388799	broad.mit.edu	37	20	55108443	55108443	+	Intron	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55108443T>C	uc010zzh.1	+						C20orf107_uc002xxz.2_Missense_Mutation_p.C16R	NM_001013646	NP_001013668	Q5JX69	CT107_HUMAN	hypothetical protein LOC388799 precursor							integral to membrane					0			Colorectal(105;0.202)			GTGCCTCACCTGCAGCTATGC	0.552													21	113	---	---	---	---	PASS
C21orf99	149992	broad.mit.edu	37	21	14417570	14417570	+	RNA	SNP	A	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14417570A>T	uc002yiy.3	+	3		c.2845A>T			C21orf99_uc002yja.3_RNA					Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						GCAAATGCAAATGGAGTTGAT	0.308													4	79	---	---	---	---	PASS
KRTAP10-10	353333	broad.mit.edu	37	21	46057319	46057319	+	5'UTR	SNP	G	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46057319G>T	uc002zfq.2	+	1					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181688	NP_859016	P60014	KR10A_HUMAN	keratin associated protein 10-10							keratin filament					0						CCAGCTCACCGCCTCCCCACT	0.507													5	49	---	---	---	---	PASS
OTC	5009	broad.mit.edu	37	X	38262963	38262963	+	Silent	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38262963C>T	uc004def.3	+	6	847	c.633C>T	c.(631-633)TTC>TTT	p.F211F		NM_000531	NP_000522	P00480	OTC_HUMAN	ornithine carbamoyltransferase precursor	211					arginine biosynthetic process|urea cycle	mitochondrial matrix|ornithine carbamoyltransferase complex	ornithine carbamoyltransferase activity			ovary(1)|breast(1)	2					L-Citrulline(DB00155)|L-Ornithine(DB00129)	CAGCGAAATTCGGAATGCACC	0.468													8	61	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	155254706	155254706	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155254706C>T	uc004fnx.3	+	8	1056	c.602C>T	c.(601-603)ACG>ATG	p.T201M		NM_182905	NP_878908			WAS protein family homolog 1																		GTGAGAGCCACGAGCCAAGGT	0.637													4	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	2618	2618	+	5'Flank	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:2618T>C	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		ttgttccttaaatagggacct	0.209													27	7	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15645	15645	+	3'UTR	SNP	T	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15645T>C	uc004coy.2	+	1					uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		ATCCATCCTCATCCTAGCAAT	0.453											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	20	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	1869072	1869072	+	IGR	DEL	C	-	-	rs60247598		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1869072delC								TMEM52 (18332 upstream) : KIAA1751 (15680 downstream)																							GCTGTGACTGCCCCCCAGTGT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4131522	4131522	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4131522delC								LOC100133612 (297645 upstream) : LOC284661 (340589 downstream)																							TGGCAGCGTTCACTGGGCCAG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	6825285	6825285	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6825285delT								DNAJC11 (63319 upstream) : CAMTA1 (20099 downstream)																							AACTTTTCTGTTTTTTTTTTT	0.433													4	2	---	---	---	---	
NBPF1	55672	broad.mit.edu	37	1	16900070	16900070	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16900070delA	uc009vos.1	-						NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TGAAACACACATGATAGATAA	0.234													4	2	---	---	---	---	
KPNA6	23633	broad.mit.edu	37	1	32636838	32636838	+	3'UTR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32636838delT	uc001bug.2	+	14					KPNA6_uc001buh.2_3'UTR|KPNA6_uc010ogx.1_3'UTR|KPNA6_uc010ogy.1_3'UTR|KPNA6_uc009vtz.2_3'UTR	NM_012316	NP_036448	O60684	IMA7_HUMAN	karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				tttatttttattttttttctt	0.378													4	2	---	---	---	---	
ERI3	79033	broad.mit.edu	37	1	44816709	44816709	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44816709delT	uc001clt.2	-						ERI3_uc010okv.1_Intron|ERI3_uc009vxg.2_Intron|ERI3_uc010okw.1_Intron|ERI3_uc001clu.2_Intron	NM_024066	NP_076971	O43414	ERI3_HUMAN	prion protein interacting protein							intracellular	exonuclease activity|metal ion binding|nucleic acid binding			ovary(2)|large_intestine(1)	3						cagagcaaacttttttttttt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48266351	48266351	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48266351delG								FOXD2 (359989 upstream) : SKINTL (301036 downstream)																							TGACAGAGGAGGCACAAGGCC	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	54882975	54882976	+	IGR	DEL	CA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54882975_54882976delCA								SSBP3 (10883 upstream) : ACOT11 (124954 downstream)																							TGAACACATGCACACACACACA	0.347													4	2	---	---	---	---	
FGGY	55277	broad.mit.edu	37	1	59812470	59812470	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59812470delT	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron	NM_018291	NP_060761	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)					tccaaaatcATTTTTTTTtaa	0.000													4	2	---	---	---	---	
DOCK7	85440	broad.mit.edu	37	1	63025117	63025117	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63025117delT	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						CTAATTAAGATTTTTTTTTTT	0.219													4	3	---	---	---	---	
WLS	79971	broad.mit.edu	37	1	68617288	68617289	+	Intron	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68617288_68617289insA	uc001def.1	-						uc001deb.1_Intron|uc001dec.1_Intron|WLS_uc001dee.2_Intron|WLS_uc001deg.1_Intron|WLS_uc009wbf.1_Intron	NM_024911	NP_079187	Q5T9L3	WLS_HUMAN	G protein-coupled receptor 177 isoform 1						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0						tgagcatcatgaaaaaaaaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	69569419	69569419	+	IGR	DEL	A	-	-	rs71777418		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69569419delA								DEPDC1 (606620 upstream) : LRRC7 (463449 downstream)																							GTCCATGATCAAAAAAAAAAA	0.388													3	3	---	---	---	---	
NEGR1	257194	broad.mit.edu	37	1	71960010	71960010	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71960010delA	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		aagccccagtaaaaactctgg	0.000													4	2	---	---	---	---	
ZZZ3	26009	broad.mit.edu	37	1	78031084	78031084	+	3'UTR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78031084delA	uc001dhq.2	-	15					ZZZ3_uc001dhr.2_3'UTR|ZZZ3_uc001dhp.2_3'UTR	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5						ATCACCACCTAAAACGCAGTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	79801912	79801913	+	IGR	DEL	TT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79801912_79801913delTT								ELTD1 (329417 upstream) : None (None downstream)																							TCCATCTCCATTTTGAGTGCAA	0.406													4	3	---	---	---	---	
LOC339524	339524	broad.mit.edu	37	1	87621113	87621113	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87621113delC	uc001dme.1	+						LOC339524_uc001dmf.2_Intron	NM_001134492	NP_001127964			heparan sulfate 2-O-sulfotransferase 1 isoform												0						ACAGCGAATTCCCCCACAGAT	0.413													4	2	---	---	---	---	
TGFBR3	7049	broad.mit.edu	37	1	92210134	92210135	+	Intron	INS	-	A	A	rs146023266	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92210134_92210135insA	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)		AAATCAATGTCAAGAAAACATC	0.436													2	4	---	---	---	---	
BRDT	676	broad.mit.edu	37	1	92420600	92420600	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92420600delT	uc001dok.3	+						BRDT_uc001dol.3_Intron|BRDT_uc010osz.1_Intron|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Intron|BRDT_uc010otb.1_Intron|BRDT_uc001dom.3_Intron	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		AACTCTGTACTTTTTTCCCCT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96989051	96989051	+	IGR	DEL	C	-	-	rs76555736	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96989051delC								None (None upstream) : PTBP2 (198124 downstream)																							TTCTTAATGACCCCCCGAGAA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	103177320	103177320	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103177320delA								OLFM3 (714530 upstream) : COL11A1 (164704 downstream)																							AGAATCAATGAATTGAGATAG	0.368													4	2	---	---	---	---	
AMY2B	280	broad.mit.edu	37	1	104118398	104118399	+	Intron	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104118398_104118399insA	uc001duq.2	+						AMY2B_uc010ouo.1_Intron|LOC648740_uc001dur.2_Intron|AMY2B_uc001dus.1_Intron	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor						carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		TAGCCCACAGGAAAAAAAAAAA	0.257													6	4	---	---	---	---	
GPSM2	29899	broad.mit.edu	37	1	109467057	109467058	+	Intron	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109467057_109467058delGT	uc010ovc.1	+						AKNAD1_uc010ovb.1_Intron|GPSM2_uc010ovd.1_Intron|GPSM2_uc010ove.1_Intron	NM_013296	NP_037428	P81274	GPSM2_HUMAN	LGN protein						G-protein coupled receptor protein signaling pathway	cell cortex|nucleus	GTPase activator activity|identical protein binding			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		taggagagacgtgtgtgtgtgt	0.000													6	3	---	---	---	---	
WDR47	22911	broad.mit.edu	37	1	109514411	109514412	+	Intron	DEL	CT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109514411_109514412delCT	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc010ovf.1_Intron	NM_001142551	NP_001136023	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		gacaagttgcctctctctctct	0.094													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	114556072	114556075	+	IGR	DEL	ATTC	-	-	rs71578801		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114556072_114556075delATTC								OLFML3 (31196 upstream) : SYT6 (75840 downstream)																							tcattcacttattcattcattcTT	0.078													4	2	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120570923	120570923	+	Intron	DEL	C	-	-	rs11364041		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120570923delC	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAAGAGTTGCATAACAGAAT	0.368			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142803302	142803303	+	Intron	INS	-	AA	AA	rs79529551		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142803302_142803303insAA	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejc.2_5'Flank					Homo sapiens PNAS-130 mRNA, complete cds.																		acaacaacaacaaACAGGATGT	0.223													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143358380	143358381	+	IGR	DEL	TT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143358380_143358381delTT								None (None upstream) : LOC100286793 (289258 downstream)																							ATACTTTGACTTTTAAATCATA	0.297													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144914057	144914058	+	Intron	INS	-	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144914057_144914058insC	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001eme.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GTGCATAATTTTTTTTCTGAGG	0.297			T	PDGFRB	MPD								3	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145058201	145058201	+	Intron	DEL	A	-	-	rs11347217		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145058201delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						AGAGGGAGGGAAAAAAAAATC	0.383													5	4	---	---	---	---	
LOC388692	388692	broad.mit.edu	37	1	149280301	149280302	+	RNA	INS	-	A	A	rs145896171	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149280301_149280302insA	uc010pbf.1	+	1		c.826_827insA				NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0						CCAATTTAGTGAAAAAAAACTG	0.411													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	150586314	150586314	+	IGR	DEL	A	-	-	rs138805506		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150586314delA								MCL1 (34178 upstream) : ENSA (8290 downstream)																							TGCCTCTGCCAAAAAACGCCC	0.413													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	158760191	158760191	+	IGR	DEL	T	-	-	rs77036041		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158760191delT								OR6N2 (12766 upstream) : MNDA (40977 downstream)																							tgatagggaattttttttttt	0.000													4	2	---	---	---	---	
FAM78B	149297	broad.mit.edu	37	1	166030568	166030568	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166030568delT	uc010plc.1	-						FAM78B_uc001gdq.2_Intron	NM_001017961		Q5VT40	FA78B_HUMAN	hypothetical protein LOC149297											central_nervous_system(1)|skin(1)	2	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)					CATCCTTCTCTTTTTTTTTCT	0.328													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	166436766	166436767	+	IGR	DEL	TT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166436766_166436767delTT								FAM78B (300560 upstream) : FMO9P (136386 downstream)																							tcttctatcattaaccacacag	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168179626	168179626	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168179626delT								TIPRL (8277 upstream) : SFT2D2 (15629 downstream)																							tctagtaaagttttttcagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168638561	168638561	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168638561delT								XCL1 (87246 upstream) : DPT (26146 downstream)																							gcttgttttctttttttttta	0.000													4	2	---	---	---	---	
C1orf105	92346	broad.mit.edu	37	1	172395705	172395706	+	Intron	INS	-	T	T	rs113449046		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172395705_172395706insT	uc001gik.2	+						PIGC_uc001gii.1_Intron|PIGC_uc001gij.1_Intron	NM_139240	NP_640333	O95561	CA105_HUMAN	hypothetical protein LOC92346											skin(1)	1						tttcaatggtcttttttttttt	0.000													4	2	---	---	---	---	
XPR1	9213	broad.mit.edu	37	1	180763840	180763840	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180763840delT	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0						agggaggttgtttggggatgg	0.015													4	2	---	---	---	---	
STX6	10228	broad.mit.edu	37	1	180934270	180934270	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180934270delT	uc009wxo.1	-									O43752	STX6_HUMAN	Homo sapiens clone 23570 mRNA sequence.						Golgi vesicle transport|intracellular protein transport|vesicle fusion	clathrin-coated vesicle|early endosome|integral to membrane|perinuclear region of cytoplasm|plasma membrane|trans-Golgi network membrane	SNAP receptor activity			ovary(1)	1						CTCTCCCTCCTCCACTGCACT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199190984	199190984	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199190984delT								MIR181A1 (362702 upstream) : NR5A2 (805786 downstream)																							atagctcagcttggggatgtt	0.000													4	2	---	---	---	---	
MDM4	4194	broad.mit.edu	37	1	204677034	204677035	+	Intron	DEL	CT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204677034_204677035delCT	uc001hbd.1	+							NM_002393		O15151	MDM4_HUMAN	mouse double minute 4 homolog						apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization	nucleus	enzyme binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)			ACCAGGACTCCTCTCAGCTTTT	0.495			A		GBM|bladder|retinoblastoma								4	2	---	---	---	---	
IL20	50604	broad.mit.edu	37	1	207041516	207041517	+	Intron	DEL	CA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207041516_207041517delCA	uc001her.2	+						IL20_uc010pry.1_Intron|IL20_uc009xby.2_Intron	NM_018724	NP_061194	Q9NYY1	IL20_HUMAN	interleukin 20 precursor						positive regulation of keratinocyte differentiation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of inflammatory response	extracellular space	cytokine activity|interleukin-20 receptor binding				0	Breast(84;0.201)			OV - Ovarian serous cystadenocarcinoma(81;0.00459)		caggcacgtgcacacacacaca	0.173													5	3	---	---	---	---	
FAIM3	9214	broad.mit.edu	37	1	207097551	207097552	+	5'Flank	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207097551_207097552delGT	uc001hey.2	-						FAIM3_uc010prz.1_5'Flank|FAIM3_uc010psa.1_5'Flank|FAIM3_uc010psb.1_5'Flank	NM_005449	NP_005440	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3 isoform a						anti-apoptosis|cellular defense response	integral to membrane				central_nervous_system(1)	1	Breast(84;0.201)					gtgtccatgagtgtgtgtgtgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213712811	213712811	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213712811delT								RPS6KC1 (266004 upstream) : PROX1 (448475 downstream)																							GTAAATAGGATTTTTGGGGTC	0.502													4	2	---	---	---	---	
CENPF	1063	broad.mit.edu	37	1	214804623	214804625	+	Intron	DEL	TTC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214804623_214804625delTTC	uc001hkm.2	+							NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F						cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		gtcacttctattcttctttttct	0.172													3	5	---	---	---	---	
RRP15	51018	broad.mit.edu	37	1	218484971	218484971	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218484971delT	uc001hlj.2	+							NM_016052	NP_057136	Q9Y3B9	RRP15_HUMAN	ribosomal RNA processing 15 homolog							mitochondrion|nucleolus	protein binding				0				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)		gcaacattgctttatcccctt	0.060													4	2	---	---	---	---	
NVL	4931	broad.mit.edu	37	1	224491205	224491205	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224491205delA	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_Intron	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)		TACATACATTAAAAAAAAAAA	0.209													6	4	---	---	---	---	
C1orf95	375057	broad.mit.edu	37	1	226734345	226734345	+	5'Flank	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226734345delT	uc010pvn.1	+							NM_001003665	NP_001003665	Q69YW2	CA095_HUMAN	hypothetical protein LOC375057							integral to membrane				ovary(1)	1	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		CCTGAAATCCTTTTTCTCCAG	0.353													4	2	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231835602	231835603	+	Intron	INS	-	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231835602_231835603insC	uc001huz.2	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_Intron|DISC1_uc010pwp.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron|DISC1_uc010pwm.1_Intron|DISC1_uc001hux.1_Intron|DISC1_uc001hvc.3_Intron|DISC1_uc010pwn.1_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				tctctacagttttcccttacat	0.000													4	2	---	---	---	---	
DISC1	27185	broad.mit.edu	37	1	231926778	231926778	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231926778delC	uc001huz.2	+						TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				GCCACAGCCACCCCCCAGGCT	0.303													4	2	---	---	---	---	
RBM34	23029	broad.mit.edu	37	1	235295562	235295562	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235295562delT	uc001hwn.2	-						RBM34_uc001hwo.2_Intron|ARID4B_uc001hwp.2_Intron	NM_015014	NP_055829	P42696	RBM34_HUMAN	RNA binding motif protein 34 isoform 1							nucleolus	nucleotide binding|RNA binding			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			GGCTTCGTGGTTTTTTTTTTT	0.323													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15182023	15182023	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15182023delG								FAM84A (391090 upstream) : NBAS (125009 downstream)																							CTGGGAGGATGGGGCCATTTT	0.433													4	2	---	---	---	---	
NBAS	51594	broad.mit.edu	37	2	15557412	15557412	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15557412delA	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4						ACTAGAACGGAAAAAAAAAGT	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19626159	19626159	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19626159delC								OSR1 (67787 upstream) : TTC32 (470359 downstream)																							AAGGCCAAATCCCAAGTTTCT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19880760	19880760	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19880760delT								OSR1 (322388 upstream) : TTC32 (215758 downstream)																							ccagctgggcttacatcattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	20271713	20271713	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20271713delA								LAPTM4A (19924 upstream) : SDC1 (128845 downstream)																							CTTTGCTTCCAAAAAAAAAAG	0.433											OREG0004833	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	5	3	---	---	---	---	
ALK	238	broad.mit.edu	37	2	29823479	29823479	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29823479delG	uc002rmy.2	-							NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	CTGATATCGTGGGGGCTGCTC	0.512			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				4	2	---	---	---	---	
SULT6B1	391365	broad.mit.edu	37	2	37400871	37400871	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37400871delC	uc002rpu.2	-						SULT6B1_uc010yni.1_Intron	NM_001032377	NP_001027549	Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member							cytoplasm	sulfotransferase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(82;0.248)				atcctgttggccttcccttca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	43299842	43299842	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43299842delA								HAAO (280091 upstream) : ZFP36L2 (149700 downstream)																							aggttaaaagaaaaaaaaaat	0.000													3	3	---	---	---	---	
PLEKHH2	130271	broad.mit.edu	37	2	43923724	43923724	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43923724delT	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)				TCACCTCCTCTTTTTTTTTCT	0.308													4	2	---	---	---	---	
C2orf34	79823	broad.mit.edu	37	2	44942839	44942839	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44942839delC	uc002rum.2	+							NM_024766	NP_079042	Q7Z624	CMKMT_HUMAN	hypothetical protein LOC79823							cytoplasm	calmodulin-lysine N-methyltransferase activity				0		all_hematologic(82;0.0892)|Acute lymphoblastic leukemia(82;0.17)				agcagttttgcccccaagggg	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	45571842	45571843	+	IGR	INS	-	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45571842_45571843insC								SIX2 (335299 upstream) : SRBD1 (43977 downstream)																							CAAGCCTGTTTCCCCCAGCACC	0.594													4	2	---	---	---	---	
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48844560	48844560	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48844560delA	uc010yol.1	+						STON1-GTF2A1L_uc002rwp.1_Intron|GTF2A1L_uc002rws.1_5'Flank|GTF2A1L_uc010yom.1_5'Flank|GTF2A1L_uc002rwt.2_5'Flank	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTTATACAACAAAAAATGGAG	0.308													4	2	---	---	---	---	
ALMS1P	200420	broad.mit.edu	37	2	73906572	73906572	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73906572delG	uc010yrl.1	+							NR_003683				RecName: Full=Putative ALMS1-like protein;												0						CTGGTGGGCTGGGGGGATGGG	0.532													4	2	---	---	---	---	
C2orf65	130951	broad.mit.edu	37	2	74860438	74860438	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74860438delA	uc002smy.2	-						C2orf65_uc010ysa.1_Intron|C2orf65_uc002smz.2_Intron	NM_138804	NP_620159	Q8TC57	CB065_HUMAN	hypothetical protein LOC130951						chromatin assembly|female gamete generation|RNA processing|spermatogenesis	integral to membrane				ovary(1)|pancreas(1)	2						acttccttgtaaaatttcatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	78297499	78297499	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78297499delA	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																		TTTTTCTCAGAAAAAAAAATA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	82675711	82675712	+	IGR	DEL	TG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82675711_82675712delTG								None (None upstream) : None (None downstream)																							actgatggaatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	84421632	84421632	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84421632delC								None (None upstream) : FUNDC2P2 (96174 downstream)																							tggtgtgtgtccagtgggtgc	0.070													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	88971780	88971780	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88971780delG								EIF2AK3 (44786 upstream) : RPIA (19396 downstream)																							gagtttaggtggtaaaagggg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89132181	89132181	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89132181delG								FLJ40330 (26056 upstream) : None (None downstream)																							GGTTGTCCTAGGGAGCAGGGA	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91681935	91681935	+	IGR	DEL	T	-	-	rs144123748	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91681935delT								None (None upstream) : LOC654342 (123257 downstream)																							ggaaaaaaaatgctataaaga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91792896	91792897	+	IGR	INS	-	G	G	rs146949792		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91792896_91792897insG								None (None upstream) : LOC654342 (12295 downstream)																							ACTTGAAAGCTttatgaactga	0.287													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	100872735	100872735	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100872735delA								AFF3 (113698 upstream) : LONRF2 (17019 downstream)																							tcccatggataagggggTGAC	0.229													4	2	---	---	---	---	
NCK2	8440	broad.mit.edu	37	2	106507728	106507728	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106507728delT	uc002tdg.2	+						NCK2_uc002tdh.2_Intron|NCK2_uc002tdi.2_Intron	NM_003581	NP_003572	O43639	NCK2_HUMAN	NCK adaptor protein 2 isoform A						axon guidance|epidermal growth factor receptor signaling pathway|negative regulation of cell proliferation|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of epidermal growth factor receptor activity|regulation of translation|signal complex assembly|T cell activation	cytosol|endoplasmic reticulum	cytoskeletal adaptor activity|receptor signaling complex scaffold activity			ovary(1)|lung(1)	2						GTTTGTTTTCTTTTTTTTTTT	0.323													4	2	---	---	---	---	
SH3RF3	344558	broad.mit.edu	37	2	109963080	109963081	+	Intron	INS	-	T	T	rs142123578	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109963080_109963081insT	uc010ywt.1	+							NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1						GCCAGATGGACTTGATGAGACA	0.505													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118465892	118465892	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118465892delA								None (None upstream) : DDX18 (106363 downstream)																							TGAGCATGAGAAAAAAACACG	0.418													4	2	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121506954	121506954	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121506954delA	uc010yyu.1	+						GLI2_uc002tmp.1_Intron			P10070	GLI2_HUMAN	SubName: Full=cDNA FLJ60878, highly similar to Homo sapiens GLI-Kruppel family member GLI2, mRNA;						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				GCTGTATTTTAAAAAAAAAAT	0.333													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133046396	133046397	+	IGR	INS	-	G	G	rs72987878	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133046396_133046397insG								NCRNA00164 (30854 upstream) : GPR39 (127750 downstream)																							tgtgtgtgtgtTTTTGTCTGTT	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133046397	133046398	+	IGR	INS	-	G	G	rs72987878	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133046397_133046398insG								NCRNA00164 (30855 upstream) : GPR39 (127749 downstream)																							gtgtgtgtgtTTTTGTCTGTTG	0.376													3	3	---	---	---	---	
NEB	4703	broad.mit.edu	37	2	152402090	152402090	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152402090delA	uc010fnx.2	-						NEB_uc002txr.2_Intron	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)		actccatctcaaaaaaaaaaa	0.050													5	3	---	---	---	---	
TANK	10010	broad.mit.edu	37	2	162089358	162089358	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162089358delA	uc002ubr.1	+						TANK_uc002ubs.2_Intron	NM_004180	NP_004171	Q92844	TANK_HUMAN	TRAF interacting protein TANK isoform a							cytosol	metal ion binding|protein binding			ovary(1)	1						TATTCAGCTTAAAAAATTCAG	0.348													4	2	---	---	---	---	
KCNH7	90134	broad.mit.edu	37	2	163394412	163394412	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163394412delT	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	AGTAGACTTCTTTTAAATCAA	0.418													4	2	---	---	---	---	
RBM45	129831	broad.mit.edu	37	2	178986131	178986136	+	Intron	DEL	ACACAC	-	-	rs11895951		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178986131_178986136delACACAC	uc002ulv.2	+							NM_152945	NP_694453	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45						cell differentiation|nervous system development	cytoplasm|nucleus	nucleotide binding|RNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			atgtatatatacacacacacacacac	0.228													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	180739777	180739777	+	IGR	DEL	T	-	-	rs76998565		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180739777delT								ZNF385B (13545 upstream) : CWC22 (69827 downstream)																							TGTCTTCTTATTTTTTTTTTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	204968054	204968054	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204968054delA								ICOS (141758 upstream) : PARD3B (442462 downstream)																							AATACTCGAGAAAGGGCAAGA	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206524326	206524327	+	IGR	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206524326_206524327delGT								PARD3B (43789 upstream) : NRP2 (22897 downstream)																							GTGGGTGTGGGTGTGTGTGTAC	0.371													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	208519778	208519778	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208519778delA								FAM119A (29713 upstream) : CCNYL1 (56486 downstream)																							atctttaattaaaaaaaaaGA	0.294													4	3	---	---	---	---	
ATG4B	23192	broad.mit.edu	37	2	242608184	242608184	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242608184delT	uc002wbv.2	+						ATG4B_uc002wbu.2_Intron|ATG4B_uc002wbw.2_Intron|ATG4B_uc010zox.1_Intron|ATG4B_uc010zoy.1_Intron|ATG4B_uc010fzp.2_Intron|ATG4B_uc010zoz.1_Intron|ATG4B_uc002wby.2_Intron	NM_013325	NP_037457	Q9Y4P1	ATG4B_HUMAN	APG4 autophagy 4 homolog B isoform a						autophagic vacuole assembly|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		GATTTTTGCGTTTTTTTTTTC	0.507													4	2	---	---	---	---	
RAD18	56852	broad.mit.edu	37	3	8955647	8955648	+	Intron	INS	-	AGTCA	AGTCA	rs144181000	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8955647_8955648insAGTCA	uc003brd.2	-						RAD18_uc003bre.2_Intron	NM_020165	NP_064550	Q9NS91	RAD18_HUMAN	postreplication repair protein hRAD18p						DNA repair	nucleus|replication fork	damaged DNA binding|ligase activity|ubiquitin protein ligase binding|Y-form DNA binding|zinc ion binding			skin(3)|ovary(2)	5				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		ATAACCACAAGAGTCAAGTCAT	0.272								Rad6_pathway					3	3	---	---	---	---	
MTMR14	64419	broad.mit.edu	37	3	9729243	9729243	+	Intron	DEL	A	-	-	rs34956746		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9729243delA	uc003brz.2	+						MTMR14_uc003bsa.2_Intron|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993	Q8NCE2	MTMRE_HUMAN	jumpy isoform 2							perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)					tgtctcaaataaaaaaaaaaa	0.269													5	3	---	---	---	---	
FGD5	152273	broad.mit.edu	37	3	14883608	14883608	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14883608delC	uc003bzc.2	+						FGD5_uc011avk.1_Intron	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5						GCCAAGTTGTCCTCAAACCAA	0.532													4	2	---	---	---	---	
DAZL	1618	broad.mit.edu	37	3	16630443	16630443	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16630443delA	uc003cbb.2	-						DAZL_uc003cba.2_Intron	NM_001351	NP_001342	Q92904	DAZL_HUMAN	deleted in azoospermia-like						germ cell development|multicellular organismal development|positive regulation of translational initiation|spermatogenesis	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding|translation activator activity				0						GAAATCAATTAAAAAAAAAGA	0.269													6	3	---	---	---	---	
RARB	5915	broad.mit.edu	37	3	25263645	25263645	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25263645delA	uc011awl.1	+							NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)	ataaggtgttactccggaggc	0.040													4	2	---	---	---	---	
ARPP21	10777	broad.mit.edu	37	3	35826124	35826124	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35826124delT	uc003cgb.2	+						ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cgf.2_Intron|ARPP21_uc003cgg.2_Intron	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD							cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3						GTCTTTGCCCTAGAAAACTAC	0.418													4	2	---	---	---	---	
LTF	4057	broad.mit.edu	37	3	46482667	46482668	+	Intron	INS	-	GT	GT			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46482667_46482668insGT	uc003cpq.2	-						LTF_uc003fzr.2_Intron|LTF_uc010hjh.2_Intron|LTF_uc003cpr.2_Intron	NM_002343	NP_002334	P02788	TRFL_HUMAN	lactotransferrin precursor						cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)	tgtgagagtgagtgtgtgtgtg	0.351													5	6	---	---	---	---	
ARIH2	10425	broad.mit.edu	37	3	48964875	48964875	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48964875delT	uc003cvb.2	+						ARIH2_uc003cvc.2_Intron|ARIH2_uc003cvf.2_5'UTR|ARIH2_uc010hkl.2_5'Flank|ARIH2_uc003cvd.1_Intron|ARIH2_uc003cve.1_Intron	NM_006321	NP_006312	O95376	ARI2_HUMAN	ariadne homolog 2						developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		GTAACACTTATTTTTTTTTTC	0.408													4	2	---	---	---	---	
SYNPR	132204	broad.mit.edu	37	3	63396412	63396412	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63396412delC	uc003dlp.2	+						SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron	NM_001130003	NP_001123475	Q8TBG9	SYNPR_HUMAN	synaptoporin isoform 1							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		atcaggttcacccccactaga	0.000													4	2	---	---	---	---	
FOXP1	27086	broad.mit.edu	37	3	71159905	71159906	+	Intron	INS	-	AAT	AAT			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71159905_71159906insAAT	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doj.2_Intron|FOXP1_uc003dok.2_Intron	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GAATCCTGACAAATAAGCTCAC	0.431			T	PAX5	ALL								4	2	---	---	---	---	
CNTN3	5067	broad.mit.edu	37	3	74418792	74418792	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74418792delA	uc003dpm.1	-							NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor						cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		AATGAACAAGAAAAAAAAAAA	0.274													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	76270197	76270197	+	IGR	DEL	T	-	-	rs78039105		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76270197delT								ZNF717 (435527 upstream) : ROBO2 (819097 downstream)																							atgaaggatctcctgtgttgt	0.000													3	3	---	---	---	---	
GTPBP8	29083	broad.mit.edu	37	3	112713742	112713742	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112713742delA	uc003dzn.2	+						GTPBP8_uc011bhy.1_Intron|GTPBP8_uc003dzp.2_Intron|GTPBP8_uc003dzo.2_Intron	NM_014170	NP_054889	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 isoform 1						barrier septum formation		GTP binding				0						TATGGAATCTAAAGTTCTTCT	0.323													1	6	---	---	---	---	
NDUFB4	4710	broad.mit.edu	37	3	120313814	120313815	+	5'Flank	DEL	GA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120313814_120313815delGA	uc003edu.2	+						NDUFB4_uc003edt.2_5'Flank	NM_004547	NP_004538	O95168	NDUB4_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|response to oxidative stress|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0				GBM - Glioblastoma multiforme(114;0.14)	NADH(DB00157)	CTCTCAGCCTGAATCCTCATGA	0.356													4	2	---	---	---	---	
PARP15	165631	broad.mit.edu	37	3	122296898	122296899	+	Intron	DEL	GT	-	-	rs80353133		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122296898_122296899delGT	uc003efm.2	+						PARP15_uc003efn.2_Intron	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5				GBM - Glioblastoma multiforme(114;0.0531)		atttctggtggttttttttttt	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	122391958	122391958	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122391958delA								PARP15 (36422 upstream) : PARP14 (7714 downstream)																							ttcccctagcaaggaaaaaaa	0.060													4	2	---	---	---	---	
ATP2C1	27032	broad.mit.edu	37	3	130677774	130677774	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130677774delT	uc003enl.2	+						ATP2C1_uc011blg.1_Intron|ATP2C1_uc011blh.1_Intron|ATP2C1_uc011bli.1_Intron|ATP2C1_uc003enk.2_Intron|ATP2C1_uc003enm.2_Intron|ATP2C1_uc003enn.2_Intron|ATP2C1_uc003eno.2_Intron|ATP2C1_uc003enp.2_Intron|ATP2C1_uc003enq.2_Intron|ATP2C1_uc003enr.2_Intron|ATP2C1_uc003ens.2_Intron|ATP2C1_uc003ent.2_Intron	NM_014382	NP_055197	P98194	AT2C1_HUMAN	calcium-transporting ATPase 2C1 isoform 1a						actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity			skin(1)	1					Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)	TGCCACCTTCTTTTTTTCATT	0.284									Hailey-Hailey_disease				4	2	---	---	---	---	
KCNAB1	7881	broad.mit.edu	37	3	155931499	155931499	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155931499delA	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CATATGTAATAAGCAGTATCC	0.313													4	2	---	---	---	---	
PRKCI	5584	broad.mit.edu	37	3	169940502	169940503	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169940502_169940503delAG	uc003fgs.2	+	1	283_284	c.45_46delAG	c.(43-48)GCAGGCfs	p.A15fs		NM_002740	NP_002731	P41743	KPCI_HUMAN	protein kinase C, iota	15_16	Regulatory domain.|Required for interaction with RAB2.				anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			ACACGGTCGCAGGCGGCGGCAG	0.728													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	176511419	176511419	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176511419delC								NAALADL2 (987993 upstream) : TBL1XR1 (227124 downstream)																							AAAAATGATACCCAGCGTGGT	0.453													4	2	---	---	---	---	
SDHAP1	255812	broad.mit.edu	37	3	195711343	195711344	+	Intron	INS	-	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195711343_195711344insT	uc011btq.1	-						SDHAP1_uc003fvx.3_Intron|SDHAP1_uc011btp.1_Intron					SubName: Full=cDNA FLJ56858, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						AAAGACTTCTCTGTGAGCTTTG	0.381													6	3	---	---	---	---	
ZDHHC19	131540	broad.mit.edu	37	3	195937292	195937293	+	Intron	INS	-	GAAA	GAAA	rs149833656	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195937292_195937293insGAAA	uc003fwc.2	-						ZDHHC19_uc010hzz.2_Intron|ZDHHC19_uc010iaa.2_Intron|ZDHHC19_uc010iab.2_Intron	NM_001039617	NP_001034706	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC domain containing 19							integral to membrane	acyltransferase activity|zinc ion binding			ovary(3)	3	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		gaggaaggaaggaaagaaagaa	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	29172	29172	+	IGR	DEL	A	-	-	rs145707628		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29172delA								None (None upstream) : ZNF595 (24055 downstream)																							TTTGAAAAAGAAAAAAAAAAG	0.348													5	3	---	---	---	---	
CPLX1	10815	broad.mit.edu	37	4	807651	807652	+	Intron	DEL	CA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:807651_807652delCA	uc003gbi.2	-						CPLX1_uc003gbj.2_Intron	NM_006651	NP_006642	O14810	CPLX1_HUMAN	complexin 1						glutamate secretion	cytosol					0				Colorectal(103;0.187)		ccagaattcccacacacacaca	0.114													4	2	---	---	---	---	
NOP14	8602	broad.mit.edu	37	4	2952604	2952605	+	Intron	DEL	AG	-	-	rs10576953		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2952604_2952605delAG	uc003ggj.1	-						C4orf10_uc003ggh.2_RNA|C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_Intron|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1						CCTTTgagacagagagagagag	0.243													7	4	---	---	---	---	
LDB2	9079	broad.mit.edu	37	4	16746997	16746997	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16746997delA	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0						TAGAACAGTGAAAAGGAAGTC	0.448													4	2	---	---	---	---	
FAM184B	27146	broad.mit.edu	37	4	17765196	17765197	+	Intron	INS	-	GAAAA	GAAAA	rs146811691	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17765196_17765197insGAAAA	uc003gpm.3	-							NM_015688	NP_056503	Q9ULE4	F184B_HUMAN	hypothetical protein LOC27146											central_nervous_system(1)	1						TTTGGCAGCGTGAAGAGGCTTT	0.401													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18123469	18123470	+	IGR	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18123469_18123470insA								LCORL (100084 upstream) : None (None downstream)																							ttgtgagctaggaaaggggtag	0.000													4	2	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21667539	21667539	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21667539delA	uc003gqh.1	-						KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				TGTCATTTTCAATTATTGTGA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	23245017	23245017	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23245017delA								GBA3 (423826 upstream) : PPARGC1A (548628 downstream)																							TTTCAAGGAGAAAAGTTGCTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	23249696	23249696	+	IGR	DEL	A	-	-	rs34627086		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23249696delA								GBA3 (428505 upstream) : PPARGC1A (543949 downstream)																							CTATTCACATAACCACCTATT	0.353													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	33171811	33171811	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33171811delA								None (None upstream) : None (None downstream)																							atgttgagtgaaaaaaaaatc	0.000													4	2	---	---	---	---	
RBM47	54502	broad.mit.edu	37	4	40528075	40528075	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40528075delT	uc003gvc.2	-						RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3						AGCATGGACCTTAGATGACGA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	43813090	43813090	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43813090delT								GRXCR1 (780417 upstream) : KCTD8 (362832 downstream)																							CTTAAAGGCCTTTTTCAACAA	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	52842353	52842353	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52842353delA								DCUN1D4 (59352 upstream) : LRRC66 (17514 downstream)																							acagaaatagaaaaaaaattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69574859	69574859	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69574859delA								UGT2B15 (38485 upstream) : UGT2B10 (106854 downstream)																							aaaaatgtgcaaaaaaaaaga	0.154													4	2	---	---	---	---	
UGT2B4	7363	broad.mit.edu	37	4	70361792	70361792	+	5'Flank	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70361792delT	uc003hek.3	-						UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_5'Flank	NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						TCTTTTTGGATTTTTTTTTTT	0.174													4	2	---	---	---	---	
CSN1S1	1446	broad.mit.edu	37	4	70799577	70799577	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70799577delG	uc003hep.1	+						CSN1S1_uc003heq.1_Intron|CSN1S1_uc003her.1_Intron	NM_001890	NP_001881	P47710	CASA1_HUMAN	casein alpha s1 isoform 1							extracellular region	protein binding|transporter activity				0						TTAGAACTATGGTGTAATATA	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	84955075	84955075	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84955075delA	uc010ikd.1	-						uc003hoz.1_Intron					Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																		tttgactatgaagggccttgt	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	109722836	109722836	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109722836delG								AGXT2L1 (38601 upstream) : COL25A1 (9042 downstream)																							aagagtgactggggatgatga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	123469827	123469827	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123469827delT								IL2 (92177 upstream) : IL21 (63956 downstream)																							tgtgaccttatttggaaatac	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	124384028	124384029	+	IGR	INS	-	A	A	rs72526568		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124384028_124384029insA								SPRY1 (59121 upstream) : LOC285419 (187393 downstream)																							AATAACTGTATCATGCACGCTT	0.322													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	128135621	128135621	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128135621delA								None (None upstream) : INTU (418499 downstream)																							AGGGTTAGGGAAAAAAGGAGG	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	130531662	130531663	+	IGR	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130531662_130531663delAC								C4orf33 (497820 upstream) : None (None downstream)																							acaaacacatacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	141422591	141422591	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141422591delT								CLGN (73776 upstream) : ELMOD2 (22761 downstream)																							AATAGAGTTGTTTTTTTTTCT	0.398													4	2	---	---	---	---	
INPP4B	8821	broad.mit.edu	37	4	143028946	143028947	+	Intron	DEL	CA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143028946_143028947delCA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					AAATTTTTATCAGACTAATTAA	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153950953	153950954	+	IGR	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153950953_153950954delAC								FHDC1 (50105 upstream) : TRIM2 (123316 downstream)																							cacacaccatacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	154336267	154336267	+	IGR	DEL	T	-	-	rs113897268		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154336267delT								MND1 (24 upstream) : KIAA0922 (51231 downstream)																							TTACAAATGATTTTTTTTTTA	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	166419901	166419902	+	IGR	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166419901_166419902delGT								CPE (420 upstream) : TLL1 (374508 downstream)																							GAGTGCAGGGGTGTGTGTGTGT	0.396													5	3	---	---	---	---	
WWC2	80014	broad.mit.edu	37	4	184067948	184067948	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184067948delA	uc010irx.2	+							NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TGAGTTGGTGAAGCCAAAAGT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190566242	190566243	+	IGR	INS	-	T	T	rs11393860		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190566242_190566243insT								None (None upstream) : FRG1 (295731 downstream)																							TAAGGAGACGCTGCTGATTAGA	0.475													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190620783	190620784	+	IGR	DEL	AA	-	-	rs34980259		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190620783_190620784delAA								None (None upstream) : FRG1 (241190 downstream)																							TGGCTACTCCAAAAGAGTAGGA	0.411													3	3	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7664377	7664377	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7664377delT	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2						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	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7						AAACATGTGATTTTTTTTTCT	0.308													4	2	---	---	---	---	
MTRR	4552	broad.mit.edu	37	5	7871264	7871266	+	Intron	DEL	CTT	-	-	rs139287124		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7871264_7871266delCTT	uc003jed.2	+						FASTKD3_uc011cmp.1_5'Flank|FASTKD3_uc003jeb.2_5'Flank|FASTKD3_uc003jec.2_5'Flank|MTRR_uc010itn.1_Intron|MTRR_uc003jee.3_Intron|MTRR_uc003jef.3_Intron|MTRR_uc003jeg.3_Intron|MTRR_uc010ito.2_Intron	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2						methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GTAACAACtccttaactgtaaat	0.227													4	6	---	---	---	---	
DAP	1611	broad.mit.edu	37	5	10708555	10708556	+	Intron	DEL	AC	-	-	rs34710292		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10708555_10708556delAC	uc003jez.3	-						DAP_uc011cmw.1_Intron	NM_004394	NP_004385	P51397	DAP1_HUMAN	death-associated protein						activation of caspase activity|cellular response to amino acid starvation|induction of apoptosis by extracellular signals|negative regulation of autophagy|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent		death domain binding				0		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)				cacatatcagacacacacacac	0.158													4	2	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21534245	21534246	+	Intron	INS	-	TG	TG	rs143137704		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21534245_21534246insTG	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						GCAGGTGTGTCTGTCACAAACA	0.520													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	24802685	24802685	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24802685delC								CDH10 (157774 upstream) : None (None downstream)																							tacaatagggccacccagatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	29520271	29520272	+	IGR	INS	-	AC	AC	rs148809826	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29520271_29520272insAC								None (None upstream) : None (None downstream)																							ACCACATACATACACACACACA	0.386													3	3	---	---	---	---	
SLC45A2	51151	broad.mit.edu	37	5	33947702	33947702	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33947702delT	uc003jid.2	-						SLC45A2_uc003jie.2_Intron	NM_016180	NP_057264	Q9UMX9	S45A2_HUMAN	membrane-associated transporter protein isoform						melanin biosynthetic process|response to stimulus|transmembrane transport|visual perception	integral to membrane|melanosome membrane				ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						GGTAGGCTGATTTTTTTTCTA	0.408													4	2	---	---	---	---	
RANBP3L	202151	broad.mit.edu	37	5	36274097	36274097	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36274097delA	uc003jkh.2	-						RANBP3L_uc011cow.1_Intron	NM_145000	NP_659437	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like isoform 2						intracellular transport					ovary(1)	1	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			caaatagaggaaaagccagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56858124	56858124	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56858124delT								ACTBL2 (79488 upstream) : PLK2 (891688 downstream)																							ctccatcctatttacctactc	0.000													4	2	---	---	---	---	
MAST4	375449	broad.mit.edu	37	5	66135417	66135417	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66135417delT	uc003jut.1	+						MAST4_uc003jur.3_Intron|MAST4_uc010iwz.2_Intron|MAST4_uc003jus.2_Intron	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GATGTGTAGGTTTTTTTTTTC	0.358													2	4	---	---	---	---	
SV2C	22987	broad.mit.edu	37	5	75577223	75577223	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75577223delA	uc003kei.1	+							NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		TATGCAAAGTAAAAAAAAAAA	0.313													6	3	---	---	---	---	
IQGAP2	10788	broad.mit.edu	37	5	75843725	75843725	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75843725delA	uc003kek.2	+							NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ATCCCACAGTAGTCTCCACCT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	88860083	88860083	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88860083delA								MEF2C (660214 upstream) : CETN3 (829448 downstream)																							TTATTGGAGGAAAAAAAAAAC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	89476501	89476501	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89476501delG								None (None upstream) : CETN3 (213030 downstream)																							AAGGAAGGGTGGGGCCAGGCC	0.507													4	2	---	---	---	---	
TTC37	9652	broad.mit.edu	37	5	94849082	94849082	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94849082delT	uc003klb.2	-							NM_014639	NP_055454	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4						taatttttaattttttttttt	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	106179887	106179891	+	IGR	DEL	GGGAG	-	-	rs67860371		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106179887_106179891delGGGAG								None (None upstream) : EFNA5 (532700 downstream)																							ctggagcagtgggaggcccagcagg	0.127													3	3	---	---	---	---	
DCP2	167227	broad.mit.edu	37	5	112313233	112313233	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112313233delT	uc003kqh.2	+						DCP2_uc011cwa.1_Intron|DCP2_uc003kqg.2_Intron	NM_152624	NP_689837	Q8IU60	DCP2_HUMAN	DCP2 decapping enzyme						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus|RNA-induced silencing complex	exoribonuclease activity, producing 5'-phosphomonoesters|manganese ion binding|protein binding|protein binding|RNA binding				0		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		AAGGAATTACTTTTTTTTTCT	0.418													4	2	---	---	---	---	
CSNK1G3	1456	broad.mit.edu	37	5	122879155	122879155	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122879155delC	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Intron|CSNK1G3_uc003ktn.2_Intron|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_5'Flank	NM_004384	NP_004375	Q9Y6M4	KC1G3_HUMAN	casein kinase 1, gamma 3 isoform 1						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)		ttagactattcccttgtacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	124474844	124474844	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124474844delC								ZNF608 (390344 upstream) : None (None downstream)																							CCTATTATAACCCCACCCCAC	0.254													4	2	---	---	---	---	
DDX46	9879	broad.mit.edu	37	5	134153642	134153642	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134153642delT	uc003kzw.2	+							NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTGtttgttgttttttttttt	0.129													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134493434	134493434	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134493434delA	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		TGACTCTGCTAACAAAGACTT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134864551	134864552	+	IGR	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134864551_134864552insA								TIFAB (76462 upstream) : NEUROG1 (5428 downstream)																							acatattttctaaaaaaaagtc	0.188													4	2	---	---	---	---	
SPOCK1	6695	broad.mit.edu	37	5	136408962	136408963	+	Intron	DEL	AG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136408962_136408963delAG	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			gaattaagcaagagagagaaag	0.000													4	2	---	---	---	---	
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139923227	139923227	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139923227delT	uc003lfs.1	+						ANKHD1-EIF4EBP3_uc011czh.1_Intron|ANKHD1-EIF4EBP3_uc003lfx.1_Intron	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ggcataggtattttttTTAAA	0.149													4	2	---	---	---	---	
FCHSD1	89848	broad.mit.edu	37	5	141032412	141032412	+	5'Flank	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141032412delC	uc003llk.2	-						FCHSD1_uc003llj.2_5'Flank	NM_033449	NP_258260	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1										FCHSD1/BRAF(2)	skin(2)|ovary(1)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			cagatgccttccccatccacc	0.000													4	2	---	---	---	---	
KCTD16	57528	broad.mit.edu	37	5	143644087	143644087	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143644087delG	uc003lnm.1	+						KCTD16_uc003lnn.1_Intron	NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			acactttggagggccaaggta	0.154													4	2	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156795896	156795899	+	Intron	DEL	TTTT	-	-	rs74720983		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156795896_156795899delTTTT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATCCCAGAGGttttttgttttttt	0.289													5	3	---	---	---	---	
ADAM19	8728	broad.mit.edu	37	5	156922002	156922002	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156922002delT	uc003lwz.2	-						ADAM19_uc003lww.1_Intron|ADAM19_uc003lwy.2_Intron|ADAM19_uc011ddr.1_Intron	NM_033274	NP_150377	Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19 preproprotein						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATATAAATCCttttttttttc	0.209													6	4	---	---	---	---	
EBF1	1879	broad.mit.edu	37	5	158332100	158332100	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158332100delT	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ATTCAGCACATTTTGCTAGCA	0.393			T	HMGA2	lipoma								4	2	---	---	---	---	
GABRB2	2561	broad.mit.edu	37	5	160799778	160799778	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160799778delT	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	tgtaattcccttttttacaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	163472944	163472944	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163472944delT								MAT2B (526611 upstream) : None (None downstream)																							TCTAATGACCTTCATTTCCAT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	168933318	168933320	+	IGR	DEL	TTG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168933318_168933320delTTG								SLIT3 (205185 upstream) : CCDC99 (77318 downstream)																							TCTGAGATTTttgttgttgttgt	0.182													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173710824	173710824	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173710824delA								HMP19 (174643 upstream) : MSX2 (440751 downstream)																							GAAGCAGAATAAAAGAGCCCT	0.443													4	2	---	---	---	---	
CDHR2	54825	broad.mit.edu	37	5	176019086	176019097	+	Intron	DEL	TGGTGGTGGTGA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176019086_176019097delTGGTGGTGGTGA	uc003mem.1	+						CDHR2_uc003men.1_Intron	NM_017675	NP_060145	Q9BYE9	CDHR2_HUMAN	protocadherin LKC precursor						homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2						gttatcgtggtggtggtggtgatggtggtggt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	3569810	3569811	+	IGR	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3569810_3569811delAC								SLC22A23 (113017 upstream) : C6orf145 (153025 downstream)																							TCATTTATCTACACACACACAC	0.223													6	3	---	---	---	---	
LYRM4	57128	broad.mit.edu	37	6	5248751	5248751	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5248751delC	uc003mwp.2	-						LYRM4_uc010jnu.2_Intron|LYRM4_uc003mwq.2_Intron	NM_020408	NP_065141	Q9HD34	LYRM4_HUMAN	LYR motif containing 4 isoform 1							mitochondrion|nucleus					0	Ovarian(93;0.11)	all_hematologic(90;0.0901)				CCTGTCTCCACCCTCATCTCC	0.433													4	2	---	---	---	---	
TXNDC5	81567	broad.mit.edu	37	6	7906907	7906907	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7906907delA	uc003mxv.2	-						TXNDC5_uc003mxw.2_Intron|TXNDC5_uc010jnz.2_Intron|TXNDC5_uc010joa.1_Intron	NM_030810	NP_110437	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 isoform 1						anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)					ACTCAGATACAAAAAAAAAAG	0.249													3	3	---	---	---	---	
ELOVL2	54898	broad.mit.edu	37	6	11005392	11005392	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11005392delA	uc003mzp.3	-							NM_017770	NP_060240	Q9NXB9	ELOV2_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)			actccatctcaaaaaaaaaaa	0.129													6	3	---	---	---	---	
PHACTR1	221692	broad.mit.edu	37	6	12839015	12839015	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12839015delC	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron|PHACTR1_uc003nai.2_Intron	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			TTAAAAATAACCCCAACCCCC	0.413													4	2	---	---	---	---	
PHACTR1	221692	broad.mit.edu	37	6	12929333	12929333	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12929333delC	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron|PHACTR1_uc003nai.2_Intron	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)			TACCTCCAATCcccctcacct	0.169													4	2	---	---	---	---	
CAP2	10486	broad.mit.edu	37	6	17412099	17412099	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17412099delA	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357	P40123	CAP2_HUMAN	adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			AAACAAGCGCAAAGGGGCAAC	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	23591863	23591863	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23591863delG								None (None upstream) : NRSN1 (534551 downstream)																							AGCCTGAGGAGGTCATCCAGT	0.368													4	2	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29949180	29949181	+	Intron	INS	-	GC	GC			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29949180_29949181insGC	uc011dmb.1	+							NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						TGCAtgtgtgtgtgtgtgtgcc	0.243													4	2	---	---	---	---	
TMEM217	221468	broad.mit.edu	37	6	37182527	37182527	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37182527delA	uc003onl.2	-						TMEM217_uc010jwr.2_Intron|TMEM217_uc010jws.2_Intron	NM_145316	NP_660359	Q8N7C4	TM217_HUMAN	transmembrane protein 217 isoform 1							integral to membrane					0						aaatattcttATACTTTATTC	0.269													4	2	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38775791	38775791	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38775791delT	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						ttcttcacagtttactatgct	0.000													4	2	---	---	---	---	
RUNX2	860	broad.mit.edu	37	6	45338127	45338127	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45338127delA	uc011dvx.1	+						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc003oxo.2_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron|RUNX2_uc011dvy.1_Intron	NM_001024630	NP_001019801	Q13950	RUNX2_HUMAN	runt-related transcription factor 2 isoform a						negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3						actgggaaggaaaaaaaaaac	0.035													4	3	---	---	---	---	
C6orf138	442213	broad.mit.edu	37	6	48081333	48081333	+	5'Flank	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48081333delC	uc011dwn.1	-							NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213							integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1						TTTTGCCTGTCCCCTTTGTGG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	53802797	53802797	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53802797delT	uc003pce.2	+											Homo sapiens cDNA FLJ32022 fis, clone NTONG1000161.																		AGAAAAACTGTTTTTTTTTTC	0.383													4	2	---	---	---	---	
DST	667	broad.mit.edu	37	6	56500154	56500155	+	Intron	DEL	CA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56500154_56500155delCA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc003pcy.3_Intron|DST_uc003pdb.2_Intron|DST_uc003pdc.3_Intron|DST_uc003pdd.3_Intron	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CACACACGTGCACACACACACA	0.193													2	4	---	---	---	---	
BEND6	221336	broad.mit.edu	37	6	56840996	56840996	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56840996delT	uc010kab.2	+						BEND6_uc003pdg.2_Intron	NM_152731	NP_689944	Q5SZJ8	BEND6_HUMAN	BEN domain containing 6												0						gtgttagtgcttttttttttt	0.060													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57267631	57267631	+	Intron	DEL	A	-	-	rs11352298		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57267631delA	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		tgggggttttaaaaaggagaa	0.239													1	5	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57388617	57388617	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57388617delG	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTAACAATCAGTGCCACAGCA	0.378													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57432144	57432145	+	Intron	INS	-	T	T	rs11435895		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57432144_57432145insT	uc003pdx.2	+							NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		gtatgcacctctaaaaaaaata	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	57557438	57557439	+	IGR	INS	-	C	C	rs140134047		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57557438_57557439insC								PRIM2 (44063 upstream) : GUSBL2 (688720 downstream)																							GGTATgctccacccccaggtaa	0.025													4	2	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69974679	69974680	+	Intron	DEL	AA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69974679_69974680delAA	uc003pev.3	+						BAI3_uc010kak.2_Intron|BAI3_uc011dxx.1_Intron|BAI3_uc003pex.1_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				AGTTACTGAGAAAAAAAAAGTG	0.297													4	2	---	---	---	---	
FILIP1	27145	broad.mit.edu	37	6	76009841	76009841	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76009841delA	uc003phy.1	-							NM_015687	NP_056502	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1											skin(3)|ovary(1)	4						CTCTACATTTAAAAAAAAAAC	0.353													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	78943977	78943978	+	IGR	INS	-	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78943977_78943978insT								HTR1B (770857 upstream) : IRAK1BP1 (633211 downstream)																							TCATATTCTCATTTTTTTTCTC	0.441													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82695174	82695175	+	IGR	INS	-	T	T	rs143546051	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82695174_82695175insT								FAM46A (232746 upstream) : IBTK (184781 downstream)																							TGAGTTCAATCTTTTTTTACTT	0.257													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82746220	82746220	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82746220delA								FAM46A (283792 upstream) : IBTK (133736 downstream)																							AATGCACTAGAAAAAAAAAAG	0.313													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	86579331	86579331	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86579331delA								SNHG5 (190880 upstream) : None (None downstream)																							CCCAAAGCACAAAAAAACCTG	0.294													5	3	---	---	---	---	
GPR63	81491	broad.mit.edu	37	6	97246106	97246106	+	3'UTR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97246106delA	uc010kcl.2	-	3					GPR63_uc003pou.2_3'UTR	NM_001143957	NP_001137429	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63							integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		CCCCAAAACCAAAAAAAAGTC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	130788139	130788139	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130788139delT								TMEM200A (23931 upstream) : LOC285733 (360185 downstream)																							GTCCCTGCCCTTCTCTTCCCA	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139819262	139819262	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139819262delA								CITED2 (123477 upstream) : None (None downstream)																							CCAGCTTCTTAAAAAAAAATT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	156971560	156971560	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156971560delT								MIR1202 (703547 upstream) : ARID1B (127526 downstream)																							ctgtgcttcattcatgtcttg	0.000													4	2	---	---	---	---	
SYTL3	94120	broad.mit.edu	37	6	159146359	159146360	+	Intron	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159146359_159146360delGT	uc003qrp.2	+						SYTL3_uc011efp.1_Intron|SYTL3_uc003qro.2_Intron|SYTL3_uc003qrq.2_Intron|SYTL3_uc003qrr.2_Intron|SYTL3_uc003qrs.2_Intron|SYTL3_uc011efq.1_Intron	NM_001009991	NP_001009991	Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3						intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		gtgtgtgtgcgtgtgtgtgtgt	0.386													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	169494791	169494793	+	IGR	DEL	TGG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169494791_169494793delTGG								SMOC2 (426120 upstream) : THBS2 (121083 downstream)																							TCTTGAGACTTGGTAAGAGAATC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	2936688	2936690	+	IGR	DEL	TCC	-	-	rs143888830		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2936688_2936690delTCC								GNA12 (52729 upstream) : CARD11 (9079 downstream)																							TATTGTGTTTTCCTCCTCAGCGT	0.542													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	12187696	12187696	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12187696delG								THSD7A (315872 upstream) : TMEM106B (63152 downstream)																							tcagccctgtggccacaagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	15219814	15219814	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15219814delT								DGKB (277264 upstream) : TMEM195 (20129 downstream)																							tgaatgtgcatttttatgtca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	19359598	19359599	+	IGR	DEL	TG	-	-	rs34297340		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19359598_19359599delTG								FERD3L (174554 upstream) : TWISTNB (375486 downstream)																							ggcctgaaactgtattcagtga	0.000													3	5	---	---	---	---	
JAZF1	221895	broad.mit.edu	37	7	28106719	28106719	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28106719delA	uc003szn.2	-							NM_175061	NP_778231	Q86VZ6	JAZF1_HUMAN	JAZF zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcriptional repressor complex	nucleic acid binding|transcription corepressor activity|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131						CCACCTGGACAAAAACTCTAG	0.453			T	SUZ12	endometrial stromal tumours								4	2	---	---	---	---	
ADCY1	107	broad.mit.edu	37	7	45625738	45625738	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45625738delT	uc003tne.3	+						ADCY1_uc003tnd.2_Intron	NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1						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 membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TGCTTTTTCCTTTCTCCCTCC	0.567													4	2	---	---	---	---	
SEPT7P2	641977	broad.mit.edu	37	7	45786551	45786551	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45786551delA	uc003tnh.2	-						SEPT7P2_uc003tnf.3_Intron	NR_024271				Homo sapiens mRNA; cDNA DKFZp313J1114 (from clone DKFZp313J1114).												0						actccatctcaaaaaaaaaaa	0.095													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	49080366	49080366	+	IGR	DEL	A	-	-	rs74729587		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49080366delA								CDC14C (113317 upstream) : VWC2 (732891 downstream)																							aactagagagaaaaaaaaaac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	55680456	55680456	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55680456delA								VOPP1 (40256 upstream) : LOC442308 (32856 downstream)																							GATTTCAGTGAATGGAGCAGT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61970608	61970609	+	IGR	INS	-	A	A	rs144105721		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61970608_61970609insA								None (None upstream) : LOC643955 (781063 downstream)																							tcacatagtttacctttctttt	0.000													2	9	---	---	---	---	
PMS2L3	5387	broad.mit.edu	37	7	75142142	75142142	+	Intron	DEL	A	-	-	rs71519365		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75142142delA	uc003udp.2	-						PMS2L3_uc003udn.2_Intron|PMS2L3_uc003udq.2_Intron	NM_005395	NP_005386			SubName: Full=Postmeiotic segregation increased 2-like 3; SubName: Full=Postmeiotic segregation increased 2-like 3, isoform CRA_b;												0						tctcaaaaagaaaaaaaaaaa	0.129								Direct_reversal_of_damage|MMR					7	5	---	---	---	---	
SRRM3	222183	broad.mit.edu	37	7	75842905	75842905	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75842905delA	uc010ldi.2	+							NM_001110199	NP_001103669			serine/arginine repetitive matrix 3												0						ttgtcagtgcaagcatggggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	77076959	77076959	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77076959delT								PION (31242 upstream) : PTPN12 (89814 downstream)																							TGATTTTTTCTTTTTTTTCCC	0.323													4	2	---	---	---	---	
ZKSCAN1	7586	broad.mit.edu	37	7	99621024	99621024	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99621024delT	uc003usk.1	+						ZKSCAN1_uc003usj.2_Intron|ZKSCAN1_uc003usl.1_Intron|ZKSCAN1_uc003usm.1_Intron	NM_003439	NP_003430	P17029	ZKSC1_HUMAN	zinc finger protein 36						viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			TACTAATGACTTTTTTTTTAT	0.393													6	4	---	---	---	---	
GPC2	221914	broad.mit.edu	37	7	99771305	99771306	+	Intron	INS	-	TCTT	TCTT	rs143309299	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99771305_99771306insTCTT	uc003utv.2	-						GPC2_uc010lgr.2_Intron|GPC2_uc003utw.1_3'UTR	NM_152742	NP_689955	Q8N158	GPC2_HUMAN	glypican 2 precursor							anchored to membrane|endoplasmic reticulum|extracellular space|plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)|pancreas(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ttctctctctctctttctttct	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	101964630	101964632	+	IGR	DEL	GGG	-	-	rs75603731		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101964630_101964632delGGG								SH2B2 (2453 upstream) : SPDYE6 (21561 downstream)																							CAGACTCAGTGGGGGCTCTGGCG	0.532													3	4	---	---	---	---	
PRKAR2B	5577	broad.mit.edu	37	7	106791144	106791152	+	Intron	DEL	AAAAAAAAA	-	-	rs72203061		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106791144_106791152delAAAAAAAAA	uc003vdx.2	+							NM_002736	NP_002727	P31323	KAP3_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|G2/M transition of mitotic cell cycle|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	centrosome|cytosol|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1						TGCTTTCTTTaaaaaaaaaaaaaaaaaaa	0.273													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	114378629	114378629	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114378629delA								FOXP2 (47537 upstream) : MDFIC (183580 downstream)																							CTGTGGACTTAAAAAAAAAAT	0.343													8	4	---	---	---	---	
CAV1	857	broad.mit.edu	37	7	116106101	116106101	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116106101delA	uc010lkd.1	+						CAV2_uc003vhv.2_Intron|CAV2_uc003vhw.2_Intron|CAV2_uc003vhx.2_Intron|CAV2_uc010lkb.1_Intron|CAV2_uc010lkc.2_Intron|CAV2_uc003vib.2_Intron|CAV2_uc003vhz.2_Intron|CAV2_uc003via.2_Intron|CAV1_uc010lke.1_Intron	NM_001753	NP_001744	Q03135	CAV1_HUMAN	caveolin 1						blood coagulation|calcium ion transport|caveola assembly|cellular response to starvation|cholesterol homeostasis|cytosolic calcium ion homeostasis|inactivation of MAPK activity|interspecies interaction between organisms|leukocyte migration|lipid storage|maintenance of protein location in cell|mammary gland involution|membrane depolarization|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of endothelial cell proliferation|negative regulation of epithelial cell differentiation|negative regulation of nitric oxide biosynthetic process|negative regulation of peptidyl-serine phosphorylation|negative regulation of protein binding|negative regulation of transcription from RNA polymerase II promoter|nitric oxide homeostasis|nitric oxide metabolic process|positive regulation of calcium ion transport into cytosol|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of metalloenzyme activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of vasoconstriction|protein homooligomerization|receptor internalization|regulation of blood coagulation|regulation of fatty acid metabolic process|regulation of nitric-oxide synthase activity|regulation of smooth muscle contraction|response to calcium ion|response to estrogen stimulus|response to hypoxia|response to progesterone stimulus|skeletal muscle tissue development|T cell costimulation|triglyceride metabolic process|vasculogenesis|vesicle organization	apical plasma membrane|basolateral plasma membrane|caveola|caveola|cytosol|endoplasmic reticulum|endosome|Golgi membrane|lipid particle|perinuclear region of cytoplasm	cholesterol binding|nitric-oxide synthase binding|peptidase activator activity|protein binding|protein complex scaffold|receptor binding				0	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			CAAATGCCTTAAAAAAGTAGA	0.368													4	2	---	---	---	---	
KCND2	3751	broad.mit.edu	37	7	119987096	119987096	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119987096delT	uc003vjj.1	+							NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)					CTCATGGCTCTTTTTTTTTTG	0.244													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	120558233	120558233	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120558233delT								TSPAN12 (60056 upstream) : ING3 (32584 downstream)																							CTACAAGAGATTTTTTTATTA	0.264													4	2	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127732380	127732381	+	3'UTR	DEL	TA	-	-	rs76223436		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127732380_127732381delTA	uc003vmi.2	+	24					SND1_uc010lle.2_3'UTR	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						GGGCTTTTTTTAAAAAAAAAAA	0.490													4	2	---	---	---	---	
SND1	27044	broad.mit.edu	37	7	127732381	127732381	+	3'UTR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127732381delA	uc003vmi.2	+	24					SND1_uc010lle.2_3'UTR	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						GGCTTTTTTTAAAAAAAAAAA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142019649	142019649	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142019649delT	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_5'Flank|uc011krq.1_5'Flank					SubName: Full=V_segment translation product; Flags: Fragment;																		aatacaaatctttttttttca	0.095													4	2	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147267255	147267256	+	Intron	INS	-	A	A	rs144961798	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147267255_147267256insA	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			attacacctgcaaaatctcttc	0.000										HNSCC(39;0.1)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	148609785	148609785	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148609785delT								EZH2 (28371 upstream) : MIR1975 (28795 downstream)																							TTGTGTGTTGTTTTTTTTTTA	0.279													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149431806	149431806	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149431806delG								KRBA1 (144 upstream) : ZNF467 (29467 downstream)																							AATTCCCACAGGACTCCTGGG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149856270	149856271	+	IGR	INS	-	A	A	rs142655888	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149856270_149856271insA								ATP6V0E2 (278484 upstream) : ACTR3C (88031 downstream)																							aacaaagctggaaaaaAATATC	0.248													1	5	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152085705	152085705	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152085705delC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		TTCAAGCACACCCTTTTTTGT	0.224			N		medulloblastoma								2	5	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3964271	3964271	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3964271delC	uc011kwk.1	-							NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		caacaacagaccccgcacagc	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	5926553	5926553	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5926553delA								None (None upstream) : MCPH1 (337568 downstream)																							TTTACCTCATAAAAAAAGATG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9755673	9755673	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9755673delT								TNKS (115818 upstream) : LOC157627 (1901 downstream)																							AGGAATTGAGTTTTTTTTGCA	0.498													4	2	---	---	---	---	
XKR6	286046	broad.mit.edu	37	8	10864597	10864597	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10864597delA	uc003wtk.1	-							NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		gagctgctacaaaaaaaagtc	0.015													4	2	---	---	---	---	
LONRF1	91694	broad.mit.edu	37	8	12603879	12603879	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12603879delC	uc003wwd.1	-							NM_152271	NP_689484	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|zinc ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(644;0.236)		acccacactgccccatgtaca	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	16496779	16496780	+	IGR	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16496779_16496780insA								MSR1 (446479 upstream) : FGF20 (353554 downstream)																							TCTATGTTAGGAAAATGTAGGT	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	18237736	18237736	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18237736delA								NAT1 (156539 upstream) : NAT2 (11019 downstream)																							CATCCCCAAGAAAGGGATTCt	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	20948027	20948027	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20948027delC								LZTS1 (835224 upstream) : GFRA2 (601503 downstream)																							TCGTCTCTTTCTTCATCCACA	0.333													4	2	---	---	---	---	
PPP3CC	5533	broad.mit.edu	37	8	22379653	22379654	+	Intron	DEL	CA	-	-	rs35520234		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22379653_22379654delCA	uc003xbs.2	+						PPP3CC_uc003xbr.1_Intron|PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron|PPP3CC_uc011kzj.1_5'Flank	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)		cacacacacgcacacacacaca	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	29635412	29635412	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29635412delA	uc003xho.2	+						uc003xhp.2_Intron					Homo sapiens, clone IMAGE:4861097, mRNA.																		CTTTGGGTAGAAAAAAAAAAA	0.368													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37143506	37143507	+	IGR	INS	-	A	A	rs111931929		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37143506_37143507insA								KCNU1 (349865 upstream) : ZNF703 (409794 downstream)																							tttctactcttaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ASH2L	9070	broad.mit.edu	37	8	37964937	37964937	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37964937delA	uc003xkt.3	+						ASH2L_uc011lbk.1_Intron|ASH2L_uc003xku.3_Intron|ASH2L_uc010lwa.2_Intron	NM_004674	NP_004665	Q9UBL3	ASH2L_HUMAN	ash2-like isoform a						hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				GTTTGGAGACAAAAAAAAATG	0.353													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	43725159	43725159	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43725159delG								POTEA (506831 upstream) : None (None downstream)																							tgaagtctatggggaaaaact	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	48026483	48026483	+	IGR	DEL	A	-	-	rs72315869		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48026483delA								BEYLA (259076 upstream) : KIAA0146 (147059 downstream)																							GACAATGAACAAAAAAAAAAA	0.274													2	4	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48343068	48343069	+	Intron	INS	-	T	T	rs148341592	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48343068_48343069insT	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				GCGCTGGACTCTGTCAGTTCAT	0.470													3	5	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48586205	48586205	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48586205delT	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_5'UTR|KIAA0146_uc010lxv.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				AGTGGATTTCTTTTTTTTTTC	0.343													15	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	58418500	58418500	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58418500delT								C8orf71 (221212 upstream) : FAM110B (488613 downstream)																							TTCTTGGAGCTTTTTACTTTT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	68783504	68783505	+	IGR	DEL	AG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68783504_68783505delAG								CPA6 (124884 upstream) : PREX2 (80843 downstream)																							GGCCTTAGGCAGAGAGAGAGAG	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72606333	72606334	+	IGR	INS	-	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72606333_72606334insT								EYA1 (331866 upstream) : MSC (147443 downstream)																							CTCCCATCTTCCATTATGATAG	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	72903716	72903716	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72903716delA	uc011lff.1	+						uc003xyy.2_Intron					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																		CTTGTCAGATAAAAAAAAAGT	0.269													4	2	---	---	---	---	
TRPA1	8989	broad.mit.edu	37	8	72963342	72963342	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72963342delA	uc003xza.2	-						uc011lff.1_Intron|uc003xyy.2_Intron	NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)	TGGCTATTATAATCATTGTTC	0.373													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	79091018	79091018	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79091018delA								None (None upstream) : PKIA (337318 downstream)																							ctaaaaatacaaaaattagcc	0.000													4	2	---	---	---	---	
CA1	759	broad.mit.edu	37	8	86250894	86250895	+	Intron	DEL	TT	-	-	rs68187707		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86250894_86250895delTT	uc003ydh.2	-						CA13_uc003ydf.1_Intron|CA1_uc010mae.1_Intron|CA1_uc003ydi.2_Intron	NM_001738	NP_001729	P00915	CAH1_HUMAN	carbonic anhydrase I						one-carbon metabolic process	Golgi apparatus	carbonate dehydratase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dichlorphenamide(DB01144)|Ethinamate(DB01031)|Ethoxzolamide(DB00311)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Levetiracetam(DB01202)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Verapamil(DB00661)|Zonisamide(DB00909)	tctttctttctttctttctttc	0.064													9	4	---	---	---	---	
CNGB3	54714	broad.mit.edu	37	8	87697131	87697132	+	Intron	INS	-	G	G			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87697131_87697132insG	uc003ydx.2	-							NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3						signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3						ttgactgtggtggggggataca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	94123072	94123072	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94123072delC								C8orf83 (93171 upstream) : FAM92A1 (589701 downstream)																							TCCCCTGACTCCCGCCACCTC	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98258733	98258734	+	IGR	DEL	AG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98258733_98258734delAG								PGCP (103012 upstream) : TSPYL5 (26981 downstream)																							ccatagtgtcagagtcatcctg	0.010													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	104090609	104090612	+	IGR	DEL	ACAA	-	-	rs79200100		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104090609_104090612delACAA								ATP6V1C1 (5325 upstream) : C8orf56 (54580 downstream)																							TGATTTCTTCACAAACATAGTCAT	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116748007	116748007	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116748007delG								TRPS1 (66779 upstream) : EIF3H (909049 downstream)																							AAGGGCTGTTGGGAAGATGTA	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	116974116	116974116	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116974116delC								TRPS1 (292888 upstream) : EIF3H (682940 downstream)																							CACCCACTCTCCAATTCTTTC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	117522403	117522404	+	IGR	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117522403_117522404delAC								TRPS1 (841175 upstream) : EIF3H (134652 downstream)																							tctcccacatacacacacaagc	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	119148222	119148222	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119148222delC								EXT1 (24164 upstream) : SAMD12 (53473 downstream)																							CACTTTGTCTCCTCTCTGGTT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	137016411	137016411	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137016411delA								KHDRBS3 (356565 upstream) : None (None downstream)																							CAAGAATGGGAAATGGGAGAG	0.448													4	2	---	---	---	---	
FAM135B	51059	broad.mit.edu	37	8	139197870	139197870	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139197870delT	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TTATCATTAGTAGTCCCTGCT	0.483										HNSCC(54;0.14)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142521226	142521226	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142521226delC								FLJ43860 (3896 upstream) : MIR1302-7 (346377 downstream)																							GGCCCGCCTACCCCCTGCTTC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	3544254	3544255	+	IGR	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3544254_3544255delAC								RFX3 (18271 upstream) : GLIS3 (279873 downstream)																							tcaaagacgtacaaaggatcaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	6287180	6287181	+	IGR	DEL	AA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6287180_6287181delAA								IL33 (29198 upstream) : TPD52L3 (41194 downstream)																							tttaatcagtaaagataaatga	0.000													4	2	---	---	---	---	
CNTLN	54875	broad.mit.edu	37	9	17409709	17409710	+	Intron	INS	-	A	A	rs149701915	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17409709_17409710insA	uc003zmz.2	+						CNTLN_uc003zmy.2_Intron|CNTLN_uc010mio.2_Intron	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)		TATATCTCAGCAAAAAAGTGGT	0.238													7	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	21767705	21767705	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21767705delC								LOC554202 (207873 upstream) : MTAP (34930 downstream)																							tgtctgagcaccaaggctgtc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	22402431	22402431	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22402431delG								CDKN2BAS (281340 upstream) : DMRTA1 (44409 downstream)																							AATATCATTTGGGGAATAACC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66459932	66459933	+	5'Flank	DEL	AA	-	-	rs112939877	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66459932_66459933delAA	uc010mng.1	-						uc004aeb.2_5'Flank|uc004aec.2_RNA					Homo sapiens cDNA, FLJ98602.																		accatatgagaagtttaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66460027	66460027	+	5'Flank	DEL	T	-	-	rs112286776		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66460027delT	uc010mng.1	-						uc004aeb.2_5'Flank|uc004aec.2_Intron					Homo sapiens cDNA, FLJ98602.																		ttgggaaggcttttcacatat	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66479263	66479266	+	IGR	DEL	TTAA	-	-	rs3068230		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66479263_66479266delTTAA								FAM74A4 (984877 upstream) : LOC442421 (17204 downstream)																							gcgctttagtttaattagatctga	0.000													4	2	---	---	---	---	
PIP5K1B	8395	broad.mit.edu	37	9	71437244	71437244	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71437244delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron	NM_003558	NP_003549	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)		ccccatctctaaaaaaaaaaa	0.114													4	3	---	---	---	---	
APBA1	320	broad.mit.edu	37	9	72047052	72047052	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72047052delG	uc004ahh.2	-							NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,						axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1						ACACTGCACTGGGGTCACACC	0.438													4	2	---	---	---	---	
NAA35	60560	broad.mit.edu	37	9	88592940	88592940	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88592940delA	uc004aoi.3	+						NAA35_uc004aoj.3_Intron|NAA35_uc004aok.1_Intron	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN	corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3						TTTTATTGTGAAAAAAAAAAC	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	90047208	90047208	+	IGR	DEL	A	-	-	rs11298575		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90047208delA								C9orf170 (272567 upstream) : DAPK1 (65450 downstream)																							ggccttagagaaaggtgactt	0.090													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101491711	101491714	+	IGR	DEL	GGGA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101491711_101491714delGGGA								GABBR2 (20536 upstream) : ANKS6 (2578 downstream)																							ACATGGATGTGGGAGGGAGAGGAA	0.525													4	2	---	---	---	---	
C9orf4	23732	broad.mit.edu	37	9	111904553	111904553	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111904553delA	uc004bdw.1	-							NM_014334	NP_055149	Q9P0K9	CI004_HUMAN	hypothetical protein LOC23732							integral to membrane					0						aataacaatcaaaaaaataat	0.000													4	2	---	---	---	---	
RABEPK	10244	broad.mit.edu	37	9	127960189	127960189	+	5'Flank	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127960189delC	uc004bpi.2	+						RABEPK_uc004bph.1_5'Flank|RABEPK_uc004bpj.2_5'Flank|RABEPK_uc004bpk.2_5'Flank|RABEPK_uc004bpl.1_5'Flank|RABEPK_uc004bpm.2_5'Flank	NM_005833	NP_005824	Q7Z6M1	RABEK_HUMAN	Rab9 effector protein with kelch motifs						receptor-mediated endocytosis|vesicle docking involved in exocytosis	endosome membrane|plasma membrane				ovary(1)	1						GAGCATTCTGCAGCTGTGAGC	0.473													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	129507178	129507178	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129507178delA								LMX1B (43867 upstream) : ZBTB43 (60107 downstream)																							agtgcacaagaaaaggtgcaa	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2146810	2146811	+	IGR	INS	-	CA	CA	rs141213219	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2146810_2146811insCA								ADARB2 (367092 upstream) : PFKP (962941 downstream)																							ATATGCATgtgcacacacacac	0.104													3	3	---	---	---	---	
CCDC3	83643	broad.mit.edu	37	10	12953203	12953204	+	Intron	INS	-	C	C	rs146918326	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12953203_12953204insC	uc001ilq.1	-						CCDC3_uc009xjb.1_Intron|CCDC3_uc001ilr.2_Intron|CCDC3_uc009xjc.1_Intron	NM_031455	NP_113643	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3 precursor							endoplasmic reticulum|extracellular region				ovary(1)	1		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			ctgttgcatcacctgcttctct	0.000													1	6	---	---	---	---	
C10orf67	256815	broad.mit.edu	37	10	23624951	23624951	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23624951delA	uc010qcx.1	-							NM_153714	NP_714925	Q8IYJ2	CJ067_HUMAN	hypothetical protein LOC256815												0						ATGGGGCCATAAAAAAAACTG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	31875616	31875616	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31875616delA								ZEB1 (57489 upstream) : ARHGAP12 (219609 downstream)																							ATTGGAGGGGAAAAAAGATGC	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	36881770	36881770	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36881770delA								FZD8 (951408 upstream) : ANKRD30A (533015 downstream)																							atagaagaggaagcagggggc	0.000													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47058662	47058663	+	Intron	DEL	AT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47058662_47058663delAT	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						acagccacacatatcacacaca	0.050													4	3	---	---	---	---	
DRGX	644168	broad.mit.edu	37	10	50590943	50590944	+	Intron	DEL	TG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50590943_50590944delTG	uc010qgq.1	-							NM_001080520	NP_001073989	A6NNA5	DRGX_HUMAN	dorsal root ganglia homeobox						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						ACTGCCACACTGTGTGTGTGTG	0.545													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	62530162	62530162	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62530162delA								ANK3 (37007 upstream) : CDK1 (7961 downstream)																							gccattgtttaagctagtgct	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	66611179	66611179	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66611179delT								ANXA2P3 (24545 upstream) : None (None downstream)																							TCTTTCTGGATTTTTTTTTGT	0.274													4	2	---	---	---	---	
RUFY2	55680	broad.mit.edu	37	10	70146113	70146113	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70146113delT	uc001job.2	-						RUFY2_uc001jnz.1_Intron|RUFY2_uc001joc.2_Intron|RUFY2_uc010qiw.1_Intron|RUFY2_uc001jod.1_Intron|RUFY2_uc009xpv.1_Intron	NM_017987	NP_060457	Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain-containing 2 isoform a							nucleus	metal ion binding			ovary(1)	1						GTGCTACTGAttttttttttc	0.149													9	4	---	---	---	---	
VCL	7414	broad.mit.edu	37	10	75867308	75867309	+	Intron	DEL	TG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75867308_75867309delTG	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706	P18206	VINC_HUMAN	vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)					ATGCATGGGTTGTGTGTGTGTG	0.475													4	3	---	---	---	---	
C10orf11	83938	broad.mit.edu	37	10	78261482	78261483	+	Intron	INS	-	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78261482_78261483insT	uc001jxi.2	+							NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					ttgcttgttgatttttttaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80694661	80694661	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80694661delA								RPS24 (878091 upstream) : LOC283050 (8423 downstream)																							GTCACCCCCTAAATTCTTAGT	0.458													4	2	---	---	---	---	
PCGF5	84333	broad.mit.edu	37	10	92927440	92927440	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92927440delG	uc001khh.2	+						PCGF5_uc001khg.2_Intron	NM_032373	NP_115749	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|PcG protein complex	zinc ion binding			lung(1)	1						CTTGAATGCTGGGCTAAGGAG	0.413													4	2	---	---	---	---	
MYOF	26509	broad.mit.edu	37	10	95157472	95157472	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95157472delA	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc001kip.3_Intron|MYOF_uc009xuf.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						AGATTAATGTAAAAAAGCAAG	0.363													4	2	---	---	---	---	
C10orf12	26148	broad.mit.edu	37	10	98638158	98638158	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98638158delA	uc009xvg.1	+						LCOR_uc001kmr.2_Intron|LCOR_uc001kms.1_Intron|LCOR_uc001kmt.1_Intron|LCOR_uc001kmu.1_Intron	NM_015652	NP_056467	Q8N655	CJ012_HUMAN	hypothetical protein LOC26148											skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		ttaggactgtaaatatattag	0.000													4	2	---	---	---	---	
TMEM180	79847	broad.mit.edu	37	10	104235864	104235864	+	3'UTR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104235864delA	uc001kvt.2	+	10					TMEM180_uc010qql.1_3'UTR|TMEM180_uc010qqm.1_Intron	NM_024789	NP_079065	Q14CX5	TM180_HUMAN	transmembrane protein 180							integral to membrane				ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		gctgttgcccaaaaaaatgga	0.149													4	2	---	---	---	---	
AFAP1L2	84632	broad.mit.edu	37	10	116134433	116134433	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116134433delA	uc001lbn.2	-						AFAP1L2_uc001lbo.2_Intron|AFAP1L2_uc010qse.1_Intron|AFAP1L2_uc001lbp.2_Intron|AFAP1L2_uc001lbr.1_Intron	NM_001001936	NP_001001936	Q8N4X5	AF1L2_HUMAN	KIAA1914 protein isoform 1						inflammatory response|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of transcription, DNA-dependent|regulation of interleukin-6 production|regulation of mitotic cell cycle	cytoplasm	protein tyrosine kinase activator activity|SH2 domain binding|SH3 domain binding			ovary(1)|breast(1)	2		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		CTAGAAGAAGAAAAAAAAAAT	0.498													4	2	---	---	---	---	
CPXM2	119587	broad.mit.edu	37	10	125488410	125488410	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125488410delT	uc001lhj.2	-									Q8N436	CPXM2_HUMAN	Homo sapiens cDNA FLJ56000 complete cds, highly similar to Carboxypeptidase-like protein X2 precursor.						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)		CCCACCCTGGTTTTTTTTCCC	0.333													4	2	---	---	---	---	
CTBP2	1488	broad.mit.edu	37	10	126733417	126733417	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126733417delC	uc009yak.2	-						CTBP2_uc009yal.2_Intron|CTBP2_uc001lif.3_Intron|CTBP2_uc001lih.3_Intron	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1						negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		AAAGCACTGGCCCAGCCTTTG	0.333													4	2	---	---	---	---	
SCGB1C1	147199	broad.mit.edu	37	11	190325	190326	+	5'Flank	DEL	CA	-	-	rs77529988		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:190325_190326delCA	uc001loa.1	+							NM_145651	NP_663626	Q8TD33	SG1C1_HUMAN	secretoglobin, family 1C, member 1 precursor							extracellular region	binding			skin(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		gtcagagcgccagttattaagc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	7815424	7815424	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7815424delA								OVCH2 (87483 upstream) : OR5P2 (2097 downstream)																							gaaataacagaaaaaaaaatt	0.000													4	2	---	---	---	---	
SOX6	55553	broad.mit.edu	37	11	16575799	16575799	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16575799delC	uc001mmi.3	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmj.2_Intron			P35712	SOX6_HUMAN	Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3						CAAAGTTATACCATGTTCATG	0.353													4	2	---	---	---	---	
HPS5	11234	broad.mit.edu	37	11	18316378	18316379	+	Intron	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18316378_18316379insA	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3						gatgagctattaaaaaaaaaaa	0.020									Hermansky-Pudlak_syndrome				4	3	---	---	---	---	
LUZP2	338645	broad.mit.edu	37	11	25009508	25009508	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25009508delT	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909	Q86TE4	LUZP2_HUMAN	leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2						tttaggctagttttggaggtt	0.075													2	4	---	---	---	---	
C11orf41	25758	broad.mit.edu	37	11	33563514	33563515	+	5'Flank	INS	-	CAGT	CAGT			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33563514_33563515insCAGT	uc001mup.3	+						C11orf41_uc001mun.1_5'Flank	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758							integral to membrane				ovary(2)	2						CAAGCTTGCCACAGTCAGCCCG	0.545													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	56566207	56566208	+	IGR	INS	-	A	A	rs142120015	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56566207_56566208insA								OR9G4 (54920 upstream) : OR5AK2 (190181 downstream)																							TGCTTCAGTAGAAAAAAAAACA	0.342													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	57668093	57668096	+	IGR	DEL	CTTT	-	-	rs145625700		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57668093_57668096delCTTT								CTNND1 (81442 upstream) : OR9Q1 (123257 downstream)																							GGATTTATAACTTTCTTCCTGACA	0.475													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	71047521	71047521	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71047521delT								SHANK2 (111713 upstream) : DHCR7 (97938 downstream)																							TGCCAAGCCATTTTTGTAGCT	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76557458	76557459	+	IGR	INS	-	GATT	GATT	rs146936155	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76557458_76557459insGATT								TSKU (48261 upstream) : ACER3 (14458 downstream)																							GAATCACCAAAgattgattgat	0.238													3	3	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	84474000	84474000	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84474000delC	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				AACTTAATATCCAAATTGAAA	0.199													4	2	---	---	---	---	
CNTN5	53942	broad.mit.edu	37	11	99278176	99278177	+	Intron	INS	-	C	C	rs148117567	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99278176_99278177insC	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)		gcaaagtccttccactcttctg	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	105374210	105374210	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105374210delT								CARD18 (364404 upstream) : GRIA4 (106590 downstream)																							ggttagggcctttttgctaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	115988844	115988844	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115988844delT								CADM1 (613603 upstream) : BUD13 (630044 downstream)																							AAGGTGGGGGTTTTTTTCCCC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124922664	124922665	+	IGR	INS	-	G	G	rs149420327	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124922664_124922665insG								CCDC15 (11281 upstream) : SLC37A2 (10348 downstream)																							ATGGTAGATAAGGGGGGATCTG	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	125435235	125435236	+	IGR	INS	-	T	T	rs144283887		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125435235_125435236insT								FEZ1 (69112 upstream) : EI24 (4062 downstream)																							Gtttttttttgttttttttttt	0.069													4	2	---	---	---	---	
ST3GAL4	6484	broad.mit.edu	37	11	126278862	126278862	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126278862delA	uc001qds.2	+						ST3GAL4_uc001qdt.2_Intron|ST3GAL4_uc009zcc.2_Intron|ST3GAL4_uc009zcd.2_Intron|ST3GAL4_uc001qdu.2_Intron|ST3GAL4_uc001qdv.2_Intron|ST3GAL4_uc009zce.2_Intron|ST3GAL4_uc001qdw.2_Intron|ST3GAL4_uc001qdx.1_Intron|ST3GAL4_uc001qdy.2_Intron|ST3GAL4_uc001qdz.2_Intron	NM_006278	NP_006269	Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase						post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		TAGACAGCCTAAAACTTTAGT	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127502679	127502679	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127502679delA								KIRREL3 (629324 upstream) : ETS1 (825977 downstream)																							AACAGGAGGCAAAAAGAGAAA	0.453													4	2	---	---	---	---	
OPCML	4978	broad.mit.edu	37	11	132476570	132476578	+	Intron	DEL	CCGTGACTG	-	-	rs71477768		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132476570_132476578delCCGTGACTG	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		GCCAATGGGACCGTGACTGCCGTGACTGC	0.478													4	2	---	---	---	---	
CCDC77	84318	broad.mit.edu	37	12	540102	540103	+	Intron	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:540102_540103insA	uc001qig.2	+						CCDC77_uc009zdk.2_Intron|CCDC77_uc010sdp.1_Intron|CCDC77_uc010sdq.1_Intron	NM_032358	NP_115734	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77 isoform a							centrosome				ovary(1)	1	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			aaaaactagccgggtgtggtgg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8209695	8209695	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8209695delT								FOXJ2 (1578 upstream) : C3AR1 (1224 downstream)																							TCATTTTCTGTTTTTAGACTA	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28038029	28038029	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28038029delT								KLHDC5 (82057 upstream) : PTHLH (72989 downstream)																							ggCACTGGCCTTATGTGCTCA	0.254													4	2	---	---	---	---	
TMTC1	83857	broad.mit.edu	37	12	29781124	29781124	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29781124delT	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					cctacttatcttatctcaact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	30685252	30685253	+	IGR	DEL	TA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30685252_30685253delTA								TMTC1 (747560 upstream) : IPO8 (96670 downstream)																							AAGGAAGAGGTATCTTGGCTTT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	39458292	39458292	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39458292delT								CPNE8 (158872 upstream) : KIF21A (228739 downstream)																							TCCATTTGGCTTTTTTTTTTT	0.358													4	2	---	---	---	---	
ARID2	196528	broad.mit.edu	37	12	46154277	46154277	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46154277delT	uc001ros.1	+						ARID2_uc001ror.2_Intron	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		tgcgtgtgtgtttttttggtg	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	52222692	52222692	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52222692delG								FIGNL2 (6484 upstream) : ANKRD33 (59101 downstream)																							TACAGGGTGAGGTAGGAAGAA	0.303													4	2	---	---	---	---	
KRT2	3849	broad.mit.edu	37	12	53043309	53043309	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53043309delT	uc001sat.2	-							NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2						keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.19)		GAACCCTTGCTTTTGGCCTAC	0.502													4	2	---	---	---	---	
SUOX	6821	broad.mit.edu	37	12	56395697	56395699	+	Intron	DEL	TGG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56395697_56395699delTGG	uc001six.2	+						SUOX_uc009zoh.2_Intron|SUOX_uc001siy.2_Intron|SUOX_uc001siz.2_Intron|SUOX_uc001sja.2_Translation_Start_Site	NM_000456	NP_000447	P51687	SUOX_HUMAN	sulfite oxidase precursor							mitochondrial intermembrane space	electron carrier activity|molybdenum ion binding|sulfite oxidase activity				0			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			TCGTTCTCTATGGTGGACAAAGT	0.502													4	2	---	---	---	---	
MARCH9	92979	broad.mit.edu	37	12	58153294	58153294	+	3'UTR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58153294delG	uc001spx.1	+	4					MARCH9_uc001spy.2_3'UTR	NM_138396	NP_612405	Q86YJ5	MARH9_HUMAN	membrane-associated RING-CH protein IX							Golgi membrane|Golgi stack|integral to membrane|lysosomal membrane|trans-Golgi network	ligase activity|zinc ion binding				0	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			ATGCAGCAGTGGGTTCTGAGT	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	58537281	58537281	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58537281delA								XRCC6BP1 (186230 upstream) : LRIG3 (728657 downstream)																							GCACAAAATTAAAAAAAACAT	0.403													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	61802060	61802060	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61802060delA								None (None upstream) : FAM19A2 (299983 downstream)																							TTTCCGAGTTAAAAAAAAATC	0.318													4	4	---	---	---	---	
OSBPL8	114882	broad.mit.edu	37	12	76772555	76772555	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76772555delT	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron|OSBPL8_uc001syh.1_Intron	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1						AGTTATGTGCttttttttttg	0.030													10	5	---	---	---	---	
UHRF1BP1L	23074	broad.mit.edu	37	12	100492517	100492518	+	Intron	INS	-	A	A	rs58825897		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100492517_100492518insA	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2						ccatctctactaaaaaaaaaaa	0.000													6	3	---	---	---	---	
MYBPC1	4604	broad.mit.edu	37	12	102008781	102008781	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102008781delT	uc001tii.2	+						MYBPC1_uc001tif.1_Intron|MYBPC1_uc001tig.2_Intron|MYBPC1_uc010svq.1_Intron|MYBPC1_uc001tih.2_Intron|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3						cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4						AGAAACTCCCTAGCAGCTATC	0.478													4	2	---	---	---	---	
C12orf48	55010	broad.mit.edu	37	12	102544892	102544893	+	Intron	INS	-	A	A	rs145644863	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102544892_102544893insA	uc001tjf.2	+						C12orf48_uc001tje.2_Intron|C12orf48_uc001tjg.2_Intron|C12orf48_uc010swa.1_Intron|C12orf48_uc001tjh.2_Intron|C12orf48_uc010swb.1_Intron|C12orf48_uc001tji.2_Intron|C12orf48_uc009zuc.2_Intron|C12orf48_uc001tjj.2_Intron|C12orf48_uc001tjk.2_Intron|C12orf48_uc009zud.2_Intron	NM_017915	NP_060385	Q9NWS1	PR1BP_HUMAN	hypothetical protein LOC55010						response to DNA damage stimulus	cytoplasm|nucleus	DNA binding				0						TGAGTTAGCTGCAACACACGTG	0.426													4	3	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119582993	119582993	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119582993delA	uc001txa.1	+							NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2						agcagggggtaaaaaaaaaat	0.005													6	5	---	---	---	---	
ZNF664	144348	broad.mit.edu	37	12	124492243	124492244	+	Intron	INS	-	T	T	rs75783556		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124492243_124492244insT	uc001ufz.2	+						ZNF664_uc001uga.2_Intron|ZNF664_uc001ugb.2_Intron	NM_152437	NP_689650	Q8N3J9	ZN664_HUMAN	zinc finger protein 664						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.000239)|OV - Ovarian serous cystadenocarcinoma(86;0.000247)|all cancers(50;0.00155)|BRCA - Breast invasive adenocarcinoma(302;0.249)		GCATTCACAGATTTTTTTTTTT	0.342													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127239814	127239814	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127239814delA	uc001uhk.3	-											Homo sapiens cDNA clone IMAGE:6160413.																		ACAAATGTGTAAAGGGAATAC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128180826	128180826	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128180826delA								None (None upstream) : TMEM132C (718465 downstream)																							ATCCAAGGGGAAAAAAAAGCA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	28469377	28469377	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28469377delT	uc001urs.1	-											full-length cDNA clone CS0DJ004YL04 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																		gtctgtgtaattttatcacat	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	29541923	29541923	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29541923delC								SLC46A3 (248773 upstream) : MTUS2 (56825 downstream)																							GAAGAAGTAGCCCAGCATATG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30333035	30333035	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30333035delC								SLC7A1 (163210 upstream) : UBL3 (5511 downstream)																							atgtcctgggcccacagagag	0.075													4	2	---	---	---	---	
C13orf36	400120	broad.mit.edu	37	13	37250412	37250412	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37250412delA	uc001uvt.3	+							NM_203451	NP_982276	A2A2V5	CM036_HUMAN	hypothetical protein LOC400120							integral to membrane				skin(1)	1						CGTTCATTATAAAAAAGAAAG	0.358													4	2	---	---	---	---	
LHFP	10186	broad.mit.edu	37	13	40047391	40047391	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40047391delT	uc001uxf.2	-							NM_005780	NP_005771	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		ACTTGACTCCTTTGAACAGGT	0.393			T	HMGA2	lipoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	44818451	44818451	+	IGR	DEL	G	-	-	rs2843391	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44818451delG								LOC121838 (213853 upstream) : SERP2 (129527 downstream)																							TGTGTTTTttgttgttgttgt	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	44980554	44980554	+	5'Flank	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44980554delA	uc001uzl.2	-											Homo sapiens hypothetical gene supported by BC025370, mRNA (cDNA clone IMAGE:3945331).																		AAAGGGAGCTAAAACTGTCTA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78619187	78619187	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78619187delA	uc001vks.2	+											Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																		AAGGAAAAATAACTAATAGAC	0.348													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102855390	102855390	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102855390delG	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)					AGACAGGCATGGAAGACAGGA	0.448													4	2	---	---	---	---	
ANKRD10	55608	broad.mit.edu	37	13	111543150	111543150	+	Intron	DEL	G	-	-	rs34765275		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111543150delG	uc001vrn.2	-						ANKRD10_uc001vrm.2_Intron	NM_017664	NP_060134	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10											central_nervous_system(1)	1	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			AAGGCTGCATGGTGAGTTTAA	0.433													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	19108678	19108680	+	IGR	DEL	ATC	-	-	rs113828350		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19108678_19108680delATC								None (None upstream) : OR11H12 (268914 downstream)																							tgatcgtcctatcatctcggtct	0.074													4	2	---	---	---	---	
TOX4	9878	broad.mit.edu	37	14	21961596	21961596	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21961596delT	uc001waz.2	+						TOX4_uc001way.2_Intron|TOX4_uc001wba.2_Intron|TOX4_uc010tlu.1_Intron|TOX4_uc010tlv.1_Intron	NM_014828	NP_055643	O94842	TOX4_HUMAN	epidermal Langerhans cell protein LCP1							chromatin|nucleus|PTW/PP1 phosphatase complex	DNA binding|protein binding			ovary(1)	1	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)		ACTCATACTGttttttttttg	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	51180431	51180431	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51180431delG								SAV1 (45408 upstream) : NIN (6051 downstream)																							ATCACCTTGTGGGCTAAGGTG	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	56814861	56814862	+	IGR	DEL	TA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56814861_56814862delTA								PELI2 (46831 upstream) : C14orf101 (231476 downstream)																							GACCTCCACTTATCTGGCCTGA	0.277													4	2	---	---	---	---	
FNTB	2342	broad.mit.edu	37	14	65417447	65417447	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65417447delA	uc010tsl.1	+						FNTB_uc010tsm.1_Intron|RAB15_uc010aqk.2_RNA|RAB15_uc001xhz.2_Intron	NM_002028	NP_002019	P49356	FNTB_HUMAN	farnesyltransferase, CAAX box, beta						protein farnesylation	microtubule associated complex	protein binding|protein farnesyltransferase activity			ovary(1)	1				all cancers(60;0.00115)|OV - Ovarian serous cystadenocarcinoma(108;0.00412)|BRCA - Breast invasive adenocarcinoma(234;0.011)		cagaggattcaaatggcttcc	0.164													4	2	---	---	---	---	
KIAA0247	9766	broad.mit.edu	37	14	70132464	70132464	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70132464delT	uc001xlk.2	+						KIAA0247_uc010aqz.2_Intron	NM_014734	NP_055549	Q92537	K0247_HUMAN	hypothetical protein LOC9766 precursor							integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)		CTTCACCTTGTTTTTTGGAAT	0.214													4	2	---	---	---	---	
NRXN3	9369	broad.mit.edu	37	14	79413605	79413605	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79413605delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		ttaccatgccaaagaggctgc	0.239													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	90517545	90517545	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90517545delG								TDP1 (6439 upstream) : KCNK13 (10563 downstream)																							ATCTCCTGTTGGGAACGCTGA	0.517													4	2	---	---	---	---	
RIN3	79890	broad.mit.edu	37	14	93083125	93083125	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93083125delA	uc001yap.2	+						RIN3_uc010auk.2_Intron|RIN3_uc001yaq.2_Intron	NM_024832	NP_079108	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3						endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding			lung(2)|ovary(1)	3		all_cancers(154;0.0701)				atgcgagaggaaatgaaattg	0.000													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106933962	106933963	+	Intron	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106933962_106933963delAC	uc010tyt.1	-						uc010tyu.1_Intron					Parts of antibodies, mostly variable regions.												0						ACACCCCTCGACACACACACAc	0.218													4	2	---	---	---	---	
GOLGA8F	100132565	broad.mit.edu	37	15	28630217	28630218	+	Intron	INS	-	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28630217_28630218insC	uc010uag.1	+						GOLGA8G_uc001zbp.3_Intron|GOLGA8G_uc001zbo.2_Intron|GOLGA8G_uc001zbn.2_Intron	NM_001164328	NP_001157800			golgi autoantigen, golgin subfamily a, 8F												0						tcttttcttttttttttttttt	0.485													9	4	---	---	---	---	
RYR3	6263	broad.mit.edu	37	15	33651357	33651357	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33651357delC	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		tccatctttacccacttccac	0.000													4	2	---	---	---	---	
ADAL	161823	broad.mit.edu	37	15	43643532	43643532	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43643532delA	uc010udo.1	+						ADAL_uc001zri.1_Intron	NM_001159280	NP_001152752	Q6DHV7	ADAL_HUMAN	adenosine deaminase-like isoform 1						adenosine catabolic process|inosine biosynthetic process|purine ribonucleoside monophosphate biosynthetic process		adenosine deaminase activity|metal ion binding				0		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		ctcacaaagcaaaaaaaaaaa	0.224													4	3	---	---	---	---	
SQRDL	58472	broad.mit.edu	37	15	45982862	45982863	+	Intron	INS	-	CCTGA	CCTGA	rs145687436	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45982862_45982863insCCTGA	uc001zvt.2	+						SQRDL_uc001zvu.2_Intron|SQRDL_uc001zvv.2_Intron	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor								oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		gattgcaaaatcctACAGTTAA	0.163													3	5	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52688811	52688811	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52688811delT	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GTTTTTTTTGTTTTTTTTTTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	53172885	53172885	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53172885delT								ONECUT1 (90676 upstream) : WDR72 (633053 downstream)																							TTTTCTTTTCTTTTTTTTTTT	0.358													2	5	---	---	---	---	
WDR72	256764	broad.mit.edu	37	15	53906143	53906144	+	Intron	INS	-	TTAT	TTAT	rs138717914	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53906143_53906144insTTAT	uc002acj.2	-							NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		CACCTAAAATCTTATTTATTTA	0.307													10	6	---	---	---	---	
NEDD4	4734	broad.mit.edu	37	15	56126729	56126730	+	Intron	INS	-	C	C	rs144235710	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56126729_56126730insC	uc002adj.2	-						NEDD4_uc002adl.2_Intron|NEDD4_uc002adi.2_Intron|NEDD4_uc010ugj.1_Intron|NEDD4_uc010bfm.2_Intron|NEDD4_uc002adk.2_Intron	NM_198400	NP_006145	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		agtggctcattctgtaatccca	0.144													2	6	---	---	---	---	
TCF12	6938	broad.mit.edu	37	15	57269743	57269744	+	Intron	INS	-	TG	TG			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57269743_57269744insTG	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		ATTCGATATTCtgtgtgtgtgt	0.208			T	TEC	extraskeletal myxoid chondrosarcoma								4	2	---	---	---	---	
ALDH1A2	8854	broad.mit.edu	37	15	58555283	58555284	+	Intron	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58555283_58555284delAC	uc010ugw.1	-							NM_170697	NP_733798	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 3						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	ctgacttaagacaCACacacag	0.084													4	2	---	---	---	---	
RNF111	54778	broad.mit.edu	37	15	59359456	59359459	+	Intron	DEL	CTCC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59359456_59359459delCTCC	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron|RNF111_uc002afw.2_Intron|RNF111_uc002afx.2_Intron	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)		ttttttttaactccctcccattct	0.074													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	81380213	81380214	+	IGR	DEL	CA	-	-	rs74493213		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81380213_81380214delCA								MESDC1 (83869 upstream) : C15orf26 (11535 downstream)																							cacatgcacccacacacacaca	0.262													3	3	---	---	---	---	
ACAN	176	broad.mit.edu	37	15	89384734	89384734	+	Intron	DEL	T	-	-	rs34936657		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89384734delT	uc010upo.1	+						ACAN_uc002bmx.2_Intron|ACAN_uc010upp.1_Intron|ACAN_uc002bna.2_Intron	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor						cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			tagaaaaaaatatgtgagccc	0.159													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94032610	94032610	+	Intron	DEL	T	-	-	rs63112662		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94032610delT	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																		aatgctactctttttttttct	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	97300140	97300141	+	IGR	INS	-	AGG	AGG			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97300140_97300141insAGG								NR2F2 (416650 upstream) : SPATA8 (26538 downstream)																							ggaggaggaaaaggaggaggag	0.391													4	2	---	---	---	---	
ZNF597	146434	broad.mit.edu	37	16	3487743	3487744	+	Intron	INS	-	AGG	AGG	rs139797653	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3487743_3487744insAGG	uc002cvd.2	-							NM_152457	NP_689670	Q96LX8	ZN597_HUMAN	zinc finger protein 597						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ATCCAAAGGTAAGGAGAGAATA	0.426													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	5620183	5620183	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5620183delT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																		TCACTCTCTCTTTTTTTTCCT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	11323202	11323203	+	IGR	INS	-	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11323202_11323203insT								CLEC16A (47158 upstream) : C16orf75 (20303 downstream)																							ttgtttgttagttttttgcttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17913091	17913091	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17913091delA								XYLT1 (348353 upstream) : NOMO2 (598092 downstream)																							GCTTAAACCTAAGATTCTCCC	0.388													4	2	---	---	---	---	
SMG1	23049	broad.mit.edu	37	16	18844064	18844064	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18844064delT	uc002dfm.2	-						SMG1_uc010bwb.2_Intron|SMG1_uc010bwa.2_Intron	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16						ctgcctgcactttttttttaa	0.065													4	2	---	---	---	---	
PDZD9	255762	broad.mit.edu	37	16	22009714	22009714	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22009714delA	uc002dka.1	-							NM_173806	NP_776167	Q8IXQ8	PDZD9_HUMAN	hypothetical protein LOC255762											pancreas(1)	1						GTACATCTTGAAAAAAAAACA	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32544622	32544622	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32544622delT								HERC2P4 (380748 upstream) : TP53TG3B (140219 downstream)																							aaaagaaaggtttagctctag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33547462	33547462	+	IGR	DEL	T	-	-	rs74393040		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33547462delT								SLC6A10P (650999 upstream) : MIR1826 (418046 downstream)																							GCATCTGAAGTTGAGTCCCAT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33972958	33972958	+	IGR	DEL	A	-	-	rs146319188		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33972958delA								MIR1826 (7366 upstream) : UBE2MP1 (430844 downstream)																							aaacagtcctattgtagaatc	0.000													13	8	---	---	---	---	
CES7	221223	broad.mit.edu	37	16	55941018	55941018	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55941018delA	uc002eir.2	-						CES7_uc002eiq.2_Intron			Q6NT32	EST5A_HUMAN	SubName: Full=Putative uncharacterized protein ENSP00000383269; Flags: Fragment;							extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)		tgacgatgatAAGATACTAAT	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	59039462	59039463	+	IGR	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59039462_59039463insA								GOT2 (271216 upstream) : None (None downstream)																							ccggcttggggaaaaaaaaaaT	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73847401	73847402	+	IGR	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73847401_73847402insA								HTA (719731 upstream) : PSMD7 (483279 downstream)																							ttcagtaaaacaaaaaaaaAGG	0.188													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73871473	73871474	+	IGR	DEL	CA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73871473_73871474delCA								HTA (743803 upstream) : PSMD7 (459207 downstream)																							TTCTTGGAAGCACACACACACT	0.292													4	2	---	---	---	---	
CNTNAP4	85445	broad.mit.edu	37	16	76557275	76557275	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76557275delT	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						ATTTTGCCCATTTTTTTTTCT	0.313													4	2	---	---	---	---	
PKD1L2	114780	broad.mit.edu	37	16	81253526	81253527	+	Intron	INS	-	TTATT	TTATT	rs141224532	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81253526_81253527insTTATT	uc002fgh.1	-						PKD1L2_uc002fgj.2_Intron	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a						neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						ttagacatgaattatttaatcc	0.282													9	5	---	---	---	---	
NECAB2	54550	broad.mit.edu	37	16	84029921	84029921	+	Intron	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84029921delC	uc002fhd.2	+						NECAB2_uc002fhe.2_Intron	NM_019065	NP_061938	Q7Z6G3	NECA2_HUMAN	neuronal calcium-binding protein 2						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity|protein binding			ovary(2)	2						ATGCTGTGTGCCCCCAGAAGG	0.338													4	2	---	---	---	---	
STX8	9482	broad.mit.edu	37	17	9444603	9444603	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9444603delA	uc002glx.2	-							NM_004853	NP_004844	Q9UNK0	STX8_HUMAN	syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1						GACACGGAACAAATGAGATGT	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	12135628	12135628	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12135628delC								MAP2K4 (88578 upstream) : MYOCD (433579 downstream)																							GGCCTGAAATCCTGCTGCTTT	0.488													4	2	---	---	---	---	
CCDC144C	348254	broad.mit.edu	37	17	20280158	20280159	+	Intron	INS	-	GC	GC	rs139801618		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20280158_20280159insGC	uc010cqy.1	+							NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						AGCTGCGGGGAGCGCGGCCGTT	0.634													4	2	---	---	---	---	
FLJ36000	284124	broad.mit.edu	37	17	21904525	21904525	+	Intron	DEL	C	-	-	rs148239380		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21904525delC	uc002gza.2	+							NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						GTGGACCGGTCTTTGGTGAGC	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25285558	25285559	+	IGR	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25285558_25285559insA								None (None upstream) : WSB1 (335547 downstream)																							aaaggaatcagaaaaaatatta	0.000													3	3	---	---	---	---	
SSH2	85464	broad.mit.edu	37	17	28120653	28120653	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28120653delT	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						GCTCTTACTCttttttttttt	0.189													4	2	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35471774	35471774	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35471774delA	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuy.2_Intron|ACACA_uc010wdb.1_Intron|ACACA_uc010wdc.1_Intron	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2						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)	CTCAATTTGGAATAAATCAAT	0.343													4	2	---	---	---	---	
TADA2A	6871	broad.mit.edu	37	17	35825918	35825919	+	Intron	INS	-	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35825918_35825919insT	uc002hnt.2	+						TADA2A_uc002hnv.2_Intron|TADA2A_uc002hnw.2_Intron|TADA2A_uc010cvb.2_Intron	NM_001488	NP_001479	O75478	TAD2A_HUMAN	transcriptional adaptor 2A isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	chromosome|PCAF complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|zinc ion binding			breast(3)|skin(1)	4						atatatatagaagtagagataa	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	41675338	41675338	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41675338delT								ETV4 (51576 upstream) : MEOX1 (42429 downstream)																							GTTTTGTTGGTTTTTTTTCCC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49469791	49469792	+	IGR	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49469791_49469792delGT								UTP18 (94501 upstream) : CA10 (237883 downstream)																							AGAATGAACCgtgtgtgtgtgt	0.257													4	3	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	49721536	49721537	+	Intron	DEL	TT	-	-	rs112789467		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49721536_49721537delTT	uc002itw.3	-						CA10_uc002itu.3_Intron|CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			GTTCCCCCCCTTTTTTTTTTTC	0.450													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	52864691	52864692	+	IGR	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52864691_52864692delAC								KIF2B (962118 upstream) : TOM1L1 (113360 downstream)																							ATGCAGGCTTACACACACACAC	0.406													4	2	---	---	---	---	
MED13	9969	broad.mit.edu	37	17	60020018	60020018	+	3'UTR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60020018delT	uc002izo.2	-	30						NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						tttgtttttgttttttttttt	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	75034046	75034047	+	IGR	INS	-	C	C	rs142776467	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75034046_75034047insC								MGAT5B (87576 upstream) : C17orf86 (50678 downstream)																							gacacatggcaccaatactgga	0.109													4	6	---	---	---	---	
RPTOR	57521	broad.mit.edu	37	17	78631273	78631273	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78631273delT	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						ACTTTCCTTCTTTTTTTTTGA	0.373													4	2	---	---	---	---	
TBCD	6904	broad.mit.edu	37	17	80852516	80852516	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80852516delT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kgb.1_5'Flank	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)			TTTAATGTCCTTTTTTGCCTT	0.269													4	2	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3874304	3874305	+	Intron	DEL	TC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3874304_3874305delTC	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc010wyw.1_5'Flank|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				gctccctctgtctctctctctc	0.351													4	2	---	---	---	---	
L3MBTL4	91133	broad.mit.edu	37	18	6285302	6285302	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6285302delG	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				atacaactaaggggaacagag	0.234													4	2	---	---	---	---	
PTPRM	5797	broad.mit.edu	37	18	8106322	8106322	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8106322delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_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)				ACATGTTGGCTTTTTTTTTTG	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	10928995	10928996	+	IGR	INS	-	GA	GA			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10928995_10928996insGA								FAM38B (227016 upstream) : GNAL (760140 downstream)																							TGCATTAACAGGAGAGAGAAAA	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	14145018	14145019	+	IGR	DEL	TA	-	-	rs34266186	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14145018_14145019delTA								ZNF519 (12589 upstream) : LOC284233 (192403 downstream)																							GGAGGCAGCGTACCCCCCCCAC	0.639													4	2	---	---	---	---	
GREB1L	80000	broad.mit.edu	37	18	19065309	19065309	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19065309delA	uc010xam.1	+						GREB1L_uc010dlp.1_Intron|GREB1L_uc010xan.1_Intron|GREB1L_uc010dlr.1_Intron	NM_001142966	NP_001136438	Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast							integral to membrane					0						GTATCCCAACAAAAAAAAAAG	0.383													4	2	---	---	---	---	
LAMA3	3909	broad.mit.edu	37	18	21475213	21475213	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21475213delG	uc002kuq.2	+						LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_Intron	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1						cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TAGCACATCTGGGTGAACAAT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	23256533	23256533	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23256533delT								ZNF521 (324319 upstream) : SS18 (339686 downstream)																							TCCAAGATCCTTTTAGAATGG	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	23495592	23495592	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23495592delA								ZNF521 (563378 upstream) : SS18 (100627 downstream)																							TCTGCAATACAAAAAAAAAGC	0.428													4	2	---	---	---	---	
KLHL14	57565	broad.mit.edu	37	18	30322270	30322270	+	Intron	DEL	T	-	-	rs34677845		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30322270delT	uc002kxm.1	-						KLHL14_uc010dmd.1_5'Flank	NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14							cytosol|endoplasmic reticulum membrane				ovary(1)	1						TAGAACGACCTTTTTCTTATA	0.358													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35316322	35316323	+	IGR	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35316322_35316323delGT								CELF4 (170322 upstream) : None (None downstream)																							TCAGAGTCCAGTGTGTGTGTGT	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35829460	35829460	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35829460delT								CELF4 (683460 upstream) : LOC647946 (957428 downstream)																							CTGTCACATCTTTGAGTATTA	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38121416	38121416	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38121416delA								LOC647946 (741134 upstream) : KC6 (938822 downstream)																							TAGGGGCATGAGGGGCGGCTT	0.488													4	2	---	---	---	---	
DYM	54808	broad.mit.edu	37	18	46657209	46657209	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46657209delT	uc002ldi.1	-						DYM_uc010xdf.1_Intron|DYM_uc002ldj.3_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin							Golgi apparatus					0						ATGGGAGCACTTGGAATAGGG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	49083366	49083366	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49083366delT	uc010xdq.1	+											Homo sapiens cDNA FLJ37617 fis, clone BRCOC2012229.																		tttgaggggattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	56467893	56467893	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56467893delA								MALT1 (50523 upstream) : ZNF532 (62168 downstream)																							aaataaaaataaaaaaaagaa	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	56727625	56727625	+	IGR	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56727625delC								LOC390858 (7179 upstream) : SEC11C (79500 downstream)																							AGCCAATCATCCCCCATGCTC	0.488													4	2	---	---	---	---	
DOK6	220164	broad.mit.edu	37	18	67130254	67130254	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67130254delT	uc002lkl.2	+							NM_152721	NP_689934	Q6PKX4	DOK6_HUMAN	docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				tcttagtccatttggatggct	0.144													4	2	---	---	---	---	
MUM1	84939	broad.mit.edu	37	19	1359911	1359911	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1359911delT	uc010xgm.1	+						MUM1_uc010dsi.2_Intron|MUM1_uc002lrz.2_Intron|MUM1_uc002lsb.2_Intron|MUM1_uc002lsc.1_Intron			Q2TAK8	MUM1_HUMAN	SubName: Full=MUM1 protein;						chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|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)		ATAAATTTGGTTTTTAAAAAA	0.368											OREG0025088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
C19orf28	126321	broad.mit.edu	37	19	3558145	3558145	+	5'Flank	DEL	C	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3558145delC	uc002lxz.2	-						C19orf28_uc002lxw.2_5'Flank|C19orf28_uc002lxx.2_5'Flank|C19orf28_uc002lxy.2_5'Flank	NM_174983	NP_778148	Q6NUT3	CS028_HUMAN	hypothetical protein LOC126321 isoform c						transmembrane transport	integral to membrane				breast(1)|pancreas(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00251)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGCAAAGAGCCCCACGTGGT	0.507													4	2	---	---	---	---	
C3	718	broad.mit.edu	37	19	6720074	6720075	+	Intron	INS	-	T	T	rs11569402		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6720074_6720075insT	uc002mfm.2	-							NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor						complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		GAGTCTCCAAACACCCCCAACC	0.455													4	2	---	---	---	---	
C3	718	broad.mit.edu	37	19	6720077	6720077	+	Intron	DEL	C	-	-	rs11569400		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6720077delC	uc002mfm.2	-							NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor						complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		TCTCCAAACACCCCCAACCGC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13688962	13688963	+	IGR	INS	-	C	C			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13688962_13688963insC								CACNA1A (71688 upstream) : CCDC130 (153611 downstream)																							cactggcattgcccccctccac	0.104													4	2	---	---	---	---	
TSHZ3	57616	broad.mit.edu	37	19	31817985	31817986	+	Intron	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31817985_31817986insA	uc002nsy.3	-							NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537						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)					TCTGTTTCATTAAAAAAAAAAC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36673143	36673144	+	IGR	INS	-	TT	TT	rs151244757	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36673143_36673144insTT								COX7A1 (29372 upstream) : ZNF565 (44 downstream)																							TTCTATATTCATTTTTTTTTAG	0.287													3	4	---	---	---	---	
ZNF527	84503	broad.mit.edu	37	19	37864139	37864140	+	Intron	DEL	GA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37864139_37864140delGA	uc010efk.1	+						ZNF527_uc002ogf.3_Intron|ZNF527_uc010xtq.1_Intron|ZNF527_uc002oge.2_Intron	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTGTGTGTGTGAGAGAGAGAGA	0.332													4	2	---	---	---	---	
ZNF527	84503	broad.mit.edu	37	19	37870362	37870362	+	Intron	DEL	C	-	-	rs34967980		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37870362delC	uc010efk.1	+						ZNF527_uc002ogf.3_Intron|ZNF527_uc010xtq.1_Intron|ZNF527_uc002oge.2_Intron	NM_032453	NP_115829	Q8NB42	ZN527_HUMAN	zinc finger protein 527						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GAAGTAAtttctttttttttt	0.129													5	3	---	---	---	---	
SIPA1L3	23094	broad.mit.edu	37	19	38467010	38467012	+	Intron	DEL	AAA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38467010_38467012delAAA	uc002ohk.2	+							NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TCCAACTTGTAAAATATTTGTAA	0.493													4	2	---	---	---	---	
CEACAM19	56971	broad.mit.edu	37	19	45186328	45186331	+	Intron	DEL	CTCT	-	-	rs71338723		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45186328_45186331delCTCT	uc002ozo.3	+						CEACAM19_uc002ozp.3_Intron	NM_020219	NP_064604	Q7Z692	CEA19_HUMAN	carcinoembryonic antigen-related cell adhesion							integral to membrane					0	Lung NSC(12;0.00308)|all_lung(12;0.00806)	Prostate(69;0.0376)				CTTTCTTGGActctctctctctct	0.299													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	48291271	48291271	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48291271delT								SEPW1 (3332 upstream) : TPRX1 (13229 downstream)																							ttttctttcattttttttttt	0.204													5	3	---	---	---	---	
ZNF160	90338	broad.mit.edu	37	19	53573669	53573669	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53573669delT	uc010eqk.2	-						ZNF160_uc002qaq.3_Intron|ZNF160_uc002qar.3_Intron	NM_001102603	NP_001096073	Q9HCG1	ZN160_HUMAN	zinc finger protein 160						hemopoiesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(134;0.02)		AACAAAAATGttttttttttt	0.134													3	3	---	---	---	---	
TGM6	343641	broad.mit.edu	37	20	2378932	2378932	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2378932delG	uc002wfy.1	+						TGM6_uc010gal.1_Intron	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6						cell death|peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)|skin(1)	4					L-Glutamine(DB00130)	tgcttcttctggggatatctt	0.000													4	2	---	---	---	---	
C20orf194	25943	broad.mit.edu	37	20	3320971	3320972	+	Intron	INS	-	C	C	rs58672154		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3320971_3320972insC	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron|C20orf194_uc010gay.1_Intron	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943												0						CCTAGTTTGTACTATAAAAAAA	0.302													4	2	---	---	---	---	
PLCB4	5332	broad.mit.edu	37	20	9421480	9421480	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9421480delA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15						GGAAAAGGTTAAAGGGAACCA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	10869748	10869748	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10869748delT								JAG1 (215054 upstream) : None (None downstream)																							TCtttttttattttttttttt	0.184													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26074256	26074257	+	IGR	INS	-	TC	TC	rs141028126	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26074256_26074257insTC								FAM182A (6704 upstream) : C20orf191 (9796 downstream)																							GCACATGTGGTCCCCCAAAGAA	0.243													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	29602180	29602180	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29602180delT								None (None upstream) : FRG1B (9699 downstream)																							aatccacatatttacatgcaa	0.000													9	4	---	---	---	---	
CBFA2T2	9139	broad.mit.edu	37	20	32182725	32182725	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32182725delG	uc002wzg.1	+						CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Intron|CBFA2T2_uc002wzf.1_Intron|CBFA2T2_uc002wzh.1_Intron|CBFA2T2_uc002wzi.1_Intron	NM_005093	NP_005084	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2						CTAAGCTGGTGGAGACCTGAA	0.353													4	2	---	---	---	---	
TRPC4AP	26133	broad.mit.edu	37	20	33656765	33656766	+	Intron	INS	-	A	A	rs139432845	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33656765_33656766insA	uc002xbk.2	-						TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453	Q8TEL6	TP4AP_HUMAN	TRPC4-associated protein isoform a						protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)			cacacacacacacacacacaca	0.332													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36039266	36039269	+	IGR	DEL	TCAT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36039266_36039269delTCAT								SRC (5447 upstream) : BLCAP (106551 downstream)																							CGGGGTCCCCtcattcattcattc	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36044277	36044278	+	IGR	INS	-	TG	TG	rs144260769	by1000genomes	TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36044277_36044278insTG								SRC (10458 upstream) : BLCAP (101542 downstream)																							tctgtGAGAGATGTGTGTGTGT	0.376													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36044353	36044354	+	IGR	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36044353_36044354delGT								SRC (10534 upstream) : BLCAP (101466 downstream)																							TTGTGTTGGGGTGTGTGTGTGG	0.525													3	3	---	---	---	---	
LPIN3	64900	broad.mit.edu	37	20	39978338	39978338	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39978338delT	uc002xjx.2	+						LPIN3_uc010ggh.2_Intron|LPIN3_uc010zwf.1_Intron	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3						fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)				GTTGCACATATTTTTTTCCCT	0.418													6	4	---	---	---	---	
DNTTIP1	116092	broad.mit.edu	37	20	44433428	44433428	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44433428delT	uc002xpk.2	+							NM_052951	NP_443183	Q9H147	TDIF1_HUMAN	terminal deoxynucleotidyltransferase interacting							nucleus				ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.0122)				gtgctcaccctttcagaatta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50535665	50535665	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50535665delA								SALL4 (116617 upstream) : ZFP64 (164886 downstream)																							CTGTAGAATTAAAAAAAAAAA	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	51061883	51061886	+	IGR	DEL	GCAA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51061883_51061886delGCAA								ZFP64 (253359 upstream) : TSHZ2 (526991 downstream)																							tatgcagagggcaagcaagcaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	55228482	55228482	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55228482delT								TFAP2C (14146 upstream) : BMP7 (515327 downstream)																							GAATCAAGTGTTCTGTGGTTG	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10704482	10704483	+	IGR	INS	-	A	A	rs141719157		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10704482_10704483insA								None (None upstream) : TPTE (202260 downstream)																							aatatcttcacaaaaaaagtag	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10705056	10705056	+	IGR	DEL	A	-	-	rs150496275		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10705056delA								None (None upstream) : TPTE (201687 downstream)																							catctcacagagttgaaattt	0.000													11	5	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11082289	11082290	+	Intron	INS	-	A	A	rs112034466		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11082289_11082290insA	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)		cttaacatcctacacacaggac	0.045													5	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11096529	11096532	+	Intron	DEL	TTTG	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11096529_11096532delTTTG	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)		tttgttttgttttgtttttgagac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11182289	11182290	+	IGR	INS	-	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11182289_11182290insT								BAGE (83352 upstream) : None (None downstream)																							ctaatttattatttttttccta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	33213324	33213325	+	IGR	INS	-	A	A			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33213324_33213325insA								SFRS15 (108893 upstream) : HUNK (32303 downstream)																							TGTTTTTGAGGAAAAAAAAAAC	0.347													4	2	---	---	---	---	
C21orf63	59271	broad.mit.edu	37	21	33797109	33797109	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33797109delT	uc002ypr.1	+						C21orf63_uc002ypq.1_Intron|C21orf63_uc002yps.1_Intron|C21orf63_uc010glw.1_Intron|C21orf63_uc002ypt.1_Intron	NM_058187	NP_478067	P58658	CU063_HUMAN	hypothetical protein LOC59271 precursor							integral to membrane	sugar binding			ovary(2)|pancreas(1)	3						GATTTCCGTATTTTTTTTATT	0.289													4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	36181169	36181169	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36181169delT	uc002yuh.2	-						RUNX1_uc002yui.2_Intron|RUNX1_uc010gmu.2_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yul.1_Intron|RUNX1_uc002yum.1_Intron	NM_001001890	NP_001001890	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						AAGATGGGTGTTTTTAGAACA	0.507			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				4	2	---	---	---	---	
RUNX1	861	broad.mit.edu	37	21	37025503	37025506	+	Intron	DEL	CTGA	-	-	rs141906989		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37025503_37025506delCTGA	uc002yut.1	-									Q01196	RUNX1_HUMAN	Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						gttggggtctctgactaataAGCC	0.083			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				5	4	---	---	---	---	
KCNJ6	3763	broad.mit.edu	37	21	39197402	39197402	+	Intron	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39197402delG	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)	gggtccacctggatgatgtgg	0.000													4	2	---	---	---	---	
NCRNA00114	400866	broad.mit.edu	37	21	40136876	40136876	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40136876delA	uc011aen.1	-						NCRNA00114_uc002yxd.3_Intron	NR_027066				Homo sapiens chromosome 21 open reading frame 24 isoform 1 (C21orf24) mRNA, complete sequence.												0						ttacaactttaaaaaataatc	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	41350443	41350444	+	IGR	DEL	GA	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41350443_41350444delGA								PCP4 (49123 upstream) : DSCAM (33899 downstream)																							AGAAAGACCTGAGAGAGAGAGA	0.564													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	42511130	42511130	+	IGR	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42511130delA								DSCAM (292091 upstream) : C21orf130 (2297 downstream)																							gaactggcctaaggtctcaac	0.164													4	2	---	---	---	---	
HSF2BP	11077	broad.mit.edu	37	21	44994245	44994246	+	Intron	INS	-	T	T	rs113806687		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44994245_44994246insT	uc002zdi.2	-						HSF2BP_uc011aey.1_Intron	NM_007031	NP_008962	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding						spermatogenesis|transcription from RNA polymerase II promoter	cytosol	binding			skin(1)	1				STAD - Stomach adenocarcinoma(101;0.18)		ttctttttctcttttttttttt	0.188													5	3	---	---	---	---	
SUMO3	6612	broad.mit.edu	37	21	46230774	46230776	+	Intron	DEL	GAG	-	-	rs141195217		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46230774_46230776delGAG	uc002zfz.1	-						SUMO3_uc011afi.1_Intron|SUMO3_uc002zga.1_Intron	NM_006936	NP_008867	P55854	SUMO3_HUMAN	small ubiquitin-like modifier protein 3						protein sumoylation	cytoplasm|kinetochore	protein binding				0				Colorectal(79;0.058)		GAGGAGCGCAGAGGAGAACGGAC	0.409													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17791160	17791160	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17791160delT								CECR1 (88422 upstream) : CECR2 (49679 downstream)																							GGCTCCTGTCttttttttttg	0.294													5	3	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26185684	26185685	+	Intron	DEL	AC	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26185684_26185685delAC	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						AAACCAGAATACACACACACAC	0.351													3	4	---	---	---	---	
TTC28	23331	broad.mit.edu	37	22	28495561	28495561	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28495561delA	uc003adp.3	-							NM_001145418	NP_001138890	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28								binding				0						TTGTGGACCTAAAAAGGCATC	0.234													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	36958245	36958246	+	IGR	DEL	GT	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36958245_36958246delGT								EIF3D (32968 upstream) : CACNG2 (1858 downstream)																							GAGGTATATGgtgtgtgtgtgt	0.490													4	2	---	---	---	---	
TMPRSS6	164656	broad.mit.edu	37	22	37469387	37469390	+	Intron	DEL	GATG	-	-	rs111916270		TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37469387_37469390delGATG	uc003aqs.1	-						TMPRSS6_uc003aqt.1_Intron	NM_153609	NP_705837	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6						angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)|skin(1)	6						GAGACCAGAAgatggatggatgga	0.162													7	4	---	---	---	---	
PHF21B	112885	broad.mit.edu	37	22	45406421	45406422	+	5'Flank	INS	-	T	T			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45406421_45406422insT	uc003bfn.2	-						PHF21B_uc003bfm.2_5'Flank|PHF21B_uc011aqk.1_5'Flank|PHF21B_uc011aql.1_5'Flank|PHF21B_uc011aqm.1_5'Flank	NM_138415	NP_612424	Q96EK2	PF21B_HUMAN	PHD finger protein 21B isoform 1								zinc ion binding			ovary(2)|skin(1)	3		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)		TCCTTTAATGATTTTTTTTTAC	0.426													4	2	---	---	---	---	
FAM19A5	25817	broad.mit.edu	37	22	48968671	48968671	+	Intron	DEL	A	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48968671delA	uc003bim.3	+							NM_001082967	NP_001076436	Q7Z5A7	F19A5_HUMAN	family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)		caagagctgtaatgtgatatg	0.000													4	2	---	---	---	---	
FRMPD4	9758	broad.mit.edu	37	X	12735428	12735428	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12735428delT	uc004cuz.1	+						FRMPD4_uc011mij.1_Intron	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4						positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						TCCTTTGTTATTTTTTTTTAA	0.378													4	2	---	---	---	---	
POLA1	5422	broad.mit.edu	37	X	24750783	24750783	+	Intron	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24750783delT	uc004dbl.2	+						POLA1_uc004dbn.2_Intron	NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)	AGCTGGTTCATTTTTTTTTTT	0.313													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	28151836	28151836	+	IGR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:28151836delT								DCAF8L1 (152270 upstream) : IL1RAPL1 (453845 downstream)																							TAGCTTTATCTTTTTTTTTTT	0.279													3	3	---	---	---	---	
COL4A5	1287	broad.mit.edu	37	X	107683189	107683189	+	5'UTR	DEL	T	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107683189delT	uc004enz.1	+	1					COL4A6_uc004env.3_5'Flank|COL4A6_uc011msn.1_5'Flank|COL4A6_uc010npk.2_5'Flank|COL4A6_uc004enw.3_5'Flank|COL4A6_uc004enx.2_5'Flank|COL4A6_uc004eny.2_5'Flank|COL4A5_uc011mso.1_5'UTR	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor						axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4						CTTCTTCTTCTTTTTTTTTTC	0.463									Alport_syndrome_with_Diffuse_Leiomyomatosis				8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	22816766	22816766	+	IGR	DEL	G	-	-			TCGA-CZ-5452-01A-01D-1501-10	TCGA-CZ-5452-11A-01D-1501-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:22816766delG								EIF1AY (61727 upstream) : RPS4Y2 (101188 downstream)																							gaacacaactggggacaagtg	0.000													4	2	---	---	---	---	
