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
CROCCL1	84809	broad.mit.edu	37	1	16945628	16945628	+	Intron	SNP	G	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16945628G>C	uc010ocf.1	-						CROCCL1_uc009vov.1_Intron|CROCCL1_uc001aze.2_Intron|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						AAAGGGCTTGGGGGATGGGCT	0.617													10	79	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16976345	16976345	+	RNA	SNP	T	C	C	rs139809665	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16976345T>C	uc010och.1	+	13		c.2190T>C			MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						CCTTGCTGAATGTCATCTCCA	0.582													7	54	---	---	---	---	PASS
PADI6	353238	broad.mit.edu	37	1	17714957	17714957	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17714957A>G	uc001bak.1	+	7	761	c.761A>G	c.(760-762)AAG>AGG	p.K254R		NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6	246					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	AACCACTTGAAGGAGACTTTC	0.537													5	172	---	---	---	---	PASS
CCDC30	728621	broad.mit.edu	37	1	43055038	43055038	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43055038A>G	uc009vwk.1	+	9	1377	c.1267A>G	c.(1267-1269)ACC>GCC	p.T423A	CCDC30_uc001chm.2_Missense_Mutation_p.T121A|CCDC30_uc001chn.2_Missense_Mutation_p.T212A|CCDC30_uc001chp.2_Missense_Mutation_p.T237A	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	423	Potential.										0						GCAAGTGAGAACCTTACAAGA	0.363													7	317	---	---	---	---	PASS
FPGT	8790	broad.mit.edu	37	1	74671277	74671277	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74671277A>G	uc001dgb.1	+	4	1583	c.1546A>G	c.(1546-1548)AAC>GAC	p.N516D	TNNI3K_uc001dgc.1_Intron|TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron|FPGT_uc010oqt.1_Missense_Mutation_p.N141D|FPGT_uc010oqu.1_Missense_Mutation_p.N262D|FPGT_uc010oqv.1_Intron	NM_003838	NP_003829	O14772	FPGT_HUMAN	fucose-1-phosphate guanyltransferase	516					fucose metabolic process	cytoplasm	fucose-1-phosphate guanylyltransferase activity|GTP binding			skin(1)	1						GTTCTCTGGTAACAAGACATG	0.363													5	391	---	---	---	---	PASS
ACADM	34	broad.mit.edu	37	1	76228484	76228484	+	3'UTR	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76228484C>A	uc001dgw.3	+	12					ACADM_uc009wbp.2_3'UTR|ACADM_uc009wbr.2_3'UTR|ACADM_uc010ore.1_3'UTR|ACADM_uc010orf.1_3'UTR|ACADM_uc001dgx.3_3'UTR|ACADM_uc010org.1_3'UTR	NM_000016	NP_000007	P11310	ACADM_HUMAN	medium-chain acyl-CoA dehydrogenase isoform a						carnitine biosynthetic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|medium-chain fatty acid catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|identical protein binding|medium-chain-acyl-CoA dehydrogenase activity			breast(2)|ovary(1)|skin(1)	4						AACTAGAACACAAGCCACTGT	0.308													10	41	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145293473	145293473	+	Missense_Mutation	SNP	C	A	A	rs57489144		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145293473C>A	uc001end.3	+	1	103	c.68C>A	c.(67-69)ACA>AAA	p.T23K	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.T23K|NOTCH2NL_uc010oyh.1_RNA|NBPF10_uc001emq.1_Missense_Mutation_p.T23K	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	23											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATCAACGAGACATTGCGCCCC	0.517													4	168	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145293535	145293535	+	Missense_Mutation	SNP	C	G	G	rs55936365	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145293535C>G	uc001end.3	+	1	165	c.130C>G	c.(130-132)CTA>GTA	p.L44V	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Missense_Mutation_p.L44V|NOTCH2NL_uc010oyh.1_RNA|NBPF10_uc001emq.1_Missense_Mutation_p.L44V	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	44											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAAATGTTTTCTAACTCAACT	0.443													6	194	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	146398399	146398399	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146398399G>A	uc001emp.3	+	13	2396	c.1198G>A	c.(1198-1200)GCC>ACC	p.A400T	uc010ozk.1_5'UTR	NM_017940	NP_060410	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC55672	129											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCATCTCCAGGCCCTCCTCAC	0.562													11	15	---	---	---	---	PASS
PGLYRP3	114771	broad.mit.edu	37	1	153275057	153275057	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153275057C>A	uc001fbn.1	-	5	609	c.556G>T	c.(556-558)GCT>TCT	p.A186S		NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor	186					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCTTCCCAAGCAGATCGTTTG	0.468													190	358	---	---	---	---	PASS
SLC26A9	115019	broad.mit.edu	37	1	205904828	205904828	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205904828A>G	uc001hdq.2	-	2	235	c.121T>C	c.(121-123)TTC>CTC	p.F41L	SLC26A9_uc001hdp.2_Missense_Mutation_p.F41L	NM_052934	NP_443166	Q7LBE3	S26A9_HUMAN	solute carrier family 26, member 9 isoform a	41						integral to membrane	chloride channel activity|secondary active sulfate transmembrane transporter activity			ovary(1)|skin(1)	2	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)			AGTTACCTGAAGGCATTGCGA	0.532													7	362	---	---	---	---	PASS
DNAH14	127602	broad.mit.edu	37	1	225525799	225525799	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225525799A>G	uc001how.2	+	66	10284	c.10069A>G	c.(10069-10071)ATT>GTT	p.I3357V	DNAH14_uc001hox.2_RNA	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1						CTTAAAGGCAATTCTGAAAAA	0.323													247	309	---	---	---	---	PASS
PGBD5	79605	broad.mit.edu	37	1	230503709	230503709	+	Intron	SNP	A	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230503709A>C	uc010pwb.1	-						PGBD5_uc001htv.2_Silent_p.L102L	NM_024554	NP_078830	Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		caaggagctcaaggtcctgca	0.119													13	124	---	---	---	---	PASS
TTC13	79573	broad.mit.edu	37	1	231067099	231067099	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231067099A>G	uc001huf.3	-	11	1276	c.1245T>C	c.(1243-1245)GAT>GAC	p.D415D	TTC13_uc009xfi.2_Silent_p.D362D|TTC13_uc009xfj.2_RNA|TTC13_uc001hug.3_Silent_p.D362D|TTC13_uc009xfk.1_Silent_p.D305D	NM_024525	NP_078801	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13 isoform a	415	TPR 7.						binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		CTGGGAGAGGATCATTCAGCA	0.353													6	409	---	---	---	---	PASS
ALK	238	broad.mit.edu	37	2	29419724	29419724	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29419724T>C	uc002rmy.2	-	28	4983	c.4076A>G	c.(4075-4077)TAC>TGC	p.Y1359C	ALK_uc010ymo.1_Missense_Mutation_p.Y291C	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1359	Protein kinase.|Cytoplasmic (Potential).				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)	CATTATCCGGTATCTAAAAGA	0.408			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		OREG0014526	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	339	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32658813	32658813	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32658813T>C	uc010ezu.2	+	13	3484	c.3350T>C	c.(3349-3351)ATT>ACT	p.I1117T		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	1117					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					ATCACCAATATTCCACAGATA	0.338													7	411	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32832647	32832647	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32832647A>G	uc010ezu.2	+	72	14330	c.14196A>G	c.(14194-14196)CGA>CGG	p.R4732R		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	4732					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					GAAACATTCGACAAGCAACAG	0.383													7	482	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109367729	109367729	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109367729G>A	uc002tem.3	+	10	1409	c.1283G>A	c.(1282-1284)CGA>CAA	p.R428Q		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	428					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						GGTGCTATTCGAGCACATAAT	0.353													5	557	---	---	---	---	PASS
TTC30B	150737	broad.mit.edu	37	2	178415784	178415784	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178415784T>C	uc002uln.2	-	1	1741	c.1708A>G	c.(1708-1710)AGC>GGC	p.S570G	TTC30B_uc010zfc.1_Missense_Mutation_p.S342G	NM_152517	NP_689730	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	570	TPR 8.				cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			GGTTCCAAGCTTTTGATAACT	0.363													7	440	---	---	---	---	PASS
INO80D	54891	broad.mit.edu	37	2	206921555	206921555	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206921555A>G	uc002vaz.3	-	4	736	c.331T>C	c.(331-333)TTT>CTT	p.F111L		NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	111					DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1						GTCAGGCTAAAGGCCATGGTA	0.522													6	358	---	---	---	---	PASS
CRYGA	1418	broad.mit.edu	37	2	209025594	209025594	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209025594C>G	uc002vcq.3	-	3	476	c.459G>C	c.(457-459)AGG>AGC	p.R153S		NM_014617	NP_055432	P11844	CRGA_HUMAN	crystallin, gamma A	153	Beta/gamma crystallin 'Greek key' 4.				visual perception		structural constituent of eye lens				0				Epithelial(149;0.067)|LUSC - Lung squamous cell carcinoma(261;0.0708)|Lung(261;0.135)		AGTCGTGGTACCTTCTGTAGT	0.562													23	45	---	---	---	---	PASS
NPRL2	10641	broad.mit.edu	37	3	50386816	50386816	+	Splice_Site	SNP	C	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50386816C>G	uc003daj.1	-	4	851	c.448_splice	c.e4+1	p.D150_splice	NPRL2_uc003dai.1_Splice_Site_p.D30_splice|CYB561D2_uc003dak.2_5'Flank|CYB561D2_uc003dal.2_5'Flank|CYB561D2_uc003dam.2_5'Flank	NM_006545	NP_006536	Q8WTW4	NPRL2_HUMAN	tumor suppressor candidate 4						negative regulation of kinase activity		protein binding|protein kinase activity			lung(1)	1						GCTGGCCATACCAATGGGCAG	0.552													24	15	---	---	---	---	PASS
IQCB1	9657	broad.mit.edu	37	3	121500624	121500624	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121500624T>C	uc010hre.1	-	13	1591	c.1376A>G	c.(1375-1377)AAG>AGG	p.K459R	IQCB1_uc003eek.2_Missense_Mutation_p.K326R|IQCB1_uc010hrf.1_RNA	NM_001023570	NP_001018864	Q15051	IQCB1_HUMAN	IQ motif containing B1 isoform a	459					cilium assembly|maintenance of organ identity|photoreceptor cell maintenance	centrosome|photoreceptor connecting cilium	calmodulin binding				0				GBM - Glioblastoma multiforme(114;0.0983)		CACTCGTTTCTTCAGTTCAAC	0.413													6	296	---	---	---	---	PASS
MBD4	8930	broad.mit.edu	37	3	129150378	129150378	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129150378A>G	uc003emh.1	-	8	1885	c.1709T>C	c.(1708-1710)CTT>CCT	p.L570P	uc003emg.2_5'Flank|MBD4_uc003emi.1_3'UTR|MBD4_uc003emj.1_Missense_Mutation_p.L564P|MBD4_uc003emk.1_Missense_Mutation_p.L252P	NM_003925	NP_003916	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	570					depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2						ATTTTCCCAAAGCCAGTCATG	0.348								BER_DNA_glycosylases					8	780	---	---	---	---	PASS
SLCO2A1	6578	broad.mit.edu	37	3	133653504	133653504	+	3'UTR	SNP	T	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133653504T>G	uc003eqa.3	-	14					SLCO2A1_uc003eqb.3_3'UTR	NM_005630	NP_005621	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1						TATAGGCAGGTGTGGAAGAGT	0.493													11	57	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505827	195505827	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505827A>G	uc011bto.1	-	3	12700	c.12240T>C	c.(12238-12240)CCT>CCC	p.P4080P	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGACAGGAAGAGGGGTGGCGT	0.597													5	89	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506555C>T	uc011bto.1	-	3	11972	c.11512G>A	c.(11512-11514)GCC>ACC	p.A3838T	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACCTGTG	0.592													3	23	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195509394	195509394	+	Silent	SNP	T	G	G	rs151068917	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195509394T>G	uc011bto.1	-	3	9133	c.8673A>C	c.(8671-8673)ACA>ACC	p.T2891T	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	767					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGCGTGACCTGTGGATATTG	0.592													5	20	---	---	---	---	PASS
C3orf34	84984	broad.mit.edu	37	3	196435556	196435556	+	5'UTR	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196435556A>G	uc011btw.1	-	2						NM_032898	NP_116287	Q96LK0	CEP19_HUMAN	hypothetical protein LOC84984							centriole|spindle pole					0	all_cancers(143;1.48e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;1.08e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00301)		GGTAAGTCAGAGGAAATCTGA	0.408													6	311	---	---	---	---	PASS
TXK	7294	broad.mit.edu	37	4	48115257	48115257	+	Silent	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48115257C>T	uc003gxx.3	-	3	227	c.141G>A	c.(139-141)AGG>AGA	p.R47R	TXK_uc003gxy.1_Silent_p.R47R	NM_003328	NP_003319	P42681	TXK_HUMAN	TXK tyrosine kinase	47						cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0						TGAGCCACGGCCTGCGACGCT	0.413													11	453	---	---	---	---	PASS
BMP2K	55589	broad.mit.edu	37	4	79800074	79800074	+	Intron	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79800074T>C	uc003hlk.2	+						BMP2K_uc003hlj.2_Silent_p.A660A|BMP2K_uc003hll.2_Silent_p.A124A	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a							nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1						CTTATTTTGCTTCACAGTAAA	0.353													5	159	---	---	---	---	PASS
CDS1	1040	broad.mit.edu	37	4	85538720	85538720	+	Silent	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85538720C>T	uc011ccv.1	+	4	844	c.346C>T	c.(346-348)CTG>TTG	p.L116L		NM_001263	NP_001254	Q92903	CDS1_HUMAN	CDP-diacylglycerol synthase 1	116	Helical; (Potential).				signal transduction|visual perception	endoplasmic reticulum membrane|integral to membrane	diacylglycerol cholinephosphotransferase activity|phosphatidate cytidylyltransferase activity			large_intestine(2)|ovary(1)|breast(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		GTTTCAGGTTCTGGGCATCCA	0.308													5	513	---	---	---	---	PASS
ABCE1	6059	broad.mit.edu	37	4	146032163	146032163	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146032163A>G	uc003ijx.2	+	8	1097	c.657A>G	c.(655-657)GGA>GGG	p.G219G	ABCE1_uc003ijy.2_Silent_p.G219G|ABCE1_uc010iot.2_RNA	NM_001040876	NP_001035809	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E, member 1	219	ABC transporter 1.				interspecies interaction between organisms|response to virus|RNA catabolic process	mitochondrion	ATP binding|ATPase activity|electron carrier activity|iron-sulfur cluster binding|ribonuclease inhibitor activity			skin(1)	1	all_hematologic(180;0.151)					ATCTTTCAGGAGGAGAGTTGC	0.368													7	572	---	---	---	---	PASS
SLC10A7	84068	broad.mit.edu	37	4	147442852	147442852	+	Silent	SNP	T	C	C	rs116538438	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147442852T>C	uc010ioz.2	-	1	272	c.18A>G	c.(16-18)AGA>AGG	p.R6R	SLC10A7_uc003ikr.2_Silent_p.R6R|SLC10A7_uc010ipa.2_Silent_p.R6R|SLC10A7_uc003iks.2_RNA|SLC10A7_uc003ikt.2_Silent_p.R6R|SLC10A7_uc003iku.3_RNA	NM_001029998	NP_001025169	Q0GE19	NTCP7_HUMAN	solute carrier family 10 (sodium/bile acid	6						integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)					CTTTCCTCATTCTCTCCAGCA	0.493													7	614	---	---	---	---	PASS
MARCH6	10299	broad.mit.edu	37	5	10400982	10400982	+	Intron	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10400982T>C	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_5'UTR|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						ACAAAGTTACTTTCATTCATT	0.328													6	358	---	---	---	---	PASS
C5orf36	285600	broad.mit.edu	37	5	93809098	93809098	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93809098A>G	uc011cuk.1	-	8	1611	c.1354T>C	c.(1354-1356)TCT>CCT	p.S452P		NM_001145678	NP_001139150	Q8IV33	K0825_HUMAN	hypothetical protein LOC285600 isoform 1	452											0		all_cancers(142;2.12e-08)|all_epithelial(76;5.95e-11)|all_lung(232;0.000996)|Lung NSC(167;0.0108)|Ovarian(174;0.0218)|Colorectal(57;0.0329)|Breast(839;0.214)|Lung SC(612;0.236)		all cancers(79;3.96e-19)		ACAGCTGAAGACCTTTCATTC	0.413													7	523	---	---	---	---	PASS
DOCK2	1794	broad.mit.edu	37	5	169477329	169477329	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169477329C>T	uc003maf.2	+	41	4221	c.4141C>T	c.(4141-4143)CAG>TAG	p.Q1381*	DOCK2_uc011der.1_RNA|DOCK2_uc010jjm.2_Nonsense_Mutation_p.Q873*	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1381	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCTGATGACCCAGTTCCCCAA	0.502													4	171	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56481876	56481876	+	Intron	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56481876T>C	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_Missense_Mutation_p.N2130S	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)			CAGAAACTTGTTAAGAGTTTT	0.438													32	60	---	---	---	---	PASS
SOBP	55084	broad.mit.edu	37	6	107811866	107811866	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107811866A>G	uc003prx.2	+	1	550	c.46A>G	c.(46-48)AGC>GGC	p.S16G	SOBP_uc003prw.1_Missense_Mutation_p.S16G	NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	16							metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		AAATAAACGGAGCAGGAAGCC	0.507													66	142	---	---	---	---	PASS
ZUFSP	221302	broad.mit.edu	37	6	116988166	116988166	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116988166T>C	uc003pxf.1	-	2	436	c.190A>G	c.(190-192)AGG>GGG	p.R64G	ZUFSP_uc010kef.1_Intron	NM_145062	NP_659499	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	64						intracellular	zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		GTATTTATCCTCTCAAAGTTT	0.348													8	767	---	---	---	---	PASS
RSPO3	84870	broad.mit.edu	37	6	127517157	127517157	+	3'UTR	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127517157T>C	uc003qar.2	+	5					RSPO3_uc003qas.1_Intron	NM_032784	NP_116173	Q9BXY4	RSPO3_HUMAN	R-spondin 3 precursor							extracellular region	heparin binding				0				GBM - Glioblastoma multiforme(226;0.0555)		CACTAGAGGGTTCCATGAGAT	0.438													6	361	---	---	---	---	PASS
C6orf103	79747	broad.mit.edu	37	6	147038067	147038067	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147038067A>T	uc010khx.2	+	15	1831	c.1790A>T	c.(1789-1791)GAT>GTT	p.D597V	C6orf103_uc003qlp.2_5'UTR|C6orf103_uc003qlq.2_RNA	NM_024694	NP_078970	Q8N7X0	CAN7L_HUMAN	hypothetical protein LOC79747	597					oxygen transport|proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|heme binding|oxygen binding			central_nervous_system(2)|lung(1)	3		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.04e-08)|GBM - Glioblastoma multiforme(68;0.0113)		CATCAGAGTGATGGATTAAAC	0.368													8	390	---	---	---	---	PASS
FBXO5	26271	broad.mit.edu	37	6	153293560	153293560	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153293560A>G	uc003qpg.2	-	4	1048	c.939T>C	c.(937-939)GCT>GCC	p.A313A	FBXO5_uc003qph.2_Silent_p.A267A	NM_012177	NP_036309	Q9UKT4	FBX5_HUMAN	F-box only protein 5 isoform a	313					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm|spindle	metal ion binding|protein binding				0		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		CTCTGGTTGAAGCATGAGGTG	0.323													7	538	---	---	---	---	PASS
CCR6	1235	broad.mit.edu	37	6	167417323	167417323	+	5'UTR	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167417323T>C	uc003qvl.2	+	3					FGFR1OP_uc011egp.1_Intron|FGFR1OP_uc003qvj.2_Intron|FGFR1OP_uc003qvk.2_Intron	NM_031409	NP_113597	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6						cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|humoral immune response	integral to plasma membrane	C-C chemokine receptor activity			ovary(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		TTTTTACATCTATCTTTTGAA	0.274													6	751	---	---	---	---	PASS
HGC6.3	100128124	broad.mit.edu	37	6	168377119	168377119	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168377119T>C	uc010kks.1	-	1	501	c.214A>G	c.(214-216)ATG>GTG	p.M72V		NM_001129895	NP_001123367	Q9UM08	Q9UM08_HUMAN	hypothetical protein LOC100128124	72											0						GTGGGGGTCATTCCCCCTGCA	0.622													5	35	---	---	---	---	PASS
CRHR2	1395	broad.mit.edu	37	7	30706921	30706921	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30706921A>G	uc003tbn.2	-	3	482	c.238T>C	c.(238-240)TAT>CAT	p.Y80H	CRHR2_uc010kvw.1_Missense_Mutation_p.Y80H|CRHR2_uc010kvx.1_Missense_Mutation_p.Y80H|CRHR2_uc010kvy.1_Intron|CRHR2_uc003tbo.2_Missense_Mutation_p.Y66H|CRHR2_uc003tbp.2_Missense_Mutation_p.Y107H	NM_001883	NP_001874	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	80	Extracellular (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4						CATTCTCGATAGGCATTCCCT	0.537													5	276	---	---	---	---	PASS
TYW1	55253	broad.mit.edu	37	7	66563615	66563615	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66563615A>G	uc003tvn.2	+	12	1621	c.1472A>G	c.(1471-1473)TAC>TGC	p.Y491C	TYW1_uc010lai.2_RNA|TYW1_uc011kef.1_Missense_Mutation_p.Y105C	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	491					tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)				CCAATAATGTACCCAGAGATC	0.473													5	292	---	---	---	---	PASS
SPDYE7P	441251	broad.mit.edu	37	7	72338316	72338316	+	RNA	SNP	T	A	A	rs142786145	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72338316T>A	uc010lal.1	-	1		c.1340A>T				NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0						TGATTAGAGATCAGATGTCAG	0.532													7	268	---	---	---	---	PASS
SEMA3A	10371	broad.mit.edu	37	7	83640554	83640554	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83640554A>G	uc003uhz.2	-	8	1185	c.870T>C	c.(868-870)CGT>CGC	p.R290R		NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor	290	Sema.				axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4						AGCAAATCAGACGAGCTTTGA	0.403													134	230	---	---	---	---	PASS
PLOD3	8985	broad.mit.edu	37	7	100860059	100860059	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100860059G>T	uc003uyd.2	-	2	574	c.118C>A	c.(118-120)CTG>ATG	p.L40M	ZNHIT1_uc003uye.2_5'Flank|ZNHIT1_uc003uyf.2_5'Flank	NM_001084	NP_001075	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase	40					protein modification process	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein binding			ovary(1)|skin(1)	2	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	GTGATCACCAGCAGCTTCTCT	0.592													49	50	---	---	---	---	PASS
PLOD3	8985	broad.mit.edu	37	7	100860060	100860060	+	Silent	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100860060C>A	uc003uyd.2	-	2	573	c.117G>T	c.(115-117)CTG>CTT	p.L39L	ZNHIT1_uc003uye.2_5'Flank|ZNHIT1_uc003uyf.2_5'Flank	NM_001084	NP_001075	O60568	PLOD3_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase	39					protein modification process	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein binding			ovary(1)|skin(1)	2	Lung NSC(181;0.168)|all_lung(186;0.215)				Succinic acid(DB00139)|Vitamin C(DB00126)	TGATCACCAGCAGCTTCTCTG	0.587													48	49	---	---	---	---	PASS
DNAJC2	27000	broad.mit.edu	37	7	102964053	102964053	+	Silent	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102964053T>C	uc003vbo.2	-	7	962	c.711A>G	c.(709-711)AAA>AAG	p.K237K	PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_5'UTR|DNAJC2_uc010lix.2_Silent_p.K237K|DNAJC2_uc003vbp.2_5'UTR|DNAJC2_uc003vbq.1_RNA	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	237	ZRF1-UBD.				'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1						ACCATTCTGCTTTTTCTTTTT	0.264													7	581	---	---	---	---	PASS
FAM71F2	346653	broad.mit.edu	37	7	128323136	128323136	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128323136G>A	uc003vnk.3	+	5	959	c.853G>A	c.(853-855)GAA>AAA	p.E285K	FAM71F2_uc010llm.1_Missense_Mutation_p.E276K|FAM71F2_uc003vnl.2_RNA|FAM71F2_uc010lln.1_RNA	NM_001012454	NP_001012457	Q6NXP2	F71F2_HUMAN	hypothetical protein LOC346653 isoform a	285											0						CAGCCTCTGGGAACAAGAGGA	0.478													70	104	---	---	---	---	PASS
INTS10	55174	broad.mit.edu	37	8	19703258	19703258	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19703258A>G	uc003wzj.2	+	16	2057	c.1926A>G	c.(1924-1926)GAA>GAG	p.E642E		NM_018142	NP_060612	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	642					snRNA processing	integrator complex	protein binding			ovary(1)	1				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		GAACTCAGGAAGGTGGGAAAA	0.413													7	385	---	---	---	---	PASS
ESCO2	157570	broad.mit.edu	37	8	27661087	27661087	+	3'UTR	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27661087A>G	uc003xgg.2	+	11					ESCO2_uc010luy.1_Intron	NM_001017420	NP_001017420	Q56NI9	ESCO2_HUMAN	establishment of cohesion 1 homolog 2						cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding			central_nervous_system(1)	1		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)		acacacacgcacacacacaTA	0.214									SC_Phocomelia_syndrome				5	38	---	---	---	---	PASS
WHSC1L1	54904	broad.mit.edu	37	8	38139060	38139060	+	Silent	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38139060T>C	uc003xli.2	-	20	4061	c.3543A>G	c.(3541-3543)GAA>GAG	p.E1181E	WHSC1L1_uc011lbm.1_Silent_p.E1181E|WHSC1L1_uc010lwe.2_Silent_p.E1132E|WHSC1L1_uc003xlh.2_5'Flank	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long	1181	SET.				cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			TGCATTCTTCTTCATCAATTA	0.308			T	NUP98	AML								8	698	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61754584	61754584	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61754584G>A	uc003xue.2	+	21	5300	c.4823G>A	c.(4822-4824)AGG>AAG	p.R1608K		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1608					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GAATGTTTCAGGGTGGAGAAG	0.433													73	140	---	---	---	---	PASS
SNX31	169166	broad.mit.edu	37	8	101629859	101629859	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101629859T>C	uc003yjr.2	-	5	572	c.421A>G	c.(421-423)AGA>GGA	p.R141G	SNX31_uc011lhb.1_Missense_Mutation_p.R42G	NM_152628	NP_689841	Q8N9S9	SNX31_HUMAN	sorting nexin 31	141					cell communication|protein transport		phosphatidylinositol binding				0	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			TCTAGGACTCTTTCAGCAGTG	0.413													8	727	---	---	---	---	PASS
ASAP1	50807	broad.mit.edu	37	8	131146582	131146582	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131146582T>C	uc003yta.1	-	14	1205	c.1177A>G	c.(1177-1179)ACA>GCA	p.T393A	ASAP1_uc003ysz.1_Missense_Mutation_p.T204A|ASAP1_uc011liw.1_Missense_Mutation_p.T386A	NM_018482	NP_060952	Q9ULH1	ASAP1_HUMAN	development and differentiation enhancing factor	393	PH.				cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4						AAGTGATATGTTCTATTATCT	0.353													7	528	---	---	---	---	PASS
KIF27	55582	broad.mit.edu	37	9	86474157	86474157	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86474157C>A	uc004ana.2	-	14	3208	c.3064G>T	c.(3064-3066)GTC>TTC	p.V1022F	KIF27_uc010mpw.2_Missense_Mutation_p.V956F|KIF27_uc010mpx.2_Missense_Mutation_p.V925F	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27	1022	Potential.				cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5						TTCTGGAGGACTTCAACTTGT	0.408													111	464	---	---	---	---	PASS
PTCH1	5727	broad.mit.edu	37	9	98229631	98229631	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98229631T>C	uc004avk.3	-	15	2515	c.2327A>G	c.(2326-2328)GAC>GGC	p.D776G	PTCH1_uc010mro.2_Missense_Mutation_p.D625G|PTCH1_uc010mrp.2_Missense_Mutation_p.D625G|PTCH1_uc010mrq.2_Missense_Mutation_p.D625G|PTCH1_uc004avl.3_Missense_Mutation_p.D625G|PTCH1_uc010mrr.2_Missense_Mutation_p.D710G|PTCH1_uc004avm.3_Missense_Mutation_p.D775G	NM_000264	NP_000255	Q13635	PTC1_HUMAN	patched isoform L	776	Extracellular (Potential).				embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GTCCGTAAGGTCCAGCCCGTC	0.468									Basal_Cell_Nevus_syndrome				6	232	---	---	---	---	PASS
C10orf111	221060	broad.mit.edu	37	10	15138321	15138321	+	3'UTR	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15138321T>C	uc001inw.2	-	2					RPP38_uc001iny.3_5'Flank|RPP38_uc009xjm.2_5'Flank|RPP38_uc001inx.3_5'Flank	NM_153244	NP_694976	Q8N326	CJ111_HUMAN	hypothetical protein LOC221060							integral to membrane					0						tcaacaacaataataataata	0.144													4	92	---	---	---	---	PASS
SLC16A9	220963	broad.mit.edu	37	10	61432539	61432539	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61432539C>G	uc010qig.1	-	3	778	c.329G>C	c.(328-330)GGC>GCC	p.G110A		NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid	110	Helical; (Potential).				urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						TACAACAATGCCATAGGAAAA	0.428													40	110	---	---	---	---	PASS
FAM35A	54537	broad.mit.edu	37	10	88911830	88911830	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88911830C>A	uc001kei.3	+	3	833	c.719C>A	c.(718-720)ACA>AAA	p.T240K		NM_019054	NP_061927	Q86V20	FA35A_HUMAN	hypothetical protein LOC54537	240										ovary(2)|skin(2)	4						TCAACTGATACAGAATTTCTC	0.388													4	120	---	---	---	---	PASS
HELLS	3070	broad.mit.edu	37	10	96350466	96350466	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96350466T>C	uc001kjt.2	+	15	1805	c.1700T>C	c.(1699-1701)CTT>CCT	p.L567P	HELLS_uc001kjs.2_Missense_Mutation_p.L551P|HELLS_uc009xul.2_Missense_Mutation_p.L469P|HELLS_uc009xum.2_Missense_Mutation_p.L437P|HELLS_uc009xun.2_Missense_Mutation_p.L443P|HELLS_uc009xuo.2_Missense_Mutation_p.L613P|HELLS_uc001kju.2_Missense_Mutation_p.L206P|HELLS_uc009xup.2_RNA|HELLS_uc009xuq.2_Missense_Mutation_p.L429P|HELLS_uc009xur.2_RNA	NM_018063	NP_060533	Q9NRZ9	HELLS_HUMAN	helicase, lymphoid-specific	567					cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		ATGATGCTACTTCGTAAATGT	0.318													7	541	---	---	---	---	PASS
CYP2C8	1558	broad.mit.edu	37	10	96824701	96824701	+	Silent	SNP	G	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96824701G>A	uc001kkb.2	-	4	593	c.498C>T	c.(496-498)CCC>CCT	p.P166P	CYP2C8_uc001kkc.2_RNA|CYP2C8_uc010qoa.1_Silent_p.P96P|CYP2C8_uc010qob.1_Silent_p.P80P|CYP2C8_uc010qoc.1_Silent_p.P64P|CYP2C8_uc010qod.1_Silent_p.P80P	NM_000770	NP_000761	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C,	166					exogenous drug catabolic process|organic acid metabolic process|oxidative demethylation|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|electron carrier activity|heme binding|oxygen binding				0		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Aminophenazone(DB01424)|Amiodarone(DB01118)|Amodiaquine(DB00613)|Benzphetamine(DB00865)|Carbamazepine(DB00564)|Cerivastatin(DB00439)|Diclofenac(DB00586)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lovastatin(DB00227)|Midazolam(DB00683)|Montelukast(DB00471)|Nicardipine(DB00622)|Paclitaxel(DB01229)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rifampin(DB01045)|Rosiglitazone(DB00412)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Tolbutamide(DB01124)|Torasemide(DB00214)|Tretinoin(DB00755)|Trimethoprim(DB00440)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zopiclone(DB01198)	GGATGAAAGTGGGATCACAGG	0.303													5	308	---	---	---	---	PASS
TLL2	7093	broad.mit.edu	37	10	98155769	98155769	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98155769C>T	uc001kml.1	-	12	1619	c.1393G>A	c.(1393-1395)GGG>AGG	p.G465R	TLL2_uc009xvf.1_Missense_Mutation_p.G443R	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	465	CUB 2.				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		ATGTCTCCCCCGCAGGTAGCT	0.527											OREG0020398	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	241	---	---	---	---	PASS
SHOC2	8036	broad.mit.edu	37	10	112764387	112764387	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112764387A>G	uc001kzl.3	+	5	1345	c.996A>G	c.(994-996)AAA>AAG	p.K332K	SHOC2_uc009xxx.2_Silent_p.K332K|SHOC2_uc010qrg.1_5'UTR|SHOC2_uc001kzn.2_Silent_p.K286K	NM_007373	NP_031399	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog	332	LRR 11.				fibroblast growth factor receptor signaling pathway|positive regulation of Ras protein signal transduction|Ras protein signal transduction	nucleus|protein phosphatase type 1 complex	protein phosphatase binding|protein phosphatase regulator activity			ovary(1)|skin(1)	2				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		GTCTTGTGAAACTGAATAGTT	0.358													8	625	---	---	---	---	PASS
HTRA1	5654	broad.mit.edu	37	10	124268184	124268184	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124268184A>G	uc001lgj.2	+	6	1146	c.1018A>G	c.(1018-1020)ATT>GTT	p.I340V		NM_002775	NP_002766	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1 precursor	340	Serine protease.				proteolysis|regulation of cell growth	extracellular space	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				CGGTGAAGTGATTGGAATTAA	0.463													6	294	---	---	---	---	PASS
FRG2B	441581	broad.mit.edu	37	10	135440141	135440141	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135440141C>T	uc010qvg.1	-	1	159	c.106G>A	c.(106-108)GAG>AAG	p.E36K		NM_001080998	NP_001074467	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	36						nucleus					0		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GGTTTCTTCTCATCTGAGCCC	0.502													6	653	---	---	---	---	PASS
LOC650368	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3427845C>T	uc010qxs.1	+	9		c.838C>T			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						CTTCAAGTGGCAGGAGCAGAA	0.587													4	74	---	---	---	---	PASS
OR5W2	390148	broad.mit.edu	37	11	55681849	55681849	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55681849A>T	uc010rir.1	-	1	210	c.210T>A	c.(208-210)GAT>GAA	p.D70E		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	70	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2						AATAGCAGAGATCACAGAAAG	0.403													125	162	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	74208320	74208320	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74208320A>G	uc001ove.2	+	2	1161	c.370A>G	c.(370-372)AGA>GGA	p.R124G						SubName: Full=Similar to Cytochrome c, somatic;																		aatgaaaaatagaaaaacact	0.000													4	100	---	---	---	---	PASS
DDX12	440081	broad.mit.edu	37	12	9571764	9571764	+	Missense_Mutation	SNP	T	G	G	rs117821635	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9571764T>G	uc010sgs.1	-	25	2675	c.2480A>C	c.(2479-2481)CAC>CCC	p.H827P	DDX12_uc001qvx.3_Missense_Mutation_p.H49P|DDX12_uc001qvy.1_Missense_Mutation_p.H49P	NM_004400	NP_004391			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12												0						CTTCCCTGGGTGTGCCTGGCC	0.642													7	47	---	---	---	---	PASS
KLRD1	3824	broad.mit.edu	37	12	10467335	10467335	+	Silent	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10467335T>C	uc001qxw.3	+	7	680	c.483T>C	c.(481-483)GCT>GCC	p.A161A	KLRD1_uc001qxx.3_Silent_p.A161A|KLRD1_uc001qxy.3_Silent_p.A130A|KLRD1_uc009zhh.2_Silent_p.A140A|KLRD1_uc009zhi.2_3'UTR|KLRD1_uc001qxz.3_Silent_p.A162A	NM_001114396	NP_001107868	Q13241	KLRD1_HUMAN	killer cell lectin-like receptor subfamily D,	161	Extracellular (Potential).|C-type lectin.				cell surface receptor linked signaling pathway|regulation of immune response	integral to membrane|plasma membrane	sugar binding|transmembrane receptor activity				0						ATGGAAATGCTTTAGATGAAT	0.333													6	345	---	---	---	---	PASS
ATF7IP	55729	broad.mit.edu	37	12	14628883	14628883	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14628883A>G	uc001rbw.2	+	11	3080	c.2922A>G	c.(2920-2922)GAA>GAG	p.E974E	ATF7IP_uc001rbu.2_Silent_p.E974E|ATF7IP_uc001rbv.1_Silent_p.E973E|ATF7IP_uc001rbx.2_Silent_p.E973E|ATF7IP_uc001rby.3_Silent_p.E974E|ATF7IP_uc001rca.2_Silent_p.E974E	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	974	Interaction with SUMO.				DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						TGGATGATGAAGAGAGTGGAG	0.358													7	493	---	---	---	---	PASS
DENND5B	160518	broad.mit.edu	37	12	31552599	31552599	+	Silent	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31552599T>C	uc001rki.1	-	16	3243	c.3057A>G	c.(3055-3057)GGA>GGG	p.G1019G	DENND5B_uc001rkh.1_Silent_p.G1054G|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	1019	PLAT.					integral to membrane				ovary(1)|central_nervous_system(1)	2						TGTATGTATGTCCTGTGATTT	0.373													6	358	---	---	---	---	PASS
MMP19	4327	broad.mit.edu	37	12	56236156	56236156	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56236156C>A	uc001sib.2	-	2	275	c.154G>T	c.(154-156)GAT>TAT	p.D52Y	MMP19_uc001sia.2_5'Flank|MMP19_uc001sid.2_RNA|MMP19_uc010spw.1_Missense_Mutation_p.D52Y	NM_002429	NP_002420	Q99542	MMP19_HUMAN	matrix metalloproteinase 19 isoform rasi-1	52					angiogenesis|cell differentiation|collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)	1						TCGGTGATATCTTCTGGCTTG	0.488													8	278	---	---	---	---	PASS
PLXNC1	10154	broad.mit.edu	37	12	94603479	94603479	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94603479A>G	uc001tdc.2	+	5	1802	c.1553A>G	c.(1552-1554)AAG>AGG	p.K518R		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	518	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3						AGTAAAGAAAAGGTAAGAGGA	0.353													6	228	---	---	---	---	PASS
MSI1	4440	broad.mit.edu	37	12	120791103	120791103	+	Silent	SNP	G	A	A	rs140182426		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120791103G>A	uc001tye.1	-	10	796	c.732C>T	c.(730-732)CCC>CCT	p.P244P		NM_002442	NP_002433	O43347	MSI1H_HUMAN	musashi 1	244					nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGACTTACCGGGGAACTGGT	0.617													43	74	---	---	---	---	PASS
LOC374491	374491	broad.mit.edu	37	13	25157668	25157668	+	RNA	SNP	G	A	A	rs138262720	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25157668G>A	uc001upm.2	+	6		c.502G>A			LOC374491_uc001upn.2_RNA|LOC374491_uc001upo.2_5'Flank					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						GGAGAAAGGCGAACAGATAAA	0.398													4	90	---	---	---	---	PASS
POSTN	10631	broad.mit.edu	37	13	38154717	38154717	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38154717T>C	uc001uwo.3	-	11	1628	c.1510A>G	c.(1510-1512)AAA>GAA	p.K504E	POSTN_uc010tet.1_Missense_Mutation_p.K32E|POSTN_uc001uwp.3_Missense_Mutation_p.K504E|POSTN_uc001uwr.2_Missense_Mutation_p.K504E|POSTN_uc001uwq.2_Missense_Mutation_p.K504E|POSTN_uc010teu.1_Missense_Mutation_p.K504E|POSTN_uc010tev.1_Missense_Mutation_p.K504E|POSTN_uc010tew.1_Missense_Mutation_p.K504E|POSTN_uc010tex.1_Missense_Mutation_p.K419E	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	504	FAS1 4.				cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TTATCTTGTTTTAACTTTTCA	0.438													7	642	---	---	---	---	PASS
FREM2	341640	broad.mit.edu	37	13	39265348	39265348	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39265348A>G	uc001uwv.2	+	1	4176	c.3867A>G	c.(3865-3867)GAA>GAG	p.E1289E		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1289	Extracellular (Potential).|CSPG 9.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ACTCTGTGGAAAAGACGGTCC	0.398													5	158	---	---	---	---	PASS
C13orf37	440145	broad.mit.edu	37	13	73293134	73293134	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73293134A>C	uc001viu.2	-	2	379	c.181T>G	c.(181-183)TCA>GCA	p.S61A		NM_001071775	NP_001065243	Q08AG7	MZT1_HUMAN	hypothetical protein LOC440145	61					gamma-tubulin complex localization	centrosome|gamma-tubulin ring complex|spindle	protein binding				0						ATAACCGATGATAAAGCTTCT	0.353													173	247	---	---	---	---	PASS
TUBGCP3	10426	broad.mit.edu	37	13	113200070	113200070	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113200070A>G	uc001vse.1	-	11	1465	c.1278T>C	c.(1276-1278)GTT>GTC	p.V426V	TUBGCP3_uc010tjq.1_Silent_p.V416V|TUBGCP3_uc001vsf.2_Silent_p.V426V	NM_006322	NP_006313	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	426					G2/M transition of mitotic cell cycle|microtubule nucleation|single fertilization	centriole|cytosol|polar microtubule	gamma-tubulin binding|structural constituent of cytoskeleton			central_nervous_system(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)					GGAAGCTCAAAACAGGATGAG	0.517													6	187	---	---	---	---	PASS
PCK2	5106	broad.mit.edu	37	14	24573183	24573183	+	3'UTR	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24573183C>T	uc001wlt.2	+	10					NRL_uc001wlq.2_Intron|PCK2_uc001wlr.1_3'UTR|PCK2_uc010tnw.1_3'UTR|PCK2_uc010tnx.1_3'UTR|PCK2_uc001wlu.3_3'UTR	NM_004563	NP_004554	Q16822	PCKGM_HUMAN	mitochondrial phosphoenolpyruvate carboxykinase						gluconeogenesis	mitochondrial matrix	GTP binding|metal ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0184)		ACCTGAGGCCCTAGTCTAGCA	0.493													3	61	---	---	---	---	PASS
SFTA3	253970	broad.mit.edu	37	14	36982445	36982445	+	5'UTR	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36982445C>T	uc001wtr.2	-	1					SFTA3_uc001wtq.2_RNA|SFTA3_uc001wts.2_Intron	NM_001101341	NP_001094811	P0C7M3	SFTA3_HUMAN	surfactant associated 3												0						GACGCCTGGACGCGGTGAGCG	0.567													9	143	---	---	---	---	PASS
PPIL5	122769	broad.mit.edu	37	14	50081105	50081105	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50081105T>C	uc001wwn.2	+	4	1460	c.1136T>C	c.(1135-1137)GTT>GCT	p.V379A	SDCCAG1_uc010anj.1_Intron|PPIL5_uc001wwo.2_Silent_p.C138C|PPIL5_uc010ank.2_Missense_Mutation_p.V320A|PPIL5_uc001wwp.2_RNA	NM_152329	NP_689542	Q96L50	LLR1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 5	379											0	all_epithelial(31;0.0021)|Breast(41;0.0124)					CTGCATTCTGTTGCCCACACT	0.388													8	799	---	---	---	---	PASS
CDC42BPB	9578	broad.mit.edu	37	14	103442383	103442383	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103442383A>G	uc001ymi.1	-	10	1456	c.1224T>C	c.(1222-1224)TGT>TGC	p.C408C		NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	408	AGC-kinase C-terminal.				actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		GATCAGAAAAACAGCTGGGAA	0.418													7	223	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106877591	106877591	+	Intron	SNP	G	C	C	rs147493442	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106877591G>C	uc010tyt.1	-						uc010tyu.1_Missense_Mutation_p.P121A					Parts of antibodies, mostly variable regions.												0						TTTTGTCTGGGCTCACACTCA	0.627													5	38	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	20643886	20643886	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20643886T>C	uc001ytg.2	-	23	3593	c.2884A>G	c.(2884-2886)ATG>GTG	p.M962V	uc010tyx.1_RNA|uc001yth.3_Missense_Mutation_p.M962V					RecName: Full=Putative HERC2-like protein 3;																		CACGTCCGCATGTCAGAGAAC	0.498													4	74	---	---	---	---	PASS
RASGRP1	10125	broad.mit.edu	37	15	38782713	38782713	+	3'UTR	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38782713A>G	uc001zke.3	-	17					RASGRP1_uc010bbe.2_RNA|RASGRP1_uc010bbf.2_3'UTR|RASGRP1_uc010bbg.2_3'UTR|RASGRP1_uc001zkd.3_3'UTR	NM_005739	NP_005730	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		AGGAAATGAGATCACTATACT	0.383													6	292	---	---	---	---	PASS
DUT	1854	broad.mit.edu	37	15	48633511	48633511	+	Silent	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48633511A>G	uc001zws.2	+	5	674	c.582A>G	c.(580-582)AGA>AGG	p.R194R	DUT_uc001zwt.2_Silent_p.R83R|DUT_uc001zwu.2_RNA|DUT_uc001zwv.2_Silent_p.R106R|DUT_uc001zww.2_Silent_p.R106R	NM_001025248	NP_001020419	P33316	DUT_HUMAN	deoxyuridine triphosphatase isoform 1 precursor	194					DNA replication|dUTP metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process	mitochondrion|nucleoplasm	dUTP diphosphatase activity|protein binding				0		all_lung(180;0.00265)		all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07)		AAGATTATAGAGGAAATGTTG	0.284								Modulation_of_nucleotide_pools					7	567	---	---	---	---	PASS
TRIP4	9325	broad.mit.edu	37	15	64717763	64717763	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64717763C>T	uc002anm.2	+	11	1551	c.1508C>T	c.(1507-1509)CCG>CTG	p.P503L		NM_016213	NP_057297	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	503					positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	ligand-dependent nuclear receptor binding|transcription coactivator activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3						AATGACTATCCGTCAGGTTGT	0.343													6	560	---	---	---	---	PASS
CSPG4	1464	broad.mit.edu	37	15	75981976	75981976	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75981976C>T	uc002baw.2	-	3	1523	c.1430G>A	c.(1429-1431)CGC>CAC	p.R477H		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	477	Extracellular (Potential).|CSPG 1.|Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition (By similarity).			RH -> HY (in Ref. 1; CAA65529).	angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3						CTCGCCATGGCGTGCCCCTCG	0.637													3	22	---	---	---	---	PASS
MEF2A	4205	broad.mit.edu	37	15	100211761	100211761	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100211761C>T	uc010urw.1	+	4	654	c.295C>T	c.(295-297)CCA>TCA	p.P99S	MEF2A_uc010urv.1_Intron|MEF2A_uc010bos.2_Intron|MEF2A_uc002bvf.2_Missense_Mutation_p.P99S|MEF2A_uc002bve.2_Intron|MEF2A_uc002bvg.2_Intron|MEF2A_uc002bvi.2_Intron|MEF2A_uc010bot.2_Intron	NM_005587	NP_005578	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A isoform 1	99					apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development	nuclear chromatin|nucleoplasm	activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding			ovary(1)	1	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			GTGCGACAGCCCAGACCCTGA	0.333													9	468	---	---	---	---	PASS
CIRH1A	84916	broad.mit.edu	37	16	69200826	69200826	+	Intron	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69200826C>A	uc002ews.3	+						CIRH1A_uc002ewr.2_3'UTR|CIRH1A_uc002ewt.3_Intron|CIRH1A_uc010cfi.2_Intron	NM_032830	NP_116219	Q969X6	CIR1A_HUMAN	cirhin							nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)		ATTATGGCTACAGCTGTTTTC	0.418													5	32	---	---	---	---	PASS
PDPR	55066	broad.mit.edu	37	16	70192394	70192394	+	3'UTR	SNP	G	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70192394G>A	uc002eyf.1	+	19					CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_3'UTR|PDPR_uc002eyg.1_3'UTR|PDPR_uc002eyh.2_3'UTR|PDPR_uc010vls.1_3'UTR	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory						glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		ACTTACGCTGGCTCCTTCTAG	0.443													3	40	---	---	---	---	PASS
ZFHX3	463	broad.mit.edu	37	16	72831125	72831125	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72831125C>A	uc002fck.2	-	9	6129	c.5456G>T	c.(5455-5457)AGT>ATT	p.S1819I	ZFHX3_uc002fcl.2_Missense_Mutation_p.S905I	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	1819					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				CAGTGCCCCACTGGTCACTGG	0.592													67	122	---	---	---	---	PASS
CLEC18B	497190	broad.mit.edu	37	16	74442881	74442881	+	3'UTR	SNP	C	G	G	rs145544284	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74442881C>G	uc002fct.2	-	13					CLEC18B_uc002fcu.2_3'UTR	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						CCAGGGCAGGCGAGGGAGCCA	0.632													17	119	---	---	---	---	PASS
CYB5D2	124936	broad.mit.edu	37	17	4046946	4046946	+	5'UTR	SNP	A	C	C	rs28372950		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4046946A>C	uc002fxm.3	+	1					ZZEF1_uc002fxe.2_5'Flank|ZZEF1_uc002fxk.1_5'Flank|CYB5D2_uc010cko.2_Intron|CYB5D2_uc002fxl.3_5'UTR	NM_144611	NP_653212	Q8WUJ1	NEUFC_HUMAN	cytochrome b5 domain containing 2						nervous system development	extracellular region	heme binding			large_intestine(2)|ovary(1)	3						CGAGAGAGAGAGCGAGAGCGC	0.602													10	93	---	---	---	---	PASS
MYH8	4626	broad.mit.edu	37	17	10300211	10300211	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10300211A>G	uc002gmm.2	-	31	4366	c.4271T>C	c.(4270-4272)CTC>CCC	p.L1424P	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1424	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TTCATTCTGGAGCCGCTGCTT	0.498									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				6	244	---	---	---	---	PASS
FAM18B2	201158	broad.mit.edu	37	17	15441469	15441469	+	Intron	SNP	C	T	T	rs139351610	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15441469C>T	uc002goq.2	-						CDRT4_uc010vvw.1_Intron|FAM18B2_uc010vvx.1_Intron|FAM18B2_uc010cor.2_3'UTR	NM_145301	NP_660344	Q96ET8	F18B2_HUMAN	hypothetical protein LOC201158 isoform 1							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0872)|BRCA - Breast invasive adenocarcinoma(8;0.0581)|READ - Rectum adenocarcinoma(1115;0.0967)		TCCAGTGTTCCGCAAAAGACA	0.393													6	460	---	---	---	---	PASS
SYNRG	11276	broad.mit.edu	37	17	35902054	35902054	+	Intron	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35902054C>T	uc002hoa.2	-						SYNRG_uc010wde.1_Intron|SYNRG_uc010wdf.1_Intron|SYNRG_uc002hoc.2_Intron|SYNRG_uc002hoe.2_Intron|SYNRG_uc002hod.2_Intron|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Intron|SYNRG_uc002hof.2_3'UTR	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1						endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2						ATAGTAAAATCTACCTTGGAA	0.363													48	290	---	---	---	---	PASS
SCPEP1	59342	broad.mit.edu	37	17	55058513	55058513	+	Silent	SNP	C	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55058513C>G	uc002iuv.3	+	2	200	c.147C>G	c.(145-147)GCC>GCG	p.A49A	SCPEP1_uc010dcl.2_RNA|SCPEP1_uc010wnk.1_5'UTR	NM_021626	NP_067639	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1 precursor	49					proteolysis	extracellular region	serine-type carboxypeptidase activity			skin(1)	1	Breast(9;2.86e-08)					GCAAGGATGCCTACATGTTCT	0.512													93	177	---	---	---	---	PASS
PSMD12	5718	broad.mit.edu	37	17	65341780	65341780	+	Intron	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65341780A>G	uc002jfy.2	-						PSMD12_uc002jga.2_Intron|PSMD12_uc002jfz.2_Intron|PSMD12_uc010det.1_3'UTR	NM_002816	NP_002807	O00232	PSD12_HUMAN	proteasome 26S non-ATPase subunit 12 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)					TATACACAGAAGTATACACTT	0.174													7	401	---	---	---	---	PASS
ABCA6	23460	broad.mit.edu	37	17	67075142	67075142	+	Missense_Mutation	SNP	T	C	C	rs148870578		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67075142T>C	uc002jhw.1	-	39	5001	c.4826A>G	c.(4825-4827)AAA>AGA	p.K1609R		NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6	1609					transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)					AGGGAGGAGTTTCCATCTCAT	0.303													7	727	---	---	---	---	PASS
SPIRE1	56907	broad.mit.edu	37	18	12493160	12493160	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12493160C>T	uc002kre.2	-	8	1147	c.1100G>A	c.(1099-1101)CGG>CAG	p.R367Q	SPIRE1_uc002krc.2_RNA|SPIRE1_uc010wzw.1_Missense_Mutation_p.R247Q|SPIRE1_uc010wzx.1_Missense_Mutation_p.R170Q|SPIRE1_uc010wzy.1_Missense_Mutation_p.R367Q	NM_001128626	NP_001122098	Q08AE8	SPIR1_HUMAN	spire homolog 1 isoform a	367						cytoskeleton|perinuclear region of cytoplasm	actin binding				0						ATGGAGGCTCCGTGGCCGTGG	0.408													5	710	---	---	---	---	PASS
NPC1	4864	broad.mit.edu	37	18	21141440	21141440	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21141440G>T	uc002kum.3	-	5	789	c.515C>A	c.(514-516)GCC>GAC	p.A172D	NPC1_uc010xaz.1_5'Flank|NPC1_uc010xba.1_Missense_Mutation_p.A17D	NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor	172					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)					GAGTCCCAGGGCCTTGTCATT	0.493													63	107	---	---	---	---	PASS
NPC1	4864	broad.mit.edu	37	18	21141441	21141441	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21141441C>T	uc002kum.3	-	5	788	c.514G>A	c.(514-516)GCC>ACC	p.A172T	NPC1_uc010xaz.1_5'Flank|NPC1_uc010xba.1_Missense_Mutation_p.A17T	NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor	172					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)					AGTCCCAGGGCCTTGTCATTA	0.488													65	105	---	---	---	---	PASS
MADCAM1	8174	broad.mit.edu	37	19	501762	501762	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:501762A>C	uc002los.2	+	4	771	c.761A>C	c.(760-762)CAG>CCG	p.Q254P	MADCAM1_uc002lot.2_Intron|MADCAM1_uc010drq.2_Intron	NM_130760	NP_570116	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion	254	Mucin-like.|Extracellular (Potential).|5.5 X 8 AA tandem repeats of [PS]-P-D-T- T-S-[QP]-E.|4.			Q -> P (in Ref. 1; AAC13661).	cell adhesion|immune response|regulation of immune response|signal transduction	integral to membrane|membrane fraction|plasma membrane					0		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCACCTCCCAGGAGCCTCCC	0.721													5	19	---	---	---	---	PASS
DPP9	91039	broad.mit.edu	37	19	4702090	4702090	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4702090A>G	uc002mba.2	-	9	1219	c.961T>C	c.(961-963)TCT>CCT	p.S321P	DPP9_uc002mbb.2_Missense_Mutation_p.S321P|DPP9_uc002mbc.2_Missense_Mutation_p.S321P	NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9	292					proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)		AGCGCAGGAGAGGGGACGTGA	0.597													5	79	---	---	---	---	PASS
GCDH	2639	broad.mit.edu	37	19	13004357	13004357	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13004357G>A	uc002mvq.2	+	6	472	c.395G>A	c.(394-396)CGG>CAG	p.R132Q	GCDH_uc010xms.1_Missense_Mutation_p.R99Q|GCDH_uc002mvp.2_Missense_Mutation_p.R132Q|GCDH_uc010xmt.1_5'UTR|GCDH_uc010xmu.1_Missense_Mutation_p.R88Q	NM_000159	NP_000150	Q92947	GCDH_HUMAN	glutaryl-Coenzyme A dehydrogenase isoform a	132					lysine catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|glutaryl-CoA dehydrogenase activity|protein binding				0						GAGCTGGAGCGGGTGGACAGT	0.587													4	176	---	---	---	---	PASS
CCDC124	115098	broad.mit.edu	37	19	18054506	18054506	+	Silent	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18054506C>T	uc010xpz.1	+	5	699	c.654C>T	c.(652-654)CCC>CCT	p.P218P	CCDC124_uc002nhs.2_Silent_p.P218P	NM_001136203	NP_001129675	Q96CT7	CC124_HUMAN	coiled-coil domain containing 124	218							DNA binding				0						GGGCCGTGCCCTTCAATGCCC	0.617													6	9	---	---	---	---	PASS
C19orf46	163183	broad.mit.edu	37	19	36499618	36499618	+	5'UTR	SNP	G	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36499618G>C	uc002ocq.1	-	1					C19orf46_uc002ocr.1_5'UTR|C19orf46_uc002ocs.1_5'UTR|C19orf46_uc010een.1_Intron	NM_001039876	NP_001034965	Q8N205	SYNE4_HUMAN	hypothetical protein LOC163183						establishment of epithelial cell apical/basal polarity	integral to nuclear outer membrane	actin binding			ovary(1)	1	all_lung(56;1.35e-06)|Lung NSC(56;2.15e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TCAGGTGAGGGCAGCCAGTAA	0.662													7	36	---	---	---	---	PASS
PRX	57716	broad.mit.edu	37	19	40903927	40903927	+	Intron	SNP	G	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40903927G>T	uc002onr.2	-						PRX_uc002onq.2_Intron|PRX_uc002ons.2_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2						axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGGAGGCTGGGAGTGGACAGG	0.582													7	11	---	---	---	---	PASS
LILRB1	10859	broad.mit.edu	37	19	55143551	55143551	+	Missense_Mutation	SNP	G	A	A	rs112916853		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55143551G>A	uc002qgj.2	+	6	864	c.524G>A	c.(523-525)CGT>CAT	p.R175H	LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Missense_Mutation_p.R175H|LILRB1_uc002qgk.2_Missense_Mutation_p.R175H|LILRB1_uc002qgm.2_Missense_Mutation_p.R175H|LILRB1_uc010erq.2_Missense_Mutation_p.R175H|LILRB1_uc010err.2_RNA	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor,	175	Ig-like C2-type 2.|Extracellular (Potential).				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		CCCCATGCCCGTGGGTCGTCC	0.577										HNSCC(37;0.09)			85	141	---	---	---	---	PASS
CST11	140880	broad.mit.edu	37	20	23431177	23431177	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23431177T>C	uc002wtf.1	-	3	417	c.383A>G	c.(382-384)TAC>TGC	p.Y128C	CST11_uc002wtg.1_Missense_Mutation_p.Y93C	NM_130794	NP_570612	Q9H112	CST11_HUMAN	cystatin 11 isoform 1 precursor	128					defense response to bacterium	cytoplasm|nucleus	cysteine-type endopeptidase inhibitor activity				0	Colorectal(13;0.0431)|Lung NSC(19;0.235)					CAAAATTTTGTACTGTTCAAA	0.408													6	462	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29653853	29653853	+	3'UTR	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29653853A>G	uc010ztl.1	+	4					FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_3'UTR					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						cactgcccctataggctgcag	0.000													3	2	---	---	---	---	PASS
RBM39	9584	broad.mit.edu	37	20	34319917	34319917	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34319917C>T	uc002xeb.2	-	4	586	c.242G>A	c.(241-243)CGG>CAG	p.R81Q	RBM39_uc002xdz.2_Missense_Mutation_p.R57Q|RBM39_uc002xea.2_5'UTR|RBM39_uc010gfn.2_5'UTR|RBM39_uc010zvm.1_Missense_Mutation_p.R81Q|RBM39_uc002xeg.2_Missense_Mutation_p.R81Q|RBM39_uc002xec.2_Missense_Mutation_p.R81Q|RBM39_uc002xed.2_5'UTR|RBM39_uc002xee.2_5'UTR|RBM39_uc002xef.2_5'UTR|RBM39_uc010zvn.1_5'UTR	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a	81	Arg/Ser-rich (RS domain).				mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					TGAGCGGCTCCGTCGCCTCTC	0.438													117	256	---	---	---	---	PASS
SGK2	10110	broad.mit.edu	37	20	42200707	42200707	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42200707C>A	uc002xkv.2	+	8	926	c.707C>A	c.(706-708)ACG>AAG	p.T236K	SGK2_uc002xkt.2_RNA|SGK2_uc002xkr.2_Missense_Mutation_p.T176K|SGK2_uc010ggm.2_Missense_Mutation_p.T176K|SGK2_uc002xks.2_Missense_Mutation_p.T175K|SGK2_uc002xku.2_Missense_Mutation_p.T176K	NM_016276	NP_057360	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2 isoform	236	Protein kinase.				intracellular protein kinase cascade|response to oxidative stress		ATP binding|potassium channel regulator activity|protein serine/threonine kinase activity|sodium channel regulator activity			lung(3)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	6		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GTGGTGCTGACGGATTTTGGC	0.577													6	153	---	---	---	---	PASS
KRTAP6-2	337967	broad.mit.edu	37	21	31971188	31971188	+	Silent	SNP	G	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31971188G>A	uc011adc.1	-	1	6	c.6C>T	c.(4-6)TGC>TGT	p.C2C	KRTAP22-1_uc011add.1_5'Flank	NM_181604	NP_853635	Q3LI66	KRA62_HUMAN	keratin associated protein 6-2	2						intermediate filament					0						AGTAGCTGCCGCACATCGTGA	0.483													6	142	---	---	---	---	PASS
SERHL2	253190	broad.mit.edu	37	22	42952207	42952207	+	Intron	SNP	C	T	T	rs142212902		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42952207C>T	uc003bcr.2	+						SERHL_uc011apm.1_Intron|SERHL2_uc011apn.1_Intron|SERHL2_uc010gyz.2_Intron|SERHL2_uc010gyy.2_Intron|SERHL2_uc011apo.1_Intron|RRP7B_uc003bcs.2_RNA	NM_014509	NP_055324	Q9H4I8	SEHL2_HUMAN	serine hydrolase-like 2							perinuclear region of cytoplasm|peroxisome	hydrolase activity				0						GTCACAGTGACAGTCCTTATA	0.587													8	121	---	---	---	---	PASS
ASB9	140462	broad.mit.edu	37	X	15287968	15287968	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15287968C>G	uc004cwl.2	-	1	276	c.29G>C	c.(28-30)GGG>GCG	p.G10A	ASB9_uc004cwk.2_Missense_Mutation_p.G10A|ASB9_uc004cwm.2_Missense_Mutation_p.G10A|ASB9_uc010ner.2_Missense_Mutation_p.G10A|ASB9_uc004cwn.2_Missense_Mutation_p.G10A	NM_001031739	NP_001026909	Q96DX5	ASB9_HUMAN	ankyrin repeat and SOCS box-containing 9 isoform	10					intracellular signal transduction						0	Hepatocellular(33;0.183)					GGGCTTGCTCCCATCCATGCC	0.572													6	203	---	---	---	---	PASS
ATRX	546	broad.mit.edu	37	X	76888748	76888748	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76888748T>C	uc004ecp.3	-	19	5313	c.5081A>G	c.(5080-5082)AAT>AGT	p.N1694S	ATRX_uc004ecq.3_Missense_Mutation_p.N1656S|ATRX_uc004eco.3_Missense_Mutation_p.N1479S	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1694	Helicase ATP-binding.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	ACTCTTCACATTCCTTCCTTG	0.383			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						6	326	---	---	---	---	PASS
PAK3	5063	broad.mit.edu	37	X	110391050	110391050	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110391050A>G	uc004epa.2	+	4	434	c.407A>G	c.(406-408)GAT>GGT	p.D136G	PAK3_uc010npt.1_Missense_Mutation_p.D121G|PAK3_uc010npu.1_Missense_Mutation_p.D121G|PAK3_uc004eoy.1_5'UTR|PAK3_uc004eoz.2_Missense_Mutation_p.D121G|PAK3_uc011mst.1_RNA|PAK3_uc010npv.1_Missense_Mutation_p.D157G|PAK3_uc010npw.1_Missense_Mutation_p.D142G	NM_001128173	NP_001121645	O75914	PAK3_HUMAN	p21-activated kinase 3 isoform d	136	Autoregulatory region (By similarity).|Linker.			VLDV -> CSRC (in Ref. 2).	multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10						GCTGTTCTAGATGTTCTCAAA	0.398										TSP Lung(19;0.15)			5	182	---	---	---	---	PASS
CXorf66	347487	broad.mit.edu	37	X	139038168	139038168	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139038168T>C	uc004fbb.2	-	3	995	c.973A>G	c.(973-975)AAT>GAT	p.N325D		NM_001013403	NP_001013421	Q5JRM2	CX066_HUMAN	hypothetical protein LOC347487 precursor	325	Cytoplasmic (Potential).					integral to membrane					0						TCACTGTCATTCACATGATCA	0.383													7	556	---	---	---	---	PASS
AFF2	2334	broad.mit.edu	37	X	148037884	148037884	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148037884C>T	uc004fcp.2	+	11	2788	c.2309C>T	c.(2308-2310)TCC>TTC	p.S770F	AFF2_uc004fcq.2_Missense_Mutation_p.S760F|AFF2_uc004fcr.2_Missense_Mutation_p.S731F|AFF2_uc011mxb.1_Missense_Mutation_p.S735F|AFF2_uc004fcs.2_Missense_Mutation_p.S737F|AFF2_uc011mxc.1_Missense_Mutation_p.S411F	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2	770					brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)					AACAACTTATCCATCAGTAAT	0.453													78	124	---	---	---	---	PASS
ZNF185	7739	broad.mit.edu	37	X	152086678	152086678	+	Silent	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152086678C>T	uc010ntv.1	+	6	448	c.411C>T	c.(409-411)ACC>ACT	p.T137T	ZNF185_uc011myg.1_Silent_p.T137T|ZNF185_uc011myh.1_Silent_p.T137T|ZNF185_uc011myi.1_Silent_p.T137T|ZNF185_uc011myj.1_Silent_p.T137T|ZNF185_uc011myk.1_Silent_p.T137T|ZNF185_uc004fgw.3_Silent_p.T2T|ZNF185_uc004fgu.2_5'Flank|ZNF185_uc004fgv.2_5'Flank	NM_007150	NP_009081	O15231	ZN185_HUMAN	zinc finger protein 185	137						cytoplasm|cytoskeleton|focal adhesion	zinc ion binding			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					ACAAGATGACCACTGAGGATT	0.557													15	93	---	---	---	---	PASS
GAB3	139716	broad.mit.edu	37	X	153906332	153906332	+	3'UTR	SNP	C	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153906332C>T	uc004fmj.1	-	10					GAB3_uc004fmk.1_3'UTR|GAB3_uc010nve.1_3'UTR|GAB3_uc004fml.1_3'UTR	NM_080612	NP_542179	Q8WWW8	GAB3_HUMAN	Gab3 protein isoform 2											ovary(1)	1	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TACACATTCTCTCTTGGTTTT	0.398													7	23	---	---	---	---	PASS
CPSF3L	54973	broad.mit.edu	37	1	1248568	1248568	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1248568delG	uc001aee.1	-						CPSF3L_uc009vjy.1_Intron|CPSF3L_uc001aef.1_Intron|CPSF3L_uc009vjz.1_Intron|CPSF3L_uc010nyj.1_Intron|CPSF3L_uc001aeg.1_Intron|CPSF3L_uc001aeh.1_Intron|CPSF3L_uc001aei.1_Intron|CPSF3L_uc001aej.1_Intron|CPSF3L_uc001aek.1_Intron	NM_017871	NP_060341	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor							Golgi apparatus|nucleus	hydrolase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		GGCCTTGCCCGGGATGCCCCC	0.652													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2861510	2861511	+	IGR	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2861510_2861511delTG								MMEL1 (297029 upstream) : ACTRT2 (76535 downstream)																							agtgtgagtctgtgtgtgtgtc	0.084													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	5869125	5869126	+	IGR	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5869125_5869126delAC								None (None upstream) : NPHP4 (53744 downstream)																							cgccactcaaacacacacacgc	0.203													4	2	---	---	---	---	
ACOT7	11332	broad.mit.edu	37	1	6396827	6396828	+	Intron	INS	-	AT	AT	rs142964827	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6396827_6396828insAT	uc001ams.2	-						ACOT7_uc010nzq.1_Intron|ACOT7_uc001amt.2_Intron|ACOT7_uc001amu.2_Intron|ACOT7_uc001amv.2_Intron|ACOT7_uc001amq.2_Intron|ACOT7_uc001amr.2_Intron	NM_181864	NP_863654	O00154	BACH_HUMAN	acyl-CoA thioesterase 7 isoform hBACHb							mitochondrion|nucleus	carboxylesterase activity|fatty-acyl-CoA binding|palmitoyl-CoA hydrolase activity				0	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		ttggggCCTTCGAGTTCAATTT	0.351													6	5	---	---	---	---	
RERE	473	broad.mit.edu	37	1	8508151	8508151	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8508151delC	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.1_Intron	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TCCAAGTCCACCACTGCCATT	0.512													4	2	---	---	---	---	
RERE	473	broad.mit.edu	37	1	8616316	8616316	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8616316delA	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GTAAATTATCAAAAAAAAAAA	0.348													3	3	---	---	---	---	
TMEM201	199953	broad.mit.edu	37	1	9652324	9652324	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9652324delA	uc001apz.2	+						TMEM201_uc001apy.2_Intron	NM_001130924	NP_001124396	Q5SNT2	TM201_HUMAN	transmembrane protein 201 isoform 1							integral to membrane|nuclear inner membrane					0	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)		CGGGAAGTGCAGGTGAGGAGC	0.577													4	2	---	---	---	---	
CLCN6	1185	broad.mit.edu	37	1	11879289	11879289	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11879289delC	uc001ate.3	+						CLCN6_uc009vnf.1_Intron|CLCN6_uc009vng.1_Intron|CLCN6_uc009vnh.1_Intron|CLCN6_uc010oat.1_Intron|CLCN6_uc010oau.1_Intron	NM_001286	NP_001277	P51797	CLCN6_HUMAN	chloride channel 6 isoform ClC-6a						cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		GCACCTGCTTCCCTCTTTGTT	0.358													15	14	---	---	---	---	
LOC440563	440563	broad.mit.edu	37	1	13184079	13184080	+	5'Flank	INS	-	T	T	rs146762683	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13184079_13184080insT	uc010obg.1	-							NM_001136561	NP_001130033	B2RXH8	B2RXH8_HUMAN	heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleic acid binding|nucleotide binding				0						GAAAAGCACAACAACATTTTTG	0.342													6	3	---	---	---	---	
CELA2A	63036	broad.mit.edu	37	1	15798219	15798220	+	Intron	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15798219_15798220insG	uc001awk.2	+							NM_033440	NP_254275	P08217	CEL2A_HUMAN	elastase 2A preproprotein						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						tataatttttaggggttcgaag	0.203													11	8	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16944979	16944981	+	RNA	DEL	AAG	-	-	rs142983965		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16944979_16944981delAAG	uc010ocf.1	-	4		c.1176_1178delCTT			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						GGATGGATAAAAGAagagcctct	0.197													9	4	---	---	---	---	
CROCCL1	84809	broad.mit.edu	37	1	16967662	16967663	+	Intron	INS	-	A	A	rs145771302		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16967662_16967663insA	uc001azg.1	-						CROCCL1_uc001azi.1_Intron|uc001azj.1_Intron					Homo sapiens mRNA for FLJ00313 protein.												0						gactctgtctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17053293	17053293	+	IGR	DEL	A	-	-	rs71304518		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17053293delA								ESPNP (6641 upstream) : CROCC (13475 downstream)																							CTCTTTTGCCAAAAAAACCAG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	17345217	17345217	+	IGR	DEL	T	-	-	rs75557632		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17345217delT								ATP13A2 (6794 upstream) : SDHB (10 downstream)																							GAACAGGTTCTTTTTTTTTTG	0.393													29	14	---	---	---	---	
ACTL8	81569	broad.mit.edu	37	1	18119311	18119311	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18119311delA	uc001bat.2	+							NM_030812	NP_110439	Q9H568	ACTL8_HUMAN	actin-like 8							cytoplasm|cytoskeleton				ovary(4)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		GACCAAAGAGAAGGCAAGGAC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	18267946	18267946	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18267946delA								ACTL8 (114390 upstream) : IGSF21 (166294 downstream)																							ggcaactgggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	19343164	19343164	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19343164delA								IFFO2 (60338 upstream) : UBR4 (55440 downstream)																							tcaaaaaaagaaaaaaaaaaG	0.015													4	2	---	---	---	---	
EIF4G3	8672	broad.mit.edu	37	1	21145553	21145553	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21145553delC	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		caccactgcacccagcTCCAT	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	27504359	27504362	+	IGR	DEL	ATGA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27504359_27504362delATGA								SLC9A1 (22908 upstream) : WDTC1 (56645 downstream)																							cactggctgcatgaatgaatgaat	0.196													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	29697408	29697408	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29697408delC								PTPRU (44093 upstream) : None (None downstream)																							CAGCTCCAAACCCCCTTCATC	0.502													4	2	---	---	---	---	
LCK	3932	broad.mit.edu	37	1	32738901	32738902	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32738901_32738902delGT	uc001bux.2	+						LCK_uc001buy.2_5'Flank|LCK_uc001buz.2_5'Flank|LCK_uc010ohc.1_5'Flank|LCK_uc001bva.2_5'Flank	NM_005356	NP_005347	P06239	LCK_HUMAN	lymphocyte-specific protein tyrosine kinase						activation of caspase activity|cellular zinc ion homeostasis|induction of apoptosis|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of T cell receptor signaling pathway|regulation of defense response to virus by virus|release of sequestered calcium ion into cytosol|response to drug|T cell costimulation|T cell differentiation|T cell receptor signaling pathway|viral reproduction	cytosol|Golgi apparatus|membrane raft|pericentriolar material|plasma membrane	ATP binding|ATPase binding|CD4 receptor binding|CD8 receptor binding|glycoprotein binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein kinase binding|protein serine/threonine phosphatase activity|SH2 domain binding			lung(3)|central_nervous_system(2)|ovary(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)	ttatgtgaaagtgtgtgtgtgt	0.134			T	TRB@	T-ALL								4	2	---	---	---	---	
DLGAP3	58512	broad.mit.edu	37	1	35342562	35342562	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35342562delC	uc001byc.2	-							NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated						cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)				ttaggaagctcccactcacac	0.000													4	2	---	---	---	---	
MTF1	4520	broad.mit.edu	37	1	38283868	38283869	+	Intron	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38283868_38283869insG	uc001cce.1	-							NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				attgagaggctgggtttttaag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	38831010	38831010	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38831010delC								POU3F1 (318560 upstream) : RRAGC (474005 downstream)																							TTTATAGAGTCCCAGAGAATG	0.423													4	2	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39802339	39802339	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39802339delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AGTGGTGTGCTTTTTTTTTTT	0.388													10	5	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39917223	39917223	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39917223delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AAATGAGTGATTTTTTTTTTA	0.358													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	40278668	40278668	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40278668delC								BMP8B (24135 upstream) : TRIT1 (28040 downstream)																							tttctgtcctccacttgtatc	0.104													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	43501475	43501476	+	IGR	INS	-	AG	AG	rs141842636		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43501475_43501476insAG								SLC2A1 (76628 upstream) : FAM183A (112118 downstream)																							tattTTTTTACAGTCTTTCAAC	0.267													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	43513649	43513649	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43513649delT								SLC2A1 (88802 upstream) : FAM183A (99945 downstream)																							CACCAGCCCCTTTGGAAGGCC	0.433													4	2	---	---	---	---	
ST3GAL3	6487	broad.mit.edu	37	1	44257088	44257091	+	Intron	DEL	TTGA	-	-	rs3082973		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44257088_44257091delTTGA	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270	Q11203	SIAT6_HUMAN	sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				tattggaCATTtgattgaatgaat	0.152													3	4	---	---	---	---	
TESK2	10420	broad.mit.edu	37	1	45858374	45858374	+	Intron	DEL	A	-	-	rs111558684		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45858374delA	uc001cns.1	-						TESK2_uc009vxr.1_Intron|TESK2_uc010olo.1_Intron|TESK2_uc009vxs.1_Intron	NM_007170	NP_009101	Q96S53	TESK2_HUMAN	testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)					actctgtctcaaaaaaaaaaa	0.000													9	6	---	---	---	---	
RAD54L	8438	broad.mit.edu	37	1	46729479	46729479	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46729479delT	uc009vye.2	+						RAD54L_uc001cpl.2_Intron|RAD54L_uc001cpm.1_Intron	NM_001142548	NP_001136020	Q92698	RAD54_HUMAN	RAD54-like protein						meiosis	nucleus	ATP binding|DNA binding|helicase activity			ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		ctactttttgtttttttttga	0.219								Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	48146050	48146050	+	IGR	DEL	C	-	-	rs141798791	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48146050delC								FOXD2 (239688 upstream) : SKINTL (421337 downstream)																							TCTGTTCACACCTGACTATGT	0.488													4	2	---	---	---	---	
AGBL4	84871	broad.mit.edu	37	1	49895461	49895462	+	Intron	DEL	TC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49895461_49895462delTC	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		ctctgctacttctctctctctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	51991992	51991992	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51991992delA								EPS15 (6997 upstream) : OSBPL9 (50859 downstream)																							ATGTCTGGTTAAATGGAGCAT	0.408													4	2	---	---	---	---	
ZCCHC11	23318	broad.mit.edu	37	1	52956166	52956166	+	Intron	DEL	A	-	-	rs113552548		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52956166delA	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Intron|ZCCHC11_uc001cuc.2_Intron	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						gaatgaCTTGAAAAAAAAAAA	0.139													13	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	56424535	56424535	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56424535delT								USP24 (743773 upstream) : PPAP2B (535898 downstream)																							TGACTCCTCCTTTTTTTTTCT	0.398													3	3	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	58923454	58923454	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58923454delA	uc001cyt.1	-							NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						CCCCCCAGTCACCTGAAATCT	0.493													4	2	---	---	---	---	
USP1	7398	broad.mit.edu	37	1	62914561	62914561	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62914561delT	uc001daj.1	+						USP1_uc001dak.1_Intron|USP1_uc001dal.1_Intron	NM_001017415	NP_001017415	O94782	UBP1_HUMAN	ubiquitin specific protease 1						DNA repair|monoubiquitinated protein deubiquitination|regulation of DNA repair|response to UV|ubiquitin-dependent protein catabolic process	nucleoplasm	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		tttcttctccttttttttttg	0.109													11	5	---	---	---	---	
SERBP1	26135	broad.mit.edu	37	1	67890362	67890362	+	Intron	DEL	A	-	-	rs3838405		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67890362delA	uc001ddv.2	-						SERBP1_uc001ddx.2_Intron|SERBP1_uc001ddy.2_Intron|SERBP1_uc001ddw.2_Intron	NM_001018067	NP_001018077	Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1 isoform 1						regulation of mRNA stability	nucleus|perinuclear region of cytoplasm	mRNA 3'-UTR binding|protein binding			skin(1)	1						TATGGGGGGGAAAAAATGAGT	0.318													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	76514056	76514057	+	IGR	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76514056_76514057delTG								ASB17 (115940 upstream) : ST6GALNAC3 (26332 downstream)																							tgtgtgtttatgtgtgtgtgtg	0.342													4	2	---	---	---	---	
LPHN2	23266	broad.mit.edu	37	1	82166395	82166396	+	Intron	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82166395_82166396insG	uc001dit.3	+						LPHN2_uc001dis.2_Intron	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		ATACTCCAGAAGGGGGAAAGAT	0.391													4	2	---	---	---	---	
COL24A1	255631	broad.mit.edu	37	1	86289636	86289636	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86289636delT	uc001dlj.2	-						COL24A1_uc001dli.2_Intron|COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)		tctttctttctttttttTTAA	0.134													4	2	---	---	---	---	
HS2ST1	9653	broad.mit.edu	37	1	87406164	87406164	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87406164delT	uc010osk.1	+						HS2ST1_uc001dmc.3_Intron	NM_012262	NP_036394	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1 isoform							Golgi membrane|integral to membrane				central_nervous_system(1)	1		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		AAGCTGCATGTTTAAGAGTTT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91917049	91917049	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91917049delT								HFM1 (46623 upstream) : CDC7 (49355 downstream)																							AATCCTTGCCTTTTTAGAAAT	0.313													4	2	---	---	---	---	
SLC44A3	126969	broad.mit.edu	37	1	95316652	95316652	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95316652delC	uc001dqv.3	+						SLC44A3_uc001dqx.3_Intron|SLC44A3_uc010otq.1_Intron|SLC44A3_uc010otr.1_Intron|SLC44A3_uc001dqw.3_Intron|SLC44A3_uc010ots.1_Intron|SLC44A3_uc009wds.2_Intron|SLC44A3_uc010ott.1_Intron|SLC44A3_uc010otu.1_Intron	NM_001114106	NP_001107578	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3 isoform 1							integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	CCTCTAGAATCCCCTCCCCTG	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	100396430	100396431	+	IGR	INS	-	AA	AA	rs141551728	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100396430_100396431insAA								AGL (6851 upstream) : SLC35A3 (39109 downstream)																							AAAAAACAGACGAGATGCAGAT	0.297													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	106433033	106433034	+	IGR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106433033_106433034insT								None (None upstream) : None (None downstream)																							CCATATGTGTATTTTTTTTTTG	0.287													6	4	---	---	---	---	
TSPAN2	10100	broad.mit.edu	37	1	115602826	115602826	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115602826delT	uc001eft.2	-							NM_005725	NP_005716	O60636	TSN2_HUMAN	tetraspan 2							integral to membrane					0	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		TTAGAGATCCTTTTTTTTTTG	0.373													11	5	---	---	---	---	
PTGFRN	5738	broad.mit.edu	37	1	117528810	117528811	+	Intron	INS	-	G	G	rs150407607	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117528810_117528811insG	uc001egv.1	+							NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator							endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		CCAAGGAGCATGGGTACTTATG	0.272													2	4	---	---	---	---	
SPAG17	200162	broad.mit.edu	37	1	118596977	118596978	+	Intron	DEL	TC	-	-	rs67079929		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118596977_118596978delTC	uc001ehk.2	-							NM_206996	NP_996879	Q6Q759	SPG17_HUMAN	sperm associated antigen 17							cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		tgaactgtagtctctctctctc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142664224	142664224	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142664224delA	uc001eiw.1	+						uc001eix.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																		aatttacaagaaaaaaaaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	144014881	144014881	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144014881delA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																		ggagaactttaaaaaaaatac	0.020													4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144865049	144865049	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144865049delT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron|PDE4DIP_uc001ema.2_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)		TCTTGGTGGCTTTTTCCTTTT	0.338			T	PDGFRB	MPD								4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144997352	144997352	+	5'Flank	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144997352delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_5'Flank|PDE4DIP_uc001ell.1_5'Flank|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_5'Flank|PDE4DIP_uc001emd.1_5'Flank|PDE4DIP_uc001emg.1_5'Flank|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ACTGTGTATGAATCCAGGGTA	0.244			T	PDGFRB	MPD								4	2	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	145001837	145001838	+	Intron	DEL	AA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145001837_145001838delAA	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron|uc001emi.3_5'Flank	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)		ggatactgttaaaagttttccc	0.084			T	PDGFRB	MPD								7	4	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145192617	145192617	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145192617delC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						TCTGCTGTGTCCTGAATCAGT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149208496	149208497	+	IGR	DEL	AG	-	-	rs58844523		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149208496_149208497delAG								LOC645166 (255442 upstream) : LOC388692 (70979 downstream)																							agcaaaaaaaaGTTTTTATTTG	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	155064466	155064466	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155064466delA								EFNA3 (4460 upstream) : EFNA1 (35883 downstream)																							CGTGGCAGGGACAGAGGCGTG	0.597											OREG0013851	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
KIRREL	55243	broad.mit.edu	37	1	157974322	157974322	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157974322delT	uc001frn.3	+						KIRREL_uc010pib.1_Intron	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor							integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)					tgttttgccctttatgagtct	0.159													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	161471481	161471481	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161471481delT								C1orf192 (133817 upstream) : FCGR2A (3724 downstream)																							TTGAAttctctttttttttga	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165677398	165677399	+	Intron	DEL	TC	-	-	rs71757383		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165677398_165677399delTC	uc001gdi.2	+											Homo sapiens carbonic anhydrase XIV (CA14) pseudogene, mRNA (cDNA clone IMAGE:4643256).																		tctctccccgtctctctctctc	0.277													4	3	---	---	---	---	
POU2F1	5451	broad.mit.edu	37	1	167381697	167381701	+	Intron	DEL	TTTGA	-	-	rs79996749		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167381697_167381701delTTTGA	uc001gec.2	+						POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron|POU2F1_uc001gef.2_Intron|POU2F1_uc001geg.2_Intron	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5						ATACAAGGACTTTGATTATAGTTGA	0.390													4	4	---	---	---	---	
ATP1B1	481	broad.mit.edu	37	1	169101269	169101270	+	RNA	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169101269_169101270insG	uc001gfs.1	+	6		c.1513_1514insG						P05026	AT1B1_HUMAN	Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)					tttttttttttttttttttttg	0.312													14	9	---	---	---	---	
SELP	6403	broad.mit.edu	37	1	169572545	169572546	+	Intron	INS	-	TGTGTG	TGTGTG	rs113236512		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169572545_169572546insTGTGTG	uc001ggi.3	-						SELP_uc001ggh.2_Intron|SELP_uc009wvr.2_Intron	NM_003005	NP_002996	P16109	LYAM3_HUMAN	selectin P precursor						platelet activation|platelet degranulation|positive regulation of platelet activation	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane fraction|platelet alpha granule membrane|platelet dense granule membrane|soluble fraction	fucose binding|glycosphingolipid binding|heparin binding|lipopolysaccharide binding|oligosaccharide binding|sialic acid binding			ovary(2)|skin(2)	4	all_hematologic(923;0.208)				Clopidogrel(DB00758)|Heparin(DB01109)|Tirofiban(DB00775)	ctctctctctctgtgtgtgtgt	0.223													6	3	---	---	---	---	
LHX4	89884	broad.mit.edu	37	1	180201350	180201351	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180201350_180201351delGT	uc001goe.1	+							NM_033343	NP_203129	Q969G2	LHX4_HUMAN	LIM homeobox protein 4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						TGGGGGAAGGGTGTGTGTGTGT	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	182413778	182413778	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182413778delT								TEDDM1 (44027 upstream) : RGSL1 (5478 downstream)																							CAGCACCCCCTGTAGGTTCTG	0.547													3	4	---	---	---	---	
C1orf21	81563	broad.mit.edu	37	1	184569996	184569996	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184569996delT	uc001gqv.1	+							NM_030806	NP_110433	Q9H246	CA021_HUMAN	chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)		TTGAATATGCTATCTTATGTG	0.368													4	2	---	---	---	---	
C1orf26	54823	broad.mit.edu	37	1	185233323	185233323	+	Intron	DEL	T	-	-	rs72023437		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185233323delT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823												0						TTGGCGCCTCTTTTTTTTTTT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	185638822	185638822	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185638822delG								IVNS1ABP (352361 upstream) : HMCN1 (64861 downstream)																							TTATAGTGGTGGTAGTCATGG	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	186251702	186251703	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186251702_186251703delGT								HMCN1 (91617 upstream) : PRG4 (13702 downstream)																							GCTCTTCGGGgtgtgtgtgtgt	0.411													5	3	---	---	---	---	
NR5A2	2494	broad.mit.edu	37	1	200018030	200018030	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200018030delA	uc001gvb.2	+						NR5A2_uc001gvc.2_Intron|NR5A2_uc009wzh.2_Intron|NR5A2_uc010pph.1_Intron	NM_205860	NP_995582	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2						embryo development|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|protein binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)					CTTGGTGCTGAAAATATGTGT	0.358													22	17	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	201516886	201516886	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201516886delC								RPS10P7 (17284 upstream) : NAV1 (100564 downstream)																							CTTTTACATTCCACACATTCT	0.214													4	2	---	---	---	---	
FMOD	2331	broad.mit.edu	37	1	203166966	203166966	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203166966delT	uc010pqi.1	-							NM_002023		Q06828	FMOD_HUMAN	fibromodulin precursor						transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)			CTCAGCCCCCTTGAGCCTCAG	0.373													4	2	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205033255	205033255	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205033255delG	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron|CNTN2_uc001hbs.2_Intron	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			gaggggcggagggggggcgcg	0.000													7	7	---	---	---	---	
SRGAP2	23380	broad.mit.edu	37	1	206611673	206611673	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206611673delT	uc001hdy.2	+						SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron|SRGAP2_uc010prv.1_Intron	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)					ACTCCTGGCCTTTTTTTTTTT	0.393													3	3	---	---	---	---	
CAMK1G	57172	broad.mit.edu	37	1	209758474	209758475	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209758474_209758475delGT	uc001hhd.2	+						CAMK1G_uc001hhf.3_Intron|CAMK1G_uc001hhe.2_Intron	NM_020439	NP_065172	Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG							Golgi membrane|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		gattgcTCTGGTGTGTGTGTGT	0.228													4	2	---	---	---	---	
HHAT	55733	broad.mit.edu	37	1	210502521	210502521	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210502521delA	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron	NM_001122834	NP_001116306	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		TTACTCTGTTAAAAAAAAAAT	0.567													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	213612852	213612853	+	IGR	INS	-	T	T	rs149874228	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213612852_213612853insT								RPS6KC1 (166045 upstream) : PROX1 (548433 downstream)																							TGTTGTTGTGgttgggttttgt	0.193													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	217315189	217315189	+	IGR	DEL	A	-	-	rs77024002		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217315189delA								ESRRG (4092 upstream) : GPATCH2 (288645 downstream)																							AAGAAAAAGGAAAAAAAAAAA	0.373													9	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	218741739	218741740	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218741739_218741740delGT								TGFB2 (123780 upstream) : LYPLAL1 (605452 downstream)																							aagagagagagTGTGTGTGTGT	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	226703801	226703801	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226703801delT								PARP1 (108000 upstream) : C1orf95 (32700 downstream)																							AATTGTAACATTTTTTTTCAA	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	227176165	227176167	+	IGR	DEL	CAG	-	-	rs10586162		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227176165_227176167delCAG								CABC1 (919 upstream) : CDC42BPA (1400 downstream)																							AGGAGAACAACAGCAGCCAGCAT	0.532													3	4	---	---	---	---	
C1orf96	126731	broad.mit.edu	37	1	229463936	229463936	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229463936delT	uc001htl.3	-						C1orf96_uc009xfc.2_Intron	NM_145257	NP_660300	Q6IQ19	CA096_HUMAN	hypothetical protein LOC126731							centrosome					0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				TCTGCTGAAGTAAGAGTTCGT	0.448													4	2	---	---	---	---	
GALNT2	2590	broad.mit.edu	37	1	230291953	230291956	+	Intron	DEL	CGAG	-	-	rs4846911	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230291953_230291956delCGAG	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				GGGGAGCAGACgagggagagagag	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232320154	232320155	+	IGR	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232320154_232320155delAC								DISC1 (143138 upstream) : SIPA1L2 (213559 downstream)																							AGAGAGACAGACACACACACAT	0.505													4	2	---	---	---	---	
ARID4B	51742	broad.mit.edu	37	1	235384018	235384018	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235384018delA	uc001hwq.2	-						ARID4B_uc001hwr.2_Intron|ARID4B_uc001hws.3_Intron|ARID4B_uc001hwt.3_Intron	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TTTTCAATGCAAAAAAAAAAT	0.209													13	10	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236704889	236704891	+	Intron	DEL	TAT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236704889_236704891delTAT	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			tatatgtcaatataaaatattta	0.202													22	23	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236704894	236704895	+	Intron	INS	-	GGTT	GGTT			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236704894_236704895insGGTT	uc001hxz.1	+						LGALS8_uc001hxw.1_Intron|LGALS8_uc001hxy.1_Intron|LGALS8_uc009xgg.1_Intron|LGALS8_uc001hya.1_Intron|LGALS8_uc001hyb.1_Intron|LGALS8_uc001hyc.1_Intron	NM_201543	NP_963837	O00214	LEG8_HUMAN	galectin-8 isoform b							cytoplasm|extracellular space	sugar binding			ovary(1)	1	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			gtcaatataaaatatttagaaa	0.213													42	23	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245612681	245612681	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245612681delT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TCCCAGTAACTTTTTTTTTTT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	395806	395807	+	IGR	INS	-	T	T	rs113860043		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:395806_395807insT								FAM150B (107498 upstream) : TMEM18 (272168 downstream)																							CCTCTTACCAGTTTTTTTTTTT	0.292													3	3	---	---	---	---	
TSSC1	7260	broad.mit.edu	37	2	3287310	3287310	+	Intron	DEL	C	-	-	rs11364682		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3287310delC	uc002qxj.2	-						TSSC1_uc002qxi.2_Intron	NM_003310	NP_003301	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		CACGTTCACACCCCGGCACAC	0.602													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	9273496	9273496	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9273496delC								MBOAT2 (129620 upstream) : ASAP2 (73398 downstream)																							tgaatgaaaacccagggagga	0.000													4	2	---	---	---	---	
KCNF1	3754	broad.mit.edu	37	2	11051386	11051386	+	5'Flank	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11051386delG	uc002rax.2	+							NM_002236	NP_002227	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F,							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		GCCTTGGTGTGGGACTGCAGA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13008302	13008303	+	IGR	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13008302_13008303delAC								TRIB2 (125446 upstream) : None (None downstream)																							atacacacatacacacacacac	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	15912666	15912667	+	IGR	INS	-	GAGA	GAGA	rs145971848	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15912666_15912667insGAGA								DDX1 (141442 upstream) : MYCNOS (167353 downstream)																							CCTGGGTGCTGGAGAGGCCTGC	0.510													5	4	---	---	---	---	
NCOA1	8648	broad.mit.edu	37	2	24928866	24928866	+	Intron	DEL	T	-	-	rs80021154		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24928866delT	uc002rfk.2	+						NCOA1_uc010eye.2_Intron|NCOA1_uc002rfi.2_Intron|NCOA1_uc002rfj.2_Intron|NCOA1_uc002rfl.2_Intron	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1										PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCACAGTTCTTTTTTTTTCA	0.308			T	PAX3	alveolar rhadomyosarcoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	25148620	25148621	+	IGR	DEL	AC	-	-	rs55633509		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25148620_25148621delAC								ADCY3 (6565 upstream) : DNAJC27 (17884 downstream)																							ccttcatgttactgtgtgtgtg	0.059													3	3	---	---	---	---	
EFR3B	22979	broad.mit.edu	37	2	25378837	25378837	+	3'UTR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25378837delT	uc010eyh.2	+	23						NM_014971	NP_055786	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B								binding				0						tgagaATCCCTTTTTAGGGTA	0.294													4	2	---	---	---	---	
PLB1	151056	broad.mit.edu	37	2	28833908	28833908	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28833908delA	uc002rmb.1	+						PLB1_uc010ezj.1_Intron|PLB1_uc002rme.1_Intron|PLB1_uc002rmf.1_Intron	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)					AAACCCAGCTAAAAACAAGCC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	41381854	41381854	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41381854delA								SLC8A1 (642279 upstream) : PKDCC (893307 downstream)																							cattgtgaagaggctggcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58763129	58763130	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58763129_58763130insT	uc002rzy.2	+											Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																		CTCTCCAAATCTTTTTTTGTGG	0.391													4	2	---	---	---	---	
AAK1	22848	broad.mit.edu	37	2	69848612	69848612	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69848612delA	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron|AAK1_uc010fdm.1_Intron	NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0						aaactccaccaaaaaaaaaaa	0.035													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	70590333	70590333	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70590333delC								FAM136A (61113 upstream) : TGFA (84086 downstream)																							AGCAGCATGTCCCATTCCAGT	0.473													4	2	---	---	---	---	
ZNF638	27332	broad.mit.edu	37	2	71592438	71592439	+	Intron	INS	-	T	T	rs141689524	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71592438_71592439insT	uc002shx.2	+						ZNF638_uc010fec.2_Intron|ZNF638_uc010yqw.1_Intron|ZNF638_uc002shw.2_Intron|ZNF638_uc002shy.2_Intron|ZNF638_uc002shz.2_Intron|ZNF638_uc002sia.2_Intron|ZNF638_uc002sib.1_Intron|ZNF638_uc010fed.2_5'Flank	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638						RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						TAAAATCTAGATTTTTGTATTG	0.262													5	3	---	---	---	---	
SFXN5	94097	broad.mit.edu	37	2	73179968	73179968	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73179968delC	uc002siq.2	-						SFXN5_uc002sio.2_Intron|SFXN5_uc010yrc.1_Intron|SFXN5_uc002sip.2_Intron|SFXN5_uc010fet.2_Intron|SFXN5_uc010fer.2_Intron|SFXN5_uc010feq.2_Intron|SFXN5_uc010fes.2_Intron	NM_144579	NP_653180	Q8TD22	SFXN5_HUMAN	sideroflexin 5						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity			ovary(1)	1						CACCCAGGGTCCCCACACTCA	0.264													4	2	---	---	---	---	
C2orf3	6936	broad.mit.edu	37	2	75907759	75907760	+	Intron	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75907759_75907760delCT	uc002sno.2	-						C2orf3_uc010ffs.2_Intron|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						ttgagtgagcctctctctctct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	84234022	84234022	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84234022delT								None (None upstream) : FUNDC2P2 (283784 downstream)																							actgagagaatttttttgcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	85793030	85793031	+	IGR	INS	-	AG	AG			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85793030_85793031insAG								GGCX (4373 upstream) : VAMP8 (11617 downstream)																							caaagaaagaaagagagagaga	0.119													3	3	---	---	---	---	
THNSL2	55258	broad.mit.edu	37	2	88473897	88473898	+	Intron	INS	-	A	A	rs138356060	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88473897_88473898insA	uc002ssz.3	+						THNSL2_uc002ssv.2_Intron|THNSL2_uc002ssw.3_Intron|THNSL2_uc002ssx.3_Intron|THNSL2_uc002sta.3_Intron|THNSL2_uc002ssy.3_Intron|THNSL2_uc010fhe.2_5'Flank	NM_018271	NP_060741	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2						threonine biosynthetic process		threonine synthase activity			ovary(1)	1						TGAAGAAGTATAAAAAATGAAA	0.356													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91629654	91629655	+	IGR	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91629654_91629655insA								None (None upstream) : LOC654342 (175537 downstream)																							Ctaaaaattttaaaaatattat	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91660726	91660726	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91660726delA								None (None upstream) : LOC654342 (144466 downstream)																							ctcttttaacaaaataacata	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91763893	91763893	+	IGR	DEL	A	-	-	rs113390568		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91763893delA								None (None upstream) : LOC654342 (41299 downstream)																							AGGCAGTTAGAAAAAAGTGCC	0.512													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91771756	91771756	+	IGR	DEL	T	-	-	rs151108925		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91771756delT								None (None upstream) : LOC654342 (33436 downstream)																							gtttagctaattttttttttt	0.000													4	2	---	---	---	---	
LOC654342	654342	broad.mit.edu	37	2	91806956	91806956	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91806956delC	uc002sts.3	-											Homo sapiens cDNA clone IMAGE:4801360.												0						aggcacggggccaccgccatg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91893495	91893496	+	IGR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91893495_91893496insT								LOC654342 (45520 upstream) : GGT8P (69872 downstream)																							TGGGATAATAATTTTTTACTAA	0.302													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91986912	91986913	+	IGR	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91986912_91986913insA								GGT8P (16759 upstream) : FKSG73 (142246 downstream)																							aagaaagaaggaaggaaagaaa	0.000													4	2	---	---	---	---	
AFF3	3899	broad.mit.edu	37	2	100454884	100454885	+	Intron	DEL	TC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100454884_100454885delTC	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6						TCCTCACTGTTCTCTCTCTACC	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	102243817	102243817	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102243817delT								RFX8 (152652 upstream) : MAP4K4 (70671 downstream)																							TTCCCACAGCTTTTTCAGTTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	104695748	104695748	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104695748delT								None (None upstream) : LOC150568 (355057 downstream)																							aagcaattgatttttctgtat	0.000													4	2	---	---	---	---	
LOC150568	150568	broad.mit.edu	37	2	105096753	105096755	+	Intron	DEL	TAT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105096753_105096755delTAT	uc002tch.2	+							NR_015399				Homo sapiens cDNA FLJ30528 fis, clone BRAWH2001037.												0						ttattgttGGTATTATTATTGGG	0.182													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106344206	106344207	+	IGR	INS	-	T	T	rs141645043	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106344206_106344207insT								FHL2 (288976 upstream) : NCK2 (17147 downstream)																							aaacactaatatttaaagtaat	0.149													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	111940843	111940843	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111940843delA								BCL2L11 (14821 upstream) : LOC541471 (24516 downstream)																							cgatcattctaaatctatatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	112424202	112424204	+	IGR	DEL	TGG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112424202_112424204delTGG								LOC541471 (171510 upstream) : ANAPC1 (102437 downstream)																							gtgatggtgatggtggtgttact	0.015													1	5	---	---	---	---	
FBLN7	129804	broad.mit.edu	37	2	112928889	112928890	+	Intron	DEL	GA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112928889_112928890delGA	uc002tho.1	+						FBLN7_uc002thn.2_Intron|FBLN7_uc010fki.1_Intron|FBLN7_uc010fkj.1_Intron	NM_153214	NP_694946	Q53RD9	FBLN7_HUMAN	fibulin 7 isoform 1						cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2						gcagggcactgagaagtcaaat	0.134													4	2	---	---	---	---	
POLR1B	84172	broad.mit.edu	37	2	113304404	113304415	+	Intron	DEL	TGCTGAGATTAC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113304404_113304415delTGCTGAGATTAC	uc002thw.2	+						POLR1B_uc010fkn.2_Intron|POLR1B_uc002thx.2_Intron|POLR1B_uc010fko.2_Intron|POLR1B_uc010fkp.2_Intron|POLR1B_uc010yxn.1_Intron|POLR1B_uc002thy.2_Intron|POLR1B_uc010yxo.1_Intron	NM_019014	NP_061887	Q9H9Y6	RPA2_HUMAN	RNA polymerase I polypeptide B isoform 1						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1						cctcccaaagtgctgagattacaggcgtgaac	0.156													10	7	---	---	---	---	
SLC35F5	80255	broad.mit.edu	37	2	114483285	114483286	+	Intron	INS	-	A	A	rs142067133	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114483285_114483286insA	uc002tku.1	-						SLC35F5_uc002tkt.2_Intron	NM_025181	NP_079457	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5						transport	integral to membrane					0						CTCAACGCCATAGAAAAAAAAA	0.386													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	117982383	117982383	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117982383delG								None (None upstream) : DDX18 (589872 downstream)																							tgagttccttgtagattctgg	0.000													4	2	---	---	---	---	
GLI2	2736	broad.mit.edu	37	2	121529114	121529115	+	Intron	DEL	AA	-	-	rs72502183		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121529114_121529115delAA	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)				GTGAAGACAGAAGATGTTTCTG	0.411													11	12	---	---	---	---	
CLASP1	23332	broad.mit.edu	37	2	122103142	122103142	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122103142delG	uc002tnc.2	-						CLASP1_uc010yyv.1_Intron|CLASP1_uc002tmz.2_Intron|CLASP1_uc002tna.2_Intron|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tmy.2_Intron	NM_015282	NP_056097	Q7Z460	CLAP1_HUMAN	CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)					AATCCCTGATGGAGGTAGGAG	0.438													4	2	---	---	---	---	
CLASP1	23332	broad.mit.edu	37	2	122216727	122216728	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122216727_122216728insT	uc002tnc.2	-						CLASP1_uc002tna.2_5'Flank|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097	Q7Z460	CLAP1_HUMAN	CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)					AAGTTTTGTTGTTTTTTTTTTT	0.243													7	4	---	---	---	---	
CLASP1	23332	broad.mit.edu	37	2	122407330	122407331	+	5'Flank	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122407330_122407331insT	uc002tnc.2	-						CLASP1_uc010yyz.1_5'Flank|CLASP1_uc010yza.1_5'Flank|CLASP1_uc010yzb.1_5'Flank|CLASP1_uc010yzc.1_5'Flank|CLASP1_uc002tng.1_5'Flank|uc002tnj.1_5'Flank|uc002tnh.2_5'Flank|uc002tni.2_5'Flank	NM_015282	NP_056097	Q7Z460	CLAP1_HUMAN	CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)					TTTTGTTTTTGTTTTTTTTTAC	0.495													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122536935	122536935	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122536935delG								TSN (11509 upstream) : None (None downstream)																							GTCAGGTGCTGGGGAATGGAT	0.468													4	2	---	---	---	---	
GYPC	2995	broad.mit.edu	37	2	127416894	127416894	+	Intron	DEL	C	-	-	rs55755786		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127416894delC	uc002tnq.2	+						GYPC_uc002tnr.2_Intron|GYPC_uc010flv.2_Intron	NM_002101	NP_002092	P04921	GLPC_HUMAN	glycophorin C isoform 1							cortical cytoskeleton|integral to plasma membrane	protein binding			central_nervous_system(1)	1	Colorectal(110;0.0533)			BRCA - Breast invasive adenocarcinoma(221;0.075)		aggaaacgtgccccagaagtg	0.055													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129550157	129550158	+	IGR	INS	-	AA	AA	rs150111646		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129550157_129550158insAA								HS6ST1 (473986 upstream) : None (None downstream)																							cacacatccacagtgtctcaca	0.050													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131065103	131065103	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131065103delG								TUBA3E (109069 upstream) : CCDC115 (30713 downstream)																							TGTAAGTCCTGGAAGACATGA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132773799	132773799	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132773799delA								C2orf27B (214565 upstream) : NCRNA00164 (131365 downstream)																							aacatgagggaaatattctga	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133103684	133103684	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133103684delT								NCRNA00164 (88142 upstream) : GPR39 (70463 downstream)																							TTTCCTTTCATTTTTTTCAAA	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133120238	133120239	+	IGR	DEL	AT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133120238_133120239delAT								NCRNA00164 (104696 upstream) : GPR39 (53908 downstream)																							ttgagatttcatatgttttaga	0.000													4	2	---	---	---	---	
NCKAP5	344148	broad.mit.edu	37	2	133970663	133970663	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133970663delG	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002ttt.1_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1								protein binding				0						GCATTCCCCAGGTCCCCAGAC	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	134601805	134601805	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134601805delC								NCKAP5 (275774 upstream) : MGAT5 (410025 downstream)																							CAAGCCCCTTCCCAAACACCT	0.527											OREG0014990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
HNMT	3176	broad.mit.edu	37	2	138718888	138718888	+	5'Flank	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138718888delA	uc002tvc.2	+						HNMT_uc002tvd.2_5'Flank|HNMT_uc002tve.2_5'Flank|HNMT_uc002tvf.2_5'Flank	NM_006895	NP_008826	P50135	HNMT_HUMAN	histamine N-methyltransferase isoform 1						respiratory gaseous exchange	cytoplasm	histamine N-methyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)	ttacaagaataaaaaaaagac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	139239881	139239881	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139239881delC	uc002tvg.2	-											full-length cDNA clone CS0DL004YM17 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																		attaaaaagtccagaaacaac	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	159612537	159612537	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159612537delC								PKP4 (74599 upstream) : DAPL1 (39292 downstream)																							AGGCTCTCTGCCCACAAGCAA	0.542											OREG0015031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	161489744	161489744	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161489744delG								RBMS1 (139426 upstream) : TANK (503722 downstream)																							CCTCATTGCTGGGGCTTACTC	0.473													4	2	---	---	---	---	
SCN1A	6323	broad.mit.edu	37	2	166894121	166894124	+	Intron	DEL	GTTT	-	-	rs139551129		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166894121_166894124delGTTT	uc010zcz.1	-						SCN1A_uc002udo.3_Intron|SCN1A_uc010fpk.2_Intron	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	AATAATCATAGTTTGTTTTTCTTT	0.206													7	6	---	---	---	---	
STK39	27347	broad.mit.edu	37	2	168956332	168956333	+	Intron	INS	-	A	A	rs147356134	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168956332_168956333insA	uc002uea.2	-							NM_013233	NP_037365	Q9UEW8	STK39_HUMAN	serine threonine kinase 39 (STE20/SPS1 homolog,						response to stress	cytoplasm|nucleus	ATP binding|protein binding|receptor signaling protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2						AAACATACCAGAAAAAAACCAT	0.356													4	2	---	---	---	---	
MYO3B	140469	broad.mit.edu	37	2	171442027	171442027	+	Intron	DEL	T	-	-	rs72013843		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171442027delT	uc002ufy.2	+						MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						CCATCCTCAATTTTTTACACC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	174582228	174582228	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174582228delA								CDCA7 (348510 upstream) : SP3 (191031 downstream)																							GGTGAATGTGAAAAAAGGTAC	0.398													4	2	---	---	---	---	
PPP1R1C	151242	broad.mit.edu	37	2	182934094	182934094	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182934094delT	uc002uoo.2	+						PPP1R1C_uc002uon.2_Intron|PPP1R1C_uc002uop.1_Intron|PPP1R1C_uc010frm.1_Intron|PPP1R1C_uc010frn.1_Intron	NM_001080545	NP_001074014	Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor)						signal transduction	cytoplasm	protein phosphatase inhibitor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0628)			TATGCTCATCTTTCCTCACAT	0.378													4	2	---	---	---	---	
SLC40A1	30061	broad.mit.edu	37	2	190437908	190437908	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190437908delC	uc002uqp.3	-						SLC40A1_uc002uqq.2_Intron	NM_014585	NP_055400	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated						anatomical structure morphogenesis|cellular iron ion homeostasis	cytoplasm|integral to plasma membrane	iron ion transmembrane transporter activity|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			TGATGAAGTACCACAAGTTTC	0.343													4	2	---	---	---	---	
ANKAR	150709	broad.mit.edu	37	2	190550347	190550347	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190550347delA	uc002uqw.1	+						ANKAR_uc002uqu.2_Intron|ANKAR_uc002uqv.1_Intron	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			gtgaggcaggaacgctggcag	0.080													4	2	---	---	---	---	
ORC2L	4999	broad.mit.edu	37	2	201780041	201780041	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201780041delT	uc002uwr.2	-						ORC2L_uc010zhj.1_Intron	NM_006190	NP_006181	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0						TTTTCTTTTCTTTTTTTTTGC	0.229													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	202817015	202817026	+	IGR	DEL	GGAGCTGGTGGT	-	-	rs11275382		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202817015_202817026delGGAGCTGGTGGT								CDK15 (58752 upstream) : FZD7 (82284 downstream)																							AGCTGGGCGGGGAGCTGGTGGTGGAGCTGGCT	0.547													3	3	---	---	---	---	
ICOS	29851	broad.mit.edu	37	2	204799436	204799436	+	5'Flank	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204799436delA	uc002vam.2	+						ICOS_uc010zip.1_5'Flank|ICOS_uc010fua.2_5'Flank	NM_012092	NP_036224	Q9Y6W8	ICOS_HUMAN	inducible T-cell co-stimulator precursor						immune response|T cell costimulation	extracellular region					0						ATAGGAGACCAAAAAAAGTAA	0.274													4	2	---	---	---	---	
MAP2	4133	broad.mit.edu	37	2	210286250	210286250	+	5'Flank	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210286250delA	uc002vdc.1	+						MAP2_uc002vdd.1_5'Flank	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	TTGCTGAGGGAAAAAAAAAAG	0.308													4	2	---	---	---	---	
TNS1	7145	broad.mit.edu	37	2	218716163	218716164	+	Intron	INS	-	AC	AC	rs10631122		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218716163_218716164insAC	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc010zjv.1_Intron|TNS1_uc010fvj.1_Intron|TNS1_uc010fvk.1_Intron|TNS1_uc010fvi.1_Intron	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGCATCCCTCTacacacacaca	0.450													4	3	---	---	---	---	
ARPC2	10109	broad.mit.edu	37	2	219091013	219091013	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219091013delA	uc002vhd.2	+						ARPC2_uc002vhe.2_Intron	NM_152862	NP_690601	O15144	ARPC2_HUMAN	actin related protein 2/3 complex subunit 2						cellular component movement	Arp2/3 protein complex|cell projection|Golgi apparatus	actin binding|structural constituent of cytoskeleton			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;1.21e-06)|all cancers(144;0.000212)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0103)		agactgtctcaaaaaaaaaaa	0.045													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220619532	220619554	+	IGR	DEL	GGCTAGTCCACAAGGTCTCTCTG	-	-	rs72448421		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220619532_220619554delGGCTAGTCCACAAGGTCTCTCTG								SLC4A3 (112831 upstream) : None (None downstream)																							TCCACCACCTGGCTAGTCCACAAGGTCTCTCTGGGCTCACCAG	0.538													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	224100936	224100936	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224100936delA								KCNE4 (180583 upstream) : SCG2 (360724 downstream)																							TCAACTCAGGAACTCCAGTAC	0.428													4	2	---	---	---	---	
COL4A4	1286	broad.mit.edu	37	2	228026652	228026652	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228026652delA	uc010zlt.1	-						COL4A3_uc002vom.1_5'Flank|COL4A3_uc002von.1_5'Flank|COL4A3_uc002voo.1_5'Flank|COL4A3_uc002vop.1_5'Flank	NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCCTTTGTACAAAAAAAAAAA	0.249													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	229725657	229725658	+	IGR	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229725657_229725658insG								SPHKAP (679296 upstream) : PID1 (163032 downstream)																							TTATTATTTAAGGATTTCTGAT	0.401													4	2	---	---	---	---	
CAB39	51719	broad.mit.edu	37	2	231617613	231617613	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231617613delA	uc002vqx.2	+						CAB39_uc010fxr.2_Intron|CAB39_uc010fxq.2_Intron	NM_016289	NP_057373	Q9Y376	CAB39_HUMAN	calcium binding protein 39						cell cycle arrest|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol	kinase binding			central_nervous_system(1)	1		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		AAAAAGAAGCAGGACTTAGAT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	232498393	232498394	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232498393_232498394delGT								C2orf57 (39401 upstream) : PTMA (74841 downstream)																							gagtgtgtgagtgtgtgtgtgc	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235126990	235126990	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235126990delG								SPP2 (141214 upstream) : ARL4C (274698 downstream)																							tggtccacatgggtgatacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	235381008	235381008	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235381008delT								SPP2 (395232 upstream) : ARL4C (20680 downstream)																							ctctcctgtgttttatgagat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236042949	236042949	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236042949delT								SH3BP4 (78593 upstream) : AGAP1 (359787 downstream)																							CTTTGATTGATTTTTTTAGCG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236117976	236117976	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236117976delA								SH3BP4 (153620 upstream) : AGAP1 (284760 downstream)																							aacatgaatgaaaatatcaac	0.000													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236551666	236551666	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236551666delA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						TTGGGAGGAGaaaatacacag	0.308													4	2	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236953411	236953412	+	Intron	INS	-	CA	CA	rs34701466		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236953411_236953412insCA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						AGGTTTGAAATcacacacacac	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	238698436	238698437	+	IGR	DEL	AG	-	-	rs113640485		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238698436_238698437delAG								LRRFIP1 (8148 upstream) : RBM44 (8951 downstream)																							acctggcagcagagagagagag	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	240638833	240638834	+	IGR	DEL	GA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240638833_240638834delGA								HDAC4 (315487 upstream) : NDUFA10 (261324 downstream)																							GTTCTGAGCTGAGAGAGAGACC	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241306754	241306754	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241306754delG								OTOS (226681 upstream) : GPC1 (68361 downstream)																							GGAAAGCGATGGGTGTTTTGC	0.438													4	2	---	---	---	---	
CRBN	51185	broad.mit.edu	37	3	3219709	3219710	+	Intron	INS	-	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3219709_3219710insC	uc003bpq.2	-						CRBN_uc003bpr.2_Intron|CRBN_uc010hbw.2_Intron|CRBN_uc011aso.1_Intron	NM_016302	NP_057386	Q96SW2	CRBN_HUMAN	cereblon						proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	Cul4A-RING ubiquitin ligase complex|cytoplasm|membrane|nucleus	ATP-dependent peptidase activity|protein binding			ovary(1)	1				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)		aacaaaaaaaaaacaaacaaaa	0.371													4	2	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10121606	10121606	+	Intron	DEL	T	-	-	rs79933580		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10121606delT	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		cttcgtcttcttttttttttt	0.119			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	13139244	13139244	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13139244delT								IQSEC1 (24627 upstream) : NUP210 (218493 downstream)																							GGGCTGAACATTTTTTTTTTC	0.378													4	3	---	---	---	---	
LOC285375	285375	broad.mit.edu	37	3	13699540	13699540	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13699540delG	uc003byd.1	+							NR_027103				Homo sapiens, clone IMAGE:5742174, mRNA.												0						GAACACGGCTGGGACGAGGGC	0.657											OREG0015414	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SLC6A6	6533	broad.mit.edu	37	3	14466834	14466834	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14466834delT	uc010heg.2	+						SLC6A6_uc010hee.1_Intron|SLC6A6_uc003byp.2_Intron|SLC6A6_uc010hef.1_Intron|SLC6A6_uc003byq.2_Intron|SLC6A6_uc003byr.2_Intron	NM_001134367	NP_001127839	P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter						cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity			ovary(1)	1						AGGGTGGAACTAGGCAAACCT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	15186241	15186241	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15186241delT								ZFYVE20 (45586 upstream) : DVWA (20628 downstream)																							TCAGATGCCCTTGCATCGTCT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	15400812	15400812	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15400812delT								SH3BP5 (17911 upstream) : METTL6 (21972 downstream)																							tctttctttcttttttttttt	0.124													2	5	---	---	---	---	
GALNTL2	117248	broad.mit.edu	37	3	15974183	15974183	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15974183delG	uc003caq.3	+							NM_054110	NP_473451	Q8N3T1	GLTL2_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1						TGGTCCCTAAGGAACCCTCAG	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	16293208	16293209	+	IGR	DEL	AG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16293208_16293209delAG								GALNTL2 (21956 upstream) : DPH3 (5360 downstream)																							ACATCAGAAcagagctgagagg	0.248													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	19845750	19845750	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19845750delC								KCNH8 (268615 upstream) : EFHB (75218 downstream)																							atctcctcaacccacaccacc	0.000													4	2	---	---	---	---	
ZNF385D	79750	broad.mit.edu	37	3	21696606	21696606	+	Intron	DEL	C	-	-	rs9810559	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21696606delC	uc003cce.2	-						ZNF385D_uc010hfb.1_Intron	NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5						gtgcaaaaaacaacaacaaca	0.169													4	2	---	---	---	---	
ZNF385D	79750	broad.mit.edu	37	3	22414784	22414785	+	5'Flank	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22414784_22414785delCT	uc010hfb.1	-									Q9H6B1	Z385D_HUMAN	Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5						TGTCTGTCTCCTCTCTCTCTCA	0.500													4	2	---	---	---	---	
NGLY1	55768	broad.mit.edu	37	3	25761840	25761840	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25761840delT	uc003cdl.2	-						NGLY1_uc010hfg.2_Intron|NGLY1_uc003cdm.2_Intron|NGLY1_uc011awo.1_Intron|NGLY1_uc003cdk.2_Intron	NM_018297	NP_060767	Q96IV0	NGLY1_HUMAN	N-glycanase 1 isoform 1						glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1						ACTGCTAACATTTTTTTTGGC	0.343													5	3	---	---	---	---	
CMTM7	112616	broad.mit.edu	37	3	32469849	32469849	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32469849delT	uc003cey.1	+						CMTM7_uc003cez.1_Intron	NM_138410	NP_612419	Q96FZ5	CKLF7_HUMAN	CKLF-like MARVEL transmembrane domain containing						chemotaxis	extracellular space|integral to membrane	cytokine activity				0						TTTTCCTTCATTTCCTCATCT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34290728	34290728	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34290728delC								PDCD6IP (379534 upstream) : None (None downstream)																							CCTCTGCCTTCCCATCATGTT	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34788144	34788144	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34788144delG								PDCD6IP (876950 upstream) : ARPP21 (892937 downstream)																							GTATAGAAGTGGTGGGACTGA	0.338													4	2	---	---	---	---	
STAC	6769	broad.mit.edu	37	3	36581580	36581581	+	Intron	DEL	AG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36581580_36581581delAG	uc003cgh.1	+						STAC_uc011aya.1_Intron	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain						intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4						agccggggtcagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	36855371	36855371	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36855371delA								DCLK3 (74019 upstream) : TRANK1 (12940 downstream)																							GCTGGTGAGGAAAAggcaggt	0.259													4	2	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41302110	41302110	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41302110delA	uc003ckv.3	-						ULK4_uc003cku.3_Intron	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		AGGTGTCCCTAAGGATTCCCA	0.488													4	2	---	---	---	---	
CACNA1D	776	broad.mit.edu	37	3	53560116	53560116	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53560116delC	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)	gagtctttgtcccagtccttc	0.000													4	2	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	61908156	61908157	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61908156_61908157delGT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		gtctgtgtgagtgtgtgtgtgt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	64829040	64829040	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64829040delA	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																		GAACCCAATGAAGCAAAGCTG	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	71901907	71901907	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71901907delA								PROK2 (67550 upstream) : RYBP (521844 downstream)																							CCTTCAATGGAAAAAAAAAAC	0.269													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	72016598	72016598	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72016598delC								PROK2 (182241 upstream) : RYBP (407153 downstream)																							ggcggatattccccactaagt	0.000													4	2	---	---	---	---	
ARL13B	200894	broad.mit.edu	37	3	93752406	93752406	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93752406delG	uc003drc.2	+						ARL13B_uc010hop.2_Intron|ARL13B_uc003drd.2_Intron|ARL13B_uc003dre.2_Intron|ARL13B_uc003drf.2_Intron|ARL13B_uc003drg.2_Intron	NM_182896	NP_878899	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 2-like 1 isoform 1								GTP binding				0						agtaaatgcagaaggaatatg	0.000													4	2	---	---	---	---	
IMPG2	50939	broad.mit.edu	37	3	100949485	100949486	+	Intron	DEL	CC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100949485_100949486delCC	uc003duq.1	-						IMPG2_uc011bhe.1_Intron|IMPG2_uc010hpj.1_Intron	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2						visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						TAGAAAGCATCCCAGCCCAAAC	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	105304476	105304476	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105304476delA								ALCAM (8733 upstream) : CBLB (72634 downstream)																							AATCGCCATTACAACTAATGA	0.348													4	2	---	---	---	---	
MORC1	27136	broad.mit.edu	37	3	108819090	108819090	+	Intron	DEL	A	-	-	rs78907417		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108819090delA	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244	Q86VD1	MORC1_HUMAN	MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8						aatctgtctcaaaaaaaaaaa	0.164													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	111800513	111800513	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111800513delT								TMPRSS7 (397 upstream) : C3orf52 (4669 downstream)																							CCCAAGGAAATAACTATATTC	0.274													4	2	---	---	---	---	
GRAMD1C	54762	broad.mit.edu	37	3	113622785	113622786	+	Intron	INS	-	TA	TA	rs149350729	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113622785_113622786insTA	uc003eaq.3	+						GRAMD1C_uc011bil.1_Intron|GRAMD1C_uc011bim.1_Intron|GRAMD1C_uc003ear.2_Intron|GRAMD1C_uc003eas.2_Intron	NM_017577	NP_060047	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C							integral to membrane				ovary(2)|skin(1)	3						CCATGTGAGTGTATCTTGTTTT	0.262													13	10	---	---	---	---	
ZDHHC23	254887	broad.mit.edu	37	3	113676174	113676174	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113676174delT	uc003eau.2	+						ZDHHC23_uc003eav.2_Intron|ZDHHC23_uc003eaw.1_5'Flank	NM_173570	NP_775841	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC domain containing 23							integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2						GTGGCATTTGTTTTTATTAGC	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	117715669	117715670	+	IGR	INS	-	AC	AC			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117715669_117715670insAC								None (None upstream) : IGSF11 (903811 downstream)																							ACCCCACCAAGacacacacaca	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	118260410	118260410	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118260410delG	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																		ACCTACCTTTGGACATGTCCC	0.468													4	2	---	---	---	---	
UPK1B	7348	broad.mit.edu	37	3	118905466	118905467	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118905466_118905467insA	uc003ecc.2	+						UPK1B_uc011bix.1_Intron|UPK1B_uc003ecd.2_5'Flank	NM_006952	NP_008883	O75841	UPK1B_HUMAN	uroplakin 1B						epithelial cell differentiation	integral to membrane	structural molecule activity				0				GBM - Glioblastoma multiforme(114;0.222)		TATGGCTTTGGTTTGGATGCTT	0.371													53	30	---	---	---	---	
NPHP3	27031	broad.mit.edu	37	3	132410210	132410212	+	Intron	DEL	TTT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132410210_132410212delTTT	uc003epe.1	-						NPHP3_uc003epd.1_Intron	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1						CAAAAAAGAATTTATAATTATTC	0.266													64	36	---	---	---	---	
XRN1	54464	broad.mit.edu	37	3	142074103	142074103	+	Intron	DEL	G	-	-	rs67564832	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142074103delG	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3						TTTAAAAAAAGAAAAAGAAAA	0.095													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	146222548	146222548	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146222548delT								PLSCR2 (8826 upstream) : PLSCR1 (10420 downstream)																							gttccttccctttttttatca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	147038259	147038260	+	IGR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147038259_147038260insT								PLSCR5 (714256 upstream) : ZIC4 (65577 downstream)																							CTTATTCTGGGTTTTTTTTTGG	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	154050182	154050182	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154050182delT								DHX36 (7896 upstream) : GPR149 (5280 downstream)																							GTGTTCAAAGTTTTTTTGTAT	0.368													4	2	---	---	---	---	
KCNAB1	7881	broad.mit.edu	37	3	156145044	156145044	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156145044delC	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron	NM_172160	NP_751892	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CTTGTGACCTCCCAGCTTCAG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	158473204	158473204	+	IGR	DEL	C	-	-	rs11352614		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158473204delC								RARRES1 (22929 upstream) : MFSD1 (46708 downstream)																							tccctggcagccactgatcct	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	159902977	159902977	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159902977delC	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																		GCAGAGTTTACCTAGTATTCT	0.328													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	162764003	162764004	+	Intron	DEL	CT	-	-	rs79510262		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162764003_162764004delCT	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																		AATATTCTCCCTGTTTCTATTT	0.450													4	2	---	---	---	---	
SEC62	7095	broad.mit.edu	37	3	169689896	169689896	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169689896delT	uc003fgg.2	+						SEC62_uc003fgh.2_Intron	NM_003262	NP_003253	Q99442	SEC62_HUMAN	translocation protein 1						cotranslational protein targeting to membrane|transmembrane transport	aggresome|endoplasmic reticulum membrane|integral to membrane|intermediate filament cytoskeleton|rough endoplasmic reticulum	protein transporter activity|receptor activity			ovary(1)	1						gccttatgcatttttttccag	0.000													4	2	---	---	---	---	
CLDN11	5010	broad.mit.edu	37	3	170140052	170140055	+	Intron	DEL	AGAC	-	-	rs144389271		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170140052_170140055delAGAC	uc003fgx.2	+						CLDN11_uc011bpt.1_Intron|CLDN11_uc003fgy.2_Intron	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CGCTGCACTGAGACAGACAAAGAA	0.275													2	5	---	---	---	---	
RPL22L1	200916	broad.mit.edu	37	3	170582966	170582966	+	3'UTR	DEL	T	-	-	rs75304609	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170582966delT	uc003fhc.3	-	4					RPL22L1_uc003fhb.3_RNA	NM_001099645	NP_001093115	Q6P5R6	RL22L_HUMAN	ribosomal protein L22-like 1						translation	ribosome	structural constituent of ribosome				0	all_cancers(22;1.96e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.137)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)			GGCACTTAAATTTTTAGGAAA	0.368													4	2	---	---	---	---	
TNIK	23043	broad.mit.edu	37	3	171156059	171156060	+	Intron	INS	-	TAAG	TAAG	rs138138378	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171156059_171156060insTAAG	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhq.2_Intron	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			AATGCAAGCATTAAGACCCACA	0.480													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	171309234	171309234	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171309234delT								TNIK (131037 upstream) : PLD1 (9386 downstream)																							TCTTGTTTTCTtttttttttc	0.025													4	3	---	---	---	---	
TNFSF10	8743	broad.mit.edu	37	3	172241184	172241185	+	5'UTR	DEL	AG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172241184_172241185delAG	uc003fid.2	-	1					TNFSF10_uc003fie.2_5'UTR|TNFSF10_uc010hwu.1_RNA	NM_003810	NP_003801	P50591	TNF10_HUMAN	tumor necrosis factor (ligand) superfamily,						activation of caspase activity|activation of pro-apoptotic gene products|cell-cell signaling|immune response|induction of apoptosis by extracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|signal transduction	extracellular space|integral to plasma membrane|soluble fraction	cytokine activity|metal ion binding|tumor necrosis factor receptor binding			skin(4)|lung(1)	5	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.67e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			TGATCCTGTCAGAGTCTGACTG	0.520													27	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	172314182	172314184	+	5'Flank	DEL	TCT	-	-	rs138385156		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172314182_172314184delTCT	uc003fif.1	-											Homo sapiens cDNA FLJ45650 fis, clone CTONG2009923.																		TAAACCAGGATCTTCTTCAGCCT	0.443													2	4	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	174862740	174862740	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174862740delG	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		tttacttcctggtaacaagtc	0.000													4	2	---	---	---	---	
NAALADL2	254827	broad.mit.edu	37	3	175394427	175394427	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175394427delA	uc003fit.2	+							NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		GCTCTTGATTAAAAAAAAAAA	0.363													4	5	---	---	---	---	
PIK3CA	5290	broad.mit.edu	37	3	178942268	178942268	+	Intron	DEL	T	-	-	rs10605725		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178942268delT	uc003fjk.2	+							NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			GATATATCTCTATATATTTGT	0.239		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			3	3	---	---	---	---	
PIK3CA	5290	broad.mit.edu	37	3	178942270	178942272	+	Intron	DEL	TAT	-	-	rs67770152		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178942270_178942272delTAT	uc003fjk.2	+							NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			TATATCTCTATATATTTGTTGGA	0.241		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			3	3	---	---	---	---	
C3orf70	285382	broad.mit.edu	37	3	184850663	184850663	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184850663delA	uc003fpd.2	-							NM_001025266	NP_001020437	A6NLC5	CC070_HUMAN	hypothetical protein LOC285382												0						gcagctagagaaaaaagagac	0.000													4	2	---	---	---	---	
IGF2BP2	10644	broad.mit.edu	37	3	185408850	185408850	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185408850delG	uc003fpo.2	-						IGF2BP2_uc010hyi.2_Intron|IGF2BP2_uc010hyj.2_Intron|IGF2BP2_uc010hyk.2_Intron|IGF2BP2_uc010hyl.2_Intron|IGF2BP2_uc003fpp.2_Intron|IGF2BP2_uc003fpq.2_Intron	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			ATGTGTACAAGGTAAAGTTAA	0.259													4	2	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188074251	188074251	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188074251delG	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		agtgtggggtgggcagtgggg	0.030			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	2	---	---	---	---	
TP63	8626	broad.mit.edu	37	3	189547434	189547434	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189547434delG	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsa.2_Intron|TP63_uc003fsb.2_Intron|TP63_uc003fsc.2_Intron|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Intron|TP63_uc003fse.1_Intron|MIR944_hsa-mir-944|MI0005769_5'Flank	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		cctagagtctggcgaggactt	0.040									Hay-Wells_syndrome	HNSCC(45;0.13)			4	2	---	---	---	---	
LEPREL1	55214	broad.mit.edu	37	3	189763258	189763258	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189763258delC	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662	Q8IVL5	P3H2_HUMAN	leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	ATTTTTCCTTCCCCCCAACCA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193424213	193424213	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193424213delT								OPA1 (8614 upstream) : LOC100128023 (286671 downstream)																							gtggatgtgatttttggatat	0.000													4	2	---	---	---	---	
ATP13A3	79572	broad.mit.edu	37	3	194168310	194168310	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194168310delT	uc003fty.3	-						ATP13A3_uc003ftz.1_Intron	NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		TTTTTTCCTGTTTTTTTTTTT	0.249													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	194436973	194436973	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194436973delT								FAM43A (27209 upstream) : C3orf21 (352042 downstream)																							TTCCTATTTATTTTGGGCTTG	0.433													4	2	---	---	---	---	
ACAP2	23527	broad.mit.edu	37	3	195016948	195016948	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195016948delA	uc003fun.3	-							NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2						ACATCACCAGAAAAAAAAAAA	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	27550	27551	+	IGR	INS	-	C	C	rs112426244	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27550_27551insC								None (None upstream) : ZNF595 (25676 downstream)																							GGGGGGGGGGGCAAGGCAAAAA	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	199852	199853	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:199852_199853delGT								ZNF595 (3760 upstream) : ZNF876P (6536 downstream)																							AGTATGGGCCgtgtgtgtgtgt	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	254032	254032	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:254032delC								ZNF876P (4261 upstream) : ZNF732 (5450 downstream)																							GTCCTTGCCACCCCTCCAGCA	0.363													4	2	---	---	---	---	
POLN	353497	broad.mit.edu	37	4	2109722	2109722	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2109722delT	uc003ger.2	-						POLN_uc010icg.1_Intron|POLN_uc010ich.1_Intron	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			atccgagcgctttgcaccttt	0.229								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
EVC	2121	broad.mit.edu	37	4	5805130	5805130	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5805130delT	uc003gil.1	+						EVC_uc003gim.1_Intron|CRMP1_uc003gin.1_Intron	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein						muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)				ATCTGCCAGGTTTTCCAAAGG	0.393													4	2	---	---	---	---	
TBC1D14	57533	broad.mit.edu	37	4	6935526	6935527	+	Intron	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6935526_6935527delTG	uc011bwg.1	+						TBC1D14_uc003gjs.3_Intron	NM_001113361	NP_001106832	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14 isoform a							intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2						cctgaggtgctgtactgagagg	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	7752123	7752123	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7752123delC								SORCS2 (7560 upstream) : LOC84740 (3694 downstream)																							GACCAGAAATCCCCAAAGGAT	0.348													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	9054331	9054333	+	IGR	DEL	AAC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9054331_9054333delAAC								LOC650293 (102205 upstream) : USP17 (305776 downstream)																							ccaaagtgaaaacaacacaattg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	10125774	10125775	+	5'Flank	INS	-	T	T	rs34563732		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10125774_10125775insT	uc003gmm.2	+											DQ573667																		ctgttttcatccttaatgtctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12080033	12080034	+	IGR	INS	-	CTT	CTT	rs145358380	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12080033_12080034insCTT								HS3ST1 (649496 upstream) : None (None downstream)																							CAAAACGAGCACTTCATCCTTC	0.431													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	12784108	12784108	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12784108delC								None (None upstream) : HSP90AB2P (550929 downstream)																							GGGTTATATACCTGGGCATTG	0.418													4	2	---	---	---	---	
FAM184B	27146	broad.mit.edu	37	4	17694653	17694657	+	Intron	DEL	CAGGC	-	-	rs139504706		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17694653_17694657delCAGGC	uc003gpm.3	-							NM_015688	NP_056503	Q9ULE4	F184B_HUMAN	hypothetical protein LOC27146											central_nervous_system(1)	1						AGGGGAACTGCAGGCTACCCActtg	0.102													4	4	---	---	---	---	
KCNIP4	80333	broad.mit.edu	37	4	21503617	21503618	+	Intron	DEL	CA	-	-	rs77637490		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21503617_21503618delCA	uc003gqh.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)				CATGcacacgcacacacacaca	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	22691269	22691270	+	IGR	INS	-	TG	TG	rs143659871	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22691269_22691270insTG								GPR125 (173597 upstream) : GBA3 (3278 downstream)																							agaggaactactgtggctgtga	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	26141885	26141885	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26141885delC								C4orf52 (210385 upstream) : RBPJ (179447 downstream)																							CCAGTGACAGCCCAGGCTGTG	0.388													4	2	---	---	---	---	
KIAA1239	57495	broad.mit.edu	37	4	37362293	37362293	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37362293delC	uc011bxz.1	+							NM_001144990	NP_001138462	Q9ULI1	K1239_HUMAN	hypothetical protein LOC57495												0						AACAAAATCTCCCCCACCTAC	0.423													4	2	---	---	---	---	
KLB	152831	broad.mit.edu	37	4	39444461	39444461	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39444461delC	uc003gua.2	+						KLB_uc011byj.1_Intron	NM_175737	NP_783864	Q86Z14	KLOTB_HUMAN	klotho beta						carbohydrate metabolic process	integral to membrane|plasma membrane	cation binding|fibroblast growth factor binding|hydrolase activity, hydrolyzing O-glycosyl compounds			skin(1)	1						tattatgattcccaggaaatt	0.000													4	2	---	---	---	---	
LIAS	11019	broad.mit.edu	37	4	39472556	39472557	+	Intron	INS	-	CAAA	CAAA	rs139815066	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39472556_39472557insCAAA	uc003guf.2	+						LIAS_uc003gug.2_Intron|LIAS_uc003guh.2_Intron	NM_006859	NP_006850	O43766	LIAS_HUMAN	lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)	ACCTTTTCTACCAGACTCCTAC	0.351													4	6	---	---	---	---	
ATP8A1	10396	broad.mit.edu	37	4	42568877	42568877	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42568877delA	uc003gwr.2	-						ATP8A1_uc003gws.2_Intron|ATP8A1_uc011byz.1_Intron	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	caccaactttaaaatggccat	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49220046	49220046	+	IGR	DEL	T	-	-	rs113422017		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49220046delT								CWH43 (155953 upstream) : None (None downstream)																							aaaggaaaaatgttgtcatgc	0.000													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49318804	49318804	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49318804delG								CWH43 (254711 upstream) : None (None downstream)																							ccaaccctcagggactctcct	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49563343	49563343	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49563343delC								CWH43 (499250 upstream) : None (None downstream)																							GTAAGAGCTTCCTTGGGTATG	0.567													6	3	---	---	---	---	
CLOCK	9575	broad.mit.edu	37	4	56309643	56309643	+	Intron	DEL	A	-	-	rs36064611		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56309643delA	uc003haz.1	-						CLOCK_uc003hba.1_Intron|CLOCK_uc010igu.1_Intron	NM_004898	NP_004889	O15516	CLOCK_HUMAN	clock						circadian rhythm|photoperiodism|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|transcription factor complex	DNA binding|histone acetyltransferase activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			actccgtctcaaaaaaaaaaa	0.090													10	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	67453877	67453878	+	IGR	DEL	TT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67453877_67453878delTT								MIR1269 (311231 upstream) : CENPC1 (884111 downstream)																							CCTGTATTCATTTTAGAATATA	0.262													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	72588820	72588820	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72588820delG								SLC4A4 (151017 upstream) : GC (18593 downstream)																							cgatctgtatggaagatctga	0.000													4	2	---	---	---	---	
AFP	174	broad.mit.edu	37	4	74306790	74306790	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74306790delT	uc003hgz.1	+						AFP_uc003hha.1_Intron|AFP_uc011cbg.1_5'Flank	NM_001134	NP_001125	P02771	FETA_HUMAN	alpha-fetoprotein precursor						transport		metal ion binding			ovary(1)	1	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GATATACACCTTTTTTTTTTC	0.358									Alpha-Fetoprotein_Hereditary_Persistence_of				7	4	---	---	---	---	
USO1	8615	broad.mit.edu	37	4	76693399	76693399	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76693399delT	uc003hiu.2	+						USO1_uc003hiv.2_Intron|USO1_uc003hiw.2_Intron	NM_003715	NP_003706	O60763	USO1_HUMAN	USO1 homolog, vesicle docking protein						intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AAGAAGGACAtttttttttga	0.114													4	2	---	---	---	---	
BMP2K	55589	broad.mit.edu	37	4	79755268	79755268	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79755268delT	uc003hlk.2	+						BMP2K_uc010ijl.1_Intron|BMP2K_uc003hlj.2_Intron	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a							nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1						TATAAACCTGTTTTATGTAGT	0.254													4	2	---	---	---	---	
PTPN13	5783	broad.mit.edu	37	4	87723299	87723300	+	Intron	INS	-	GTGT	GTGT	rs1894958	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87723299_87723300insGTGT	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron|PTPN13_uc003hqc.1_Intron	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TCAAGATTTTAgtgtgtgtgtg	0.248													5	3	---	---	---	---	
FAM190A	401145	broad.mit.edu	37	4	91990507	91990507	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91990507delT	uc003hsv.3	+						FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2						TTCATTTCACTTTTTTTTTTC	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	93154480	93154480	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93154480delT								FAM190A (631111 upstream) : GRID2 (71070 downstream)																							TAAGAAAGGCTTTTTTTTAAA	0.373													3	3	---	---	---	---	
SMARCAD1	56916	broad.mit.edu	37	4	95202130	95202133	+	Intron	DEL	AGTT	-	-	rs34519004		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95202130_95202133delAGTT	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron|SMARCAD1_uc011cdw.1_Intron	NM_020159	NP_064544	Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		AACAATAGAAAGTTAGTAGACTGT	0.304													11	7	---	---	---	---	
PPP3CA	5530	broad.mit.edu	37	4	101984180	101984180	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101984180delT	uc011cen.1	-						PPP3CA_uc003hvu.2_Intron|PPP3CA_uc010ilj.2_Intron|PPP3CA_uc003hvt.2_Intron|PPP3CA_uc003hvs.2_Intron|PPP3CA_uc010ilk.2_Intron	NM_000944	NP_000935	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha						protein dephosphorylation	calcineurin complex|cytosol|nucleus	calcium ion binding|calmodulin binding			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		CTGTGTTTTGTTTTTTTTTTT	0.313													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	105706044	105706044	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105706044delT								CXXC4 (289986 upstream) : TET2 (361899 downstream)																							tattcttcagttttttttttc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	109411853	109411856	+	IGR	DEL	GATA	-	-	rs34818113		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109411853_109411856delGATA								LEF1 (322275 upstream) : LOC285456 (47490 downstream)																							atagatagatgatagatagataga	0.078													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	113395298	113395298	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113395298delT								ALPK1 (31537 upstream) : NEUROG2 (39376 downstream)																							tggattttgcttttttatcta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	120283186	120283186	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120283186delT								FABP2 (39870 upstream) : PDE5A (132366 downstream)																							ttcggggtggtgggaattaat	0.000													4	2	---	---	---	---	
PRDM5	11107	broad.mit.edu	37	4	121641072	121641072	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121641072delT	uc003idn.2	-						PRDM5_uc003ido.2_Intron|PRDM5_uc010ine.2_Intron	NM_018699	NP_061169	Q9NQX1	PRDM5_HUMAN	PR domain containing 5						histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2						AGGGGAACTATTTTTGATATC	0.393													4	2	---	---	---	---	
TNIP3	79931	broad.mit.edu	37	4	122053415	122053415	+	3'UTR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122053415delT	uc010ing.2	-	11					TNIP3_uc010inh.2_3'UTR|TNIP3_uc011cgj.1_3'UTR	NM_024873	NP_079149	Q96KP6	TNIP3_HUMAN	TNFAIP3 interacting protein 3											ovary(1)	1						acaTATGCACTTTAAATCAAC	0.294													4	2	---	---	---	---	
FGF2	2247	broad.mit.edu	37	4	123765802	123765803	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123765802_123765803insT	uc003iev.1	+							NM_002006	NP_001997	P09038	FGF2_HUMAN	fibroblast growth factor 2						activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing	extracellular space	fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|lung(1)|central_nervous_system(1)	3					Pentosan Polysulfate(DB00686)	ttctttctttctttttttTTga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	128146063	128146064	+	IGR	INS	-	CT	CT	rs145816368	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128146063_128146064insCT								None (None upstream) : INTU (408056 downstream)																							cagggttgggactctgcaccgg	0.000													3	4	---	---	---	---	
ELF2	1998	broad.mit.edu	37	4	140053604	140053605	+	Intron	DEL	CA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140053604_140053605delCA	uc003ihp.1	-						ELF2_uc003ihq.2_Intron	NM_201999	NP_973728	Q15723	ELF2_HUMAN	E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)					catgtgcatgcacacacacaca	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	141777363	141777363	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141777363delT								TBC1D9 (99892 upstream) : RNF150 (9362 downstream)																							TTGCTTTCCATTCCTTATATT	0.119													4	2	---	---	---	---	
RNF150	57484	broad.mit.edu	37	4	142019847	142019847	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142019847delC	uc003iio.1	-						RNF150_uc010iok.1_Intron|RNF150_uc003iip.1_Intron	NM_020724	NP_065775	Q9ULK6	RN150_HUMAN	ring finger protein 150 precursor							integral to membrane	zinc ion binding			ovary(1)	1	all_hematologic(180;0.162)					ATAAAAACAACAATAAATTCA	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	146332744	146332744	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146332744delC								OTUD4 (231912 upstream) : SMAD1 (70207 downstream)																							ccactcaccaccgagcagctt	0.000													4	2	---	---	---	---	
ZNF827	152485	broad.mit.edu	37	4	146709315	146709315	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146709315delT	uc003ikn.2	-						ZNF827_uc003ikm.2_Intron|ZNF827_uc010iox.2_Intron|ZNF827_uc003ikl.2_Intron	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)					TGGATAACCATTTTTTTTTGC	0.303													4	2	---	---	---	---	
DCLK2	166614	broad.mit.edu	37	4	151000965	151000965	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151000965delC	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)					CTCTGTTGGACCCTCGGTGTG	0.478													4	2	---	---	---	---	
DCLK2	166614	broad.mit.edu	37	4	151088313	151088313	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151088313delA	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)					GAAAAATGCCAAAAAAAAAAT	0.418													4	3	---	---	---	---	
SH3D19	152503	broad.mit.edu	37	4	152059255	152059255	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152059255delA	uc010ipl.1	-						SH3D19_uc003imb.2_Intron|SH3D19_uc003imc.2_Intron|SH3D19_uc003ime.2_Intron|SH3D19_uc010ipm.2_Intron	NM_001009555	NP_001009555	Q5HYK7	SH319_HUMAN	SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				GAAATGGTTGAAAAAAACACT	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	152980267	152980267	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152980267delT								PET112L (298121 upstream) : FBXW7 (262144 downstream)																							AAAACGAAGCTTTTTAGAAAT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	153185910	153185910	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153185910delA								PET112L (503764 upstream) : FBXW7 (56501 downstream)																							TCATTATTTTAAAAAAATTTA	0.368													4	2	---	---	---	---	
RNF175	285533	broad.mit.edu	37	4	154674130	154674130	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154674130delA	uc003int.2	-						RNF175_uc003inu.1_Intron	NM_173662	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175							integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				CACGGTAAATAAAAAAAGTGC	0.199													4	2	---	---	---	---	
FSTL5	56884	broad.mit.edu	37	4	162644025	162644025	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162644025delG	uc003iqh.2	-						FSTL5_uc003iqi.2_Intron|FSTL5_uc010iqv.2_Intron	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a							extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TGAGACTTCTGGGCCTTGAAT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	164201932	164201932	+	IGR	DEL	T	-	-	rs71823749		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164201932delT								NAF1 (113859 upstream) : NPY1R (43185 downstream)																							TTCTAATGCATTTTTTTTTGG	0.348													3	3	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164640644	164640645	+	Intron	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164640644_164640645delTG	uc003iqs.1	-							NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				aataaacagatgtgtgtgtgtg	0.000													4	2	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164869836	164869840	+	Intron	DEL	AAGAC	-	-	rs71600654		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164869836_164869840delAAGAC	uc003iqs.1	-							NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				AACAGGAGTAAAGACAAGAAGAAAA	0.366													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	183769717	183769717	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183769717delT								ODZ3 (45540 upstream) : DCTD (41528 downstream)																							aagttttttgttttttttttt	0.000													4	3	---	---	---	---	
WWC2	80014	broad.mit.edu	37	4	184226387	184226387	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184226387delA	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|WWC2_uc003ivn.3_Intron|WWC2_uc010irz.2_Intron|WWC2_uc003ivo.3_Intron	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)		gagactggagaaaaaaaaagg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	187829098	187829098	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187829098delT								FAT1 (181248 upstream) : None (None downstream)																							GGTGATCTTATTTTTTTTAGT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188980665	188980665	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188980665delT								ZFP42 (54466 upstream) : TRIML2 (31762 downstream)																							ACTTTTTCCCTCACGTTTCTC	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	189296527	189296527	+	IGR	DEL	G	-	-	rs140775290		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189296527delG								TRIML1 (227878 upstream) : None (None downstream)																							gattgacgctgggaaatgaag	0.000													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190511955	190511956	+	IGR	INS	-	T	T	rs142515391		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190511955_190511956insT								None (None upstream) : FRG1 (350018 downstream)																							ATGGAACCTTGTTTTTTCTCTA	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190599848	190599851	+	IGR	DEL	ACTC	-	-	rs146229730		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190599848_190599851delACTC								None (None upstream) : FRG1 (262123 downstream)																							AAACAAACAAACTCACTCACCAAA	0.265													4	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190703942	190703942	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190703942delC								None (None upstream) : FRG1 (158032 downstream)																							CTGCTTCCTTCCCATGACCCC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190735956	190735957	+	IGR	INS	-	G	G	rs67994415		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190735956_190735957insG								None (None upstream) : FRG1 (126017 downstream)																							TGCTTTTTTTAAAAAAATACTA	0.252													4	2	---	---	---	---	
AHRR	57491	broad.mit.edu	37	5	345079	345080	+	Intron	INS	-	GTG	GTG	rs148647331	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:345079_345080insGTG	uc003jav.2	+						AHRR_uc003jaw.2_Intron|AHRR_uc010isy.2_Intron|AHRR_uc010isz.2_Intron	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			breast(2)	2			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			tgtgtgaggttgggggctgtgt	0.109													4	2	---	---	---	---	
C5orf55	116349	broad.mit.edu	37	5	442070	442078	+	3'UTR	DEL	TTTGGCAAT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:442070_442078delTTTGGCAAT	uc010ita.2	-	1					EXOC3_uc003jba.2_5'Flank	NM_138464	NP_612473	Q8N2X6	CE055_HUMAN	hypothetical protein LOC116349 precursor							extracellular region					0						TCCTAAAAGCTTTGGCAATTTTGGCAATT	0.282													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2201688	2201688	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2201688delT								IRX4 (318808 upstream) : IRX2 (544593 downstream)																							TAAACCAATGTTTGCTAGCCT	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2719297	2719298	+	IGR	INS	-	TAC	TAC	rs138223898	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2719297_2719298insTAC								IRX4 (836417 upstream) : IRX2 (26983 downstream)																							CTTGTCTCTGTTGTCTCTAAGA	0.371													2	4	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5186610	5186611	+	Intron	DEL	TG	-	-	rs144280497		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5186610_5186611delTG	uc003jdl.2	+						ADAMTS16_uc003jdk.1_Intron|ADAMTS16_uc003jdj.1_Intron	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						TATAAGCCTCTGTAAGCCTGTG	0.376													3	3	---	---	---	---	
ADCY2	108	broad.mit.edu	37	5	7763151	7763152	+	Intron	INS	-	TTTC	TTTC			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7763151_7763152insTTTC	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						AGTGCTTTCATTTTCTTTGTtt	0.198													3	3	---	---	---	---	
CTNND2	1501	broad.mit.edu	37	5	11237135	11237135	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11237135delT	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						ctttcttttcttttttttttt	0.149													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	22105211	22105211	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22105211delT	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						ttttcttttctttttttttga	0.000										HNSCC(59;0.17)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	26149627	26149628	+	IGR	INS	-	ACA	ACA	rs146477836	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26149627_26149628insACA								None (None upstream) : CDH9 (731081 downstream)																							catcatcaaccacaacaacaac	0.000													4	2	---	---	---	---	
CDH6	1004	broad.mit.edu	37	5	31293938	31293938	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31293938delA	uc003jhe.1	+						CDH6_uc003jhd.1_Intron	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						CGTAAATAGTAAAAAAAAAAA	0.209													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	33501371	33501373	+	IGR	DEL	ACA	-	-	rs139809402		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33501371_33501373delACA								TARS (33177 upstream) : ADAMTS12 (25914 downstream)																							tctctgttccacatggtgttggc	0.084													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	34179632	34179632	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34179632delA								C1QTNF3 (136315 upstream) : RAI14 (476801 downstream)																							aaaagaaaagaaaaaaaaaaa	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	39666174	39666175	+	IGR	INS	-	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39666174_39666175insC								DAB2 (240839 upstream) : None (None downstream)																							TCAGGATTTTTCCCCTAATTCC	0.218													4	2	---	---	---	---	
ZNF131	7690	broad.mit.edu	37	5	43149815	43149815	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43149815delT	uc011cpw.1	+						ZNF131_uc010ivl.1_Intron|ZNF131_uc003jnj.3_Intron|ZNF131_uc003jnk.2_Intron|ZNF131_uc003jnn.3_Intron|ZNF131_uc003jnl.1_Intron|ZNF131_uc010ivm.1_Intron	NM_003432	NP_003423	P52739	ZN131_HUMAN	zinc finger protein 131							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						atggtcaggcttttttttatt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	56013390	56013390	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56013390delA								ANKRD55 (484204 upstream) : MAP3K1 (97510 downstream)																							ATATGAGGACAAAAAAAAAGG	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	57678772	57678772	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57678772delA								ACTBL2 (900136 upstream) : PLK2 (71040 downstream)																							TACAGTGTAGAAAAAAAAGAT	0.383													4	2	---	---	---	---	
CWC27	10283	broad.mit.edu	37	5	64205952	64205952	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64205952delT	uc003jtn.1	+						CWC27_uc010iwt.1_Intron	NM_005869	NP_005860	Q6UX04	CWC27_HUMAN	serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0						gtggatgtcctttttattgac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	67849485	67849485	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67849485delC								PIK3R1 (251838 upstream) : SLC30A5 (540333 downstream)																							aactcctcttccattaaattt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	74601192	74601192	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74601192delC								ANKRD31 (68489 upstream) : HMGCR (30962 downstream)																							tgggtcctgaccatgaatttc	0.000													6	4	---	---	---	---	
AP3B1	8546	broad.mit.edu	37	5	77337647	77337648	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77337647_77337648insT	uc003kfj.2	-							NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		tctttcttttctttttttttga	0.208									Hermansky-Pudlak_syndrome				4	2	---	---	---	---	
BHMT2	23743	broad.mit.edu	37	5	78384221	78384222	+	Intron	INS	-	T	T	rs4020529		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78384221_78384222insT	uc003kft.2	+						BHMT2_uc011cth.1_Intron	NM_017614	NP_060084	Q9H2M3	BHMT2_HUMAN	betaine-homocysteine methyltransferase 2						methionine biosynthetic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00063)|Lung NSC(167;0.00171)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;2.09e-45)|Epithelial(54;9.3e-41)|all cancers(79;4.09e-36)	L-Methionine(DB00134)	gtgtgtgtgtgGTTatatacat	0.208													8	5	---	---	---	---	
MSH3	4437	broad.mit.edu	37	5	80037053	80037053	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80037053delT	uc003kgz.2	+							NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CCTGTTCTTGTTTTTTTTTTG	0.358								MMR					9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	94800112	94800112	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94800112delT								FAM81B (13968 upstream) : TTC37 (11 downstream)																							CCAAATTAAATTTTTTTTTTT	0.294													11	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	98301019	98301020	+	IGR	INS	-	T	T	rs141731585	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98301019_98301020insT								CHD1 (38781 upstream) : None (None downstream)																							TTCCGAGCATCttttttttttg	0.074													3	3	---	---	---	---	
TMEM232	642987	broad.mit.edu	37	5	110011328	110011328	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110011328delC	uc011cvh.1	-						TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;							integral to membrane					0						caccttTTCTCCACCCccagc	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	110395934	110395934	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110395934delT								SLC25A46 (297452 upstream) : TSLP (9844 downstream)																							actgaattaattttttaaatg	0.000													4	2	---	---	---	---	
CAMK4	814	broad.mit.edu	37	5	110819196	110819196	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110819196delG	uc011cvj.1	+						CAMK4_uc003kpf.2_Intron|CAMK4_uc010jbv.2_Intron|CAMK4_uc003kpg.2_Intron	NM_001744	NP_001735	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		GAGAGCAGCTGGGGGTCAGAA	0.373													4	2	---	---	---	---	
EPB41L4A	64097	broad.mit.edu	37	5	111600227	111600228	+	Intron	INS	-	A	A	rs10660118		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111600227_111600228insA	uc003kpv.1	-						EPB41L4A_uc003kpw.1_3'UTR	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)		ACTGGTGACTGAAAAAAAAAAA	0.257													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	119231678	119231678	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119231678delC								FAM170A (260162 upstream) : PRR16 (568341 downstream)																							CTGCCTCCTTCCCCAGACTTC	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	129217738	129217738	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129217738delG								ADAMTS19 (143362 upstream) : CHSY3 (22785 downstream)																							ttgttgaggtgggaccactgt	0.000													4	2	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	130840783	130840783	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130840783delT	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvq.2_Intron|RAPGEF6_uc003kvr.2_Intron|RAPGEF6_uc011cxe.1_Intron|RAPGEF6_uc010jdk.2_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		ATTTCTTTCCTTTTTTTTTTT	0.308													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	134403321	134403321	+	Intron	DEL	G	-	-	rs143583387	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134403321delG	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																		TGAGTGGCCTGGACCACGGGC	0.557													4	2	---	---	---	---	
SIL1	64374	broad.mit.edu	37	5	138297801	138297801	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138297801delT	uc003ldm.2	-						SIL1_uc003ldn.2_Intron|SIL1_uc003ldo.2_Intron|SIL1_uc003ldp.2_Intron|SIL1_uc003ldq.1_Intron	NM_022464	NP_071909	Q9H173	SIL1_HUMAN	SIL1 protein precursor						intracellular protein transport|protein folding|transmembrane transport	endoplasmic reticulum lumen	unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			tattggtttcttttttttttc	0.000									Marinesco-Sj_gren_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	141372846	141372846	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141372846delA								RNF14 (4094 upstream) : GNPDA1 (7392 downstream)																							AAAACAAACCAAAAAAGGAAA	0.338													4	2	---	---	---	---	
GNPDA1	10007	broad.mit.edu	37	5	141384864	141384864	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141384864delC	uc003lmf.3	-						GNPDA1_uc003lmg.3_Intron|GNPDA1_uc010jgh.2_Intron|GNPDA1_uc003lmh.3_Intron	NM_005471	NP_005462	P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1						generation of precursor metabolites and energy|glucosamine catabolic process|N-acetylglucosamine metabolic process|single fertilization	cytoplasm	glucosamine-6-phosphate deaminase activity|hydrolase activity				0		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTACCATTTCTTTCTCTTTG	0.468													4	2	---	---	---	---	
C5orf46	389336	broad.mit.edu	37	5	147280951	147280951	+	Intron	DEL	A	-	-	rs113443820		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147280951delA	uc010jgp.2	-						C5orf46_uc003lou.2_Intron	NM_206966	NP_996849	Q6UWT4	CE046_HUMAN	hypothetical protein LOC389336 precursor							extracellular region					0						GATTAAAAAGAAAAAAAAAAA	0.224													4	2	---	---	---	---	
SPINK5	11005	broad.mit.edu	37	5	147488628	147488628	+	Intron	DEL	T	-	-	rs113070270		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147488628delT	uc003lox.2	+						SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTTCTCCCCTGATTGTGTCA	0.333													7	13	---	---	---	---	
ABLIM3	22885	broad.mit.edu	37	5	148583266	148583268	+	Intron	DEL	ATT	-	-	rs72371258		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148583266_148583268delATT	uc003lpy.2	+						ABLIM3_uc003lpz.1_Intron|ABLIM3_uc003lqa.1_Intron|ABLIM3_uc003lqb.2_Intron|ABLIM3_uc003lqc.1_Intron|ABLIM3_uc003lqd.1_Intron|ABLIM3_uc003lqf.2_Intron|ABLIM3_uc003lqe.1_Intron	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3						axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			ovary(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			catcaccaccattattattacca	0.049													3	3	---	---	---	---	
GRPEL2	134266	broad.mit.edu	37	5	148724445	148724445	+	5'Flank	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148724445delA	uc003lqj.2	+						GRPEL2_uc011dca.1_5'Flank	NM_152407	NP_689620	Q8TAA5	GRPE2_HUMAN	GrpE-like 2, mitochondrial precursor						protein folding	mitochondrial matrix	adenyl-nucleotide exchange factor activity|chaperone binding|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			agtcgataagaagggcattag	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154390227	154390227	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154390227delT								MRPL22 (41257 upstream) : KIF4B (3033 downstream)																							ctcttcttcctctctctctct	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	154390229	154390229	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154390229delT								MRPL22 (41259 upstream) : KIF4B (3031 downstream)																							cttcttcctctctctctctct	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157586906	157586906	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157586906delA								CLINT1 (300738 upstream) : EBF1 (536018 downstream)																							TGCAATTTGTATGACTTTCTG	0.517													4	2	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168151747	168151748	+	Intron	INS	-	C	C	rs149192628	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168151747_168151748insC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			caccgttggatccccccgtggc	0.064													5	4	---	---	---	---	
SLIT3	6586	broad.mit.edu	37	5	168430907	168430907	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168430907delG	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTGGGGATGTGGGGATTTATC	0.507													4	2	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169145427	169145427	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169145427delT	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AGTCAAAAGATTTTTTTTTCC	0.303													4	2	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169375471	169375472	+	Intron	INS	-	TC	TC			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169375471_169375472insTC	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|FAM196B_uc003mag.2_Intron	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			catcccctacatctctctctct	0.094													4	2	---	---	---	---	
C5orf47	133491	broad.mit.edu	37	5	173402116	173402117	+	Intron	INS	-	CTA	CTA	rs138292711	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173402116_173402117insCTA	uc003mcv.2	+									Q569G3	CE047_HUMAN	Homo sapiens chromosome 5 open reading frame 47, mRNA (cDNA clone IMAGE:4823612), partial cds.												0						atgaacttcctctacctcagct	0.000													3	3	---	---	---	---	
C5orf47	133491	broad.mit.edu	37	5	173409912	173409913	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173409912_173409913insA	uc003mcv.2	+									Q569G3	CE047_HUMAN	Homo sapiens chromosome 5 open reading frame 47, mRNA (cDNA clone IMAGE:4823612), partial cds.												0						gtctcaaaaacaaaacaaaaca	0.000													4	2	---	---	---	---	
COL23A1	91522	broad.mit.edu	37	5	177680094	177680094	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177680094delG	uc003mje.2	-						COL23A1_uc010jkt.2_Intron	NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		AGGTAGGGGTGGGGTCTCCAG	0.627													4	2	---	---	---	---	
COL23A1	91522	broad.mit.edu	37	5	177978494	177978494	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177978494delC	uc003mje.2	-							NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		CCAAATTGATCCCTCTTTGGG	0.468											OREG0017103	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
RASGEF1C	255426	broad.mit.edu	37	5	179620837	179620840	+	Intron	DEL	CAGA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179620837_179620840delCAGA	uc003mlr.2	-							NM_175062	NP_778232	Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			gaagttTACGCAGACAAAGTCCCC	0.289													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	351533	351533	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:351533delG								DUSP22 (180 upstream) : IRF4 (40219 downstream)																							CTCCAAGAAAGAAAAATAGGC	0.473													4	2	---	---	---	---	
EXOC2	55770	broad.mit.edu	37	6	529405	529409	+	Intron	DEL	AAAGA	-	-	rs10608942		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:529405_529409delAAAGA	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GAGGGCTGGCAAAGAAAAGTCTTCT	0.483													4	3	---	---	---	---	
EXOC2	55770	broad.mit.edu	37	6	551443	551443	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:551443delG	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GCAGGAGAGAGGAGGCCCTGC	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	5824726	5824726	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5824726delG								FARS2 (52910 upstream) : NRN1 (173509 downstream)																							GTGTTCTTGTGGGAGGTGGCA	0.592													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	7266722	7266723	+	IGR	INS	-	G	G	rs148522985	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7266722_7266723insG								RREB1 (15030 upstream) : SSR1 (14567 downstream)																							tctggccccccccagagctgga	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	7276104	7276106	+	IGR	DEL	AAA	-	-	rs138424967		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7276104_7276106delAAA								RREB1 (24412 upstream) : SSR1 (5184 downstream)																							CAAATTACTTAAAAAATCCGAGA	0.438											OREG0017176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
SSR1	6745	broad.mit.edu	37	6	7295301	7295301	+	Intron	DEL	A	-	-	rs35998405		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7295301delA	uc003mxf.3	-						SSR1_uc003mxg.3_Intron|SSR1_uc010jny.2_Intron	NM_003144	NP_003135	P43307	SSRA_HUMAN	signal sequence receptor, alpha precursor						cotranslational protein targeting to membrane|positive regulation of cell proliferation	endoplasmic reticulum membrane|integral to membrane	signal sequence binding				0	Ovarian(93;0.0398)					AAAAACCATTAAAAAAATTAA	0.323													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	7496884	7496884	+	IGR	DEL	G	-	-	rs11291955		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7496884delG								RIOK1 (78616 upstream) : DSP (44986 downstream)																							TCGAGTACGTGGAAGGACGTG	0.512													4	2	---	---	---	---	
TXNDC5	81567	broad.mit.edu	37	6	8010372	8010372	+	Intron	DEL	G	-	-	rs74771844		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8010372delG	uc003mxw.2	-							NM_001145549	NP_001139021	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 isoform 3						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)					attcaggggagacaaaattca	0.095													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	11090831	11090831	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11090831delA								ELOVL2 (46207 upstream) : LOC221710 (3435 downstream)																							GGAGAACATTAAAAAAATTAC	0.303													4	2	---	---	---	---	
RANBP9	10048	broad.mit.edu	37	6	13626252	13626252	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13626252delA	uc003nbb.2	-						RANBP9_uc003nba.2_Intron	NM_005493	NP_005484	Q96S59	RANB9_HUMAN	RAN binding protein 9						axon guidance|microtubule nucleation|protein complex assembly	cytosol|microtubule associated complex|nucleus	Ran GTPase binding			lung(1)|skin(1)	2	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)			ACAAAACAGGAAAAAAAAATT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	15098007	15098007	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15098007delA								CD83 (960861 upstream) : JARID2 (147727 downstream)																							aaaaaaaaacaaaaaaaaaga	0.035													4	2	---	---	---	---	
JARID2	3720	broad.mit.edu	37	6	15438664	15438667	+	Intron	DEL	GTAC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15438664_15438667delGTAC	uc003nbj.2	+						JARID2_uc011diu.1_Intron|JARID2_uc011div.1_Intron|JARID2_uc011diw.1_Intron	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein						central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TGAGGGAGATGTACGTACGTAGCT	0.461													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	21515817	21515818	+	IGR	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21515817_21515818delAC								CDKAL1 (283185 upstream) : SOX4 (78154 downstream)																							GAATTTATTTACACACACACAC	0.366													4	2	---	---	---	---	
ALDH5A1	7915	broad.mit.edu	37	6	24526383	24526384	+	Intron	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24526383_24526384delTG	uc003neg.2	+						ALDH5A1_uc003nef.2_Intron	NM_001080	NP_001071	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5A1 isoform 2 precursor						acetate metabolic process|central nervous system development|galactosylceramide metabolic process|gamma-aminobutyric acid catabolic process|glucose metabolic process|glutamate metabolic process|glutamine metabolic process|glutathione metabolic process|glycerophospholipid metabolic process|neurotransmitter catabolic process|neurotransmitter secretion|protein homotetramerization|respiratory electron transport chain|short-chain fatty acid metabolic process|succinate metabolic process	mitochondrial matrix|soluble fraction	succinate-semialdehyde dehydrogenase activity				0					Chlormerodrin(DB00534)|NADH(DB00157)|Succinic acid(DB00139)	ACCCAGTCCTTGTGTGTGTGTG	0.411													4	2	---	---	---	---	
KIAA0319	9856	broad.mit.edu	37	6	24613908	24613908	+	Intron	DEL	A	-	-	rs71739209		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24613908delA	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2						CATTTGAGGGAAAAAAAAAAA	0.338													4	2	---	---	---	---	
PGBD1	84547	broad.mit.edu	37	6	28252200	28252200	+	Intron	DEL	C	-	-	rs71548313		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28252200delC	uc003nky.2	+						PGBD1_uc003nkz.2_Intron	NM_032507	NP_115896	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1						viral reproduction	membrane|nucleus	scavenger receptor activity|sequence-specific DNA binding transcription factor activity			ovary(4)	4						GAAGTGCATTCCCCCCCCCCA	0.209													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	28374339	28374339	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28374339delA								ZSCAN12 (6795 upstream) : ZSCAN23 (18948 downstream)																							TTCATGTTTTAAAAAAAAAGA	0.209													4	2	---	---	---	---	
GABBR1	2550	broad.mit.edu	37	6	29599691	29599691	+	Intron	DEL	A	-	-	rs3215531		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29599691delA	uc003nmt.3	-						GABBR1_uc003nmu.3_Intron|GABBR1_uc011dlr.1_Intron|GABBR1_uc011dls.1_Intron	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1						gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)	GCTTTTCTTTAAAAAAAAAGG	0.413													6	3	---	---	---	---	
LOC285830	285830	broad.mit.edu	37	6	29712289	29712289	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29712289delC	uc003nnp.2	-						LOC285830_uc011dlz.1_Intron|LOC285830_uc003rsi.3_Intron	NR_026972				Homo sapiens cDNA FLJ35429 fis, clone SMINT2002126.												0						CCTTCTAAGGCCCCACTGTGC	0.532													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	30423458	30423459	+	IGR	DEL	CA	-	-	rs139670903		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30423458_30423459delCA								TRIM39 (108826 upstream) : HLA-E (33812 downstream)																							CTATGCTAGGCACacactatta	0.213													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	31383128	31383128	+	IGR	DEL	T	-	-	rs67294703		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31383128delT								MICA (38 upstream) : HCP5 (47829 downstream)																							CGtattattattttttttttt	0.075													4	4	---	---	---	---	
TCP11	6954	broad.mit.edu	37	6	35101781	35101781	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35101781delA	uc003okd.2	-						TCP11_uc003ojz.1_Intron|TCP11_uc003oka.2_Intron|TCP11_uc003okb.2_Intron|TCP11_uc003okc.2_Intron|TCP11_uc011dsu.1_Intron|TCP11_uc011dsv.1_Intron|TCP11_uc011dsw.1_Intron	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5						AAGCTGGGGGAAAAAAAATCC	0.353													4	2	---	---	---	---	
GUCA1A	2978	broad.mit.edu	37	6	42145611	42145611	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42145611delG	uc003orx.2	+						GUCA1A_uc011duo.1_Intron|GUCA1A_uc010jxt.2_Intron	NM_000409	NP_000400	P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)						signal transduction|visual perception	membrane	calcium ion binding|calcium sensitive guanylate cyclase activator activity				0	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;5.54e-05)|Epithelial(12;0.000167)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCCCATCCCTGGGGGTGCAGT	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	43192594	43192594	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43192594delT								CUL9 (270 upstream) : C6orf108 (775 downstream)																							CTCCCAACtcttttttttttt	0.299													6	3	---	---	---	---	
LOC100132354	100132354	broad.mit.edu	37	6	43881778	43881778	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43881778delT	uc011dvm.1	+							NR_024478				Homo sapiens cDNA FLJ38229 fis, clone FCBBF2004256.												0						CCTCTCTCTGTTAGGACTAGC	0.547													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	48996630	48996630	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48996630delT								C6orf138 (917687 upstream) : MUT (402364 downstream)																							TGGGGTAAAATTTTTTATCCA	0.398													4	2	---	---	---	---	
COL21A1	81578	broad.mit.edu	37	6	55990774	55990778	+	Intron	DEL	TTTAC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55990774_55990778delTTTAC	uc003pcs.2	-						COL21A1_uc010jzz.2_5'Flank|COL21A1_uc011dxg.1_5'Flank|COL21A1_uc011dxh.1_5'Flank|COL21A1_uc003pct.1_Intron|COL21A1_uc011dxi.1_Intron|COL21A1_uc003pcu.1_Intron	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TAGCCCATTGTTTACTTTATCTCta	0.137													10	6	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57336549	57336550	+	Intron	INS	-	A	A	rs137992363		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57336549_57336550insA	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)		GTTTTCCTCTGAAAAAAATTAA	0.262													3	4	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57497965	57497966	+	Intron	DEL	TG	-	-	rs146591848		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57497965_57497966delTG	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)		GTAATTTTTTTGTGTGTATCTG	0.317													4	2	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	65987343	65987347	+	Intron	DEL	AATTA	-	-	rs145692139		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65987343_65987347delAATTA	uc011dxu.1	-							NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						aaagttaattaattaaaaaaaaaag	0.000													4	2	---	---	---	---	
COL9A1	1297	broad.mit.edu	37	6	70982029	70982029	+	Intron	DEL	T	-	-	rs111249380		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70982029delT	uc003pfg.3	-						COL9A1_uc003pfe.3_Intron|COL9A1_uc003pff.3_Intron	NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor						axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4						TTTTCCAAACTTTTTTTTTTT	0.398													4	2	---	---	---	---	
RIMS1	22999	broad.mit.edu	37	6	72674389	72674389	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72674389delA	uc003pga.2	+							NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)				ggtttaggggaaaaaaaaaat	0.000													6	3	---	---	---	---	
MRAP2	112609	broad.mit.edu	37	6	84760705	84760705	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84760705delT	uc003pkg.3	+						MRAP2_uc010kbo.2_Intron	NM_138409	NP_612418	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2						positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding			skin(2)	2						GGCATGCTCATTTTTCAGGGT	0.473													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	85964748	85964748	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85964748delT								TBX18 (490849 upstream) : NT5E (194554 downstream)																							TCCACACGGGTtttctcccat	0.189													4	2	---	---	---	---	
PNRC1	10957	broad.mit.edu	37	6	89789429	89789430	+	5'Flank	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89789429_89789430insT	uc003pmv.2	+						PNRC1_uc003pmu.2_5'Flank|PNRC1_uc003pmx.2_5'Flank	NM_006813	NP_006804	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding				0		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		GGTCTGATCTATTTTTCTtagt	0.134										Multiple Myeloma(7;0.094)			4	2	---	---	---	---	
UBE2J1	51465	broad.mit.edu	37	6	90047599	90047599	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90047599delT	uc010kcb.2	-						UBE2J1_uc003pnc.2_Intron	NM_016021	NP_057105	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1							endoplasmic reticulum membrane|integral to membrane	ATP binding|ubiquitin-protein ligase activity				0		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		ATTGCTCTGGTTCTTTTCCAT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	93432441	93432442	+	IGR	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93432441_93432442delCT								None (None upstream) : EPHA7 (517300 downstream)																							tgacacttgactctcttgcctc	0.000													2	4	---	---	---	---	
EPHA7	2045	broad.mit.edu	37	6	93995864	93995865	+	Intron	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93995864_93995865delAC	uc003poe.2	-						EPHA7_uc003pof.2_Intron|EPHA7_uc011eac.1_Intron	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		GTTTTTCCTTacacacacacac	0.203													3	3	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112492418	112492418	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112492418delT	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		ctgtctctccttttttttttt	0.100													11	5	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112563257	112563257	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112563257delC	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron|LAMA4_uc003pvw.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TGAGCAGATTCCCCAAGTAAA	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	112646702	112646702	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112646702delT								LAMA4 (70874 upstream) : RFPL4B (21830 downstream)																							ccagagactatttttttTTTC	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	114056175	114056176	+	IGR	INS	-	GT	GT	rs140677001	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114056175_114056176insGT								None (None upstream) : MARCKS (122351 downstream)																							CCTCTTCCTCCGTGTGTGTGTG	0.396													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	114872887	114872887	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114872887delA								HS3ST5 (209347 upstream) : None (None downstream)																							AAATAATTACAAAAATTTGAA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	143373508	143373508	+	IGR	DEL	T	-	-	rs113081051		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143373508delT								HIVEP2 (107170 upstream) : AIG1 (6992 downstream)																							ATTCATCTGCTTTTTTTTGAC	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	148202592	148202592	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148202592delG								SAMD5 (311435 upstream) : SASH1 (461137 downstream)																							tatcctccctggggacataat	0.000													4	2	---	---	---	---	
MTHFD1L	25902	broad.mit.edu	37	6	151345976	151345976	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151345976delT	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		TTGTTTTGGGTTTTTTTTGag	0.219													4	2	---	---	---	---	
SYNE1	23345	broad.mit.edu	37	6	152868776	152868776	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152868776delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		tagtctttccaaaaaaaagat	0.000										HNSCC(10;0.0054)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157758904	157758904	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157758904delA								C6orf35 (14111 upstream) : ZDHHC14 (43653 downstream)																							ACTAAATCCTAAAAATGATTA	0.343													4	2	---	---	---	---	
GTF2H5	404672	broad.mit.edu	37	6	158592454	158592454	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158592454delG	uc003qrd.2	+							NM_207118	NP_997001	Q6ZYL4	TF2H5_HUMAN	general transcription factor IIH, polypeptide 5						nucleotide-excision repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;5.98e-18)|BRCA - Breast invasive adenocarcinoma(81;2.83e-05)		cctgactagtgggctacctta	0.000								Direct_reversal_of_damage|NER					4	2	---	---	---	---	
FNDC1	84624	broad.mit.edu	37	6	159692702	159692702	+	3'UTR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159692702delT	uc010kjv.2	+	23						NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1							extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GCTTCTCTACTTTTTTTTGTT	0.418													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	160371387	160371387	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160371387delG								MAS1 (42282 upstream) : IGF2R (18744 downstream)																							ttttggctttggggatacctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	161204811	161204812	+	IGR	INS	-	GA	GA	rs148671196	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161204811_161204812insGA								PLG (30466 upstream) : MAP3K4 (208010 downstream)																							GGTTTGGAGTTGAGAGAGCTCT	0.554													4	3	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	162982422	162982423	+	Intron	INS	-	A	A	rs150126059	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162982422_162982423insA	uc003qtx.3	-						PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		gtgagatgcagacaagatggta	0.030													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164458815	164458818	+	IGR	DEL	TGAG	-	-	rs149375607		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164458815_164458818delTGAG								QKI (463923 upstream) : None (None downstream)																							TAGAAAAGACTGAGAGCCTTTTAG	0.490													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	164506994	164506994	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164506994delC								QKI (512102 upstream) : None (None downstream)																							GGGCAGGGGGCCAGGGGTGAG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166133125	166133126	+	IGR	INS	-	GT	GT	rs148352462	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166133125_166133126insGT								PDE10A (57541 upstream) : C6orf176 (204410 downstream)																							gtgtgcaacaggtgtaacccag	0.000													2	5	---	---	---	---	
FGFR1OP	11116	broad.mit.edu	37	6	167435747	167435748	+	Intron	INS	-	AC	AC	rs10624685		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167435747_167435748insAC	uc003qvj.2	+						CCR6_uc003qvl.2_Intron|FGFR1OP_uc011egp.1_Intron|FGFR1OP_uc003qvk.2_Intron	NM_007045	NP_008976	O95684	FR1OP_HUMAN	FGFR1 oncogene partner isoform a						G2/M transition of mitotic cell cycle|microtubule anchoring|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell proliferation	centrosome|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity|protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(1)	1		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)		GAGCTGCCCCAacacacacaca	0.342			T	FGFR1	MPD|NHL								6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	168052216	168052217	+	IGR	INS	-	TG	TG	rs149093424		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168052216_168052217insTG								TCP10 (254218 upstream) : C6orf123 (133004 downstream)																							acgtgtgtgaatgtgtggtgca	0.000													4	2	---	---	---	---	
THBS2	7058	broad.mit.edu	37	6	169630315	169630316	+	Intron	INS	-	A	A	rs141816534	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169630315_169630316insA	uc003qwt.2	-							NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor						cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		TGTAATTGGGCAAAAACTCCTT	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170428709	170428709	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170428709delC								C6orf208 (225740 upstream) : LOC154449 (134713 downstream)																							CCACATTAGGCCCTAAGCACA	0.502													4	2	---	---	---	---	
PRKAR1B	5575	broad.mit.edu	37	7	740305	740305	+	Intron	DEL	A	-	-	rs79787649	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:740305delA	uc003siu.1	-						PRKAR1B_uc003siv.2_Intron|PRKAR1B_uc003siw.1_Intron	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		aaatttatttaaaaaaaaaag	0.000													2	4	---	---	---	---	
KIAA1908	114796	broad.mit.edu	37	7	1616995	1616995	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1616995delT	uc003sla.2	+						KIAA1908_uc003sky.1_Intron|KIAA1908_uc003skz.1_Intron	NR_021487				Homo sapiens mRNA for KIAA1908 protein, partial cds.												0						aattaatctctttttttttgc	0.000													3	3	---	---	---	---	
MAD1L1	8379	broad.mit.edu	37	7	2025905	2025915	+	Intron	DEL	TGTGATGCACC	-	-	rs72429272		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2025905_2025915delTGTGATGCACC	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		ttcaagtacgtgtgatgcacctgtgtgaccc	0.114													4	4	---	---	---	---	
SNX8	29886	broad.mit.edu	37	7	2352148	2352148	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2352148delC	uc003slw.2	-							NM_013321	NP_037453	Q9Y5X2	SNX8_HUMAN	sorting nexin 8						cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		TCACGTGCCTCCCCTTACACT	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	13788628	13788628	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13788628delT								None (None upstream) : ETV1 (142230 downstream)																							TACTGTTCCATTTTACAAATC	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	20526961	20526961	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20526961delG								ITGB8 (71583 upstream) : ABCB5 (128284 downstream)																							tgcactatcagggggcctgag	0.000													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23747555	23747556	+	5'Flank	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23747555_23747556delAC	uc003sws.3	+						STK31_uc003swt.3_5'Flank|STK31_uc011jze.1_5'Flank|STK31_uc010kuq.2_5'Flank	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						accctgtcttacacacacacac	0.000													4	2	---	---	---	---	
SNX10	29887	broad.mit.edu	37	7	26349594	26349595	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26349594_26349595insT	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.2_Intron	NM_013322	NP_037454	Q9Y5X0	SNX10_HUMAN	sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0						atagtaaacAATTTTTTTTGGC	0.178													4	2	---	---	---	---	
CHN2	1124	broad.mit.edu	37	7	29306563	29306565	+	Intron	DEL	CCT	-	-	rs75030331		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29306563_29306565delCCT	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058	P52757	CHIO_HUMAN	beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2						GGCCCTTCTCCCTCCTCAAGGTG	0.478													0	7	---	---	---	---	
SEPT7	989	broad.mit.edu	37	7	35925791	35925792	+	Intron	INS	-	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35925791_35925792insC	uc010kxc.2	+						SEPT7_uc011kat.1_Intron|SEPT7_uc011kau.1_Intron|SEPT7_uc011kav.1_Intron|SEPT7_uc003tey.2_Intron	NM_001788	NP_001779	Q16181	SEPT7_HUMAN	cell division cycle 10 isoform 1						cilium morphogenesis|cytokinesis|mitosis|protein heterooligomerization|regulation of embryonic cell shape	cilium axoneme|cleavage furrow|condensed chromosome kinetochore|midbody|nucleus|septin complex|spindle|stress fiber	GTP binding|protein binding|structural molecule activity				0						CTTTTTTCTTAATGTGAAAACC	0.337													4	3	---	---	---	---	
EEPD1	80820	broad.mit.edu	37	7	36268793	36268793	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36268793delG	uc003tfa.2	+							NM_030636	NP_085139	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0						GGTTTGGTGTGGGCTCTTCAA	0.473													4	2	---	---	---	---	
AMPH	273	broad.mit.edu	37	7	38424703	38424703	+	Intron	DEL	A	-	-	rs72507353		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38424703delA	uc003tgu.2	-						AMPH_uc003tgv.2_Intron|AMPH_uc003tgt.2_Intron	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						GTTGTTAGTTaaaaaaaaaaa	0.318													13	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	41682955	41682955	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41682955delG								C7orf10 (782598 upstream) : INHBA (45648 downstream)																							CACTCCTGATGGGGTCAAGGA	0.308													4	2	---	---	---	---	
VOPP1	81552	broad.mit.edu	37	7	55560961	55560961	+	Intron	DEL	G	-	-	rs35821539		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55560961delG	uc003tqs.2	-						VOPP1_uc003tqq.2_Intron|VOPP1_uc010kzh.2_Intron|VOPP1_uc010kzi.2_Intron|VOPP1_uc011kcr.1_Intron	NM_030796	NP_110423	Q96AW1	VOPP1_HUMAN	EGFR-coamplified and overexpressed protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic vesicle membrane|endosome|integral to organelle membrane	signal transducer activity				0						CTGGCAAACTGGCAAACTCTT	0.478													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57609387	57609387	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57609387delA								ZNF716 (76122 upstream) : None (None downstream)																							TTTCATTTCTAAATATGCTAT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57698975	57698976	+	IGR	INS	-	AGTG	AGTG	rs145904451	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57698975_57698976insAGTG								ZNF716 (165710 upstream) : None (None downstream)																							AAAAAATGTACAGTGAGGGAAT	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61831566	61831566	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61831566delA								None (None upstream) : LOC643955 (920106 downstream)																							tcgcaaggacaaaaaaccaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	63249743	63249743	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63249743delA								LOC100287704 (437592 upstream) : ZNF727 (256078 downstream)																							TTTGAACATTAAAAAAAAAAG	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65897520	65897520	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65897520delC								NCRNA00174 (32125 upstream) : LOC493754 (95926 downstream)																							CAACTAGTTACCCATATACAT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67420362	67420362	+	IGR	DEL	A	-	-	rs35306410		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67420362delA								STAG3L4 (633850 upstream) : None (None downstream)																							CCTGAGAGAGAAAGGGAGGAA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	69058688	69058688	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69058688delA								None (None upstream) : AUTS2 (5217 downstream)																							AGAGGGATATAAAAATTTAGC	0.323													4	2	---	---	---	---	
CALN1	83698	broad.mit.edu	37	7	71733316	71733316	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71733316delA	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				TGAAGCAGACAAAAAAAAAGA	0.463													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	71953677	71953677	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71953677delT								CALN1 (41541 upstream) : TYW1B (70052 downstream)																							ACCCATTCACtttttttttag	0.259													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	82180618	82180618	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82180618delA								CACNA2D1 (107587 upstream) : PCLO (202703 downstream)																							ACTGAAGCAGAAAAAAAAATT	0.299													4	2	---	---	---	---	
DMTF1	9988	broad.mit.edu	37	7	86803665	86803666	+	Intron	INS	-	A	A	rs144869061	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86803665_86803666insA	uc003uih.2	+						DMTF1_uc003uii.2_Intron|DMTF1_uc003uij.2_Intron|DMTF1_uc011khb.1_Intron|DMTF1_uc003uik.2_Intron|DMTF1_uc003uil.2_Intron|DMTF1_uc003uim.1_Intron|DMTF1_uc003uin.2_Intron	NM_001142327	NP_001135799	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1						cell cycle	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(14;0.0058)					AGAGAGGTAATTTTTTTTAAAT	0.267													5	8	---	---	---	---	
ABCB1	5243	broad.mit.edu	37	7	87196055	87196063	+	Intron	DEL	AAGGATAAG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87196055_87196063delAAGGATAAG	uc003uiz.1	-						ABCB1_uc011khc.1_Intron	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	TCATTTTACTAAGGATAAGAACGACACCC	0.392													94	58	---	---	---	---	
BRI3	25798	broad.mit.edu	37	7	97917895	97917895	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97917895delC	uc003upi.2	+						BRI3_uc011kip.1_Intron	NM_015379	NP_056194	O95415	BRI3_HUMAN	brain protein I3 isoform a							integral to membrane					0	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)					TGCCCTGCAGCCCAGCTCAGC	0.398													4	2	---	---	---	---	
LHFPL3	375612	broad.mit.edu	37	7	104456754	104456754	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104456754delT	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3							integral to membrane					0						CCTAGTTTCCTTTTAGCTTAG	0.413													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111829438	111829439	+	Intron	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111829438_111829439delCT	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				GTAAAAATGCCTAAGATCCAGT	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	111993430	111993430	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111993430delA								ZNF277 (9441 upstream) : IFRD1 (69796 downstream)																							GGGGTCAGAGAAAGGGCAGAG	0.483													4	2	---	---	---	---	
TES	26136	broad.mit.edu	37	7	115893920	115893921	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115893920_115893921delGT	uc003vho.2	+						TES_uc011kmy.1_Intron|TES_uc003vhp.2_Intron|uc003vhq.1_RNA	NM_015641	NP_056456	Q9UGI8	TES_HUMAN	testin isoform 1						negative regulation of cell proliferation	cytoplasm|focal adhesion|nucleus|protein complex	zinc ion binding				0	Lung NSC(10;0.0137)|all_lung(10;0.0148)	Breast(660;0.0602)	STAD - Stomach adenocarcinoma(10;0.00878)			gtgtgtgggggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	117857717	117857718	+	IGR	INS	-	AA	AA	rs141687883	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117857717_117857718insAA								NAA38 (24839 upstream) : ANKRD7 (6994 downstream)																							gctgctagaggaaaaaaaaacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128736164	128736164	+	IGR	DEL	T	-	-	rs66837005		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128736164delT								TPI1P2 (38871 upstream) : LOC407835 (30161 downstream)																							GGAATGAATCttttttttttt	0.174													5	4	---	---	---	---	
COPG2	26958	broad.mit.edu	37	7	130283027	130283027	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130283027delT	uc003vqh.1	-							NM_012133	NP_036265	Q9UBF2	COPG2_HUMAN	coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)					tcaaggatgcttttttttttg	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	131317113	131317114	+	IGR	INS	-	AAAACAAAACAAAAC	AAAACAAAACAAAAC	rs140275119	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131317113_131317114insAAAACAAAACAAAAC								PODXL (75737 upstream) : PLXNA4 (490978 downstream)																							TAGATGTGTTAaaaacaaaaca	0.045													4	2	---	---	---	---	
PLXNA4	91584	broad.mit.edu	37	7	131954424	131954424	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131954424delT	uc003vra.3	-							NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1						AAAAAAGATCTTTTTTTTTTT	0.363													9	5	---	---	---	---	
SLC13A4	26266	broad.mit.edu	37	7	135408592	135408592	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135408592delG	uc003vta.2	-						SLC13A4_uc003vtb.2_Intron|SLC13A4_uc003vtc.1_Intron	NM_012450	NP_036582	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate							integral to plasma membrane	sodium:sulfate symporter activity				0						GATGTTCTCTGGGGCCAAAAG	0.453													4	2	---	---	---	---	
KIAA1549	57670	broad.mit.edu	37	7	138544349	138544349	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138544349delT	uc011kql.1	-						KIAA1549_uc011kqi.1_Intron|KIAA1549_uc003vuk.3_Intron|KIAA1549_uc011kqj.1_Intron|KIAA1549_uc011kqk.1_Intron	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230						ccaaactccatttcttcaact	0.000			O	BRAF	pilocytic astrocytoma								4	2	---	---	---	---	
TBXAS1	6916	broad.mit.edu	37	7	139565461	139565461	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139565461delG	uc011kqv.1	+						TBXAS1_uc003vvh.2_Intron|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Intron|TBXAS1_uc003vvi.2_Intron|TBXAS1_uc003vvj.2_Intron|TBXAS1_uc011kqw.1_Intron|TBXAS1_uc011kqx.1_Intron	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)					aggaggaggaggaagaggagg	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	140146782	140146782	+	IGR	DEL	T	-	-	rs76501180		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140146782delT								RAB19 (20732 upstream) : MKRN1 (6058 downstream)																							gtagcatgggttagtggttgc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149449512	149449512	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149449512delA								KRBA1 (17850 upstream) : ZNF467 (11761 downstream)																							ataccaagacaaaaaaacacg	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149599100	149599100	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149599100delG								ATP6V0E2 (21314 upstream) : ACTR3C (345202 downstream)																							TATAGGATGTGGGTAACCAGA	0.308													4	2	---	---	---	---	
PRKAG2	51422	broad.mit.edu	37	7	151531593	151531594	+	Intron	INS	-	A	A	rs146658971	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151531593_151531594insA	uc003wkk.2	-						PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		ggtttctgtttaaaTAAAGGCA	0.282													4	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152109853	152109854	+	Intron	INS	-	GA	GA	rs147369369		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152109853_152109854insGA	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)		TATTGTGGTGGGGGGGATGGTG	0.322			N		medulloblastoma								6	3	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153814975	153814975	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153814975delG	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			TTCCGCTCACGGTAGGACCCA	0.532													4	2	---	---	---	---	
DPP6	1804	broad.mit.edu	37	7	153961720	153961722	+	Intron	DEL	TTA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153961720_153961722delTTA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			gatgatgatgttaatgatgttaa	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	157279059	157279060	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157279059_157279060delGT								DNAJB6 (68927 upstream) : PTPRN2 (52691 downstream)																							GTTTGGAGGGgtgtgtgtgtgt	0.421													4	3	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	158342323	158342323	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158342323delA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCCTGCAGCCAGGGCTCGCTC	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	158962702	158962703	+	IGR	INS	-	A	A	rs148187097		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158962702_158962703insA								VIPR2 (25053 upstream) : None (None downstream)																							AGCAGAAACACGATGATCATGG	0.569													4	2	---	---	---	---	
C8orf42	157695	broad.mit.edu	37	8	481173	481174	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:481173_481174insT	uc003wpd.2	-						C8orf42_uc011kwg.1_Intron	NM_175075	NP_778250	Q86YL5	CH042_HUMAN	hypothetical protein LOC157695												0		Ovarian(12;0.0481)|Colorectal(14;0.0815)|Hepatocellular(245;0.0968)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;5.16e-14)|OV - Ovarian serous cystadenocarcinoma(5;7.35e-07)|BRCA - Breast invasive adenocarcinoma(11;4.17e-06)|COAD - Colon adenocarcinoma(149;0.0255)		aattaaatggctttttttttct	0.000													6	3	---	---	---	---	
ARHGEF10	9639	broad.mit.edu	37	8	1892667	1892667	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1892667delT	uc003wpr.2	+						ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc010lre.2_Intron	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CAGGATGGGGTTTGGTGCCAC	0.602													4	2	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	2861156	2861156	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2861156delT	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		gggctggggattaaacaagga	0.060													4	2	---	---	---	---	
DEFA1B	728358	broad.mit.edu	37	8	6878507	6878508	+	5'Flank	INS	-	AGAT	AGAT	rs138289435	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6878507_6878508insAGAT	uc003wqz.1	-							NM_005217	NP_005208	P59665	DEF1_HUMAN	defensin, alpha 3 preproprotein						chemotaxis|defense response to bacterium|defense response to fungus|immune response|killing of cells of other organism|response to virus	extracellular space					0						CAGACCTGCCCGTGTGTCCTGG	0.609													4	2	---	---	---	---	
MFHAS1	9258	broad.mit.edu	37	8	8642675	8642675	+	3'UTR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8642675delT	uc003wsj.1	-	3						NM_004225	NP_004216	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TTGCATGGACTTTTTGTCCTC	0.433													4	2	---	---	---	---	
ERI1	90459	broad.mit.edu	37	8	8870434	8870435	+	Intron	DEL	TT	-	-	rs35319524		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8870434_8870435delTT	uc011kwu.1	+						ERI1_uc003wsk.2_Intron	NM_153332	NP_699163	Q8IV48	ERI1_HUMAN	three prime histone mRNA exonuclease 1						gene silencing by RNA|rRNA 3'-end processing	cytoplasm|histone pre-mRNA 3'end processing complex|nucleolus	3'-5' exonuclease activity|histone pre-mRNA stem-loop binding|metal ion binding|ribosome binding|rRNA binding				0					Adenosine monophosphate(DB00131)	ttcaataaagtttaagctgtgt	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	9248913	9248913	+	IGR	DEL	G	-	-	rs150812218	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9248913delG								PPP1R3B (239829 upstream) : TNKS (164532 downstream)																							tatgaacaacggggatgcaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	12453422	12453422	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12453422delC	uc003wvy.3	-						uc003wwc.3_Intron					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		GCACACATTGCCCCCTGGGTC	0.308													4	2	---	---	---	---	
SGCZ	137868	broad.mit.edu	37	8	14967890	14967890	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14967890delC	uc003wwq.2	-							NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		CAATGATCATCTGGTCGTTCC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	16830853	16830853	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16830853delT								MSR1 (780553 upstream) : FGF20 (19481 downstream)																							AAAAAAACTATTTACCTTCTC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	17004290	17004293	+	IGR	DEL	TTTT	-	-	rs66578394		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17004290_17004293delTTTT								EFHA2 (24142 upstream) : ZDHHC2 (9543 downstream)																							TTTTCTAttctttttttttttttt	0.201													3	3	---	---	---	---	
SCARA5	286133	broad.mit.edu	37	8	27759939	27759939	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27759939delC	uc003xgj.2	-						SCARA5_uc010luz.2_Intron	NM_173833	NP_776194	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		CAGTACAGAGCCCACCAGCCT	0.657													4	2	---	---	---	---	
HMBOX1	79618	broad.mit.edu	37	8	28908874	28908875	+	3'UTR	INS	-	AACC	AACC	rs147395804	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28908874_28908875insAACC	uc003xhd.3	+	10					HMBOX1_uc003xhc.3_Intron|HMBOX1_uc010lve.2_RNA|HMBOX1_uc003xhe.2_3'UTR|HMBOX1_uc011lay.1_3'UTR|HMBOX1_uc003xhf.2_3'UTR|HMBOX1_uc003xhg.2_3'UTR	NM_001135726	NP_001129198	Q6NT76	HMBX1_HUMAN	homeobox containing 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)		CAGTAAATAATAACCAACCAAC	0.455													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	30175664	30175664	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30175664delA								DCTN6 (134605 upstream) : RBPMS (66280 downstream)																							aaaagaatgcaaaaAAAAGTA	0.189													4	2	---	---	---	---	
NRG1	3084	broad.mit.edu	37	8	32616602	32616602	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32616602delT	uc003xiv.2	+						NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc011lbg.1_Intron|NRG1_uc011lbh.1_Intron|NRG1_uc003xja.2_Intron	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CCAGAGAGTATTTTTTTTTTT	0.343													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	32691962	32691962	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32691962delG								NRG1 (69404 upstream) : FUT10 (536384 downstream)																							aaggattgctgggaaaacttg	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	36274728	36274729	+	IGR	DEL	CC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36274728_36274729delCC								UNC5D (622548 upstream) : KCNU1 (367113 downstream)																							atactcctttccctattttatt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37213327	37213328	+	IGR	INS	-	ATGG	ATGG	rs138900066	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37213327_37213328insATGG								KCNU1 (419686 upstream) : ZNF703 (339973 downstream)																							TAGATAGACACatggatggatg	0.243													4	3	---	---	---	---	
BRF2	55290	broad.mit.edu	37	8	37704284	37704284	+	Intron	DEL	A	-	-	rs78433761		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37704284delA	uc003xkk.2	-							NM_018310	NP_060780	Q9HAW0	BRF2_HUMAN	RNA polymerase III transcription initiation						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter|transcription initiation, DNA-dependent	nucleoplasm	protein binding|zinc ion binding				0		Lung NSC(58;0.118)|all_lung(54;0.195)	BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;1.81e-10)			agactccaagaaaaaaaaaaa	0.234													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	39952449	39952449	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39952449delA								IDO2 (78539 upstream) : C8orf4 (58540 downstream)																							cagctgagGCAGGTGAGGAGA	0.244													4	2	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40717563	40717563	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40717563delA	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			attaaggactaatcccagctc	0.085													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	52865657	52865657	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52865657delC								PCMTD1 (53922 upstream) : ST18 (157735 downstream)																							agccactgcacccagcctacg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	59417498	59417499	+	IGR	DEL	CA	-	-	rs139007405		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59417498_59417499delCA								CYP7A1 (4778 upstream) : SDCBP (48229 downstream)																							ctgtctGTGTcacacacacaca	0.010													3	4	---	---	---	---	
NKAIN3	286183	broad.mit.edu	37	8	63313173	63313173	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63313173delT	uc010lyq.1	+							NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				atccctcagcttttttttgtc	0.129													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	68914901	68914902	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68914901_68914902insT	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						CTTCTTAATCATTTTTTTTTTC	0.292													4	2	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	69002479	69002480	+	Intron	INS	-	TTA	TTA			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69002479_69002480insTTA	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						TATGTTTCTGGTCTTCTCATTT	0.287													0	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	80783815	80783816	+	RNA	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80783815_80783816insT	uc003ybn.2	-	1		c.157_158insA								Homo sapiens cDNA FLJ30770 fis, clone FEBRA2000734.																		TGGGAGTAGCCTTTGACACAGT	0.599													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	98864930	98864930	+	IGR	DEL	G	-	-	rs35775446		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98864930delG								LAPTM4B (101 upstream) : MATN2 (16381 downstream)																							GCTTTTTTTTGGGGGGGGGAG	0.403													11	9	---	---	---	---	
UBR5	51366	broad.mit.edu	37	8	103405043	103405044	+	Intron	INS	-	AG	AG	rs139457107	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103405043_103405044insAG	uc003ykr.1	-						UBR5_uc003yks.1_Intron	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			AGCCTGTTATCAGGTCTCCCCA	0.396													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103732216	103732226	+	IGR	DEL	TTCTCCAACTC	-	-	rs36212769		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103732216_103732226delTTCTCCAACTC								KLF10 (64233 upstream) : AZIN1 (106311 downstream)																							ATTTCCCCATttctccaactcttctccaact	0.408													4	2	---	---	---	---	
ZFPM2	23414	broad.mit.edu	37	8	106537196	106537196	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106537196delA	uc003ymd.2	+							NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GGCACAAGGGAAAAAAAAAGT	0.383													4	2	---	---	---	---	
OXR1	55074	broad.mit.edu	37	8	107385597	107385597	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107385597delT	uc003ymf.2	+							NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			AAACAATAAATTTTTTTTACT	0.348													4	2	---	---	---	---	
ANGPT1	284	broad.mit.edu	37	8	108334542	108334543	+	Intron	INS	-	T	T	rs150946602	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108334542_108334543insT	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron|ANGPT1_uc003ymp.3_5'Flank	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)			AACATGTCAAATAAAAAATAAG	0.272													12	12	---	---	---	---	
RSPO2	340419	broad.mit.edu	37	8	108919438	108919438	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108919438delA	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660	Q6UXX9	RSPO2_HUMAN	R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			AGAGTAAAGGAAATGAATCAA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	109192895	109192896	+	IGR	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109192895_109192896insA								RSPO2 (96982 upstream) : EIF3E (21077 downstream)																							atcttttcatgaaaaaaaaaat	0.000													4	2	---	---	---	---	
PKHD1L1	93035	broad.mit.edu	37	8	110460747	110460747	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110460747delT	uc003yne.2	+							NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			gtttgtttggttttttttttt	0.090										HNSCC(38;0.096)			7	4	---	---	---	---	
FBXO32	114907	broad.mit.edu	37	8	124535939	124535939	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124535939delA	uc003yqr.2	-						FBXO32_uc003yqq.2_Intron|FBXO32_uc010mdk.2_Intron	NM_058229	NP_478136	Q969P5	FBX32_HUMAN	F-box only protein 32 isoform 1											skin(3)|breast(2)|lung(1)	6	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AGTCATTAAGAAAAAAAAATT	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	129968524	129968524	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129968524delA								MIR1208 (806090 upstream) : GSDMC (791919 downstream)																							ATTCACCTGTAAAATAGATAT	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	130581705	130581705	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130581705delA								None (None upstream) : GSDMC (178738 downstream)																							aacaaaaatcaaaaaaaaata	0.000													4	2	---	---	---	---	
TG	7038	broad.mit.edu	37	8	133919380	133919381	+	Intron	INS	-	AT	AT			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133919380_133919381insAT	uc003ytw.2	+						TG_uc010mdw.2_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGAACCATCTGCTCCTTGAGAG	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	136133508	136133508	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136133508delG								MIR30D (316320 upstream) : LOC286094 (112866 downstream)																							ATTGCCACCTGGGCAGGGACG	0.408													4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	140769188	140769188	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140769188delA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						GGGTTGGGGTATAAGGACAGC	0.627													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	143211511	143211512	+	IGR	INS	-	CCAG	CCAG	rs142432498	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143211511_143211512insCCAG								MIR1302-7 (343837 upstream) : NCRNA00051 (68205 downstream)																							CCAGACGCCACCCAGCCGTGGT	0.589													6	4	---	---	---	---	
BAI1	575	broad.mit.edu	37	8	143604685	143604686	+	Intron	INS	-	G	G	rs139774464	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143604685_143604686insG	uc003ywm.2	+							NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1						axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					AACCGAGGCTTGAAGGGAGGGC	0.649													4	2	---	---	---	---	
BAI1	575	broad.mit.edu	37	8	143604687	143604688	+	Intron	INS	-	GGG	GGG	rs7465311	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143604687_143604688insGGG	uc003ywm.2	+							NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1						axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCGAGGCTTGAAGGGAGGGCCT	0.649													4	2	---	---	---	---	
CPSF1	29894	broad.mit.edu	37	8	145627569	145627569	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145627569delT	uc003zcj.2	-						CPSF1_uc003zck.1_Intron|CPSF1_uc011lle.1_Intron|MIR1234_hsa-mir-1234|MI0006324_5'Flank|CPSF1_uc011llf.1_Intron	NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,						mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding			skin(1)	1	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			ATCTCCTCCCTTTTCACTGCC	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	1917849	1917849	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1917849delT								DMRT2 (860296 upstream) : SMARCA2 (97493 downstream)																							tcgtttctccttttttttttG	0.328													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	3800851	3800851	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3800851delT								RFX3 (274868 upstream) : GLIS3 (23277 downstream)																							actgaagatcttggtcctata	0.000													4	2	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	6794744	6794744	+	Intron	DEL	A	-	-	rs111867924		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6794744delA	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc010mhw.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc010mhv.2_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						TAATATTCTTAAAAAAAAATG	0.294													4	2	---	---	---	---	
ZDHHC21	340481	broad.mit.edu	37	9	14589624	14589624	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14589624delA	uc003zlg.1	-									Q8IVQ6	ZDH21_HUMAN	Homo sapiens HSPC097 mRNA, partial cds.						nitric oxide metabolic process|regulation of nitric-oxide synthase activity	Golgi membrane|integral to membrane	palmitoyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(50;4.31e-06)		AAGGCTGAACAAAAAAAAATT	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	15126782	15126783	+	Intron	INS	-	ACA	ACA	rs140668609	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15126782_15126783insACA	uc003zln.1	-											Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																		gaaggaggaggaggagaaggag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	17130269	17130269	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17130269delA								BNC2 (259483 upstream) : CNTLN (4769 downstream)																							CAGAAATGTCAAACCAGGTCA	0.299													4	2	---	---	---	---	
ELAVL2	1993	broad.mit.edu	37	9	23783466	23783466	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23783466delA	uc003zpu.2	-						ELAVL2_uc003zps.2_Intron|ELAVL2_uc003zpt.2_Intron|ELAVL2_uc003zpv.2_Intron|ELAVL2_uc003zpw.2_Intron	NM_004432	NP_004423	Q12926	ELAV2_HUMAN	ELAV (embryonic lethal, abnormal vision,						regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		GCCATGCACTAACCTGAAAAC	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	26550469	26550469	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26550469delA								TUSC1 (871613 upstream) : C9orf82 (290215 downstream)																							aaggaaaaagaaaaaaaaaaT	0.184													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	30305979	30305979	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30305979delT								None (None upstream) : None (None downstream)																							acaactattctttttttaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	34069894	34069894	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34069894delT								UBAP2 (20947 upstream) : DCAF12 (16487 downstream)																							aacaaagaggttttattgtaa	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	38797322	38797322	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38797322delT								C9orf122 (174047 upstream) : CNTNAP3 (275444 downstream)																							tccttttcaattttttggaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	40747141	40747141	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40747141delA								FAM74A3 (24462 upstream) : ZNF658 (13561 downstream)																							ATTTCTTTTTAAAAACCTGAA	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	46918853	46918853	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:46918853delC								KGFLP1 (170468 upstream) : None (None downstream)																							CCCCCTACATCCCATACTTGA	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68393606	68393606	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68393606delA								FAM27B (599417 upstream) : MIR1299 (608633 downstream)																							tgtttgttggaaaaagttctt	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68418203	68418204	+	IGR	INS	-	TG	TG	rs145604244		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68418203_68418204insTG								FAM27B (624014 upstream) : MIR1299 (584035 downstream)																							AGAAAATTAGATGTGTGTGTTT	0.262													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68810602	68810602	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68810602delC								None (None upstream) : MIR1299 (191637 downstream)																							ATGGACAATTCTTTTTTTTTT	0.473													6	3	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668426	71668427	+	Intron	INS	-	GG	GG	rs58150402	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668426_71668427insGG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						gatggatggatagatagataga	0.059													13	6	---	---	---	---	
FXN	2395	broad.mit.edu	37	9	71668427	71668428	+	Intron	INS	-	TG	TG	rs75408130	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71668427_71668428insTG	uc004aha.2	+						FXN_uc011lrr.1_Intron|FXN_uc004agz.2_Intron	NM_000144	NP_000135	Q16595	FRDA_HUMAN	frataxin isoform 1 preproprotein						cellular iron ion homeostasis|cellular response to hydrogen peroxide|heme biosynthetic process|ion transport|iron incorporation into metallo-sulfur cluster|negative regulation of apoptosis|negative regulation of release of cytochrome c from mitochondria|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity|protein autoprocessing|regulation of ferrochelatase activity|response to iron ion	cytosol|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferric iron binding|ferrous iron binding|ferroxidase activity|iron chaperone activity|protein binding				0						atggatggatagatagatagat	0.059													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	73147858	73147858	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73147858delG								KLF9 (118285 upstream) : TRPM3 (2110 downstream)																							GGAAGGAAATGGACTGAAAAA	0.428													4	2	---	---	---	---	
TRPM3	80036	broad.mit.edu	37	9	73409009	73409009	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73409009delT	uc004aid.2	-						TRPM3_uc004ahu.2_Intron|TRPM3_uc004ahv.2_Intron|TRPM3_uc004ahw.2_Intron|TRPM3_uc004ahx.2_Intron|TRPM3_uc004ahy.2_Intron|TRPM3_uc004ahz.2_Intron|TRPM3_uc004aia.2_Intron|TRPM3_uc004aib.2_Intron|TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aie.2_Intron|TRPM3_uc004aif.2_Intron|TRPM3_uc004aig.2_Intron	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9						GGATAGCAGATTTTTTTTTTT	0.303													3	3	---	---	---	---	
TMC1	117531	broad.mit.edu	37	9	75430880	75430881	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75430880_75430881insA	uc004aiz.1	+						TMC1_uc010moz.1_Intron|TMC1_uc004aja.1_Intron|TMC1_uc004ajb.1_Intron|TMC1_uc004ajc.1_Intron|TMC1_uc010mpa.1_Intron	NM_138691	NP_619636	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1						sensory perception of sound	integral to membrane				ovary(1)	1						TCACTGTGTTTAAAAAAAAAAA	0.208													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	79651590	79651591	+	IGR	DEL	TC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79651590_79651591delTC								FOXB2 (15721 upstream) : VPS13A (140770 downstream)																							tctttctctgtctctctctctc	0.322													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	82929029	82929029	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82929029delT								TLE4 (587372 upstream) : None (None downstream)																							agctcctccctttttgtattt	0.065													4	2	---	---	---	---	
UBQLN1	29979	broad.mit.edu	37	9	86292480	86292481	+	Intron	INS	-	AAAAC	AAAAC	rs138593223	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86292480_86292481insAAAAC	uc004amv.2	-						UBQLN1_uc004amw.2_Intron	NM_013438	NP_038466	Q9UMX0	UBQL1_HUMAN	ubiquilin 1 isoform 1						apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0						tctatctcaaaaaaacaaaaca	0.099													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93685597	93685597	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93685597delT								SYK (24764 upstream) : AUH (290502 downstream)																							TTTTCAACTCTTTTTAGCATA	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	96197407	96197407	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96197407delT								C9orf129 (88711 upstream) : FAM120AOS (1489 downstream)																							tctttctttctttttttctga	0.015													4	2	---	---	---	---	
PHF2	5253	broad.mit.edu	37	9	96425001	96425002	+	Intron	INS	-	ATGG	ATGG	rs149000761	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96425001_96425002insATGG	uc004aub.2	+						PHF2_uc011lug.1_Intron|PHF2_uc004auc.2_5'Flank	NM_005392	NP_005383	O75151	PHF2_HUMAN	PHD finger protein 2						liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		tgaatgaataaatggatggatg	0.074													13	10	---	---	---	---	
HSD17B3	3293	broad.mit.edu	37	9	99001467	99001467	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99001467delG	uc004awa.1	-						HSD17B3_uc010msc.1_Intron	NM_000197	NP_000188	P37058	DHB3_HUMAN	estradiol 17 beta-dehydrogenase 3						androgen biosynthetic process|male genitalia development	endoplasmic reticulum membrane|microsome	binding|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity				0		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)			NADH(DB00157)	CAGCCACCCAGGACACCAGCC	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	100723505	100723506	+	IGR	DEL	TG	-	-	rs35108435		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100723505_100723506delTG								HEMGN (16371 upstream) : ANP32B (21983 downstream)																							Agtgtgtgtctgtgtgtgtgtg	0.351													3	3	---	---	---	---	
ANKS6	203286	broad.mit.edu	37	9	101518338	101518338	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101518338delT	uc004ayu.2	-						ANKS6_uc004ayt.2_Intron|ANKS6_uc004ayv.1_Intron|ANKS6_uc004ayw.1_Intron|ANKS6_uc004ayx.1_Intron|ANKS6_uc004ayy.1_Intron	NM_173551	NP_775822	Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain											ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)				tcaggtttcatttttttccct	0.080													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	109040113	109040113	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109040113delG	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																		GGTGGATGGTGGACTGTAGGT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	110447935	110447935	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110447935delT								KLF4 (195888 upstream) : None (None downstream)																							AGACCACATATTTTCTCAGAA	0.259													4	2	---	---	---	---	
PTPN3	5774	broad.mit.edu	37	9	112154661	112154661	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112154661delT	uc004bed.2	-						PTPN3_uc004beb.2_Intron|PTPN3_uc004bec.2_Intron|PTPN3_uc010mtu.2_Intron|PTPN3_uc011lwg.1_Intron|PTPN3_uc011lwh.1_Intron|PTPN3_uc011lwd.1_Intron|PTPN3_uc011lwe.1_Intron|PTPN3_uc011lwf.1_Intron	NM_002829	NP_002820	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type						negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3						TTGGAAGTGATTTTTTTTTTt	0.159													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115709965	115709966	+	IGR	INS	-	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115709965_115709966insC								SLC46A2 (56772 upstream) : ZNF883 (49436 downstream)																							TTTTATCAAGACCCCCTGGGAG	0.475													4	2	---	---	---	---	
ZNF618	114991	broad.mit.edu	37	9	116813347	116813348	+	3'UTR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116813347_116813348insT	uc004bid.2	+	15					ZNF618_uc004bic.2_3'UTR|ZNF618_uc011lxi.1_3'UTR|ZNF618_uc011lxj.1_3'UTR|ZNF618_uc010mvb.2_3'UTR	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCTCCCTAACATTTTAGCAATT	0.337													4	2	---	---	---	---	
AMBP	259	broad.mit.edu	37	9	116825464	116825464	+	Intron	DEL	A	-	-	rs7034544	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116825464delA	uc004bie.3	-						AMBP_uc011lxk.1_Intron|AMBP_uc010mvc.1_Intron	NM_001633	NP_001624	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin preproprotein						cell adhesion|female pregnancy|heme catabolic process|interspecies interaction between organisms|negative regulation of immune response|negative regulation of JNK cascade|protein-chromophore linkage	extracellular region|plasma membrane	calcium channel inhibitor activity|calcium oxalate binding|heme binding|IgA binding|protein homodimerization activity|serine-type endopeptidase inhibitor activity|transporter activity			skin(1)	1					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	CTGCTTGCAGAAAAAAAAAAA	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	117753552	117753553	+	IGR	DEL	GT	-	-	rs72049105		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117753552_117753553delGT								TNFSF8 (60782 upstream) : TNC (29253 downstream)																							TTTtgtgtgcgtgtgtgtgtgt	0.366													5	3	---	---	---	---	
PAPPA	5069	broad.mit.edu	37	9	119011890	119011890	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119011890delA	uc004bjn.2	+						PAPPA_uc011lxp.1_Intron|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9						caatgttgccaaaactgaagt	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	123131841	123131842	+	IGR	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123131841_123131842insA								MIR147 (124513 upstream) : CDK5RAP2 (19306 downstream)																							CCCTTTTGCTTAAAAAAAAAAG	0.267													4	2	---	---	---	---	
LHX6	26468	broad.mit.edu	37	9	124972160	124972160	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124972160delT	uc010mvw.2	-						LHX6_uc004blx.3_Intron|LHX6_uc004bly.3_Intron	NM_014368	NP_055183	Q9UPM6	LHX6_HUMAN	LIM homeobox protein 6 isoform 1						cell maturation|cerebral cortex GABAergic interneuron migration|cerebral cortex radially oriented cell migration|cerebral cortex tangential migration	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TGTGATGAtcttttttttttt	0.085													8	4	---	---	---	---	
RABGAP1	23637	broad.mit.edu	37	9	125723668	125723669	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125723668_125723669insA	uc011lzh.1	+						RABGAP1_uc004bnl.3_Intron|RABGAP1_uc004bnm.1_Intron	NM_012197	NP_036329	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1						cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5						gcacttaaaccaaaaaaactgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126109642	126109643	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126109642_126109643delGT								STRBP (78799 upstream) : CRB2 (8805 downstream)																							gtgtatgctggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	126763463	126763463	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126763463delT								DENND1A (71046 upstream) : LHX2 (10426 downstream)																							AGAGAAATCATTTTTTTTTTT	0.453													4	2	---	---	---	---	
FAM125B	89853	broad.mit.edu	37	9	129267958	129267959	+	3'UTR	DEL	TA	-	-	rs71654764		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129267958_129267959delTA	uc004bqh.1	+	10					FAM125B_uc011lzy.1_3'UTR|FAM125B_uc010mxd.2_3'UTR|FAM125B_uc010mxe.1_5'Flank	NM_033446	NP_258257	Q9H7P6	F125B_HUMAN	hypothetical protein LOC89853 isoform 1						protein transport	late endosome membrane					0						tgtgtgtgtgtatatgtgtgtg	0.421													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133021949	133021949	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133021949delT								NCS1 (22366 upstream) : ASS1 (298145 downstream)																							aggttcattgttttaccatac	0.000													4	2	---	---	---	---	
VAV2	7410	broad.mit.edu	37	9	136819574	136819574	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136819574delA	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		GAAAGGACCCAAAGTACTCAG	0.597													4	2	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140615677	140615677	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140615677delC	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		CTCACACTCACCCCTCCCAGA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2343534	2343534	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2343534delT								ADARB2 (563816 upstream) : PFKP (766218 downstream)																							GTAGGTTGAGTTTTTTTTTTG	0.423													4	2	---	---	---	---	
PFKP	5214	broad.mit.edu	37	10	3161275	3161276	+	Intron	INS	-	AACTT	AACTT			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3161275_3161276insAACTT	uc001igp.2	+						PFKP_uc001igq.2_Intron|PFKP_uc009xhr.2_Intron|PFKP_uc009xhs.1_Intron|PFKP_uc009xht.2_Intron|PFKP_uc009xhu.2_Intron	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet						glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		AACCGAGAAGCAAAAGCTTGAC	0.495													8	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	3576115	3576115	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3576115delT	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																		TGGACATACATTTTAGAAAAC	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	7197841	7197841	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7197841delT								PRKCQ (575603 upstream) : SFMBT2 (6408 downstream)																							AAGCAAAAGCTTTAGTGACTA	0.458													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11145155	11145155	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11145155delA	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|uc001ikn.1_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						TCAGAATTCGAAAAAAATCCA	0.378													4	2	---	---	---	---	
CELF2	10659	broad.mit.edu	37	10	11353404	11353404	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11353404delA	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc010qbo.1_Intron|CELF2_uc010qbp.1_Intron	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						gctcacaaccaaaaaaaaccc	0.000													4	2	---	---	---	---	
BEND7	222389	broad.mit.edu	37	10	13511366	13511366	+	Intron	DEL	A	-	-	rs5783325		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13511366delA	uc001imm.2	-						BEND7_uc001imn.2_Intron|BEND7_uc001imo.3_Intron	NM_152751	NP_689964	Q8N7W2	BEND7_HUMAN	BEN domain containing 7 isoform 1								protein binding			ovary(1)|breast(1)	2						CGCCTCTCTCATGCTAAGGGT	0.428													2	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	16451548	16451549	+	IGR	DEL	CA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16451548_16451549delCA								FAM188A (549029 upstream) : PTER (27418 downstream)																							cacgcgcacgcacacacacaca	0.277													4	2	---	---	---	---	
TRDMT1	1787	broad.mit.edu	37	10	17240034	17240034	+	Intron	DEL	A	-	-	rs75435003		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17240034delA	uc001iop.2	-						TRDMT1_uc001ioq.2_Intron|TRDMT1_uc001ior.2_Intron|TRDMT1_uc001ios.2_Intron|TRDMT1_uc009xjt.2_Intron|TRDMT1_uc010qcd.1_Intron	NM_004412	NP_004403	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1 isoform						tRNA processing	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|RNA binding			ovary(1)	1						actccatctcaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	20731941	20731941	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20731941delA								PLXDC2 (162826 upstream) : NEBL (336964 downstream)																							TTGAAATGTCAAGGGAGCATG	0.413													4	2	---	---	---	---	
MPP7	143098	broad.mit.edu	37	10	28592226	28592226	+	5'Flank	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28592226delC	uc009xla.2	-						MPP7_uc010qdv.1_5'Flank	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1						GCAAGTTCCACCCCTGCCCGC	0.607													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30469797	30469798	+	IGR	INS	-	CA	CA	rs149210569	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30469797_30469798insCA								KIAA1462 (65377 upstream) : MTPAP (128933 downstream)																							aaacatgcactcacacacacac	0.287													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30986798	30986799	+	Intron	DEL	TT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30986798_30986799delTT	uc010qdx.1	+											SubName: Full=cDNA FLJ59642, highly similar to Supervillin;																		agaatagtgctttttaaaagca	0.183													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	35150838	35150839	+	IGR	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35150838_35150839delCT								PARD3 (46915 upstream) : CUL2 (147969 downstream)																							TCCTACCGCCCTCTCTCTCTCC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44237840	44237840	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44237840delC								ZNF32 (93514 upstream) : HNRNPA3P1 (45020 downstream)																							cattgcctttcccccacctcg	0.134													4	2	---	---	---	---	
SYT15	83849	broad.mit.edu	37	10	46958639	46958640	+	3'UTR	DEL	GC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46958639_46958640delGC	uc001jea.2	-	8					SYT15_uc001jdz.2_Intron|SYT15_uc001jeb.2_3'UTR	NM_031912	NP_114118	Q9BQS2	SYT15_HUMAN	synaptotagmin XV isoform a							integral to membrane|plasma membrane					0						GTATAAACCTGCGCACACACAC	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	50467776	50467776	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50467776delT								C10orf128 (71369 upstream) : C10orf71 (39411 downstream)																							AAAGTAAACCTTTTTTTGCCT	0.289													4	2	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51488750	51488752	+	Intron	DEL	CAC	-	-	rs1551690		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51488750_51488752delCAC	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|AGAP7_uc001jio.2_5'Flank	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		agcagacacacacaaaaaaggga	0.113													5	4	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51488753	51488754	+	Intron	INS	-	G	G	rs143472113	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51488753_51488754insG	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|AGAP7_uc001jio.2_5'Flank	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		agacacacacaaaaaagggaga	0.114													5	4	---	---	---	---	
PARG	8505	broad.mit.edu	37	10	51491281	51491283	+	Intron	DEL	AGA	-	-	rs35397545		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51491281_51491283delAGA	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		gcctctggctagaagaagcctgt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	61205881	61205882	+	IGR	INS	-	GC	GC			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61205881_61205882insGC								FAM13C (83220 upstream) : SLC16A9 (204640 downstream)																							tgtgtgtgtgtgtgtattcaca	0.000													4	2	---	---	---	---	
HERC4	26091	broad.mit.edu	37	10	69808944	69808944	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69808944delA	uc001jng.3	-						HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron|HERC4_uc001jnj.2_Intron	NM_022079	NP_071362	Q5GLZ8	HERC4_HUMAN	hect domain and RLD 4 isoform a						cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3						ctctgcaattaaaaaaaaaaa	0.000													4	2	---	---	---	---	
COL13A1	1305	broad.mit.edu	37	10	71709756	71709757	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71709756_71709757delGT	uc001jpr.1	+						COL13A1_uc001jqj.1_Intron|COL13A1_uc001jps.1_Intron|COL13A1_uc001jpt.1_Intron|COL13A1_uc001jpu.1_Intron|COL13A1_uc001jpv.1_Intron|COL13A1_uc001jpx.1_Intron|COL13A1_uc001jpw.1_Intron|COL13A1_uc001jpy.1_Intron|COL13A1_uc001jpz.1_Intron|COL13A1_uc001jqa.1_Intron|COL13A1_uc001jqc.1_Intron|COL13A1_uc001jqb.1_Intron|COL13A1_uc001jql.2_Intron|COL13A1_uc001jqd.1_Intron|COL13A1_uc001jqe.1_Intron|COL13A1_uc001jqf.1_Intron|COL13A1_uc001jqg.1_Intron|COL13A1_uc001jqh.1_Intron|COL13A1_uc001jqi.1_Intron|COL13A1_uc010qjf.1_Intron	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1						cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)	ttgtgtgtgcgtgtgtgtgtAC	0.322													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	72413603	72413604	+	IGR	INS	-	TG	TG	rs138513597	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72413603_72413604insTG								PRF1 (51072 upstream) : ADAMTS14 (18955 downstream)																							cacttactagctgtgtggcttt	0.074													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	72764667	72764668	+	IGR	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72764667_72764668insG								PCBD1 (116126 upstream) : UNC5B (207630 downstream)																							TGGCTGTGGCTGGGGCCTTACC	0.624													4	2	---	---	---	---	
SLC29A3	55315	broad.mit.edu	37	10	73100017	73100017	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73100017delC	uc001jrr.3	+						SLC29A3_uc001jrs.3_Intron|SLC29A3_uc010qjq.1_Intron|SLC29A3_uc001jrt.3_Intron|SLC29A3_uc001jru.3_Intron	NM_018344	NP_060814	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (nucleoside						nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|late endosome membrane|lysosomal membrane	nucleoside transmembrane transporter activity				0						CCCACATTGACCCCCAGGCCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	77195949	77195949	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77195949delT								C10orf41 (27210 upstream) : MIR606 (116267 downstream)																							agaagctgtattgtgctgggc	0.149													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	80023194	80023194	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80023194delA	uc010qlp.1	+											SubName: Full=cDNA FLJ57363;																		GTGTTGGAGGAAGGGTCTAGA	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	81076921	81076921	+	IGR	DEL	T	-	-	rs11306322		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81076921delT								ZMIZ1 (636 upstream) : PPIF (30299 downstream)																							CCGATTGAAGTTTTAGGAACA	0.552											OREG0020308	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	82057637	82057637	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82057637delT								MAT1A (8203 upstream) : DYDC1 (38227 downstream)																							CTATGTAttcttttttttttt	0.219													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	85946455	85946456	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85946455_85946456delGT								C10orf99 (1406 upstream) : CDHR1 (8061 downstream)																							ggtatgtatggtgtgtgtgtgg	0.074													4	2	---	---	---	---	
FAM190B	54462	broad.mit.edu	37	10	86140277	86140278	+	Intron	INS	-	T	T	rs138543680	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86140277_86140278insT	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14											ovary(3)|skin(1)	4						atgctcatatatggcgtgtgtg	0.030													2	4	---	---	---	---	
FAM190B	54462	broad.mit.edu	37	10	86210990	86210991	+	Intron	DEL	TT	-	-	rs79298770	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86210990_86210991delTT	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron|FAM190B_uc001kdi.1_Intron|FAM190B_uc010qme.1_Intron	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14											ovary(3)|skin(1)	4						TATAGAAAGGTTTTTTTTTTGG	0.183													4	2	---	---	---	---	
GRID1	2894	broad.mit.edu	37	10	87951952	87951953	+	Intron	DEL	CA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87951952_87951953delCA	uc001kdl.1	-						GRID1_uc009xsu.1_Intron	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	gacacctgcgcacacacacaca	0.262										Multiple Myeloma(13;0.14)			4	2	---	---	---	---	
GLUD1	2746	broad.mit.edu	37	10	88847839	88847839	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88847839delA	uc001keh.2	-						GLUD1_uc001keg.2_Intron|GLUD1_uc010qmp.1_Intron	NM_005271	NP_005262	P00367	DHE3_HUMAN	glutamate dehydrogenase 1 precursor						glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)	actctgtttcaaaaaaaaaac	0.109													4	2	---	---	---	---	
PANK1	53354	broad.mit.edu	37	10	91377618	91377618	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91377618delA	uc001kgp.1	-						PANK1_uc001kgn.1_Intron|PANK1_uc001kgo.1_Intron|PANK1_uc009xtu.1_Intron	NM_148977	NP_683878	Q8TE04	PANK1_HUMAN	pantothenate kinase 1 isoform alpha						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)	ttttcttttgaaaaataattg	0.000													4	2	---	---	---	---	
TCTN3	26123	broad.mit.edu	37	10	97424226	97424226	+	Intron	DEL	A	-	-	rs71954790		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97424226delA	uc001klb.3	-						TCTN3_uc001kla.3_Intron|TCTN3_uc010qoi.1_Intron	NM_015631	NP_056446	Q6NUS6	TECT3_HUMAN	tectonic 3 isoform a precursor						apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		AGACACAAGGAAATGAATATC	0.383													2	6	---	---	---	---	
ARHGAP19	84986	broad.mit.edu	37	10	99019585	99019586	+	Intron	INS	-	TGTTTTGTTTTGTTT	TGTTTTGTTTTGTTT	rs147834614	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99019585_99019586insTGTTTTGTTTTGTTT	uc001knb.2	-						ARHGAP19_uc001kmy.2_Intron|ARHGAP19_uc001kna.2_Intron|ARHGAP19_uc009xvi.2_Intron|ARHGAP19_uc009xvj.2_Intron|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		attaaaaaacctgttttgtttt	0.104													19	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	102617680	102617682	+	IGR	DEL	TTG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102617680_102617682delTTG								PAX2 (27983 upstream) : FAM178A (54644 downstream)																							GTGCAATCTTttgttgttgttgt	0.227													4	2	---	---	---	---	
SH3PXD2A	9644	broad.mit.edu	37	10	105380475	105380476	+	Intron	DEL	AG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105380475_105380476delAG	uc001kxj.1	-						SH3PXD2A_uc010qqr.1_Intron|SH3PXD2A_uc010qqs.1_Intron|SH3PXD2A_uc010qqt.1_Intron|SH3PXD2A_uc009xxn.1_Intron|SH3PXD2A_uc010qqu.1_Intron	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1						cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		CTCTTATTTAagagagagagag	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	110977139	110977140	+	IGR	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110977139_110977140delTG								None (None upstream) : XPNPEP1 (647384 downstream)																							TGTGTACAAATGTGTGTGTGTG	0.356													4	2	---	---	---	---	
ATE1	11101	broad.mit.edu	37	10	123685921	123685921	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123685921delA	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2						protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				atctgtaaataaaaaaataaa	0.109													4	2	---	---	---	---	
HTRA1	5654	broad.mit.edu	37	10	124239301	124239302	+	Intron	INS	-	GGAGAT	GGAGAT	rs143793652	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124239301_124239302insGGAGAT	uc001lgj.2	+							NM_002775	NP_002766	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1 precursor						proteolysis|regulation of cell growth	extracellular space	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				CGTGGGCCCGAGGAGATGGCGA	0.579													5	3	---	---	---	---	
CPXM2	119587	broad.mit.edu	37	10	125655131	125655131	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125655131delT	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)		TCTCTAGGACTTTTTTGTTCT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	126069059	126069060	+	IGR	INS	-	CC	CC	rs143683830	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126069059_126069060insCC								CHST15 (215853 upstream) : OAT (16812 downstream)																							tccatgctcctcctgactcccc	0.114													4	2	---	---	---	---	
FANK1	92565	broad.mit.edu	37	10	127685480	127685480	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127685480delT	uc001ljh.3	+						FANK1_uc009yan.2_Intron|FANK1_uc001lji.2_Intron	NM_145235	NP_660278	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				TGGAATTCAATTTTTTTTTTT	0.318													7	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130236874	130236874	+	IGR	DEL	G	-	-	rs139514550	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130236874delG								MKI67 (312406 upstream) : None (None downstream)																							tggggtgtgtggtgtgtgtgt	0.000													4	2	---	---	---	---	
EBF3	253738	broad.mit.edu	37	10	131760659	131760659	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131760659delT	uc001lki.1	-						EBF3_uc010qur.1_3'UTR	NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		TCTCGCTTAATTTTTTTTTTC	0.468													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133470681	133470682	+	IGR	INS	-	A	A	rs72565542	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133470681_133470682insA								TCERG1L (360697 upstream) : PPP2R2D (277278 downstream)																							TGGGTCTGATCCCAGCCTCAGG	0.505													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133506905	133506906	+	IGR	INS	-	A	A	rs138336062	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133506905_133506906insA								TCERG1L (396921 upstream) : PPP2R2D (241054 downstream)																							AATTATTCAGGAAAAAAAATGC	0.455													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	133777929	133777929	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133777929delG								PPP2R2D (7878 upstream) : BNIP3 (3258 downstream)																							ATTGCTTCCAGGCCCTTTTGT	0.433													4	2	---	---	---	---	
HBG2	3048	broad.mit.edu	37	11	5598736	5598737	+	Intron	INS	-	GT	GT	rs34344140	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5598736_5598737insGT	uc001mak.1	-									P69892	HBG2_HUMAN	Homo sapiens hemoglobin gamma-G (HBG2) mRNA, partial cds.						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		agagagagagagtgtgtgtgtg	0.233													3	3	---	---	---	---	
LMO1	4004	broad.mit.edu	37	11	8270290	8270290	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8270290delT	uc001mgg.1	-						LMO1_uc009yfo.1_Intron|LMO1_uc001mgh.1_Intron	NM_002315	NP_002306	P25800	RBTN1_HUMAN	LIM domain only 1						cell proliferation|multicellular organismal development|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;1.59e-07)|BRCA - Breast invasive adenocarcinoma(625;0.203)		CAAGAAACACTTTACAGACAG	0.552			T|A	TRD@	T-ALL|neuroblastoma	neuroblastoma							4	2	---	---	---	---	
SBF2	81846	broad.mit.edu	37	11	9978117	9978118	+	Intron	INS	-	C	C	rs34154767		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9978117_9978118insC	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		ctTAACTCTTTTTTTTTTTTTT	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	15271498	15271498	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15271498delG								INSC (2746 upstream) : SOX6 (716498 downstream)																							AGGTTGGAATGGGGGGTGGCT	0.468													4	2	---	---	---	---	
PLEKHA7	144100	broad.mit.edu	37	11	16973224	16973224	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16973224delA	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						ACCATATGGGAAAGGAGATGG	0.313													4	2	---	---	---	---	
SERGEF	26297	broad.mit.edu	37	11	17814860	17814860	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17814860delA	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron	NM_012139	NP_036271	Q9UGK8	SRGEF_HUMAN	deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1						AGCCTATAGGAAAAAAAAAGC	0.428													4	2	---	---	---	---	
ZDHHC13	54503	broad.mit.edu	37	11	19164290	19164290	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19164290delT	uc001mpi.2	+						ZDHHC13_uc001mpj.2_Intron	NM_019028	NP_061901	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC domain containing 13 isoform						positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|palmitoyltransferase activity|signal transducer activity|zinc ion binding				0						tttttttttcttttttttttg	0.114													7	4	---	---	---	---	
HTATIP2	10553	broad.mit.edu	37	11	20390813	20390813	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20390813delT	uc009yia.1	+						HTATIP2_uc009yib.1_Intron|HTATIP2_uc001mpx.2_Intron|HTATIP2_uc001mpz.2_Intron	NM_006410	NP_006401	Q9BUP3	HTAI2_HUMAN	HIV-1 Tat interactive protein 2, 30kDa isoform						angiogenesis|anti-apoptosis|apoptosis|cell differentiation|cellular amino acid metabolic process|induction of apoptosis|interspecies interaction between organisms|nuclear import|regulation of angiogenesis|regulation of transcription from RNA polymerase II promoter	cytoplasm|nuclear envelope	NAD binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor|protein binding|transcription coactivator activity				0						CGTTGGGTGGTTTATCATATG	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	20553086	20553086	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20553086delT								PRMT3 (22209 upstream) : SLC6A5 (67860 downstream)																							TGGAAAGGAGTTTTGGCGTCC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	22341120	22341121	+	IGR	INS	-	TTG	TTG	rs144277177	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22341120_22341121insTTG								ANO5 (36207 upstream) : SLC17A6 (18546 downstream)																							TAGCAGTAGTTTTGTTGTTTTC	0.238													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	26181286	26181286	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26181286delA								None (None upstream) : ANO3 (29543 downstream)																							AGGTCACATTAAAATGGTGTC	0.353													4	2	---	---	---	---	
CSTF3	1479	broad.mit.edu	37	11	33163765	33163765	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33163765delA	uc001muh.2	-						CSTF3_uc001mui.2_Intron|CSTF3_uc001muj.2_Intron	NM_001326	NP_001317	Q12996	CSTF3_HUMAN	cleavage stimulation factor subunit 3 isoform 1						mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0						actcagagagaaaaaaaaaag	0.055													6	3	---	---	---	---	
ALKBH3	221120	broad.mit.edu	37	11	43911687	43911688	+	Intron	INS	-	TA	TA	rs151062224	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43911687_43911688insTA	uc001mxs.2	+						ALKBH3_uc009ykp.2_Intron|ALKBH3_uc001mxt.2_Intron|ALKBH3_uc009ykq.2_Intron	NM_139178	NP_631917	Q96Q83	ALKB3_HUMAN	AlkB homolog 3						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation	mitochondrion|nucleoplasm	damaged DNA binding|DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0					Vitamin C(DB00126)	TGTTCACTGACTTGCTTCAAAT	0.361								Direct_reversal_of_damage			OREG0020905	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	45666951	45666953	+	IGR	DEL	GGA	-	-	rs35676376		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45666951_45666953delGGA								SYT13 (359067 upstream) : CHST1 (3474 downstream)																							tgaacaaactggaggctgtaact	0.000													6	3	---	---	---	---	
PTPRJ	5795	broad.mit.edu	37	11	48073337	48073337	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48073337delT	uc001ngp.3	+						PTPRJ_uc001ngo.3_Intron	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8						ttctctggcaTTTTgagcatg	0.065													4	2	---	---	---	---	
PTPRJ	5795	broad.mit.edu	37	11	48170376	48170376	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48170376delT	uc001ngp.3	+							NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8						tgtttccaagttttttttctt	0.000													3	3	---	---	---	---	
MED19	219541	broad.mit.edu	37	11	57476034	57476034	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57476034delT	uc001nla.1	-						MED19_uc001nlb.2_Intron	NM_153450	NP_703151	A0JLT2	MED19_HUMAN	mediator complex subunit 19						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(2)	2						TTGAAAACCATTAGGTAGTTC	0.363													4	2	---	---	---	---	
OR9Q1	219956	broad.mit.edu	37	11	57938965	57938965	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57938965delC	uc001nmj.2	+							NM_001005212	NP_001005212	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.222)				GGCAAAGATTCCTCAACCTTT	0.433													4	2	---	---	---	---	
TMEM132A	54972	broad.mit.edu	37	11	60696555	60696559	+	Intron	DEL	AAACT	-	-	rs139814160		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60696555_60696559delAAACT	uc001nqj.2	+						TMEM132A_uc001nqi.2_Intron|TMEM132A_uc001nqk.2_Intron|TMEM132A_uc001nql.1_Intron	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1						TGTGTCCACCAAACTAAACTCCTTC	0.551													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	61259801	61259802	+	IGR	DEL	CA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61259801_61259802delCA								C11orf66 (1402 upstream) : LRRC10B (16470 downstream)																							ctcagacacgcacacacacaca	0.045													4	2	---	---	---	---	
FADS1	3992	broad.mit.edu	37	11	61577090	61577090	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61577090delT	uc010rlm.1	-						FADS1_uc001nsh.2_Intron|FADS1_uc010rln.1_Intron	NM_013402	NP_037534	O60427	FADS1_HUMAN	fatty acid desaturase 1						cell-cell signaling|cellular response to starvation|electron transport chain|icosanoid biosynthetic process|phospholipid biosynthetic process|regulation of cell differentiation|regulation of transcription, DNA-dependent|transport	endoplasmic reticulum membrane|integral to membrane|microsome	C-5 sterol desaturase activity|heme binding|protein binding			central_nervous_system(1)	1					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TGCCCATGTCTTTTTTTTAAA	0.463													3	3	---	---	---	---	
MACROD1	28992	broad.mit.edu	37	11	63822357	63822357	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63822357delC	uc001nyh.2	-							NM_014067	NP_054786	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1												0						GTGACAAATACCCCCACTACT	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	64345919	64345920	+	IGR	INS	-	C	C	rs141443095	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64345919_64345920insC								SLC22A11 (6921 upstream) : SLC22A12 (12362 downstream)																							AGCGTGGGGGACTGGGCCTGGC	0.619													7	6	---	---	---	---	
CLCF1	23529	broad.mit.edu	37	11	67137398	67137398	+	Intron	DEL	A	-	-	rs72387381		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67137398delA	uc001okq.2	-						LOC100130987_uc010rpo.1_Intron|CLCF1_uc010rpp.1_Intron	NM_013246	NP_037378	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1 precursor						B cell differentiation|cytokine-mediated signaling pathway|JAK-STAT cascade|negative regulation of neuron apoptosis|positive regulation of astrocyte differentiation|positive regulation of B cell proliferation|positive regulation of immunoglobulin production|positive regulation of isotype switching to IgE isotypes|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	ciliary neurotrophic factor receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity				0			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)			ATCTGGGCAGAAAAAAACGGC	0.537													4	3	---	---	---	---	
SHANK2	22941	broad.mit.edu	37	11	70570145	70570145	+	Intron	DEL	T	-	-	rs11342822		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70570145delT	uc001oqc.2	-							NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			AAGTTCAttcttttttttttt	0.219													12	10	---	---	---	---	
ANKRD42	338699	broad.mit.edu	37	11	82917426	82917426	+	Intron	DEL	G	-	-	rs35649629		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82917426delG	uc001ozz.1	+						ANKRD42_uc009yvi.1_Intron|ANKRD42_uc010rsv.1_Intron|ANKRD42_uc001paa.2_Intron|ANKRD42_uc001pab.1_Intron	NM_182603	NP_872409	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42											skin(1)	1						GGCTGTCTGCGTTGTTTTAAG	0.294													7	6	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	84584326	84584326	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84584326delA	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)				aaggtggaggaaaaagccaca	0.000													4	2	---	---	---	---	
CCDC89	220388	broad.mit.edu	37	11	85398239	85398239	+	5'Flank	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85398239delC	uc001pau.1	-							NM_152723	NP_689936	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89							cytoplasm|nucleus					0		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				gaatgcctttcctactttgtc	0.000													4	2	---	---	---	---	
PICALM	8301	broad.mit.edu	37	11	85747358	85747358	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85747358delG	uc001pbm.2	-						PICALM_uc001pbl.2_Intron|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron	NM_007166	NP_009097	Q13492	PICAL_HUMAN	phosphatidylinositol-binding clathrin assembly						clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				ATTTGTGAAAGGGATCATAAA	0.308			T	MLLT10|MLL	TALL|AML|								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	85932129	85932130	+	IGR	INS	-	G	G	rs138163110	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85932129_85932130insG								PICALM (151229 upstream) : EED (23685 downstream)																							TGTGGGGGAGTGGGGGGGGGAT	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	90651341	90651341	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90651341delT								MIR1261 (48971 upstream) : None (None downstream)																							GCCTAATTCATTTATTTTGCC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	91815811	91815813	+	IGR	DEL	AGA	-	-	rs58395274	byFrequency	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91815811_91815813delAGA								None (None upstream) : FAT3 (269449 downstream)																							TCTGGCTTGTAGAAGTGATTCAG	0.305													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	100254974	100254974	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100254974delG								CNTN5 (27502 upstream) : ARHGAP42 (303433 downstream)																							ctccctgggagggagtgtcca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	101889365	101889365	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101889365delA								KIAA1377 (17574 upstream) : C11orf70 (28809 downstream)																							aacaaaaaacaaaaaaaaaaa	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	106378999	106379000	+	IGR	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106378999_106379000insG								AASDHPPT (409580 upstream) : GUCY1A2 (178910 downstream)																							ACATGGGCAGAGGGGGAAATTC	0.475													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	113906205	113906206	+	IGR	DEL	CA	-	-	rs72448961		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113906205_113906206delCA								HTR3A (45173 upstream) : ZBTB16 (24225 downstream)																							ACATCAGCATcacacacacaca	0.490													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	116383281	116383281	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116383281delC								None (None upstream) : BUD13 (235607 downstream)																							ACCTGTCTGGCCCCCAAATAA	0.537													4	2	---	---	---	---	
DSCAML1	57453	broad.mit.edu	37	11	117545168	117545168	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117545168delC	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GAAGGAACTGCCATGATCCTC	0.537													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	120014924	120014924	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120014924delC								TRIM29 (6061 upstream) : OAF (66823 downstream)																							GGGCCCTGTGCCCCCCCACCC	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	126928852	126928852	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126928852delT								KIRREL3 (55497 upstream) : None (None downstream)																							ggacagagaattttttttttt	0.020													5	3	---	---	---	---	
ADAMTS8	11095	broad.mit.edu	37	11	130289404	130289405	+	Intron	INS	-	CC	CC			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130289404_130289405insCC	uc001qgg.3	-							NM_007037	NP_008968	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1						negative regulation of cell proliferation|proteolysis	proteinaceous extracellular matrix	heparin binding|integrin binding|low affinity phosphate transmembrane transporter activity|metalloendopeptidase activity|zinc ion binding			central_nervous_system(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		tgatgcatgaacagtggtcttt	0.040													6	3	---	---	---	---	
ADAMTS8	11095	broad.mit.edu	37	11	130289407	130289408	+	Intron	INS	-	ACCTGCCT	ACCTGCCT			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130289407_130289408insACCTGCCT	uc001qgg.3	-							NM_007037	NP_008968	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1						negative regulation of cell proliferation|proteolysis	proteinaceous extracellular matrix	heparin binding|integrin binding|low affinity phosphate transmembrane transporter activity|metalloendopeptidase activity|zinc ion binding			central_nervous_system(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		tgcatgaacagtggtctttgaa	0.040													6	3	---	---	---	---	
SNX19	399979	broad.mit.edu	37	11	130782544	130782545	+	Intron	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130782544_130782545insG	uc001qgk.3	-						SNX19_uc010sce.1_Intron|SNX19_uc010scf.1_Intron|SNX19_uc010scg.1_Intron|SNX19_uc001qgl.3_Intron|SNX19_uc009zcx.1_Intron	NM_014758	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		GAGTTGTGGCTGGTGCTTTACA	0.416													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	131236714	131236715	+	IGR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131236714_131236715insT								SNX19 (450332 upstream) : NTM (3656 downstream)																							CCTGAAGGCCATTGGGAAATTT	0.391													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	132226154	132226154	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132226154delG								NTM (19439 upstream) : OPCML (58723 downstream)																							tagcaaggttggacagaagtg	0.000													4	2	---	---	---	---	
GLB1L3	112937	broad.mit.edu	37	11	134179342	134179342	+	Intron	DEL	T	-	-	rs79490965		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134179342delT	uc009zdf.2	+						GLB1L3_uc010scu.1_Intron|GLB1L3_uc001qho.3_Intron	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		agaaaaattgttttttttttt	0.060													17	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134898458	134898458	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134898458delT								B3GAT1 (616646 upstream) : None (None downstream)																							GTGCATTATCTTTTTTTTGCA	0.388													4	2	---	---	---	---	
NINJ2	4815	broad.mit.edu	37	12	761344	761345	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:761344_761345insA	uc001qil.2	-						NINJ2_uc010sds.1_Intron	NM_016533	NP_057617	Q9NZG7	NINJ2_HUMAN	ninjurin 2						nervous system development|neuron cell-cell adhesion|tissue regeneration	integral to plasma membrane				ovary(2)	2	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)			gaatacacaagaaaaaaaaatc	0.000													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2208194	2208194	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2208194delG	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	CTGTGTGGCTGGGGAAGCCCT	0.353													4	2	---	---	---	---	
EFCAB4B	84766	broad.mit.edu	37	12	3737393	3737394	+	Intron	INS	-	TCTT	TCTT	rs150027786	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3737393_3737394insTCTT	uc010sen.1	-						EFCAB4B_uc001qmi.1_Intron	NM_001144958	NP_001138430	Q9BSW2	EFC4B_HUMAN	EF-hand calcium binding domain 4B isoform a						activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			cttcctttctctctttctttct	0.168													4	6	---	---	---	---	
ATF7IP	55729	broad.mit.edu	37	12	14532924	14532925	+	Intron	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14532924_14532925delTG	uc001rbw.2	+						ATF7IP_uc010shs.1_Intron|ATF7IP_uc001rbu.2_Intron|ATF7IP_uc001rbv.1_Intron|ATF7IP_uc001rbx.2_Intron	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						gtgatgtatttgtgtgtgtgtg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	28988420	28988420	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28988420delT								CCDC91 (285322 upstream) : FAR2 (313812 downstream)																							gtggtgttgatttttttctac	0.000													4	2	---	---	---	---	
PDZRN4	29951	broad.mit.edu	37	12	41717213	41717213	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41717213delA	uc010skn.1	+							NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				ATAGATATCTAAAAAAAGATA	0.214													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	45862578	45862579	+	IGR	DEL	AC	-	-	rs138905800		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45862578_45862579delAC								ANO6 (28391 upstream) : LOC400027 (257231 downstream)																							tcaaaacaaaacagatatgatc	0.134													1	5	---	---	---	---	
DNAJC22	79962	broad.mit.edu	37	12	49738171	49738171	+	5'Flank	DEL	T	-	-	rs76048711		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49738171delT	uc001rua.2	+						DNAJC22_uc001rub.2_5'Flank	NM_024902	NP_079178	Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22						protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)	1						CGTCCTCttcttttttttttt	0.219													4	2	---	---	---	---	
DIP2B	57609	broad.mit.edu	37	12	51122129	51122130	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51122129_51122130insA	uc001rwv.2	+						DIP2B_uc009zlt.2_Intron	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6						aaactccatctaaaaaaaaaaa	0.124													6	3	---	---	---	---	
GALNT6	11226	broad.mit.edu	37	12	51780887	51780887	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51780887delT	uc001ryl.1	-						GALNT6_uc010snh.1_Intron	NM_007210	NP_009141	Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6						protein O-linked glycosylation	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2						GTTTGCATAAttttttttttt	0.184													3	3	---	---	---	---	
IGFBP6	3489	broad.mit.edu	37	12	53491636	53491638	+	In_Frame_Del	DEL	GGA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53491636_53491638delGGA	uc001sbu.1	+	1	201_203	c.135_137delGGA	c.(133-138)GTGGAG>GTG	p.E48del		NM_002178	NP_002169	P24592	IBP6_HUMAN	insulin-like growth factor binding protein 6	48	IGFBP N-terminal.				negative regulation of cell proliferation|regulation of cell growth|signal transduction					ovary(1)	1						GGGGCTGCGTGGAGGAGGAGGAT	0.640													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	54837213	54837213	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54837213delT								ITGA5 (24163 upstream) : GTSF1 (12524 downstream)																							TTCCTTTTCATTATAAAAATA	0.189													4	2	---	---	---	---	
HMGA2	8091	broad.mit.edu	37	12	66355519	66355520	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66355519_66355520delGT	uc001ssx.2	+							NM_003483	NP_003474	P52926	HMGA2_HUMAN	high mobility group AT-hook 2 isoform a						cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/LPP(161)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/RAD51B(11)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/CCNB1IP1(2)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/COX6C(2)	soft_tissue(159)|bone(27)|salivary_gland(22)	208	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)		CCAGGATAGAgtgtgtgtgtgt	0.361			T	 LHFP|RAD51L1|LPP|HEI10|COX6C|CMKOR1|NFIB|ALDH2|CCNB1IP1|EBF1|WIF1|FHIT	lipoma|leiomyoma|pleiomorphic salivary gland adenoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	74669120	74669120	+	Intron	DEL	T	-	-	rs113849001		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74669120delT	uc009zrx.1	-						uc001sxc.2_Intron					Homo sapiens cDNA clone IMAGE:3926153, partial cds.																		TTTTTTGGGGTTTTTTTTTTT	0.303													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77092249	77092249	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77092249delC								OSBPL8 (138660 upstream) : ZDHHC17 (65605 downstream)																							ttttgttcttccctgaacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80608305	80608305	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80608305delA								PPP1R12A (279070 upstream) : PTPRQ (229821 downstream)																							GTGTGCACAGAAATCCAGATG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	84465314	84465314	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84465314delC								TMTC2 (937251 upstream) : SLC6A15 (787955 downstream)																							gtccagaagtccaggagtccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	90146628	90146628	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90146628delT								LOC338758 (40900 upstream) : None (None downstream)																							GTTTCATAGGTTTTCCATCTC	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	92726260	92726260	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92726260delG								BTG1 (186587 upstream) : CLLU1OS (87610 downstream)																							ggcaagcaatggcagacacat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	94415688	94415688	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94415688delA								CRADD (127072 upstream) : PLXNC1 (126811 downstream)																							CTTGGCTGACAAAAAAAAAAG	0.398													3	3	---	---	---	---	
DRAM1	55332	broad.mit.edu	37	12	102308264	102308264	+	Intron	DEL	T	-	-	rs66919603		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102308264delT	uc001tix.2	+						DRAM1_uc010svv.1_Intron	NM_018370	NP_060840	Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1						apoptosis|autophagy	integral to membrane|lysosomal membrane				ovary(1)	1						cttcttcttcttttttttttt	0.139													25	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102363738	102363738	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102363738delA								DRAM1 (46339 upstream) : CCDC53 (42980 downstream)																							tttaagaactaatactaatcc	0.000													4	2	---	---	---	---	
BTBD11	121551	broad.mit.edu	37	12	107747816	107747816	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107747816delT	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3						tttttttctgtttttattgta	0.100													4	2	---	---	---	---	
PWP1	11137	broad.mit.edu	37	12	108082782	108082782	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108082782delA	uc001tmo.1	+						PWP1_uc001tmn.1_Intron|PWP1_uc009zuu.1_Intron	NM_007062	NP_008993	Q13610	PWP1_HUMAN	periodic tryptophan protein 1						transcription, DNA-dependent	nucleus					0						TCTAGGATCTAAAAAAAAAAG	0.328													13	7	---	---	---	---	
WSCD2	9671	broad.mit.edu	37	12	108624350	108624350	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108624350delA	uc001tms.2	+						WSCD2_uc001tmt.2_Intron|WSCD2_uc001tmu.2_Intron	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2							integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3						tatgtcacccaaaaagtaagt	0.129													4	2	---	---	---	---	
PPP1CC	5501	broad.mit.edu	37	12	111171319	111171319	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111171319delT	uc001tru.2	-							NM_002710	NP_002701	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma						cell division|glycogen metabolic process|mitotic prometaphase|triglyceride catabolic process	cleavage furrow|condensed chromosome kinetochore|cytosol|midbody|MLL5-L complex|nuclear speck|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|protein binding|protein kinase binding|protein serine/threonine phosphatase activity			lung(2)|central_nervous_system(1)	3						CACTGTCACCTTTGAACATAG	0.343													4	2	---	---	---	---	
RASAL1	8437	broad.mit.edu	37	12	113550969	113550969	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113550969delG	uc001tum.1	-						RASAL1_uc010syp.1_Intron|RASAL1_uc001tul.2_Intron|RASAL1_uc001tun.1_Intron|RASAL1_uc010syq.1_Intron|RASAL1_uc001tuo.3_Intron|RASAL1_uc010syr.1_Intron	NM_004658	NP_004649	O95294	RASL1_HUMAN	RAS protein activator like 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	metal ion binding|phospholipid binding|Ras GTPase activator activity			ovary(2)|skin(2)	4						TACAGATTGAGGGTCTGTCTT	0.289													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115300988	115300988	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115300988delC								TBX3 (179019 upstream) : None (None downstream)																							CTACTGAATTCCCCAGGCCTC	0.423													4	2	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119553681	119553682	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119553681_119553682insT	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						aagtgatttgatttttttttta	0.134													4	2	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124952583	124952584	+	Intron	INS	-	TCC	TCC	rs147189850	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124952583_124952584insTCC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		caccctcatcatcctcatcacc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	128584430	128584431	+	IGR	INS	-	TG	TG			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128584430_128584431insTG								None (None upstream) : TMEM132C (314860 downstream)																							TTCCATCACACTGTCCGAATAA	0.436													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	130576969	130576969	+	IGR	DEL	C	-	-	rs12424919	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130576969delC								LOC100190940 (50082 upstream) : FZD10 (70063 downstream)																							GATAAGACCGCCCGACGTGAT	0.522													4	2	---	---	---	---	
GPR133	283383	broad.mit.edu	37	12	131530814	131530814	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131530814delC	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GGTCAGTGCTCCCTCCCTGGT	0.632													2	4	---	---	---	---	
EP400	57634	broad.mit.edu	37	12	132501413	132501414	+	Intron	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132501413_132501414delCT	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400						histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		TTTGCCATTGCTCTCTCCTCCC	0.550													3	3	---	---	---	---	
GOLGA3	2802	broad.mit.edu	37	12	133365502	133365503	+	Intron	INS	-	AC	AC			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133365502_133365503insAC	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		ccccgacccagacagaccccgc	0.312													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31275042	31275043	+	IGR	INS	-	AG	AG			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31275042_31275043insAG								USPL1 (41356 upstream) : ALOX5AP (12572 downstream)																							ctccagttccaagagtctaaac	0.000													4	2	---	---	---	---	
NBEA	26960	broad.mit.edu	37	13	36246099	36246099	+	3'UTR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36246099delT	uc001uvb.2	+	58					NBEA_uc010abi.2_3'UTR|NBEA_uc010tef.1_3'UTR|NBEA_uc001uvd.2_3'UTR	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TGATGCTAACTTTTTTTTTCT	0.348													4	2	---	---	---	---	
UFM1	51569	broad.mit.edu	37	13	38935215	38935215	+	3'UTR	DEL	T	-	-	rs111718532	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38935215delT	uc001uwu.2	+	6						NM_016617	NP_057701	P61960	UFM1_HUMAN	ubiquitin-fold modifier 1 precursor						protein ufmylation	cytoplasm|nucleus	protein binding				0		Lung NSC(96;3.18e-06)|Prostate(109;0.00314)|Breast(139;0.0199)|Lung SC(185;0.0743)		all cancers(112;1.05e-08)|Epithelial(112;1.44e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000855)|BRCA - Breast invasive adenocarcinoma(63;0.00342)|GBM - Glioblastoma multiforme(144;0.0132)		CTTTTGATAATTTTTTTTTTT	0.318													9	4	---	---	---	---	
LHFP	10186	broad.mit.edu	37	13	39917692	39917692	+	3'UTR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39917692delA	uc001uxf.2	-	4						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)		TCCTCACCTTAAAAAAAAAAA	0.313			T	HMGA2	lipoma								2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	45906077	45906077	+	IGR	DEL	T	-	-	rs34411594		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45906077delT								GTF2F2 (47840 upstream) : TPT1 (5227 downstream)																							TACAAGTAGATTTTTtttttc	0.194													4	3	---	---	---	---	
CPB2	1361	broad.mit.edu	37	13	46665556	46665556	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46665556delA	uc001vaw.2	-						uc001vau.1_Intron|uc001vav.1_Intron|CPB2_uc001vax.2_Intron	NM_001872	NP_001863	Q96IY4	CBPB2_HUMAN	plasma carboxypeptidase B2 isoform a						blood coagulation|fibrinolysis|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		aagtggagataaaatgcatga	0.000													4	2	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52819942	52819942	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52819942delT	uc001vgm.1	-						uc001vgn.2_Intron					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						gactccccaattttttttttt	0.000													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	54913567	54913567	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54913567delT								MIR1297 (27384 upstream) : None (None downstream)																							TCaatttttatttttttactt	0.299													4	2	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60449555	60449555	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60449555delT	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.2_Intron	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		gaaACGTACATTTTTTTTCAC	0.254													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	73230957	73230957	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73230957delT								DACH1 (789627 upstream) : C13orf37 (51538 downstream)																							CATACTCctcttccctcaagg	0.368													4	2	---	---	---	---	
KLF12	11278	broad.mit.edu	37	13	74508281	74508282	+	Intron	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74508281_74508282insG	uc001vjf.2	-						KLF12_uc010aeq.2_Intron|KLF12_uc001vjg.3_Intron	NM_007249	NP_009180	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		agataaattgaggggttttttt	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78956704	78956704	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78956704delC	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																		CTTCAACATTCCCCAGTGTGC	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	87152813	87152814	+	IGR	DEL	TT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87152813_87152814delTT								SLITRK6 (779330 upstream) : None (None downstream)																							tgacactgacttaaggaaggaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90970594	90970594	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90970594delG								MIR622 (87063 upstream) : LOC144776 (572614 downstream)																							AGCAGGCAGAGGATAAAATGT	0.353													4	2	---	---	---	---	
FGF14	2259	broad.mit.edu	37	13	102655129	102655129	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102655129delA	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)					ACTATTTTGGAAAAGGATCTC	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	107065082	107065083	+	IGR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107065082_107065083insT								DAOA (921700 upstream) : EFNB2 (77015 downstream)																							caaagcttatattttatccgtc	0.000													4	4	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110809226	110809227	+	Intron	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110809226_110809227delTG	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			tgtgtctgtctgtgtgtgtgtg	0.302													4	2	---	---	---	---	
RASA3	22821	broad.mit.edu	37	13	114795042	114795043	+	Intron	DEL	GT	-	-	rs68004915		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114795042_114795043delGT	uc001vui.2	-						RASA3_uc010tkk.1_Intron|RASA3_uc001vuj.2_Intron|RASA3_uc010tkl.1_Intron|RASA3_uc010aha.1_Intron	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			CATCATCCTGGTGGGCCAGGAC	0.604													4	2	---	---	---	---	
CHD8	57680	broad.mit.edu	37	14	21895574	21895577	+	Intron	DEL	ACTT	-	-	rs60595107		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21895574_21895577delACTT	uc001was.1	-						CHD8_uc001war.1_Intron	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8						ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		AGGAGCACTCACTTGAGCTTGCTC	0.520													4	3	---	---	---	---	
TGM1	7051	broad.mit.edu	37	14	24732008	24732008	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24732008delC	uc001wod.2	-						TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1						cell envelope organization|keratinization|peptide cross-linking	cornified envelope|intrinsic to membrane	acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	TAGCAGAAATCCCCCAACTCA	0.572													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	25603154	25603154	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25603154delT								STXBP6 (83983 upstream) : None (None downstream)																							attcaggatctgctaaaacac	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26669325	26669325	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26669325delA								None (None upstream) : NOVA1 (245765 downstream)																							GACCCACTAGAAAAAAAAAGT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	32018541	32018542	+	IGR	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32018541_32018542delTG								HEATR5A (91861 upstream) : NUBPL (12049 downstream)																							tttctatttctgtgaagaatgt	0.000													4	2	---	---	---	---	
ARHGAP5	394	broad.mit.edu	37	14	32586147	32586147	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32586147delT	uc001wrl.2	+						ARHGAP5_uc001wrm.2_Intron|ARHGAP5_uc001wrn.2_Intron|ARHGAP5_uc001wro.2_Intron|ARHGAP5_uc001wrp.2_Intron	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b						cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(4)|central_nervous_system(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		CAATAAGCCATTTTTTTTTCT	0.338													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	35357053	35357053	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35357053delT								BAZ1A (12200 upstream) : C14orf19 (52075 downstream)																							CTCAACCCAATTTTTTTTTCA	0.224													5	3	---	---	---	---	
NID2	22795	broad.mit.edu	37	14	52509260	52509260	+	Intron	DEL	A	-	-	rs3841694		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52509260delA	uc001wzo.2	-						NID2_uc010tqs.1_Intron|NID2_uc010tqt.1_Intron|NID2_uc001wzp.2_Intron	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor							basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					TCCTCCTTCTACTCCACTACA	0.428													4	12	---	---	---	---	
DAAM1	23002	broad.mit.edu	37	14	59734208	59734208	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59734208delA	uc001xdz.1	+						DAAM1_uc001xea.1_Intron|DAAM1_uc001xeb.1_Intron	NM_014992	NP_055807	Q9Y4D1	DAAM1_HUMAN	dishevelled-associated activator of						actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)		TGCTTAACTTAAAAAAAAAAA	0.239													4	2	---	---	---	---	
PRKCH	5583	broad.mit.edu	37	14	61955294	61955294	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61955294delT	uc001xfn.2	+						PRKCH_uc010tsa.1_Intron|PRKCH_uc010tsb.1_Intron	NM_006255	NP_006246	P24723	KPCL_HUMAN	protein kinase C, eta						intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		TAGAGTACCATTACAGTGTCA	0.418													4	2	---	---	---	---	
SYNE2	23224	broad.mit.edu	37	14	64682283	64682284	+	Intron	INS	-	C	C	rs138806575	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64682283_64682284insC	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_Intron|SYNE2_uc010aqa.2_Intron|SYNE2_uc001xgq.2_Intron|SYNE2_uc001xgr.2_Intron|SYNE2_uc010tsi.1_Intron|SYNE2_uc001xgs.2_Intron|SYNE2_uc001xgt.2_5'Flank	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						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)		CTCGATGCCAACCCCCTCTCCT	0.505													8	4	---	---	---	---	
DPF3	8110	broad.mit.edu	37	14	73260392	73260393	+	Intron	DEL	GA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73260392_73260393delGA	uc001xnc.2	-						DPF3_uc001xnf.2_Intron|DPF3_uc010ari.1_Intron|DPF3_uc010ttq.1_Intron	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		AGCCCCAGGGGAGAGAGAGACA	0.510													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	80366268	80366268	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80366268delG								NRXN3 (35510 upstream) : DIO2 (297602 downstream)																							aaacctgcctgggtaataccc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	82244810	82244810	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82244810delT								SEL1L (244605 upstream) : None (None downstream)																							GACTATTATCTTTTACCTTGT	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	87625653	87625653	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87625653delA								None (None upstream) : GALC (678511 downstream)																							CAGGTTTTAGAAAAAAAAAAA	0.323													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	89523107	89523107	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89523107delG								TTC8 (178773 upstream) : FOXN3 (99410 downstream)																							GTCTCCGTCTGGCCCTGAAAG	0.562													4	2	---	---	---	---	
ITPK1	3705	broad.mit.edu	37	14	93479650	93479650	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93479650delA	uc001ybg.2	-						ITPK1_uc001ybe.2_Intron|ITPK1_uc001ybf.2_Intron|ITPK1_uc001ybh.2_Intron	NM_014216	NP_055031	Q13572	ITPK1_HUMAN	inositol 1,3,4-triphosphate 5/6 kinase isoform						blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		AAACAAAAACAAAAAAAATCC	0.433													4	2	---	---	---	---	
KIAA1409	57578	broad.mit.edu	37	14	94145085	94145085	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94145085delT	uc001ybv.1	+						KIAA1409_uc001ybs.1_Intron	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578							integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		ACGTATAAAGTTTTTTTACAT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95515562	95515562	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95515562delA								GSC (279063 upstream) : DICER1 (37003 downstream)																							ggaacatgccaaacatgctcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	96281630	96281631	+	IGR	INS	-	G	G	rs148376721	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96281630_96281631insG								TCL1A (101097 upstream) : C14orf132 (224031 downstream)																							tgcgatgtaaaTGGCCATTTAC	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	97631167	97631168	+	IGR	DEL	TT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97631167_97631168delTT								VRK1 (283217 upstream) : C14orf64 (760779 downstream)																							AGAGGCCCCCTTTTTTTTTCCT	0.386													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98317865	98317865	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98317865delG								VRK1 (969915 upstream) : C14orf64 (74082 downstream)																							GGTTGATGTTGGAACAATTCC	0.512													4	2	---	---	---	---	
EVL	51466	broad.mit.edu	37	14	100486121	100486122	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100486121_100486122insA	uc001ygt.2	+						EVL_uc001ygv.2_Intron	NM_016337	NP_057421	Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)				CTGGTTCTCACAAAAAAAACAG	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	100654124	100654124	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100654124delT								DEGS2 (28112 upstream) : YY1 (50978 downstream)																							ttctgcagacttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	101261254	101261254	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101261254delA								DLK1 (59780 upstream) : MEG3 (31191 downstream)																							agtagtaaagaaaaaaaaaag	0.000													4	3	---	---	---	---	
WDR20	91833	broad.mit.edu	37	14	102657963	102657963	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102657963delT	uc001ykz.2	+						WDR20_uc001yky.1_Intron|WDR20_uc001yla.2_Intron|WDR20_uc001ylb.2_Intron|WDR20_uc010txu.1_Intron|WDR20_uc001ylc.2_Intron|WDR20_uc001yld.2_Intron|WDR20_uc001yle.2_Intron|WDR20_uc001ylf.2_Intron	NM_144574	NP_653175	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20 isoform 2												0						AGAAATACAATTTTTTTTATG	0.473													4	2	---	---	---	---	
RCOR1	23186	broad.mit.edu	37	14	103128931	103128931	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103128931delT	uc001ymb.2	+							NM_015156	NP_055971	Q9UKL0	RCOR1_HUMAN	REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1						TGTGTGGATCTTTTTTTTTTC	0.542													3	3	---	---	---	---	
AMN	81693	broad.mit.edu	37	14	103388647	103388647	+	5'Flank	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103388647delG	uc001ymg.3	+						AMN_uc001ymh.3_5'Flank	NM_030943	NP_112205	Q9BXJ7	AMNLS_HUMAN	amnionless protein precursor						lipid metabolic process|lipoprotein metabolic process|multicellular organismal development	integral to membrane|plasma membrane					0				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCATGGGACAGGGGCACTGCG	0.537													4	2	---	---	---	---	
TNFAIP2	7127	broad.mit.edu	37	14	103599519	103599520	+	Intron	DEL	AC	-	-	rs112674096		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103599519_103599520delAC	uc001ymm.1	+						TNFAIP2_uc010awo.1_Intron|TNFAIP2_uc010txz.1_Intron|TNFAIP2_uc010tya.1_Intron	NM_006291	NP_006282	Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2						angiogenesis|cell differentiation	extracellular space				central_nervous_system(1)	1		Melanoma(154;0.155)	Epithelial(46;0.191)			gcacatgtgaacacacacgcaT	0.252													2	5	---	---	---	---	
TDRD9	122402	broad.mit.edu	37	14	104472524	104472524	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104472524delA	uc001yom.3	+						TDRD9_uc001yon.3_Intron	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9						cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TCATACTTTTAAAAAAAAAGT	0.313													6	4	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107099093	107099094	+	Intron	INS	-	G	G	rs140761011	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107099093_107099094insG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						GGTACCCTGCAGGAGGTTTGTG	0.540													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20413795	20413796	+	IGR	DEL	AG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20413795_20413796delAG								None (None upstream) : GOLGA6L6 (323298 downstream)																							ccttaactgtagagagactaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20427031	20427032	+	IGR	DEL	CA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20427031_20427032delCA								None (None upstream) : GOLGA6L6 (310062 downstream)																							AGACACCTAGCACAGAGTTTAG	0.411													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20512761	20512761	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20512761delG								None (None upstream) : GOLGA6L6 (224333 downstream)																							TGCTTAGTAAGGGCTCCATGG	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24174273	24174274	+	IGR	DEL	TT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24174273_24174274delTT								NDN (241823 upstream) : PWRN2 (235652 downstream)																							GAAGTAACTCTTTACTATTTCT	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	24350910	24350910	+	IGR	DEL	T	-	-	rs66860732		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24350910delT								NDN (418460 upstream) : PWRN2 (59016 downstream)																							gatctcattctttttttcagc	0.000													4	2	---	---	---	---	
UBE3A	7337	broad.mit.edu	37	15	25650315	25650319	+	Intron	DEL	AACTC	-	-	rs138698137		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25650315_25650319delAACTC	uc001zaq.2	-						UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453	Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		GAGACTGTTAAACTCAACTCTTTCC	0.224													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	29058664	29058664	+	5'Flank	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29058664delT	uc010uaq.1	+											DL491344																		ttttgtaccctttttttctca	0.144													4	2	---	---	---	---	
SCG5	6447	broad.mit.edu	37	15	32979276	32979279	+	Intron	DEL	GGAG	-	-	rs66696288		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32979276_32979279delGGAG	uc001zha.2	+						SCG5_uc001zgz.2_Intron	NM_001144757	NP_001138229	P05408	7B2_HUMAN	secretogranin V isoform 1						intracellular protein transport|neuropeptide signaling pathway|peptide hormone processing|regulation of hormone secretion	extracellular region|stored secretory granule	enzyme inhibitor activity|GTP binding|unfolded protein binding				0		all_lung(180;7.32e-08)		all cancers(64;6.48e-17)|Epithelial(43;1.23e-11)|GBM - Glioblastoma multiforme(186;1.39e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0212)		GAGAAAGAAAGGAGGGAGACTGAG	0.495													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	34665582	34665583	+	IGR	INS	-	A	A	rs28460021		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34665582_34665583insA								LPCAT4 (6187 upstream) : GOLGA8A (5689 downstream)																							AAAAAAAAACCAAAAAAAAAAG	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	41214344	41214344	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41214344delC								VPS18 (18172 upstream) : DLL4 (7203 downstream)																							GAGAGTGGCACCCAGAGGGGT	0.532													4	2	---	---	---	---	
LRRC57	255252	broad.mit.edu	37	15	42837102	42837103	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42837102_42837103insA	uc001zqd.1	-						LRRC57_uc001zqc.2_Intron	NM_153260	NP_694992	Q8N9N7	LRC57_HUMAN	leucine rich repeat containing 57												0		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)		ATAAGCTGTCTATAGAGAAAAA	0.252													18	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	45999470	45999470	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45999470delA								SQRDL (15992 upstream) : None (None downstream)																							TTATGCACTGAAGCCTTTCTG	0.313													4	2	---	---	---	---	
ATP8B4	79895	broad.mit.edu	37	15	50400581	50400581	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50400581delA	uc001zxu.2	-						ATP8B4_uc010ber.2_Intron|ATP8B4_uc010ufd.1_Intron|ATP8B4_uc010ufe.1_Intron	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		cacccctgctaaaaaccctgc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	52382887	52382887	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52382887delA								MAPK6 (24426 upstream) : BCL2L10 (18937 downstream)																							aaagtcaagtaaaaaaaatta	0.000													4	2	---	---	---	---	
UNC13C	440279	broad.mit.edu	37	15	54661144	54661144	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54661144delA	uc002ack.2	+						UNC13C_uc002acl.2_Intron	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		AGTAGGACATAACCATGTTAA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	55149853	55149854	+	IGR	DEL	AA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55149853_55149854delAA								UNC13C (229048 upstream) : RSL24D1 (323667 downstream)																							caactgaattaaaaaatattga	0.040													4	2	---	---	---	---	
RAB27A	5873	broad.mit.edu	37	15	55578573	55578574	+	Intron	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55578573_55578574delTG	uc002acr.2	-							NM_183235	NP_899058	P51159	RB27A_HUMAN	Ras-related protein Rab-27A						small GTPase mediated signal transduction	dendrite|exocytic vesicle|late endosome|lysosome|melanosome	GTP binding|GTPase activity			ovary(1)	1				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		agacaaatgttgtgtgtgtgtg	0.000													4	3	---	---	---	---	
ZNF280D	54816	broad.mit.edu	37	15	57138420	57138420	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57138420delA	uc002adw.1	-							NM_001002843	NP_001002843	Q6N043	Z280D_HUMAN	suppressor of hairy wing homolog 4 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		gatacactacaaaaaaaaaat	0.085													10	5	---	---	---	---	
CGNL1	84952	broad.mit.edu	37	15	57842136	57842136	+	3'UTR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57842136delG	uc002aeg.2	+	19					CGNL1_uc010bfw.2_3'UTR	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		AGACGCTGCTGGGGAAGGTCA	0.498													4	2	---	---	---	---	
ADAM10	102	broad.mit.edu	37	15	59016843	59016844	+	Intron	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59016843_59016844delAC	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)		aggaagctgaacagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	59883939	59883940	+	IGR	DEL	AA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59883939_59883940delAA								FAM81A (68188 upstream) : GCNT3 (20042 downstream)																							ACATTTTTTTAAAATCCCCATG	0.386													4	2	---	---	---	---	
NARG2	79664	broad.mit.edu	37	15	60736578	60736578	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60736578delA	uc002agp.2	-						NARG2_uc002ago.2_Intron|NARG2_uc002agq.3_Intron	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a							nucleus				ovary(1)|lung(1)	2						AAGCCAGGGGAAAAAAAAGGC	0.299													4	2	---	---	---	---	
VPS13C	54832	broad.mit.edu	37	15	62238847	62238848	+	Intron	INS	-	A	A	rs11405697		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62238847_62238848insA	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2						ATTTTAAAACCAAAAAAAAAAA	0.287													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	63752711	63752711	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63752711delT								CA12 (78636 upstream) : USP3 (44099 downstream)																							ggaatcagcctcccaaaaggt	0.095													4	2	---	---	---	---	
LCTL	197021	broad.mit.edu	37	15	66858647	66858647	+	5'Flank	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66858647delA	uc002aqc.2	-						LCTL_uc002aqd.3_5'Flank|LCTL_uc010bhw.2_5'Flank	NM_207338	NP_997221	Q6UWM7	LCTL_HUMAN	lactase-like precursor						carbohydrate metabolic process	endoplasmic reticulum membrane|integral to membrane	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(2)	2						CCCAGCTGCCAAAAAAAAAAC	0.478													4	3	---	---	---	---	
SMAD3	4088	broad.mit.edu	37	15	67366844	67366844	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67366844delG	uc002aqj.2	+							NM_005902	NP_005893	P84022	SMAD3_HUMAN	mothers against decapentaplegic homolog 3						activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding			large_intestine(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		TAGGCAGCGTGGATGTTGCAA	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	67489422	67489423	+	IGR	INS	-	TCCTTC	TCCTTC	rs140896383	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67489422_67489423insTCCTTC								SMAD3 (1890 upstream) : AAGAB (3946 downstream)																							tcttaaaaccatcctctggcct	0.000													5	4	---	---	---	---	
AAGAB	79719	broad.mit.edu	37	15	67524417	67524417	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67524417delC	uc002aqk.3	-						AAGAB_uc002aql.2_Intron|AAGAB_uc010uju.1_Intron	NM_024666	NP_078942	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin-binding protein p34						protein transport	cytoplasm					0						catagagaaaccccatctcta	0.000													6	5	---	---	---	---	
NEO1	4756	broad.mit.edu	37	15	73365779	73365780	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73365779_73365780delGT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor						axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1						catgagttgggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	76103193	76103193	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76103193delT								DNM1P35 (70691 upstream) : UBE2Q2 (32429 downstream)																							TTGTGCCCCATTTCCACCACA	0.373													4	2	---	---	---	---	
SGK269	79834	broad.mit.edu	37	15	77493968	77493969	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77493968_77493969insA	uc002bcm.2	-							NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member						cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)		ATTTACCTCATAAAAAAATGAT	0.337													4	2	---	---	---	---	
CHRNA5	1138	broad.mit.edu	37	15	78864325	78864325	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78864325delT	uc002bdy.2	+						CHRNA5_uc002bdz.2_Intron	NM_000745	NP_000736	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5						behavioral response to nicotine	cell junction|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(1)|central_nervous_system(1)|skin(1)	3						GCAAAGAGGATTTTTTTTTCA	0.373													4	2	---	---	---	---	
ADAMTSL3	57188	broad.mit.edu	37	15	84363867	84363868	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84363867_84363868delGT	uc002bjz.3	+						ADAMTSL3_uc002bjy.1_Intron|ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)			tgcatgtgtggtgtgtgtgtgt	0.158													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84768168	84768171	+	IGR	DEL	GTAT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84768168_84768171delGTAT								ADAMTSL3 (59577 upstream) : LOC388152 (99429 downstream)																							tgaacctttagtatgtatgtgtga	0.211													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84944245	84944245	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84944245delT								LOC388152 (45325 upstream) : GOLGA6L5 (103493 downstream)																							tctTTCCTCCTTTTTTTTTTT	0.184													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85903397	85903398	+	IGR	INS	-	AAG	AAG	rs143977499	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85903397_85903398insAAG								PDE8A (221027 upstream) : AKAP13 (20473 downstream)																							gtagaccggtaaaggagggtga	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87640295	87640295	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87640295delT								AGBL1 (68012 upstream) : NCRNA00052 (479865 downstream)																							ACTCCATGGATTTAAGCCAGC	0.294													4	2	---	---	---	---	
SLCO3A1	28232	broad.mit.edu	37	15	92568253	92568256	+	Intron	DEL	ATCT	-	-	rs139571931		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92568253_92568256delATCT	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)			tcatccatccatctgtctatccat	0.113													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	98789483	98789483	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98789483delT								ARRDC4 (272416 upstream) : FAM169B (190908 downstream)																							tcctcctcaattttttgagat	0.000													4	2	---	---	---	---	
FAM169B	283777	broad.mit.edu	37	15	99045963	99045963	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99045963delT	uc002buk.1	-							NM_182562	NP_872368	Q8N8A8	F169B_HUMAN	hypothetical protein LOC283777												0						actataatggtggatacatgt	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	99581191	99581191	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99581191delT								PGPEP1L (30167 upstream) : SYNM (64095 downstream)																							atgtacttcctttagtggagt	0.000													4	2	---	---	---	---	
LASS3	204219	broad.mit.edu	37	15	101013501	101013501	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101013501delC	uc002bvz.2	-						LASS3_uc002bwa.2_Intron|LASS3_uc002bwb.2_Intron	NM_178842	NP_849164	Q8IU89	CERS3_HUMAN	LAG1 longevity assurance homolog 3							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(2)|pancreas(1)|skin(1)	4	Lung NSC(78;0.0018)|all_lung(78;0.00278)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000867)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)			ACACACACTGCCCCCCAACAC	0.388													4	2	---	---	---	---	
RAB11FIP3	9727	broad.mit.edu	37	16	551284	551284	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:551284delC	uc002chf.2	+						RAB11FIP3_uc010uuf.1_Intron|RAB11FIP3_uc010uug.1_Intron	NM_014700	NP_055515	O75154	RFIP3_HUMAN	rab11-family interacting protein 3 isoform 1						cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)				tgcctctagacccccatttca	0.224													4	2	---	---	---	---	
NUBP2	10101	broad.mit.edu	37	16	1836992	1836993	+	Intron	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1836992_1836993insG	uc002cmw.3	+						NUBP2_uc002cmx.3_Intron|NUBP2_uc010brx.2_Intron	NM_012225	NP_036357	Q9Y5Y2	NUBP2_HUMAN	nucleotide binding protein 2 (MinD homolog, E.							microtubule organizing center|nucleus	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding|protein binding				0						GTCCTGGTGAAGGGGGTTAGCG	0.653													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8609498	8609498	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8609498delC								A2BP1 (846158 upstream) : TMEM114 (10005 downstream)																							CAAGCAAGGACCCAGCAATCC	0.517													4	2	---	---	---	---	
EMP2	2013	broad.mit.edu	37	16	10671270	10671270	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10671270delC	uc002czx.2	-							NM_001424	NP_001415	P54851	EMP2_HUMAN	epithelial membrane protein 2						cell proliferation	integral to membrane					0						TTTTTAGACTCCCCCCTGGCC	0.562													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12370656	12370656	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12370656delG	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						CCTGCAGAGTGGGCATATATG	0.438													4	2	---	---	---	---	
SNX29	92017	broad.mit.edu	37	16	12421593	12421594	+	Intron	DEL	AG	-	-	rs3975335		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12421593_12421594delAG	uc002dby.3	+							NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1						GGAGAGAGACAGAGAGAGGAAA	0.391													4	2	---	---	---	---	
MKL2	57496	broad.mit.edu	37	16	14348283	14348283	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14348283delG	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dcj.2_Intron	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5						cttttactctggggtccagct	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	19282968	19282970	+	IGR	DEL	TTG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19282968_19282970delTTG								SYT17 (4415 upstream) : LOC728276 (14135 downstream)																							tgttgttgttttgttgttgttgt	0.350													3	3	---	---	---	---	
ACSM2B	348158	broad.mit.edu	37	16	20559164	20559164	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20559164delC	uc002dhj.3	-						ACSM2B_uc002dhk.3_Intron|ACSM2B_uc010bwf.1_Intron	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member						fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5						ttgtctctctccccaaatctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	24684203	24684204	+	5'Flank	DEL	AG	-	-	rs68092029		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24684203_24684204delAG	uc002dml.1	-											Homo sapiens cDNA FLJ45256 fis, clone BRHIP2016125.																		ttttgaacctagatagttcatc	0.000													4	4	---	---	---	---	
IL4R	3566	broad.mit.edu	37	16	27368165	27368165	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27368165delA	uc002don.2	+						IL4R_uc002dop.3_Intron|IL4R_uc010bxy.2_Intron|IL4R_uc002doo.2_Intron	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a						immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2						tgatggtgagaacatatttca	0.259													4	2	---	---	---	---	
C16orf54	283897	broad.mit.edu	37	16	29755469	29755469	+	3'UTR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29755469delA	uc002dtp.2	-	2					uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|uc002dtq.1_5'Flank	NM_175900	NP_787096	Q6UWD8	CP054_HUMAN	hypothetical protein LOC283897							integral to membrane					0						GGGGAGGGGGACTCCAGGTGG	0.657													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32181823	32181824	+	IGR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32181823_32181824insT								HERC2P4 (17949 upstream) : TP53TG3B (503017 downstream)																							GAAGCACATGCTTTAATAGTAT	0.421													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32304771	32304775	+	Intron	DEL	TTTTA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32304771_32304775delTTTTA	uc002edb.2	-											Homo sapiens similar to protein phosphatase 2A 48 kDa regulatory subunit isoform 1; serine/threonine protein phosphatase 2A, 48kDa regulatory subunit; PP2A, subunit B, PR48 isoform; PP2A B subunit PR48; NY-REN-8 antigen, mRNA (cDNA clone IMAGE:5272051).																		CAGAAAATTCTTTTATTTTAAGGTG	0.380													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33532015	33532016	+	IGR	INS	-	TT	TT	rs147576683	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33532015_33532016insTT								SLC6A10P (635552 upstream) : MIR1826 (433492 downstream)																							CATCTTAAAAGTTTAACTTGCA	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33536122	33536122	+	IGR	DEL	T	-	-	rs79037717		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33536122delT								SLC6A10P (639659 upstream) : MIR1826 (429386 downstream)																							ATTAAAAAAATGCCCATTTCC	0.264													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33960743	33960743	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33960743delG								None (None upstream) : MIR1826 (4765 downstream)																							TATTTTTTTTGGCAATCTTTC	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33967631	33967631	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33967631delA								MIR1826 (2039 upstream) : UBE2MP1 (436171 downstream)																							TTCAAGGAGGAAAAAAACTGA	0.249													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34467855	34467855	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34467855delT								UBE2MP1 (63093 upstream) : LOC283914 (129932 downstream)																							TTGGGAGCACTTTACCAGGAG	0.617													4	2	---	---	---	---	
VPS35	55737	broad.mit.edu	37	16	46710949	46710949	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46710949delA	uc002eef.3	-						VPS35_uc002eed.2_Intron|VPS35_uc002eee.2_Intron	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35						protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AGATTACATGAAAAAAAAAAG	0.154													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	47749719	47749719	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47749719delT								PHKB (14286 upstream) : ABCC12 (367165 downstream)																							AGCTGGAAGGTTTTAGGCAAA	0.348													4	2	---	---	---	---	
ZNF423	23090	broad.mit.edu	37	16	49685264	49685264	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49685264delA	uc002efs.2	-						ZNF423_uc010vgn.1_Intron	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)				GAAGGAGAAGAAGGCCTGGGA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51201702	51201702	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51201702delT								SALL1 (16519 upstream) : None (None downstream)																							CTGTGTACCCTTTTTGGTCAA	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	51872647	51872647	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51872647delT								SALL1 (687464 upstream) : TOX3 (599271 downstream)																							aagcctgCCATTTTTATTCCA	0.154													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54406719	54406719	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54406719delC								IRX3 (86341 upstream) : IRX5 (558392 downstream)																							AATAAAAAGGCCACAAGGAAG	0.478													4	2	---	---	---	---	
SLC12A3	6559	broad.mit.edu	37	16	56933197	56933198	+	Intron	INS	-	AGG	AGG	rs150655528	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56933197_56933198insAGG	uc010ccm.2	+						SLC12A3_uc002ekd.3_Intron|SLC12A3_uc010ccn.2_Intron	NM_001126108	NP_001119580	P55017	S12A3_HUMAN	solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	gaggccgaggcaggatcacccg	0.020													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	57620761	57620762	+	IGR	INS	-	A	A	rs146356848	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57620761_57620762insA								GPR114 (9663 upstream) : GPR56 (32888 downstream)																							tttcaaaaaagaaaaaaaattg	0.000													4	2	---	---	---	---	
CCDC113	29070	broad.mit.edu	37	16	58312699	58312700	+	Intron	INS	-	TTTT	TTTT	rs112414360		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58312699_58312700insTTTT	uc002ene.2	+						CCDC113_uc010vid.1_Intron	NM_014157	NP_054876	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113 isoform 1							protein complex					0						ACGAAGGATGATTTGTTTTTTT	0.366													16	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	64281751	64281751	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64281751delC								None (None upstream) : CDH11 (698934 downstream)																							TTATTGAAGTCCCCCCCATCA	0.408													4	2	---	---	---	---	
CDH11	1009	broad.mit.edu	37	16	65075852	65075853	+	Intron	DEL	AG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65075852_65075853delAG	uc002eoi.2	-						CDH11_uc002eoj.2_Intron|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Intron	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		GGAGGAACTCAGAGAGAGAGAG	0.535			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			5	3	---	---	---	---	
CKLF	51192	broad.mit.edu	37	16	66598930	66598931	+	Intron	INS	-	A	A	rs147094672	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66598930_66598931insA	uc002eow.2	+						CKLF_uc002eox.1_Intron|CKLF_uc002eot.2_Intron|CKLF_uc002eou.2_Intron|CKLF_uc002eov.2_Intron|CMTM1_uc002epb.3_5'Flank|CMTM1_uc002epc.3_5'Flank|CMTM1_uc002epd.3_5'Flank|CMTM1_uc002epe.3_5'Flank|CMTM1_uc002epf.3_5'Flank|CMTM1_uc002epg.3_5'Flank|CMTM1_uc002eph.3_5'Flank|CMTM1_uc002epi.3_5'Flank|CMTM1_uc002epl.3_5'Flank|CMTM1_uc002epj.3_5'Flank|CMTM1_uc002epk.3_5'Flank|CMTM1_uc002epa.3_5'Flank|CMTM1_uc002epn.3_5'Flank|CMTM1_uc002epo.3_5'Flank|CMTM1_uc002epp.3_5'Flank|CMTM1_uc002epq.3_5'Flank|CMTM1_uc010cds.2_5'Flank|CMTM1_uc002epr.3_5'Flank|CMTM1_uc002epm.3_5'Flank|CMTM1_uc010cdt.1_5'Flank	NM_016951	NP_058647	Q9UBR5	CKLF_HUMAN	chemokine-like factor isoform a						cell proliferation|lymphocyte chemotaxis|macrophage chemotaxis|neutrophil chemotaxis|secretion by cell	extracellular space|integral to membrane	chemokine activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0689)|Epithelial(162;0.217)		GAGAATAAAGGAAAAAAAATGG	0.431													4	2	---	---	---	---	
CLEC18C	283971	broad.mit.edu	37	16	70005953	70005954	+	Intron	INS	-	GAG	GAG	rs3884125		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70005953_70005954insGAG	uc002exy.2	+							NM_182619	NP_872425	Q8NCF0	CL18C_HUMAN	secretory protein LOC348174 precursor							extracellular region	sugar binding				0						agaaaaagagaaagaaagaaaa	0.104													4	2	---	---	---	---	
AARS	16	broad.mit.edu	37	16	70312708	70312708	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70312708delA	uc002eyn.1	-							NM_001605	NP_001596	P49588	SYAC_HUMAN	alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)	AAATTGGGGGAAAAAAAAAAG	0.095													4	2	---	---	---	---	
VAC14	55697	broad.mit.edu	37	16	70772081	70772081	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70772081delC	uc002ezm.2	-						VAC14_uc010cfw.2_Intron|VAC14_uc002ezn.2_Intron|VAC14_uc010cfx.1_Intron	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog						interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				GGGGCAGTTTCCCCCAAGAAT	0.582											OREG0023918	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	71384586	71384586	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71384586delA								FTSJD1 (61073 upstream) : CALB2 (8040 downstream)																							ctgaattttgaagggatacaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74857592	74857592	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74857592delG								FA2H (48871 upstream) : WDR59 (49879 downstream)																							TGAGCACCTAGGGGACTGGTG	0.542													4	2	---	---	---	---	
CFDP1	10428	broad.mit.edu	37	16	75340341	75340341	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75340341delG	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron	NM_006324	NP_006315	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1						CCAGACTGCTGGGACTGAACA	0.517													4	2	---	---	---	---	
BCMO1	53630	broad.mit.edu	37	16	81290017	81290017	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81290017delC	uc002fgn.1	+						BCMO1_uc002fgm.1_Intron|BCMO1_uc010vnp.1_Intron	NM_017429	NP_059125	Q9HAY6	BCDO1_HUMAN	beta-carotene 15,15'-monooxygenase						retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding|monooxygenase activity				0						GTCACTGTGTCCCAGGCTTGG	0.408													4	2	---	---	---	---	
ATP2C2	9914	broad.mit.edu	37	16	84409462	84409462	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84409462delA	uc002fhx.2	+						ATP2C2_uc010chj.2_Intron	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						ttgtagacagaaaaaaaGGAG	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84572097	84572097	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84572097delG								KIAA1609 (33809 upstream) : COTL1 (27109 downstream)																							acacccagaagggggatgtgt	0.025													4	2	---	---	---	---	
ZCCHC14	23174	broad.mit.edu	37	16	87493617	87493621	+	Frame_Shift_Del	DEL	TGCTG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87493617_87493621delTGCTG	uc002fjz.1	-	2	303_307	c.276_280delCAGCA	c.(274-282)CACAGCAAAfs	p.H92fs	ZCCHC14_uc002fka.1_RNA	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	92_94					cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)		CACTCACCTTTGCTGTGTTTTCCTA	0.551													245	121	---	---	---	---	
BANP	54971	broad.mit.edu	37	16	88028644	88028644	+	Intron	DEL	G	-	-	rs67802113		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88028644delG	uc002fkr.2	+						BANP_uc002fkp.2_Intron|BANP_uc002fkq.2_Intron|BANP_uc010vow.1_Intron|BANP_uc002fks.3_Intron|BANP_uc002fko.1_Intron|BANP_uc010vov.1_Intron	NM_079837	NP_524576	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein isoform b						cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0				BRCA - Breast invasive adenocarcinoma(80;0.00551)		TTATGGCCTTGGGGGTCCTCA	0.537													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88226494	88226494	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88226494delG								BANP (115571 upstream) : ZNF469 (267385 downstream)																							tgatgatggtggtggtgatgg	0.000													4	2	---	---	---	---	
ANKRD11	29123	broad.mit.edu	37	16	89465401	89465401	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89465401delT	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GCATCATCAGTTTTTTAAAAT	0.502													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	89747189	89747189	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89747189delT								C16orf55 (9514 upstream) : CDK10 (5887 downstream)																							caattatgtcttttttttttc	0.000													3	3	---	---	---	---	
NXN	64359	broad.mit.edu	37	17	712307	712308	+	Intron	DEL	AC	-	-	rs75797391		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:712307_712308delAC	uc002fsa.2	-						NXN_uc010vqd.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		AGTGAGATCAACAGAGTCCTCC	0.441													3	3	---	---	---	---	
RILP	83547	broad.mit.edu	37	17	1550439	1550439	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1550439delT	uc002ftd.2	-						SCARF1_uc002fsy.1_5'Flank|SCARF1_uc002fsz.1_5'Flank|SCARF1_uc002fta.1_5'Flank|SCARF1_uc010cjv.1_5'Flank	NM_031430	NP_113618	Q96NA2	RILP_HUMAN	Rab interacting lysosomal protein						endosome to lysosome transport|protein transport	late endosome membrane|lysosomal membrane|phagocytic vesicle membrane	Rab GTPase binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TAAtttttaattttttttttt	0.294													5	3	---	---	---	---	
METT10D	79066	broad.mit.edu	37	17	2335940	2335940	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2335940delA	uc002fut.2	-						METT10D_uc002fuu.3_Intron|METT10D_uc010cka.2_Intron|METT10D_uc002fuv.2_Intron|METT10D_uc010vqx.1_Intron|METT10D_uc010vqy.1_Intron	NM_024086	NP_076991	Q86W50	MET16_HUMAN	methyltransferase 10 domain containing								methyltransferase activity				0						gagttttcacaaaaaaaaaac	0.159													4	2	---	---	---	---	
ENO3	2027	broad.mit.edu	37	17	4855466	4855467	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4855466_4855467insT	uc002gab.3	+						ENO3_uc010vsr.1_Intron|ENO3_uc002gac.3_Intron|ENO3_uc010vss.1_Intron|ENO3_uc010vst.1_5'Flank	NM_053013	NP_443739	P13929	ENOB_HUMAN	enolase 3						gluconeogenesis|glycolysis	phosphopyruvate hydratase complex	magnesium ion binding|phosphopyruvate hydratase activity			ovary(1)	1						CTGTGAGGTCCttttttttgtt	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	4973839	4973839	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4973839delA								GPR172B (18535 upstream) : ZFP3 (7915 downstream)																							acacagtgagaaaaaaacagt	0.045													4	2	---	---	---	---	
DLG4	1742	broad.mit.edu	37	17	7109660	7109660	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7109660delT	uc002get.3	-						DLG4_uc010vtm.1_5'Flank|DLG4_uc010vtn.1_5'Flank|DLG4_uc010cly.2_Intron|DLG4_uc010vto.1_Intron|DLG4_uc002geu.2_Intron	NM_001365	NP_001356	P78352	DLG4_HUMAN	post-synaptic density protein 95 isoform 1						axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2						AGTAACAATCTTACACTTCTC	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	7203505	7203505	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7203505delT								YBX2 (5629 upstream) : EIF5A (6813 downstream)																							CTGtcttctctttttttttgt	0.239													4	2	---	---	---	---	
FGF11	2256	broad.mit.edu	37	17	7347356	7347356	+	3'UTR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7347356delG	uc002ggz.2	+	5					FGF11_uc010vtw.1_3'UTR|FGF11_uc010cmi.2_3'UTR|FGF11_uc010vtx.1_3'UTR|FGF11_uc002gha.3_3'UTR|CHRNB1_uc002ghb.2_5'Flank|CHRNB1_uc010vty.1_5'Flank|CHRNB1_uc010vtz.1_5'Flank	NM_004112	NP_004103	Q92914	FGF11_HUMAN	fibroblast growth factor 11						cell-cell signaling|nervous system development|signal transduction		growth factor activity				0		Prostate(122;0.157)				GATGAGTTCTGGAAAAGACCC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	11103473	11103474	+	IGR	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11103473_11103474insA								PIRT (362055 upstream) : SHISA6 (41266 downstream)																							TCCAGGCAATGAAAAAAAAATG	0.337													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	14951942	14951943	+	IGR	INS	-	A	A	rs138655443	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14951942_14951943insA								HS3ST3B1 (702450 upstream) : PMP22 (181154 downstream)																							AAAGAAGGAGGAAAAAAAAGAT	0.401													10	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	16745185	16745185	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16745185delA								LOC162632 (37366 upstream) : TNFRSF13B (87664 downstream)																							AGGCTGAAAGAAAAAAAAAAA	0.567													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	18293315	18293316	+	IGR	INS	-	TC	TC	rs140161091		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18293315_18293316insTC								EVPLL (357 upstream) : LOC339240 (29966 downstream)																							cctgctccacatctctttctgt	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20883157	20883157	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20883157delC	uc002gyk.1	+											Homo sapiens hypothetical protein LOC339260, mRNA (cDNA clone IMAGE:5168338), partial cds.																		CCTTCCATCTCCCACAATGTT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21268899	21268900	+	IGR	DEL	CT	-	-	rs145973959		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21268899_21268900delCT								MAP2K3 (50350 upstream) : KCNJ12 (10799 downstream)																							CTGGATTCCCCTGTGGAGGCTT	0.614													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21542186	21542186	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21542186delT								C17orf51 (64455 upstream) : FAM27L (283184 downstream)																							ATTACTTGGCTTTTTTTGATG	0.244													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21544829	21544829	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21544829delT								C17orf51 (67098 upstream) : FAM27L (280541 downstream)																							ctgtttttgattttttttttc	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21548362	21548374	+	IGR	DEL	AAAAGGCCTGTGG	-	-	rs112577776	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21548362_21548374delAAAAGGCCTGTGG								C17orf51 (70631 upstream) : FAM27L (276996 downstream)																							AATGTAAGAAAAAAGGCCTGTGGGAAGGACTAT	0.465													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21564653	21564654	+	IGR	INS	-	C	C	rs112230591		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21564653_21564654insC								C17orf51 (86922 upstream) : FAM27L (260716 downstream)																							agaactactagctgaggcagtt	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25319139	25319140	+	IGR	INS	-	AAG	AAG	rs144466474	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25319139_25319140insAAG								None (None upstream) : WSB1 (301966 downstream)																							CTCCACACAATAAGGTCACAGG	0.599													3	3	---	---	---	---	
SLC13A2	9058	broad.mit.edu	37	17	26807350	26807350	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26807350delA	uc002hbh.2	+						SLC13A2_uc010wal.1_Intron|SLC13A2_uc010wam.1_Intron|SLC13A2_uc010wan.1_Intron|SLC13A2_uc010wao.1_Intron|SLC13A2_uc002hbi.2_Intron	NM_003984	NP_003975	Q13183	S13A2_HUMAN	solute carrier family 13, member 2 isoform b							integral to plasma membrane|membrane fraction	low affinity sodium:dicarboxylate symporter activity				0	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)	aggccttgtcaaaaaaaaaaT	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	27705657	27705658	+	IGR	INS	-	A	A	rs76598004		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27705657_27705658insA								NUFIP2 (84491 upstream) : TAOK1 (12285 downstream)																							TTCAACAACTGAAAAAAAAAAT	0.342													4	2	---	---	---	---	
CCDC55	84081	broad.mit.edu	37	17	28499865	28499865	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28499865delA	uc002heu.2	+						CCDC55_uc002hev.2_Intron|CCDC55_uc010wbl.1_Intron|CCDC55_uc010wbm.1_Intron|CCDC55_uc002hex.2_Intron	NM_032141	NP_115517	Q9H0G5	NSRP1_HUMAN	coiled-coil domain containing 55 isoform 1						developmental process|nucleocytoplasmic transport|regulation of alternative nuclear mRNA splicing, via spliceosome	nuclear speck|ribonucleoprotein complex	mRNA binding|protein binding				0						ACTTGCAGGGAAAAAAAAAAC	0.313													4	3	---	---	---	---	
LRRC37B2	147172	broad.mit.edu	37	17	28959145	28959145	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28959145delA	uc002hfl.3	+						LRRC37B2_uc010csj.1_Intron|LRRC37B2_uc010wbq.1_Intron|LRRC37B2_uc010csi.2_Intron					RecName: Full=Putative LRRC37B-like protein 2;												0						AAAATATTTGAAAAAAAAATT	0.408													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	30003887	30003888	+	IGR	INS	-	TT	TT	rs138358114	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30003887_30003888insTT								MIR365-2 (101347 upstream) : C17orf79 (174997 downstream)																							agtcacttgacctctgttttct	0.089													4	2	---	---	---	---	
ACCN1	40	broad.mit.edu	37	17	31357946	31357946	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31357946delT	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	NM_001094	NP_001085	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)	cttgtggaggttttttgcatc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	35097977	35097978	+	IGR	INS	-	AG	AG	rs55929531		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35097977_35097978insAG								MRM1 (132571 upstream) : LHX1 (196521 downstream)																							gtgtgtgtataagagtgtgtgc	0.173													4	2	---	---	---	---	
ACACA	31	broad.mit.edu	37	17	35467011	35467011	+	Intron	DEL	A	-	-	rs3841372		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35467011delA	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)	CAGCaaaaagaaaaaaaaaag	0.318													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	37196001	37196002	+	Intron	DEL	AG	-	-	rs3072622		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37196001_37196002delAG	uc002hrd.1	+											Homo sapiens cDNA FLJ43826 fis, clone TESTI4002703.																		GAATACAGACAGAAAAGAATTT	0.297													14	11	---	---	---	---	
PLXDC1	57125	broad.mit.edu	37	17	37283089	37283089	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37283089delT	uc002hrg.2	-						PLXDC1_uc002hrh.2_Intron|PLXDC1_uc002hri.2_Intron|PLXDC1_uc002hrj.1_Intron|PLXDC1_uc002hrk.1_Intron	NM_020405	NP_065138	Q8IUK5	PXDC1_HUMAN	plexin domain containing 1 precursor						angiogenesis	cytoplasm|extracellular region|integral to membrane|tight junction				ovary(1)|kidney(1)|skin(1)	3						aatccatttatttttttctca	0.000													4	2	---	---	---	---	
GRB7	2886	broad.mit.edu	37	17	37902870	37902870	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37902870delA	uc002hsr.2	+						GRB7_uc002hss.2_Intron|GRB7_uc010cwc.2_Intron|GRB7_uc002hst.2_Intron	NM_005310	NP_005301	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7						blood coagulation|epidermal growth factor receptor signaling pathway|leukocyte migration|negative regulation of translation|positive regulation of cell migration|stress granule assembly	cytosol|focal adhesion|stress granule	phosphatidylinositol binding|protein kinase binding|SH3/SH2 adaptor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			aaactgtctcaaaaaaaaaaa	0.184													5	5	---	---	---	---	
MSL1	339287	broad.mit.edu	37	17	38291470	38291470	+	3'UTR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38291470delG	uc002hub.2	+	9					MSL1_uc002hua.3_3'UTR|MSL1_uc002hud.2_3'UTR	NM_001012241	NP_001012241	Q68DK7	MSL1_HUMAN	hampin						histone H4-K16 acetylation	MSL complex					0						AACTCTTGGTGGTGGGATAGA	0.433													4	2	---	---	---	---	
CDC6	990	broad.mit.edu	37	17	38450980	38450980	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38450980delT	uc002huj.1	+							NM_001254	NP_001245	Q99741	CDC6_HUMAN	cell division cycle 6 protein						cell division|DNA replication|DNA replication checkpoint|M/G1 transition of mitotic cell cycle|mitosis|negative regulation of cell proliferation|negative regulation of DNA replication|positive regulation of cell cycle cytokinesis|positive regulation of chromosome segregation|regulation of cyclin-dependent protein kinase activity|regulation of mitotic anaphase|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm|spindle midzone|spindle pole	ATP binding|kinase binding|nucleoside-triphosphatase activity			ovary(2)|breast(1)	3						ACCCAAGCGCttttttttttt	0.194													9	5	---	---	---	---	
JUP	3728	broad.mit.edu	37	17	39783570	39783571	+	Intron	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39783570_39783571delCT	uc010wfs.1	-						KRT17_uc002hxh.2_5'Flank|KRT17_uc010wft.1_5'Flank|uc010cxq.1_RNA|uc002hxi.1_RNA	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		CTCTTCACCACTCACACAGTCA	0.515													4	2	---	---	---	---	
DUSP3	1845	broad.mit.edu	37	17	41849588	41849588	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41849588delA	uc002ied.3	-						DUSP3_uc002iee.3_Intron|DUSP3_uc002ief.1_Intron	NM_004090	NP_004081	P51452	DUS3_HUMAN	dual specificity phosphatase 3						inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of JNK cascade|negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of mitotic cell cycle|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|immunological synapse|nucleoplasm	MAP kinase phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		Breast(137;0.00725)		BRCA - Breast invasive adenocarcinoma(366;0.116)		CCCTACCCCCAAAACACCACT	0.478													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	45183182	45183182	+	IGR	DEL	T	-	-	rs111953194		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45183182delT								GOSR2 (78188 upstream) : CDC27 (12131 downstream)																							TAATTTTCCCTTTTGGCAATT	0.378													4	2	---	---	---	---	
NFE2L1	4779	broad.mit.edu	37	17	46124994	46124995	+	5'Flank	INS	-	CCGCCAACGTT	CCGCCAACGTT	rs137972774	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46124994_46124995insCCGCCAACGTT	uc002imz.3	+						NFE2L1_uc002ina.3_5'Flank|NFE2L1_uc002inb.3_5'Flank|NFE2L1_uc002inc.1_5'Flank	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1						anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1						CACCTCTCACAccgccaacgtt	0.475													4	2	---	---	---	---	
CBX1	10951	broad.mit.edu	37	17	46154619	46154619	+	Intron	DEL	T	-	-	rs66733136		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46154619delT	uc002ind.3	-						CBX1_uc002ine.3_Intron	NM_006807	NP_006798	P83916	CBX1_HUMAN	heterochromatin protein 1-beta							nuclear heterochromatin|nucleoplasm|spindle	chromatin binding|enzyme binding				0						TACAGCAAACttttttttttt	0.189													8	4	---	---	---	---	
ACSF2	80221	broad.mit.edu	37	17	48529656	48529657	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48529656_48529657insA	uc002iqu.2	+						ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron	NM_025149	NP_079425	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			ATGTCGCATTGAAAAAAAAAAT	0.267													4	2	---	---	---	---	
SPAG9	9043	broad.mit.edu	37	17	49094881	49094888	+	Intron	DEL	GAGAGAGA	-	-	rs72176610		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49094881_49094888delGAGAGAGA	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron|SPAG9_uc002ita.2_Intron|SPAG9_uc002ite.2_Intron	NM_001130528	NP_001124000	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GAACCTGTCTgagagagagagagagaga	0.067													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49469791	49469792	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49469791_49469792delGT								UTP18 (94501 upstream) : CA10 (237883 downstream)																							AGAATGAACCgtgtgtgtgtgt	0.257													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49547764	49547765	+	IGR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49547764_49547765insT								UTP18 (172474 upstream) : CA10 (159910 downstream)																							GAGTTCAGGCGTTTTTTTTTTT	0.391													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	51792531	51792531	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51792531delA								None (None upstream) : KIF2B (107708 downstream)																							TTTACAGACCAAAAAAAATCA	0.294													4	2	---	---	---	---	
SCPEP1	59342	broad.mit.edu	37	17	55055742	55055743	+	Intron	DEL	TT	-	-	rs111704494		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55055742_55055743delTT	uc002iuv.3	+						SCPEP1_uc010dcl.2_Intron|SCPEP1_uc010wnk.1_Intron	NM_021626	NP_067639	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1 precursor						proteolysis	extracellular region	serine-type carboxypeptidase activity			skin(1)	1	Breast(9;2.86e-08)					AATCTCACTCTTTTTTTTTTTT	0.391													4	2	---	---	---	---	
TMEM49	81671	broad.mit.edu	37	17	57815135	57815135	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57815135delT	uc002ixu.3	+						TMEM49_uc010wog.1_Intron|TMEM49_uc010woh.1_Intron|TMEM49_uc010woi.1_Intron|TMEM49_uc010woj.1_Intron	NM_030938	NP_112200	Q96GC9	VMP1_HUMAN	transmembrane protein 49						autophagy|cell adhesion	endoplasmic reticulum|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane|vacuolar membrane					0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;1.15e-09)|all cancers(12;1.15e-08)			CCTTCAAAGAttttttttttt	0.159													13	6	---	---	---	---	
MRC2	9902	broad.mit.edu	37	17	60765432	60765432	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60765432delC	uc002jad.2	+						MRC2_uc002jae.2_Intron|MRC2_uc002jaf.2_Intron	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2						endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3						ATTTGAAGATCCCCTGGAGTG	0.532													4	2	---	---	---	---	
PRKCA	5578	broad.mit.edu	37	17	64529824	64529824	+	Intron	DEL	A	-	-	rs66936053		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64529824delA	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	TGCCGCCCCCACTGGCCAGGC	0.537													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	65306200	65306200	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65306200delA								HELZ (64881 upstream) : PSMD12 (30420 downstream)																							ctcaaaaaagaaaaaaaaaaa	0.199													2	4	---	---	---	---	
ARSG	22901	broad.mit.edu	37	17	66346080	66346080	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66346080delG	uc002jhc.2	+						ARSG_uc002jhb.1_Intron	NM_014960	NP_055775	Q96EG1	ARSG_HUMAN	Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACCACATATTGGGTTGGCAAA	0.289													4	2	---	---	---	---	
PRKAR1A	5573	broad.mit.edu	37	17	66526759	66526762	+	3'UTR	DEL	TAAC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66526759_66526762delTAAC	uc002jhg.2	+	11					PRKAR1A_uc002jhh.2_3'UTR|PRKAR1A_uc002jhi.2_3'UTR|PRKAR1A_uc002jhj.2_3'UTR|PRKAR1A_uc002jhk.2_3'UTR|PRKAR1A_uc002jhl.2_3'UTR|PRKAR1A_uc002jhm.2_Intron	NM_212471	NP_997636	P10644	KAP0_HUMAN	cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding			adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1)	12	Breast(10;1.64e-13)					TTTGGAGCATTAACTAAATGCTCA	0.402			T|Mis|N|F|S	RET	papillary thyroid	myxoma|endocrine|papillary thyroid			Carney_Complex|Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial|Cardiac_Myxomas_Familial_Clustering_of				7	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69177242	69177243	+	Intron	INS	-	AG	AG	rs147601450	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69177242_69177243insAG	uc002jis.3	-											Homo sapiens cDNA clone IMAGE:5267277.																		Aacacacacacacgcacgcaca	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	70185057	70185059	+	IGR	DEL	TGA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70185057_70185059delTGA								SOX9 (62505 upstream) : SLC39A11 (457027 downstream)																							atagtggtagtgatgatggtggt	0.000													4	5	---	---	---	---	
SDK2	54549	broad.mit.edu	37	17	71535571	71535571	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71535571delC	uc010dfm.2	-							NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2						cell adhesion	integral to membrane				ovary(2)	2						CTCAGCACAGCCAGGAGTGGG	0.662													4	2	---	---	---	---	
CDR2L	30850	broad.mit.edu	37	17	72992087	72992087	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72992087delT	uc002jml.3	+							NM_014603	NP_055418	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like												0	all_lung(278;0.226)					TGCCTAAATCTTTTTTttttt	0.264													3	3	---	---	---	---	
CASKIN2	57513	broad.mit.edu	37	17	73505227	73505228	+	Intron	DEL	GG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73505227_73505228delGG	uc002joc.2	-						CASKIN2_uc010wsc.1_Intron|CASKIN2_uc002jod.2_Intron	NM_020753	NP_065804	Q8WXE0	CSKI2_HUMAN	cask-interacting protein 2 isoform a							cytoplasm				pancreas(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			AAGAGGAGCTGGGGCCACCCCC	0.639													4	2	---	---	---	---	
CYTH1	9267	broad.mit.edu	37	17	76739900	76739900	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76739900delT	uc002jvw.2	-							NM_017456	NP_059430	Q15438	CYH1_HUMAN	cytohesin 1 isoform 2						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						cttcttctcatttaagagtga	0.060													4	2	---	---	---	---	
HRNBP3	146713	broad.mit.edu	37	17	77244837	77244837	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77244837delG	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044	A6NFN3	RFOX3_HUMAN	hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)			CTGAGGCAATGGGGGTCCCCG	0.597													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	78139038	78139038	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78139038delT								EIF4A3 (18100 upstream) : CARD14 (4795 downstream)																							aattttcatgtttttttcttt	0.000													4	2	---	---	---	---	
BAIAP2	10458	broad.mit.edu	37	17	79038402	79038403	+	Intron	INS	-	T	T	rs151068539	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79038402_79038403insT	uc002jzg.2	+						BAIAP2_uc002jyz.3_Intron|BAIAP2_uc002jza.2_Intron|BAIAP2_uc002jzc.2_Intron|BAIAP2_uc002jzb.2_Intron|BAIAP2_uc002jzd.2_Intron|BAIAP2_uc002jzf.2_Intron|BAIAP2_uc002jze.2_Intron|BAIAP2_uc010wuh.1_Intron	NM_017451	NP_059345	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2 isoform 2						axonogenesis|filopodium assembly|insulin receptor signaling pathway|regulation of actin cytoskeleton organization|response to bacterium	cell junction|cytoskeleton|cytosol|filopodium|nucleus|ruffle	cytoskeletal adaptor activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding				0	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CCCAGAGAGTCTTTTTTTGCTT	0.589													4	2	---	---	---	---	
WDR45L	56270	broad.mit.edu	37	17	80582052	80582053	+	Intron	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80582052_80582053delAC	uc002kfq.2	-						WDR45L_uc002kfr.2_Intron	NM_019613	NP_062559	Q5MNZ6	WIPI3_HUMAN	WDR45-like						autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1	Breast(20;0.00106)|all_neural(118;0.0952)	all_cancers(8;0.101)|all_epithelial(8;0.198)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.0835)			TAACACACATACACACACACAG	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	313296	313297	+	IGR	INS	-	C	C			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:313296_313297insC								THOC1 (45237 upstream) : COLEC12 (6059 downstream)																							TTAGTTTTTTTCCCATGTCATC	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	2308157	2308158	+	IGR	DEL	CT	-	-	rs71661900		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2308157_2308158delCT								C18orf2 (900976 upstream) : METTL4 (229367 downstream)																							tctctctctcctctctctctct	0.327													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	5705554	5705555	+	IGR	INS	-	CA	CA	rs143817924	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5705554_5705555insCA								EPB41L3 (74912 upstream) : TMEM200C (184629 downstream)																							GGacacacatgcacacacacac	0.307													4	2	---	---	---	---	
KIAA0802	23255	broad.mit.edu	37	18	8785010	8785011	+	Intron	INS	-	T	T	rs142102394	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8785010_8785011insT	uc002knr.2	+						KIAA0802_uc002knq.2_Intron|KIAA0802_uc010dkw.1_Intron	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255												0						GTTGGGCTCCGttttttttgtt	0.361													11	6	---	---	---	---	
GNAL	2774	broad.mit.edu	37	18	11857357	11857357	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11857357delA	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron|GNAL_uc010wzt.1_5'Flank	NM_001142339	NP_001135811	P38405	GNAL_HUMAN	guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1						TCAAAGGGGGAAAAAAAGCAG	0.478													4	2	---	---	---	---	
IMPA2	3613	broad.mit.edu	37	18	11986027	11986027	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11986027delG	uc002kqp.1	+						IMPA2_uc002kqo.1_Intron|IMPA2_uc010dlb.1_Intron|IMPA2_uc002kqq.1_Intron	NM_014214	NP_055029	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2						inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)	gcaggcaagtgggggccttga	0.090													4	2	---	---	---	---	
IMPA2	3613	broad.mit.edu	37	18	11996999	11997000	+	Intron	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11996999_11997000delAC	uc002kqp.1	+						IMPA2_uc002kqo.1_Intron|IMPA2_uc010dlb.1_Intron|IMPA2_uc002kqq.1_Intron	NM_014214	NP_055029	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2						inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)	CACCACAGCAacacacacacac	0.223													4	2	---	---	---	---	
IMPA2	3613	broad.mit.edu	37	18	11999918	11999919	+	Intron	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11999918_11999919delCT	uc002kqp.1	+						IMPA2_uc002kqo.1_Intron|IMPA2_uc010dlb.1_Intron|IMPA2_uc002kqq.1_Intron	NM_014214	NP_055029	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2						inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)	TCTAAGGCCCCTCTCTCACCTC	0.282													4	2	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13299844	13299844	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13299844delA	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146	O15165	CR001_HUMAN	hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)		cctgtctcttaaaaaaaaaaG	0.224													4	2	---	---	---	---	
ROCK1	6093	broad.mit.edu	37	18	18548273	18548273	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18548273delT	uc002kte.2	-							NM_005406	NP_005397	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)					ATCCTAtttcttttttttttt	0.164													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	24316308	24316308	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24316308delA								LOC728606 (32706 upstream) : AQP4 (115702 downstream)																							gagagcagagaaatggggcag	0.000													4	2	---	---	---	---	
MEP1B	4225	broad.mit.edu	37	18	29774790	29774790	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29774790delT	uc002kxj.3	+							NM_005925	NP_005916	Q16820	MEP1B_HUMAN	meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2						tgcttaaacattttttttttt	0.060													4	2	---	---	---	---	
KIAA1328	57536	broad.mit.edu	37	18	34459159	34459159	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34459159delT	uc002kzz.2	+							NM_020776	NP_065827	Q86T90	K1328_HUMAN	hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)		tttggatgggttttttttttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	38557012	38557013	+	IGR	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38557012_38557013delCT								None (None upstream) : KC6 (503225 downstream)																							caagggtaagctctctctctct	0.000													4	2	---	---	---	---	
PIK3C3	5289	broad.mit.edu	37	18	39555241	39555241	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39555241delG	uc002lap.2	+						PIK3C3_uc010xcl.1_Intron	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3						cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(8)|ovary(1)|breast(1)	10						TTTATAATCTGGAGctgcagt	0.169										TSP Lung(28;0.18)			4	2	---	---	---	---	
HAUS1	115106	broad.mit.edu	37	18	43703722	43703722	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43703722delG	uc002lbu.2	+						HAUS1_uc002lbv.2_Intron	NM_138443	NP_612452	Q96CS2	HAUS1_HUMAN	coiled-coil domain containing 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole				ovary(1)	1						GTTATATAAAGGTTTTACCTG	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	45062005	45062006	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45062005_45062006delGT	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																		GTGAGGTATGGTGTGTGTGTGT	0.297													4	2	---	---	---	---	
LIPG	9388	broad.mit.edu	37	18	47096075	47096076	+	Intron	INS	-	T	T	rs35711840		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47096075_47096076insT	uc002ldv.2	+						LIPG_uc002ldu.1_Intron|LIPG_uc010xdh.1_Intron	NM_006033	NP_006024	Q9Y5X9	LIPE_HUMAN	endothelial lipase precursor						cholesterol homeostasis|high-density lipoprotein particle remodeling|phospholipid catabolic process|phospholipid homeostasis|positive regulation of cholesterol transport|positive regulation of high-density lipoprotein particle clearance|reverse cholesterol transport	extracellular space	heparin binding|lipoprotein lipase activity|phospholipase A1 activity|protein binding|triglyceride lipase activity			ovary(1)|skin(1)	2						TCACAAGaaacttttttttttt	0.109													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53527787	53527789	+	IGR	DEL	ACC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53527787_53527789delACC								TCF4 (224602 upstream) : TXNL1 (742266 downstream)																							TAGGAAAATGACCACAGGTGAGA	0.360													4	2	---	---	---	---	
ZNF532	55205	broad.mit.edu	37	18	56567279	56567280	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56567279_56567280insT	uc002lho.2	+						ZNF532_uc002lhp.2_Intron|ZNF532_uc010xeg.1_Intron|ZNF532_uc002lhr.2_Intron|ZNF532_uc002lhs.2_Intron	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2						tgtcctctttatttttgatttt	0.000													4	2	---	---	---	---	
PIGN	23556	broad.mit.edu	37	18	59740227	59740227	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59740227delA	uc002lii.3	-						PIGN_uc002lij.3_Intron	NM_176787	NP_789744	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphotransferase activity, for other substituted phosphate groups			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5		Colorectal(73;0.187)				CAACATCAATAAAAAAAACTA	0.214													3	3	---	---	---	---	
DOK6	220164	broad.mit.edu	37	18	67198915	67198916	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67198915_67198916insT	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)				ACCATTTCAGATTTTAAGCACT	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68079733	68079733	+	IGR	DEL	T	-	-	rs111425830		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68079733delT								SOCS6 (82299 upstream) : None (None downstream)																							tctgtctctcttttttttttt	0.144													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68278263	68278264	+	IGR	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68278263_68278264insT								SOCS6 (280829 upstream) : None (None downstream)																							TGCACACATCATTTTTTCCACC	0.426													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76596645	76596645	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76596645delA								None (None upstream) : SALL3 (143630 downstream)																							CATTTGCTTTAAAAAAAAAAA	0.244													4	3	---	---	---	---	
MPND	84954	broad.mit.edu	37	19	4348661	4348661	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4348661delT	uc002mae.2	+						MPND_uc010dtx.2_Intron|MPND_uc002mag.2_Intron|MPND_uc002maf.2_Intron|MPND_uc002mah.2_Intron|MPND_uc002mai.2_Intron	NM_032868	NP_116257	Q8N594	MPND_HUMAN	MPN domain containing isoform 1								peptidase activity			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		tgttgaattcttttttttttt	0.164													4	2	---	---	---	---	
KDM4B	23030	broad.mit.edu	37	19	5033760	5033761	+	Intron	DEL	TC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5033760_5033761delTC	uc002mbq.3	+						KDM4B_uc010xil.1_Intron|KDM4B_uc010xim.1_Intron	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1						TATTGGTTCTTCTCTCTCTCTC	0.559													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	6337473	6337473	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6337473delT								ACER1 (3833 upstream) : CLPP (23990 downstream)																							tttttttttcttttttttttt	0.000													2	4	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7128635	7128635	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7128635delA	uc002mgd.1	-						INSR_uc002mge.1_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	aggtttgggcaaaaaaaaaaa	0.000													9	5	---	---	---	---	
SLC44A2	57153	broad.mit.edu	37	19	10727846	10727846	+	Intron	DEL	T	-	-	rs33959587		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10727846delT	uc002mpe.3	+							NM_001145056	NP_001138528	Q8IWA5	CTL2_HUMAN	solute carrier family 44, member 2 isoform 2						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	choline transmembrane transporter activity|signal transducer activity			ovary(1)	1			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	tccgcccgcctggggctccca	0.100													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13100297	13100298	+	IGR	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13100297_13100298delTG								DAND5 (14730 upstream) : NFIX (6286 downstream)																							ggatgggtgttgtgtgtgtgcg	0.114													4	2	---	---	---	---	
CD97	976	broad.mit.edu	37	19	14507483	14507484	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14507483_14507484insT	uc002myl.2	+						CD97_uc002mym.2_Intron|CD97_uc002myn.2_Intron	NM_078481	NP_510966	P48960	CD97_HUMAN	CD97 antigen isoform 1 precursor						cell adhesion|cell-cell signaling|cellular component movement|immune response|inflammatory response|neuropeptide signaling pathway	extracellular space|integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)|breast(1)	4						GCCTTCAGGGCTGGAGTGCCCT	0.604													4	2	---	---	---	---	
HSH2D	84941	broad.mit.edu	37	19	16267796	16267796	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16267796delA	uc002ndp.3	+						HSH2D_uc002ndr.2_Intron|HSH2D_uc010ead.2_Intron	NM_032855	NP_116244	Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing							cytoplasm|nucleus					0						actccatctcaaaaaaaaaaa	0.204													4	2	---	---	---	---	
SIN3B	23309	broad.mit.edu	37	19	16955787	16955787	+	Intron	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16955787delC	uc002ney.1	+						SIN3B_uc002new.2_Intron|SIN3B_uc002nex.2_Intron|SIN3B_uc002nez.1_Intron	NM_015260	NP_056075	O75182	SIN3B_HUMAN	SIN3 homolog B, transcription regulator						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	protein binding			ovary(2)	2						tttgcatactcccacggggtt	0.000													4	2	---	---	---	---	
IFI30	10437	broad.mit.edu	37	19	18285679	18285679	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18285679delA	uc002nic.1	+						PIK3R2_uc002nib.1_Intron	NM_006332	NP_006323	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30						antigen processing and presentation of exogenous peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway	cell junction|extracellular region|lysosome	oxidoreductase activity, acting on a sulfur group of donors				0						actccatctcaaaaaaaaaaa	0.204													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	18493065	18493077	+	IGR	DEL	GGGGGCACCCTGA	-	-	rs72057616		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18493065_18493077delGGGGGCACCCTGA								PGPEP1 (12302 upstream) : GDF15 (3891 downstream)																							AGATGTTGTTGGGGGCACCCTGAGGGGGCACCC	0.582													4	3	---	---	---	---	
ZNF506	440515	broad.mit.edu	37	19	19917502	19917502	+	Intron	DEL	A	-	-	rs35646134		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19917502delA	uc010eci.2	-						ZNF506_uc002nog.2_Intron|ZNF506_uc002noh.3_Intron|ZNF506_uc010ecj.1_Intron	NM_001099269	NP_001092739	Q5JVG8	ZN506_HUMAN	zinc finger protein 506 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding				0						TTATGCCACTAAATTTTTGGA	0.333													12	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	29877141	29877141	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29877141delG	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																		TGTCCTCAGCGGGAGAGCCTC	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31873812	31873813	+	IGR	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31873812_31873813delTG								TSHZ3 (33622 upstream) : ZNF507 (962701 downstream)																							TGTGAACAGCTGTGTGTGTGTG	0.500													4	2	---	---	---	---	
ZNF507	22847	broad.mit.edu	37	19	32843388	32843389	+	Intron	INS	-	C	C	rs72050439		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32843388_32843389insC	uc002nte.2	+						ZNF507_uc002ntc.2_Intron|ZNF507_uc010xrn.1_Intron|ZNF507_uc002ntd.2_Intron	NM_001136156	NP_001129628	Q8TCN5	ZN507_HUMAN	zinc finger protein 507						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(110;0.162)					GTCTTTTTTTTTTTTTCTTGGC	0.406													4	2	---	---	---	---	
WTIP	126374	broad.mit.edu	37	19	34985297	34985297	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34985297delA	uc002nvm.2	+							NM_001080436	NP_001073905			Wilms tumor 1 interacting protein												0	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			catttctattaaaaaaaaaaa	0.264													25	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36417111	36417111	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36417111delG								TYROBP (17925 upstream) : LRFN3 (10911 downstream)																							tctgggctccggtgacaccac	0.000													4	2	---	---	---	---	
SPTBN4	57731	broad.mit.edu	37	19	41061823	41061824	+	Intron	INS	-	A	A	rs148222208	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41061823_41061824insA	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron|SPTBN4_uc002ooa.2_Intron	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			accctgtctccaaaaaaaaaga	0.213													2	4	---	---	---	---	
STRN4	29888	broad.mit.edu	37	19	47230393	47230394	+	Intron	INS	-	T	T	rs150908378	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47230393_47230394insT	uc002pfl.2	-						STRN4_uc002pfm.2_Intron|STRN4_uc010xyf.1_Intron|STRN4_uc010xyg.1_Intron	NM_013403	NP_037535	Q9NRL3	STRN4_HUMAN	zinedin isoform 1							cytoplasm|membrane	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding				0		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		CATTTCAGCCCAGCTGCCCATT	0.594													5	4	---	---	---	---	
SLC6A16	28968	broad.mit.edu	37	19	49831252	49831252	+	5'Flank	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49831252delT	uc002pmz.2	-						SLC6A16_uc002pna.2_5'Flank	NM_014037	NP_054756	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16							integral to membrane|intracellular	neurotransmitter:sodium symporter activity			skin(2)|ovary(1)|kidney(1)	4		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		atggtcggaatttttttcttt	0.000													4	2	---	---	---	---	
AP2A1	160	broad.mit.edu	37	19	50297928	50297928	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50297928delT	uc002ppn.2	+						AP2A1_uc010enj.1_Intron|AP2A1_uc002ppo.2_Intron	NM_014203	NP_055018	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1						axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|Golgi to endosome transport|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|clathrin coat of trans-Golgi network vesicle|cytosol	protein binding|protein transporter activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		ATGAtctttctttttttttga	0.015													4	2	---	---	---	---	
KLK2	3817	broad.mit.edu	37	19	51374185	51374185	+	5'Flank	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51374185delC	uc002ptv.2	+						KLK2_uc010eog.2_5'Flank|KLK2_uc010yck.1_5'Flank|KLK2_uc002ptu.2_5'Flank|KLK2_uc002ptt.2_5'Flank|KLK2_uc010ycl.1_5'Flank|KLK2_uc010ycm.1_5'Flank	NM_005551	NP_005542	P20151	KLK2_HUMAN	kallikrein 2, prostatic isoform 1						proteolysis		serine-type endopeptidase activity			ovary(1)|skin(1)	2		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.00871)		ACAGGGACTACCCAGGGCCCT	0.597			T	ETV4	prostate								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54097707	54097710	+	IGR	DEL	TGAG	-	-	rs138447832		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54097707_54097710delTGAG								ZNF331 (14184 upstream) : LOC284379 (5177 downstream)																							AATGCATGGATGAGTGAGTCCCAT	0.397													3	4	---	---	---	---	
CACNG7	59284	broad.mit.edu	37	19	54417543	54417544	+	Intron	DEL	AA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54417543_54417544delAA	uc002qcr.1	+						CACNG7_uc010era.1_Intron	NM_031896	NP_114102	P62955	CCG7_HUMAN	voltage-dependent calcium channel gamma-7						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(1)	1	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		aaaaaaaaagaaaaaaagaaaa	0.233													6	8	---	---	---	---	
ATRN	8455	broad.mit.edu	37	20	3489906	3489907	+	Intron	INS	-	AG	AG	rs147450740	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3489906_3489907insAG	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2						tgtaatgagtcaaatattgaaa	0.000													4	3	---	---	---	---	
RASSF2	9770	broad.mit.edu	37	20	4794429	4794430	+	Intron	DEL	GT	-	-	rs11468773		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4794429_4794430delGT	uc002wld.2	-						RASSF2_uc002wle.2_Intron|RASSF2_uc002wlf.2_Intron	NM_170774	NP_739580	P50749	RASF2_HUMAN	Ras association domain family 2						cell cycle|signal transduction	nucleus	protein binding			ovary(3)|lung(2)|large_intestine(1)	6						agtgtgtggcgtgtgtgtgtgt	0.094													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	6827397	6827397	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6827397delA								BMP2 (66487 upstream) : None (None downstream)																							ttggaagtggaaaaaaatatt	0.124													4	2	---	---	---	---	
RRBP1	6238	broad.mit.edu	37	20	17624036	17624036	+	Intron	DEL	T	-	-	rs113680800		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17624036delT	uc002wpv.1	-						RRBP1_uc002wpu.2_Intron|RRBP1_uc002wpw.1_Intron|RRBP1_uc010gcl.1_Intron	NM_001042576	NP_001036041	Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1						protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1						AGAGCTCCTCTTTTTTTTTTT	0.468													1	5	---	---	---	---	
BANF2	140836	broad.mit.edu	37	20	17707692	17707693	+	Intron	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17707692_17707693delTG	uc002wpz.2	+						BANF2_uc010zrs.1_Intron|BANF2_uc002wqa.2_Intron	NM_178477	NP_848572	Q9H503	BAFL_HUMAN	barrier to autointegration factor 2 isoform 1							cytoplasm|nucleus	DNA binding			skin(1)	1						agTTTAAGTCTGTGTGTGTGAA	0.173													4	2	---	---	---	---	
C20orf72	92667	broad.mit.edu	37	20	17970349	17970349	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17970349delT	uc002wqh.2	+						C20orf72_uc010gco.2_Intron|C20orf72_uc010gcp.2_Intron	NM_052865	NP_443097	Q9BQP7	CT072_HUMAN	hypothetical protein LOC92667												0						TTCTTGGGCCTTTTTTTTTTT	0.269													4	5	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19612436	19612437	+	Intron	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19612436_19612437delGT	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						atgagtgagagtgtgtgtgtgt	0.040													4	2	---	---	---	---	
C20orf26	26074	broad.mit.edu	37	20	20258528	20258528	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20258528delG	uc002wru.2	+						C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)		gccccttcatgggactggctt	0.000													4	2	---	---	---	---	
CST2	1470	broad.mit.edu	37	20	23807931	23807932	+	5'Flank	INS	-	A	A	rs147780642	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23807931_23807932insA	uc002wtq.1	-							NM_001322	NP_001313	P09228	CYTT_HUMAN	cystatin SA precursor							extracellular region	cysteine-type endopeptidase inhibitor activity				0						CATTATTCAATAAAAAAACTTA	0.401													4	2	---	---	---	---	
TMEM90B	79953	broad.mit.edu	37	20	24472812	24472813	+	Intron	INS	-	CA	CA	rs147257578	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24472812_24472813insCA	uc002wtw.1	+							NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B						response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0						AGAGCCTTCTCTCCACACCCCC	0.609													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	25986379	25986380	+	IGR	INS	-	T	T	rs146152485	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25986379_25986380insT								FAM182B (137593 upstream) : LOC100134868 (4055 downstream)																							taaaccatttattaaagatcct	0.000													0	6	---	---	---	---	
C20orf191	149934	broad.mit.edu	37	20	26088971	26088971	+	Intron	DEL	A	-	-	rs76867961	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26088971delA	uc002wvj.3	-							NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0						CAGTATGCTTAAAAAAAAAGA	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26210810	26210812	+	IGR	DEL	ACA	-	-	rs149589991		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26210810_26210812delACA								MIR663 (21896 upstream) : None (None downstream)																							CTTCAAAATCACAACAACTTTAT	0.177													3	3	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29631052	29631052	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29631052delA	uc010ztl.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						AGGATATAAGAAGCTAGTAAA	0.333													4	2	---	---	---	---	
FRG1B	284802	broad.mit.edu	37	20	29638538	29638538	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29638538delT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						AGAGCAAGAATTTTTAAAGAA	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	31131990	31131991	+	IGR	DEL	GA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31131990_31131991delGA								C20orf112 (7790 upstream) : C20orf203 (88671 downstream)																							aagaaggggtgagagagaggca	0.079													5	3	---	---	---	---	
PIGU	128869	broad.mit.edu	37	20	33266439	33266439	+	5'Flank	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33266439delT	uc002xas.2	-						PIGU_uc010zul.1_5'Flank|PIGU_uc002xat.2_5'Flank|PIGU_uc010gev.1_5'Flank	NM_080476	NP_536724	Q9H490	PIGU_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0						tttactacacttttttttata	0.000													4	2	---	---	---	---	
ERGIC3	51614	broad.mit.edu	37	20	34135825	34135826	+	Intron	INS	-	T	T			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34135825_34135826insT	uc002xct.2	+						ERGIC3_uc002xcr.1_Intron|ERGIC3_uc010zvg.1_Intron|ERGIC3_uc002xcs.2_Intron|ERGIC3_uc002xcu.2_Intron|ERGIC3_uc002xcv.2_Intron	NM_015966	NP_057050	Q9Y282	ERGI3_HUMAN	serologically defined breast cancer antigen 84						vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi apparatus|integral to membrane	protein binding			large_intestine(2)|ovary(1)	3	Lung NSC(9;0.00489)|all_lung(11;0.00729)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			cattttaactatttttaagtgt	0.025													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	36034550	36034551	+	IGR	DEL	GT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36034550_36034551delGT								SRC (731 upstream) : BLCAP (111269 downstream)																							CAGGGGGCGGgtgtgtgtgtgt	0.406													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	38807106	38807107	+	IGR	INS	-	A	A	rs112851302		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38807106_38807107insA								LOC339568 (953715 upstream) : MAFB (507412 downstream)																							aagcagttgctaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	39273281	39273281	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39273281delA								None (None upstream) : MAFB (41238 downstream)																							CCTGGGTGCCAAGGGAACTCG	0.313													4	2	---	---	---	---	
PTPRT	11122	broad.mit.edu	37	20	41535378	41535379	+	Intron	INS	-	G	G			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41535378_41535379insG	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				acaccctgtgagggggacaggg	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42403762	42403762	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42403762delG								GTSF1L (48120 upstream) : TOX2 (139730 downstream)																							ggaagggagtgggcgtgaggc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46824917	46824918	+	IGR	DEL	GA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46824917_46824918delGA								SULF2 (409557 upstream) : LOC284749 (163736 downstream)																							ggggggtggggagagagagaga	0.010													4	2	---	---	---	---	
DOK5	55816	broad.mit.edu	37	20	53093187	53093187	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53093187delG	uc002xwy.2	+						DOK5_uc010gin.2_Intron|DOK5_uc002xwz.2_Intron	NM_018431	NP_060901	Q9P104	DOK5_HUMAN	docking protein 5								insulin receptor binding			ovary(1)	1			Colorectal(105;0.202)			AATACACCCTGGAGGTCCACG	0.517													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	53294071	53294072	+	IGR	INS	-	G	G	rs140274215	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53294071_53294072insG								DOK5 (26362 upstream) : None (None downstream)																							cctaggggagagggtggcagcc	0.074													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	54920689	54920690	+	IGR	DEL	CA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54920689_54920690delCA								MC3R (95818 upstream) : C20orf108 (13293 downstream)																							cacacacatgcacacacacaca	0.401													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56514552	56514552	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56514552delG								PMEPA1 (228011 upstream) : C20orf85 (211431 downstream)																							GCATGAGTGTGGGAGGGAGTC	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56614677	56614677	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56614677delA								PMEPA1 (328136 upstream) : C20orf85 (111306 downstream)																							TTTGTCTCATAAACCCTGCCC	0.562													4	2	---	---	---	---	
VAPB	9217	broad.mit.edu	37	20	57020342	57020342	+	3'UTR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57020342delC	uc002xza.2	+	6					VAPB_uc002xzb.2_RNA|VAPB_uc010zzo.1_3'UTR|VAPB_uc002xzc.2_3'UTR|uc002xzd.1_5'Flank	NM_004738	NP_004729	O95292	VAPB_HUMAN	VAMP-associated protein B/C						cell death|endoplasmic reticulum unfolded protein response|positive regulation of viral genome replication|sphingolipid metabolic process|virus-host interaction	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	beta-tubulin binding|enzyme binding|protein heterodimerization activity|protein homodimerization activity|structural molecule activity			kidney(1)	1	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			ACTTCCAGCGCCCAGGTCCAA	0.507													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57998787	57998787	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57998787delC								EDN3 (97741 upstream) : PHACTR3 (153777 downstream)																							TGGCACGGCTCCCTCCTCCCT	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59310008	59310008	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59310008delT								MIR646 (426383 upstream) : CDH4 (517551 downstream)																							CCCCCCCCTCTTTTTTTTTGC	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	59605065	59605065	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59605065delC								MIR646 (721440 upstream) : CDH4 (222494 downstream)																							gttgcttcctcccttgttgct	0.154													4	2	---	---	---	---	
CDH4	1002	broad.mit.edu	37	20	60330425	60330426	+	Intron	DEL	CA	-	-	rs112783033		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60330425_60330426delCA	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ccacacacaccacacacacaca	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	61737877	61737879	+	IGR	DEL	ACA	-	-	rs143378318		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61737877_61737879delACA								HAR1A (2140 upstream) : MIR124-3 (71973 downstream)																							ggttggcaggacaacaacagtcc	0.241													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9419242	9419242	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9419242delA								None (None upstream) : None (None downstream)																							GGAAATTTTTAAAAAGAGGAC	0.303													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10590343	10590343	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10590343delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		ACTTCCCTTATTTTTTATGGG	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10644105	10644106	+	IGR	DEL	AC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10644105_10644106delAC								None (None upstream) : TPTE (262637 downstream)																							TATAAAATGTACACACACACAG	0.322													4	2	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11028703	11028704	+	Intron	INS	-	TG	TG	rs138520594	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11028703_11028704insTG	uc002yit.1	-						TPTE_uc002yis.1_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		cGAGTTTGTTTTGTTATTAAAT	0.144													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11040504	11040504	+	Intron	DEL	C	-	-	rs71231228		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11040504delC	uc002yit.1	-						TPTE_uc002yis.1_5'Flank	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)		ATCATGACATCCCCCCTCCAA	0.313													15	9	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11042951	11042952	+	Intron	DEL	CC	-	-	rs468234		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11042951_11042952delCC	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gagtgctagacctggaaatgca	0.000													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11050563	11050564	+	Intron	DEL	TC	-	-	rs59708944		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11050563_11050564delTC	uc002yit.1	-							NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ACTCATATGTTCTTTCTTTTCC	0.257													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11089271	11089273	+	Intron	DEL	CAC	-	-	rs150553952		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11089271_11089273delCAC	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)		gtaatcccaacactttggaaggc	0.089													4	3	---	---	---	---	
TIAM1	7074	broad.mit.edu	37	21	32796415	32796415	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32796415delA	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						TCAGAAAAGGAAAATGGTCTA	0.244													4	2	---	---	---	---	
ITSN1	6453	broad.mit.edu	37	21	35205301	35205301	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35205301delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytd.2_Intron|ITSN1_uc010gmk.2_Intron|ITSN1_uc010gml.2_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc002yte.2_Intron|ITSN1_uc002yti.1_Intron	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4						CAGAGCCTTGTTTCTAGACgt	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	35357846	35357849	+	IGR	DEL	ACCA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35357846_35357849delACCA								ATP5O (69688 upstream) : MRPS6 (87974 downstream)																							acacacacacaccacacacacaca	0.044													4	2	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	42221428	42221428	+	5'Flank	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42221428delA	uc002yyq.1	-						DSCAM_uc002yyr.1_5'Flank	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				ccccaagtgcaggcccttctt	0.139													4	2	---	---	---	---	
UBASH3A	53347	broad.mit.edu	37	21	43826184	43826185	+	Intron	INS	-	TT	TT	rs117834816	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43826184_43826185insTT	uc002zbe.2	+						UBASH3A_uc002zbf.2_Intron|UBASH3A_uc010gpc.2_Intron|UBASH3A_uc010gpd.2_Intron|UBASH3A_uc010gpe.2_Intron	NM_018961	NP_061834	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing,							cytosol|nucleus				ovary(3)	3						GGGCTGAAGCGGGTAGCCAGGG	0.658													6	3	---	---	---	---	
PKNOX1	5316	broad.mit.edu	37	21	44450371	44450380	+	3'UTR	DEL	GTGTGTGTGT	-	-	rs112515074		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44450371_44450380delGTGTGTGTGT	uc002zcq.1	+	11					PKNOX1_uc011aex.1_3'UTR	NM_004571	NP_004562	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1								sequence-specific DNA binding			large_intestine(2)	2						CTTCTTTCAAgtgtgtgtgtgtgtgtgtgt	0.252													6	3	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45815574	45815574	+	Intron	DEL	G	-	-	rs67099101		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45815574delG	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						ggggtgtggagggctgtggag	0.249													9	4	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45824662	45824663	+	Intron	INS	-	TGA	TGA			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45824662_45824663insTGA	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						GACAGTGACTGTGATGATAGTG	0.119													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	46144381	46144382	+	IGR	DEL	CT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46144381_46144382delCT								C21orf29 (12886 upstream) : UBE2G2 (44574 downstream)																							AAGGCTCTGGCTCTGTGGGGAA	0.510													3	3	---	---	---	---	
SLC7A4	6545	broad.mit.edu	37	22	21389728	21389728	+	5'Flank	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21389728delA	uc002zud.2	-						SLC7A4_uc002zue.2_5'Flank|MIR649_hsa-mir-649|MI0003664_5'Flank	NM_004173	NP_004164	O43246	CTR4_HUMAN	solute carrier family 7 (cationic amino acid						cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity			ovary(1)|lung(1)	2	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	ccctgtatctaaaaaaaaaaa	0.000													2	4	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26387880	26387881	+	Intron	INS	-	GAAAG	GAAAG	rs112698629		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26387880_26387881insGAAAG	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron|MYO18B_uc010gva.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						GGGACAGACTTGAAACTATCTT	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27159770	27159770	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27159770delC								MIAT (44821 upstream) : MN1 (984496 downstream)																							cctcatggtgccctgagcaca	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	32580245	32580245	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32580245delA								C22orf42 (25002 upstream) : RFPL2 (6177 downstream)																							AGTTCATTTTAAAAAAAACTC	0.254													4	2	---	---	---	---	
CACNG2	10369	broad.mit.edu	37	22	37053814	37053814	+	Intron	DEL	G	-	-	rs73884126	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37053814delG	uc003aps.1	-							NM_006078	NP_006069	Q9Y698	CCG2_HUMAN	voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0						AGGTCTGTGTGTTTCCTTTGC	0.453													3	4	---	---	---	---	
NCF4	4689	broad.mit.edu	37	22	37273071	37273072	+	Intron	DEL	CT	-	-	rs67925316		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37273071_37273072delCT	uc003apy.3	+						NCF4_uc003apz.3_Intron	NM_000631	NP_000622	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4 isoform 1						cell communication|immune response|oxidation-reduction process	cytosol|NADPH oxidase complex	phosphatidylinositol binding|protein dimerization activity			ovary(1)	1						TACAGCCCCACTCTGTGCCCAG	0.401													4	3	---	---	---	---	
SLC16A8	23539	broad.mit.edu	37	22	38478263	38478263	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38478263delT	uc003auu.2	-							NM_013356	NP_037488	O95907	MOT3_HUMAN	solute carrier family 16, member 8						blood coagulation|leukocyte migration|pyruvate metabolic process	integral to plasma membrane|membrane fraction	lactate transmembrane transporter activity|secondary active monocarboxylate transmembrane transporter activity|symporter activity				0	Melanoma(58;0.045)				Pyruvic acid(DB00119)	TCCGCACCCCTTTAACCTTCA	0.657													4	2	---	---	---	---	
PLA2G6	8398	broad.mit.edu	37	22	38512446	38512446	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38512446delT	uc003auy.1	-						PLA2G6_uc003auz.1_Intron|PLA2G6_uc003ava.1_Intron|PLA2G6_uc003avb.2_Intron|PLA2G6_uc010gxk.1_Intron|PLA2G6_uc003aux.1_5'Flank	NM_003560	NP_003551	O60733	PA2G6_HUMAN	phospholipase A2, group VI isoform a						cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)	caaaagttggtttttttgaaa	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	41090245	41090245	+	IGR	DEL	T	-	-	rs11364756		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41090245delT								MCHR1 (11428 upstream) : SLC25A17 (75396 downstream)																							GTAATTTGGatttttttttat	0.209													2	4	---	---	---	---	
TCF20	6942	broad.mit.edu	37	22	42592061	42592061	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42592061delT	uc003bcj.1	-						TCF20_uc003bck.1_Intron|TCF20_uc003bnt.2_Intron	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5						TAGCTGGGCATTTGCATAAGT	0.547													4	2	---	---	---	---	
EFCAB6	64800	broad.mit.edu	37	22	44133610	44133611	+	Intron	DEL	CA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44133610_44133611delCA	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)				cacatatattcacacacacaca	0.000													4	2	---	---	---	---	
KIAA1644	85352	broad.mit.edu	37	22	44665409	44665410	+	Intron	DEL	AC	-	-	rs142804654		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44665409_44665410delAC	uc003bet.2	-							NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor							integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				cacacaatatacacacacacca	0.010													4	2	---	---	---	---	
KIAA1644	85352	broad.mit.edu	37	22	44705822	44705822	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44705822delG	uc003bet.2	-							NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor							integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)				CATGCTTGCAGGGGGAAGCGG	0.542													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	48536721	48536722	+	IGR	INS	-	CCTTCTATACTCTCT	CCTTCTATACTCTCT	rs146926394	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48536721_48536722insCCTTCTATACTCTCT								TBC1D22A (966999 upstream) : FAM19A5 (348566 downstream)																							GAGTGGAGGGCCTGCTGGAGTC	0.490													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	49698355	49698356	+	IGR	INS	-	GTT	GTT	rs147355343	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49698355_49698356insGTT								FAM19A5 (550613 upstream) : C22orf34 (109820 downstream)																							tttctcctgaggttgttttgag	0.218													3	4	---	---	---	---	
C22orf34	348645	broad.mit.edu	37	22	49926611	49926612	+	Intron	INS	-	AGCAAAGG	AGCAAAGG	rs140740821	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49926611_49926612insAGCAAAGG	uc003biq.2	-											Homo sapiens cDNA FLJ42972 fis, clone BRSTN2019129.												0						GCCACAGTCACAGCAAAGGAGC	0.480													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	1359863	1359864	+	IGR	DEL	TC	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1359863_1359864delTC								CRLF2 (28333 upstream) : CSF2RA (27829 downstream)																							TGAGTGTGGATCTCTCTGAGGG	0.559													3	3	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2152478	2152479	+	Intron	DEL	CA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2152478_2152479delCA	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CAGCTAGACCCACACACACACA	0.455													4	2	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2346976	2346976	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2346976delA	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				TTCAACATATAATCTGTTATT	0.204													4	2	---	---	---	---	
CD99	4267	broad.mit.edu	37	X	2621485	2621485	+	Intron	DEL	A	-	-	rs138008773	by1000genomes	TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2621485delA	uc004cqm.2	+						CD99_uc010nda.2_Intron|CD99_uc004cqn.2_Intron|CD99_uc004cqo.2_Intron	NM_002414	NP_002405	P14209	CD99_HUMAN	CD99 antigen isoform a precursor						cell adhesion	cytoplasm|integral to plasma membrane				skin(1)	1						aaacccacataaaacgcgctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6515078	6515078	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6515078delA								VCX3A (61919 upstream) : HDHD1A (451883 downstream)																							AATAAATGGCAAAAAAAAATC	0.333													4	2	---	---	---	---	
TBL1X	6907	broad.mit.edu	37	X	9534046	9534047	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9534046_9534047insA	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_Intron	NM_001139466	NP_001132938	O60907	TBL1X_HUMAN	transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)				ACCTGCATTTTAAAAAAAATTT	0.337													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	15931066	15931067	+	IGR	INS	-	A	A	rs74868438		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15931066_15931067insA								AP1S2 (57966 upstream) : GRPR (210357 downstream)																							TAACTATCTGGATGGAgatgat	0.188													4	2	---	---	---	---	
CTPS2	56474	broad.mit.edu	37	X	16728589	16728589	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16728589delG	uc004cxk.2	-						CTPS2_uc004cxl.2_Intron|CTPS2_uc004cxm.2_Intron	NM_001144002	NP_001137474	Q9NRF8	PYRG2_HUMAN	cytidine triphosphate synthase II						glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine nucleotide biosynthetic process	cytosol	ATP binding|CTP synthase activity			ovary(1)	1	Hepatocellular(33;0.0997)					tgacccttatgatatcagctc	0.114													3	3	---	---	---	---	
SH3KBP1	30011	broad.mit.edu	37	X	19719655	19719655	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19719655delA	uc004czm.2	-						SH3KBP1_uc004czl.2_Intron	NM_031892	NP_114098	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1 isoform a						apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding				0						AGGCTCTACTAACACCATGTC	0.468													4	2	---	---	---	---	
PRDX4	10549	broad.mit.edu	37	X	23684182	23684183	+	5'Flank	INS	-	GCGA	GCGA	rs148383808		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23684182_23684183insGCGA	uc004dam.2	+							NM_006406	NP_006397	Q13162	PRDX4_HUMAN	peroxiredoxin 4						cell redox homeostasis|I-kappaB phosphorylation		thioredoxin peroxidase activity			upper_aerodigestive_tract(1)	1						AGGGATAAAACGCGAGCTATTC	0.510													4	3	---	---	---	---	
MAOB	4129	broad.mit.edu	37	X	43703254	43703254	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43703254delA	uc004dfz.3	-						MAOB_uc011mkx.1_Intron|MAOB_uc011mky.1_Intron|MAOB_uc010nhj.2_Intron	NM_000898	NP_000889	P27338	AOFB_HUMAN	monoamine oxidase B						xenobiotic metabolic process	integral to membrane|mitochondrial outer membrane	electron carrier activity|primary amine oxidase activity			ovary(1)|central_nervous_system(1)	2					Amantadine(DB00915)|Bupropion(DB01156)|Carbidopa(DB00190)|Citalopram(DB00215)|Dopamine(DB00988)|Entacapone(DB00494)|Furazolidone(DB00614)|Ginkgo biloba(DB01381)|Ibuprofen(DB01050)|Imipramine(DB00458)|Iproniazid(DB04818)|Isocarboxazid(DB01247)|Levodopa(DB01235)|Maprotiline(DB00934)|Meclizine(DB00737)|Moclobemide(DB01171)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Rasagiline(DB01367)|Selegiline(DB01037)|Tranylcypromine(DB00752)	CCACTATATCAAAATGTCTAT	0.348													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	45768753	45768753	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45768753delG								MIR222 (162223 upstream) : ZNF673 (537871 downstream)																							gttttttgcaggaagaaatgg	0.000													4	2	---	---	---	---	
ZNF673	55634	broad.mit.edu	37	X	46333091	46333092	+	3'UTR	DEL	TT	-	-	rs150712140		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46333091_46333092delTT	uc004dgn.3	+	6					ZNF673_uc004dgp.3_3'UTR|ZNF673_uc010nhl.2_3'UTR|ZNF673_uc004dgm.3_3'UTR	NM_001129898	NP_001123370	Q5JUW0	ZN673_HUMAN	zinc finger family member 673 isoform 1						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0						tcagtgaatctttttttttttt	0.030													3	3	---	---	---	---	
PHF16	9767	broad.mit.edu	37	X	46787131	46787131	+	Intron	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46787131delA	uc004dgx.2	+						PHF16_uc004dgy.2_Intron	NM_001077445	NP_001070913	Q92613	JADE3_HUMAN	PHD finger protein 16						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0						cacctggcTTAATCTCCCCAG	0.264													4	2	---	---	---	---	
PAGE1	8712	broad.mit.edu	37	X	49454898	49454898	+	Intron	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49454898delG	uc004dom.2	-							NM_003785	NP_003776	O75459	GAGB1_HUMAN	P antigen family, member 1						cellular defense response					skin(1)	1	Ovarian(276;0.236)					GGAGTCTGTTGGCAGAAAACA	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	65294244	65294244	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65294244delA								VSIG4 (34277 upstream) : HEPH (88419 downstream)																							AATTTCCTTTAAAAAAAATTA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	65684759	65684760	+	IGR	INS	-	TTGA	TTGA			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65684759_65684760insTTGA								HEPH (197531 upstream) : EDA2R (130723 downstream)																							ccatactatatttgattagggc	0.000													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	99717146	99717146	+	IGR	DEL	G	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99717146delG								PCDH19 (51875 upstream) : TNMD (122644 downstream)																							ATCATGCCTAGAACCCATGGT	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	106698292	106698292	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106698292delT								CXorf41 (210820 upstream) : PRPS1 (173362 downstream)																							accttgtacattttttttgcc	0.070													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	106741132	106741133	+	IGR	DEL	TG	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106741132_106741133delTG								CXorf41 (253660 upstream) : PRPS1 (130521 downstream)																							TGTTTCTGGATGTGTGTGTGTG	0.505													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	108863555	108863555	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108863555delC								NXT2 (75642 upstream) : KCNE1L (3376 downstream)																							AGCCCAGCGTCCCTGATTCTT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	111868600	111868600	+	IGR	DEL	T	-	-	rs66753630		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111868600delT								ZCCHC16 (168127 upstream) : LHFPL1 (5280 downstream)																							cagggctgggttttttttttt	0.050													3	3	---	---	---	---	
FAM70A	55026	broad.mit.edu	37	X	119408802	119408803	+	Intron	INS	-	TT	TT			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119408802_119408803insTT	uc004eso.3	-						FAM70A_uc004esp.3_Intron|FAM70A_uc010nqo.2_Intron	NM_017938	NP_060408	Q5JRV8	FA70A_HUMAN	hypothetical protein LOC55026 isoform 1							integral to membrane				lung(1)|breast(1)	2						TTAGAGAACTCTTAACACTCAT	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	125855509	125855509	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125855509delC								DCAF12L1 (168667 upstream) : CXorf64 (98238 downstream)																							GGTGACCCATCCAGAGGTTGC	0.388													4	2	---	---	---	---	
ZDHHC9	51114	broad.mit.edu	37	X	128950130	128950131	+	Intron	INS	-	A	A			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128950130_128950131insA	uc004euv.2	-						ZDHHC9_uc004euw.2_Intron|ZDHHC9_uc004eux.1_Intron|ZDHHC9_uc004euy.1_Intron	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9							endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1						tttgtttcaataaatacagttg	0.000													4	2	---	---	---	---	
BCORL1	63035	broad.mit.edu	37	X	129163624	129163626	+	Intron	DEL	TTC	-	-	rs7060792		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129163624_129163626delTTC	uc004evb.1	+						BCORL1_uc004evc.1_Intron	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						ATTTttttttttctctctctctc	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	129450049	129450049	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129450049delT								ZNF280C (47176 upstream) : SLC25A14 (23861 downstream)																							tattttctcctttttttctga	0.000													4	2	---	---	---	---	
SLC25A14	9016	broad.mit.edu	37	X	129498997	129499009	+	Intron	DEL	ATCTAATAAGCAC	-	-	rs67555915		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129498997_129499009delATCTAATAAGCAC	uc004evn.1	+						SLC25A14_uc011mut.1_3'UTR|SLC25A14_uc011muu.1_3'UTR|SLC25A14_uc010nrg.2_3'UTR|SLC25A14_uc004evo.1_Intron|SLC25A14_uc004evp.1_Intron|SLC25A14_uc004evq.1_Intron|SLC25A14_uc004evr.1_Intron	NM_003951	NP_003942	O95258	UCP5_HUMAN	solute carrier family 25, member 14 isoform						aerobic respiration|mitochondrial transport	integral to plasma membrane|mitochondrial inner membrane	binding			ovary(1)	1						TAGCTTCTATATCTAATAAGCACATCTATTATT	0.366													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	136870752	136870752	+	IGR	DEL	C	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136870752delC								ZIC3 (216495 upstream) : LOC158696 (826140 downstream)																							tctccatcctccagatgagga	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	144526521	144526521	+	IGR	DEL	A	-	-	rs139609700		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144526521delA								SPANXN1 (188793 upstream) : SLITRK2 (372826 downstream)																							atgctggattaaaaaaaaaag	0.000													4	2	---	---	---	---	
IDS	3423	broad.mit.edu	37	X	148606186	148606186	+	Intron	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148606186delT	uc004fcw.3	-						IDS_uc010nsu.1_Intron|uc004fcz.2_Intron	NM_000202	NP_000193	P22304	IDS_HUMAN	iduronate-2-sulfatase isoform a precursor							lysosome	iduronate-2-sulfatase activity|metal ion binding				0	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					aggtgGtttctttttttttct	0.005													4	3	---	---	---	---	
MAMLD1	10046	broad.mit.edu	37	X	149637898	149637899	+	Intron	DEL	TT	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149637898_149637899delTT	uc004fee.1	+						MAMLD1_uc011mxt.1_Intron|MAMLD1_uc011mxu.1_Intron|MAMLD1_uc011mxv.1_Intron|MAMLD1_uc011mxw.1_5'Flank	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1						male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)					tctctctctctttctctctgtc	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	150099681	150099681	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150099681delA								CD99L2 (32502 upstream) : HMGB3 (52082 downstream)																							aagtacaaataaaaaaaagaa	0.179													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	151310875	151310876	+	IGR	INS	-	TG	TG			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151310875_151310876insTG								MAGEA10 (3850 upstream) : GABRA3 (24758 downstream)																							tgaaatatatatgtgtgtctac	0.000													4	2	---	---	---	---	
MAGEA3	4102	broad.mit.edu	37	X	151939271	151939284	+	5'Flank	DEL	TTTTGTTGCGTAGA	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151939271_151939284delTTTTGTTGCGTAGA	uc004fgp.2	-							NM_005362	NP_005353	P43357	MAGA3_HUMAN	melanoma antigen family A, 3												0	Acute lymphoblastic leukemia(192;6.56e-05)					GCTTTCCCTGTTTTGTTGCGTAGATTTTGTTGCT	0.449													8	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	152900273	152900274	+	IGR	INS	-	G	G	rs71844359		TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152900273_152900274insG								FAM58A (35641 upstream) : DUSP9 (7623 downstream)																							CTAAACAGTGCCCCCCCAAAAT	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9965005	9965005	+	IGR	DEL	A	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9965005delA								TTTY22 (314151 upstream) : None (None downstream)																							cctagaagataaaaaagttat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9980352	9980352	+	IGR	DEL	T	-	-			TCGA-CJ-5681-01A-11D-1534-10	TCGA-CJ-5681-11A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9980352delT								TTTY22 (329498 upstream) : None (None downstream)																							AAGGCCTTTCTTTTTTAATGC	0.289													2	4	---	---	---	---	
