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
VPS13D	55187	broad.mit.edu	37	1	12445359	12445359	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12445359A>G	uc001atv.2	+	59	11552	c.11411A>G	c.(11410-11412)GAA>GGA	p.E3804G	VPS13D_uc001atw.2_Missense_Mutation_p.E3779G|VPS13D_uc001atx.2_Missense_Mutation_p.E2991G|VPS13D_uc009vnl.2_RNA	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3803					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CGTTCATATGAAGTGGATGAA	0.373													6	326	---	---	---	---	PASS
TNNI3K	51086	broad.mit.edu	37	1	74835124	74835124	+	Nonsense_Mutation	SNP	C	T	T	rs41289190	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74835124C>T	uc001dgf.1	+	16	1573	c.1522C>T	c.(1522-1524)CGA>TGA	p.R508*	TNNI3K_uc001dgc.1_Nonsense_Mutation_p.R609*|TNNI3K_uc001dgd.2_Nonsense_Mutation_p.R609*|TNNI3K_uc001dge.1_Nonsense_Mutation_p.R609*	NM_015978	NP_057062	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform b	508	Protein kinase.					cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10						TATGTTTTGCCGAGAGGTGTC	0.448													6	617	---	---	---	---	PASS
RPAP2	79871	broad.mit.edu	37	1	92789679	92789679	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92789679C>T	uc001dot.2	+	8	1311	c.1202C>T	c.(1201-1203)TCT>TTT	p.S401F	RPAP2_uc009wdh.2_RNA	NM_024813	NP_079089	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	401						integral to membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)		CCCGAAGCCTCTCTGGTTAAA	0.408													5	259	---	---	---	---	PASS
SLC6A17	388662	broad.mit.edu	37	1	110716594	110716594	+	Splice_Site	SNP	G	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110716594G>A	uc009wfq.2	+	4	906	c.445_splice	c.e4-1	p.V149_splice		NM_001010898	NP_001010898	Q9H1V8	S6A17_HUMAN	solute carrier family 6, member 17						alanine transport|glycine transport|leucine transport|proline transport	cell junction|integral to plasma membrane|synaptic vesicle membrane	neurotransmitter:sodium symporter activity			ovary(1)|pancreas(1)	2		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		CTTGTCCCCAGGTCTGTCTCT	0.582													5	362	---	---	---	---	PASS
NBPF10	100132406	broad.mit.edu	37	1	145293212	145293212	+	5'Flank	SNP	G	C	C	rs4382783		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145293212G>C	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_5'UTR|NOTCH2NL_uc010oyh.1_Intron|NBPF10_uc001emq.1_5'Flank	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CTCGAACCTTGTTTTTGTGGT	0.468													5	24	---	---	---	---	PASS
MRPL9	65005	broad.mit.edu	37	1	151733944	151733944	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151733944G>T	uc001eyv.2	-	5	656	c.571C>A	c.(571-573)CGC>AGC	p.R191S	MRPL9_uc009wmz.2_RNA	NM_031420	NP_113608	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9 precursor	191					translation	mitochondrial ribosome	structural constituent of ribosome			ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AAGAAGTGGCGGGCAACTATT	0.463													4	188	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214819651	214819651	+	Silent	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214819651A>G	uc001hkm.2	+	13	6912	c.6738A>G	c.(6736-6738)GCA>GCG	p.A2246A		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2342	Potential.|2-1.|2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGGAGCAAGCAGAGATACAGA	0.378													5	155	---	---	---	---	PASS
DEGS1	8560	broad.mit.edu	37	1	224363513	224363513	+	5'UTR	SNP	G	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224363513G>T	uc001hoi.2	+	1						NM_144780	NP_659004	O15121	DEGS1_HUMAN	degenerative spermatocyte homolog 1, lipid						sphingolipid metabolic process|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	electron carrier activity|protein binding|sphingolipid delta-4 desaturase activity				0	Breast(184;0.193)			GBM - Glioblastoma multiforme(131;0.00643)		CATCGCTTGGGCCTCCTCCAC	0.701													5	30	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237586402	237586402	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237586402A>G	uc001hyl.1	+	12	979	c.859A>G	c.(859-861)AGC>GGC	p.S287G		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	287	Cytoplasmic (By similarity).|MIR 4.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GTGGAGTGGAAGCCACATAAG	0.418													5	169	---	---	---	---	PASS
MDH1	4190	broad.mit.edu	37	2	63822630	63822630	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63822630A>G	uc002scj.1	+	3	232	c.176A>G	c.(175-177)GAC>GGC	p.D59G	MDH1_uc010ypv.1_Missense_Mutation_p.D77G|MDH1_uc010ypw.1_Intron	NM_005917	NP_005908	P40925	MDHC_HUMAN	cytosolic malate dehydrogenase	59					gluconeogenesis|tricarboxylic acid cycle	centrosome|cytosol	L-malate dehydrogenase activity|malic enzyme activity			kidney(2)	2					NADH(DB00157)	GAACTGCAAGACTGTGCCCTT	0.443													6	286	---	---	---	---	PASS
TGFBRAP1	9392	broad.mit.edu	37	2	105915065	105915065	+	Silent	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105915065C>T	uc002tcq.2	-	3	870	c.786G>A	c.(784-786)GCG>GCA	p.A262A	TGFBRAP1_uc010fjc.2_Silent_p.A32A|TGFBRAP1_uc002tcr.3_Silent_p.A262A	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	262	CNH.				regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						CGTCATCGAGCGCTATGACGT	0.542													38	49	---	---	---	---	PASS
STEAP3	55240	broad.mit.edu	37	2	120012306	120012306	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120012306G>A	uc002tlp.2	+	5	1224	c.1067G>A	c.(1066-1068)CGG>CAG	p.R356Q	STEAP3_uc002tlq.2_Missense_Mutation_p.R366Q|STEAP3_uc002tlr.2_Missense_Mutation_p.R356Q|STEAP3_uc010fle.2_Missense_Mutation_p.R356Q	NM_018234	NP_060704	Q658P3	STEA3_HUMAN	dudulin 2 isoform b	356	Ferric oxidoreductase.|Vesicular (Potential).				apoptosis|cell cycle|cellular iron ion homeostasis|protein secretion|transferrin transport|transmembrane transport	endosome membrane|integral to membrane|multivesicular body	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			central_nervous_system(2)|skin(1)	3						GAGGTCTGGCGGATGGAGATC	0.607													37	71	---	---	---	---	PASS
AMMECR1L	83607	broad.mit.edu	37	2	128631624	128631624	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128631624T>C	uc002tpl.2	-	3	436	c.185A>G	c.(184-186)GAG>GGG	p.E62G	AMMECR1L_uc002tpm.2_Missense_Mutation_p.E62G	NM_031445	NP_113633	Q6DCA0	AMERL_HUMAN	AMME chromosomal region gene 1-like	62										central_nervous_system(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)		TGACACATTCTCCCGTCCACT	0.557													6	243	---	---	---	---	PASS
MIR663B	100302269	broad.mit.edu	37	2	133015512	133015512	+	5'Flank	SNP	C	T	T	rs75932541		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133015512C>T	hsa-mir-663b|MI0006336	-						NCRNA00164_uc002ttj.3_RNA																	0						AACGGTAGCCCCTCGGCGGCC	0.682													4	21	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179621360	179621360	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179621360T>C	uc010zfh.1	-	44	10554	c.10330A>G	c.(10330-10332)AGT>GGT	p.S3444G	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc002unb.2_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	3461							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGAGATACACTTTCAAAAACC	0.393													6	250	---	---	---	---	PASS
CD200R1	131450	broad.mit.edu	37	3	112647851	112647851	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112647851G>A	uc003dzk.1	-	4	745	c.512C>T	c.(511-513)GCA>GTA	p.A171V	CD200R1_uc003dzj.1_Missense_Mutation_p.A194V|CD200R1_uc011bhx.1_Missense_Mutation_p.A149V|CD200R1_uc003dzl.1_3'UTR|CD200R1_uc003dzm.1_3'UTR	NM_170780	NP_740750	Q8TD46	MO2R1_HUMAN	CD200 receptor 1 isoform d	171	Ig-like C2-type.|Extracellular (Potential).				interspecies interaction between organisms|regulation of immune response	extracellular region|integral to membrane|plasma membrane	receptor activity			ovary(2)|pancreas(1)	3						TGGCTTCCCTGCAACTGCCTT	0.478													24	118	---	---	---	---	PASS
FSTL1	11167	broad.mit.edu	37	3	120114667	120114667	+	3'UTR	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120114667A>G	uc003eds.2	-	11					FSTL1_uc011bjh.1_3'UTR|MIR198_hsa-mir-198|MI0000240_5'Flank	NM_007085	NP_009016	Q12841	FSTL1_HUMAN	follistatin-like 1 precursor						BMP signaling pathway	extracellular space	calcium ion binding|heparin binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.189)		aaaaaagaagagacagggcca	0.318													5	108	---	---	---	---	PASS
ATR	545	broad.mit.edu	37	3	142266679	142266679	+	Missense_Mutation	SNP	C	T	T	rs146504354		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142266679C>T	uc003eux.3	-	16	3367	c.3245G>A	c.(3244-3246)CGT>CAT	p.R1082H		NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	1082					cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						TTCTCCAATACGCAGCAATAA	0.373								Other_conserved_DNA_damage_response_genes					5	388	---	---	---	---	PASS
CENPC1	1060	broad.mit.edu	37	4	68359666	68359666	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68359666T>G	uc003hdd.1	-	14	2409	c.2226A>C	c.(2224-2226)AGA>AGC	p.R742S	CENPC1_uc010ihj.1_RNA|CENPC1_uc010ihk.1_RNA|CENPC1_uc010ihl.2_5'UTR|CENPC1_uc010ihm.1_Missense_Mutation_p.R742S	NM_001812	NP_001803	Q03188	CENPC_HUMAN	centromere protein C 1	742	MIF2 homology domain II.				mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2						TCAAACGTGTTCTCTTGGTCC	0.368													9	475	---	---	---	---	PASS
UGT2B10	7365	broad.mit.edu	37	4	69681749	69681749	+	Silent	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69681749A>G	uc003hee.2	+	1	37	c.12A>G	c.(10-12)AAA>AAG	p.K4K	UGT2B10_uc011cam.1_Silent_p.K4K	NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2B10 isoform 1	4					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(3)|ovary(2)	5						TGGCTCTGAAATGGACTACAG	0.383													7	343	---	---	---	---	PASS
ADAMTS3	9508	broad.mit.edu	37	4	73280688	73280688	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73280688C>T	uc003hgk.1	-	4	542	c.505G>A	c.(505-507)GCT>ACT	p.A169T		NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1	169					collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATCATTCCAGCCTAGAGAAAG	0.318													5	396	---	---	---	---	PASS
PRKG2	5593	broad.mit.edu	37	4	82064076	82064076	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82064076A>G	uc003hmh.2	-	10	1293	c.1279T>C	c.(1279-1281)TCC>CCC	p.S427P	PRKG2_uc011ccf.1_Missense_Mutation_p.S7P|PRKG2_uc011ccg.1_Missense_Mutation_p.S7P|PRKG2_uc011cch.1_Missense_Mutation_p.S427P	NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	427					platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7						AGTGCTTTGGACAGCTTCCAG	0.438													5	179	---	---	---	---	PASS
NHEDC1	150159	broad.mit.edu	37	4	103826800	103826800	+	Silent	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103826800A>G	uc003hww.2	-	11	1325	c.1203T>C	c.(1201-1203)TCT>TCC	p.S401S	NHEDC1_uc003hwu.2_Silent_p.S401S|NHEDC1_uc010ilm.2_Silent_p.S168S|NHEDC1_uc003hwv.2_RNA|NHEDC1_uc011cev.1_Silent_p.S174S	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1	401						integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		GAGTGGCAACAGATATGCCTA	0.303													6	189	---	---	---	---	PASS
CD180	4064	broad.mit.edu	37	5	66479740	66479740	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66479740T>C	uc003juy.2	-	3	1079	c.931A>G	c.(931-933)AAA>GAA	p.K311E		NM_005582	NP_005573	Q99467	CD180_HUMAN	CD180 molecule precursor	311	LRR 9.|Extracellular (Potential).				inflammatory response|innate immune response	integral to membrane|plasma membrane	receptor activity			ovary(1)	1		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		GGTAACCCTTTCAAGTGAGTT	0.448													5	185	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469440	75469440	+	Intron	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469440A>G	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CAGAGCTACAATGCATTTAGT	0.418													8	253	---	---	---	---	PASS
SV2C	22987	broad.mit.edu	37	5	75469483	75469483	+	Intron	SNP	G	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75469483G>A	uc003kei.1	+						uc003kej.2_RNA	NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		GACTTTTTGCGAGCCTTCCCA	0.393													11	401	---	---	---	---	PASS
RASA1	5921	broad.mit.edu	37	5	86682657	86682657	+	Silent	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86682657A>G	uc003kiw.2	+	23	2980	c.2862A>G	c.(2860-2862)GAA>GAG	p.E954E	RASA1_uc010jav.2_RNA|RASA1_uc003kix.2_Silent_p.E777E|RASA1_uc011ctv.1_Silent_p.E787E|RASA1_uc011ctw.1_Silent_p.E788E|RASA1_uc010jaw.2_Silent_p.E776E	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	954					cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CCTACATGGAAGGTGTCAATC	0.289													9	633	---	---	---	---	PASS
CAST	831	broad.mit.edu	37	5	96103643	96103643	+	Silent	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96103643T>C	uc003klz.1	+	27	2121	c.1959T>C	c.(1957-1959)GCT>GCC	p.A653A	CAST_uc003klt.2_Silent_p.A640A|CAST_uc003klu.2_Silent_p.A736A|CAST_uc003klv.2_Silent_p.A714A|CAST_uc003klw.2_Silent_p.A717A|CAST_uc003klx.2_Silent_p.A695A|CAST_uc003kly.2_Silent_p.A701A|CAST_uc011cuo.1_Silent_p.A699A|CAST_uc011cur.1_Silent_p.A639A|CAST_uc011cus.1_Silent_p.A640A|CAST_uc003kma.1_Silent_p.A611A|CAST_uc011cut.1_Silent_p.A581A|CAST_uc003kmb.2_Silent_p.A599A|CAST_uc003kmc.2_Silent_p.A653A|CAST_uc003kmd.2_Silent_p.A631A|CAST_uc003kme.2_Silent_p.A612A|CAST_uc003kmf.2_Silent_p.A618A|CAST_uc003kmh.2_Silent_p.A367A|CAST_uc010jbj.2_Silent_p.A368A|CAST_uc010jbk.2_Silent_p.A368A|CAST_uc010jbl.1_Silent_p.A376A|CAST_uc003kmi.2_RNA|CAST_uc003kmj.2_Silent_p.A375A|CAST_uc003kmk.2_RNA|ERAP1_uc003kml.2_Intron	NM_001042443	NP_001035908	P20810	ICAL_HUMAN	calpastatin isoform i	653							calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		CCATTGATGCTCTCTCAGGAG	0.438													87	130	---	---	---	---	PASS
CAST	831	broad.mit.edu	37	5	96103644	96103644	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96103644C>T	uc003klz.1	+	27	2122	c.1960C>T	c.(1960-1962)CTC>TTC	p.L654F	CAST_uc003klt.2_Missense_Mutation_p.L641F|CAST_uc003klu.2_Missense_Mutation_p.L737F|CAST_uc003klv.2_Missense_Mutation_p.L715F|CAST_uc003klw.2_Missense_Mutation_p.L718F|CAST_uc003klx.2_Missense_Mutation_p.L696F|CAST_uc003kly.2_Missense_Mutation_p.L702F|CAST_uc011cuo.1_Missense_Mutation_p.L700F|CAST_uc011cur.1_Missense_Mutation_p.L640F|CAST_uc011cus.1_Missense_Mutation_p.L641F|CAST_uc003kma.1_Missense_Mutation_p.L612F|CAST_uc011cut.1_Missense_Mutation_p.L582F|CAST_uc003kmb.2_Missense_Mutation_p.L600F|CAST_uc003kmc.2_Missense_Mutation_p.L654F|CAST_uc003kmd.2_Missense_Mutation_p.L632F|CAST_uc003kme.2_Missense_Mutation_p.L613F|CAST_uc003kmf.2_Missense_Mutation_p.L619F|CAST_uc003kmh.2_Missense_Mutation_p.L368F|CAST_uc010jbj.2_Missense_Mutation_p.L369F|CAST_uc010jbk.2_Missense_Mutation_p.L369F|CAST_uc010jbl.1_Missense_Mutation_p.L377F|CAST_uc003kmi.2_RNA|CAST_uc003kmj.2_Missense_Mutation_p.L376F|CAST_uc003kmk.2_RNA|ERAP1_uc003kml.2_Intron	NM_001042443	NP_001035908	P20810	ICAL_HUMAN	calpastatin isoform i	654							calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		CATTGATGCTCTCTCAGGAGA	0.438													88	131	---	---	---	---	PASS
PCDHAC2	56134	broad.mit.edu	37	5	140391226	140391226	+	3'UTR	SNP	A	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140391226A>C	uc003lii.2	+	4					PCDHA1_uc003lha.2_3'UTR|PCDHA1_uc003lhb.2_3'UTR|PCDHA2_uc003lhd.2_3'UTR|PCDHA3_uc003lhf.2_3'UTR|PCDHA4_uc003lhi.2_3'UTR|PCDHA4_uc003lhh.1_3'UTR|PCDHA5_uc003lhk.1_3'UTR|PCDHA5_uc003lhl.2_3'UTR|PCDHA6_uc003lhn.2_3'UTR|PCDHA6_uc003lho.2_3'UTR|PCDHA7_uc003lhq.2_3'UTR|PCDHA8_uc003lhs.2_3'UTR|PCDHA9_uc003lhu.2_3'UTR|PCDHA10_uc003lhw.2_3'UTR|PCDHA10_uc003lhx.2_3'UTR|PCDHA11_uc003lia.2_3'UTR|PCDHA12_uc003lic.2_3'UTR|PCDHA13_uc003lie.1_3'UTR|PCDHA13_uc003lif.2_3'UTR|PCDHAC1_uc003lih.2_3'UTR	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCGTGCCAAGACTTCTGCTGG	0.363													48	87	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176687168	176687168	+	Silent	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176687168A>G	uc003mfr.3	+	14	5283	c.5145A>G	c.(5143-5145)GAA>GAG	p.E1715E	NSD1_uc003mft.3_Silent_p.E1446E|NSD1_uc003mfs.1_Silent_p.E1612E|NSD1_uc011dfx.1_Silent_p.E1363E	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1715	PHD-type 3.				negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		TGTGCTCAGAAGGTAAGAAAT	0.368			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			5	156	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38942198	38942198	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38942198T>G	uc003ooe.1	+	83	12676	c.12076T>G	c.(12076-12078)TTG>GTG	p.L4026V	DNAH8_uc003oog.1_Missense_Mutation_p.L475V	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						ACGCGCAGGTTTGAAAAGAAC	0.383													68	97	---	---	---	---	PASS
GRIK2	2898	broad.mit.edu	37	6	102337563	102337563	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102337563A>G	uc003pqp.3	+	11	1822	c.1573A>G	c.(1573-1575)AAG>GAG	p.K525E	GRIK2_uc003pqn.2_Missense_Mutation_p.K525E|GRIK2_uc003pqo.3_Missense_Mutation_p.K525E|GRIK2_uc010kcw.2_Missense_Mutation_p.K525E	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	525	Extracellular (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)	TGTTCGAGAGAAGGTCATCGA	0.378													5	158	---	---	---	---	PASS
TXLNB	167838	broad.mit.edu	37	6	139583779	139583779	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139583779C>A	uc011eds.1	-	5	984	c.819G>T	c.(817-819)CAG>CAT	p.Q273H		NM_153235	NP_694967	Q8N3L3	TXLNB_HUMAN	taxilin beta	273	Potential.					cytoplasm				large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		CTGTGTTCTCCTGACAGAGCT	0.463													5	355	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82582250	82582250	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82582250T>G	uc003uhx.2	-	5	8308	c.8019A>C	c.(8017-8019)GAA>GAC	p.E2673D	PCLO_uc003uhv.2_Missense_Mutation_p.E2673D|PCLO_uc010lec.2_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2604					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TCTTGGAAACTTCAGTAGTGA	0.458													38	98	---	---	---	---	PASS
TRPV5	56302	broad.mit.edu	37	7	142622569	142622569	+	Intron	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142622569C>T	uc003wby.1	-						TRPV5_uc003wbz.2_3'UTR	NM_019841	NP_062815	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel,						protein tetramerization	apical plasma membrane|integral to plasma membrane	calcium channel activity			ovary(3)|central_nervous_system(2)|skin(1)	6	Melanoma(164;0.059)					GCTTCGTTTCCAGCACCATCA	0.512													3	26	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151921114	151921114	+	Nonsense_Mutation	SNP	A	T	T	rs4024337		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151921114A>T	uc003wla.2	-	20	3528	c.3309T>A	c.(3307-3309)TGT>TGA	p.C1103*	MLL3_uc003wkz.2_Nonsense_Mutation_p.C164*	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	1103	PHD-type 6.				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)		CACATTGTCTACATTGCAGAA	0.338			N		medulloblastoma								5	147	---	---	---	---	PASS
COL14A1	7373	broad.mit.edu	37	8	121282409	121282409	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121282409C>A	uc003yox.2	+	26	3474	c.3209C>A	c.(3208-3210)ACC>AAC	p.T1070N	COL14A1_uc003yoz.2_Missense_Mutation_p.T35N	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	1070	VWFA 2.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			ACAGATGGAACCCAAGTAAGG	0.373													134	168	---	---	---	---	PASS
ZHX1	11244	broad.mit.edu	37	8	124265629	124265629	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124265629T>C	uc003yqe.2	-	3	2988	c.2558A>G	c.(2557-2559)GAT>GGT	p.D853G	C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.2_Missense_Mutation_p.D853G|ZHX1_uc003yqg.2_Intron|ZHX1_uc010mdi.2_Missense_Mutation_p.D853G	NM_007222	NP_009153	Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	853	Required for repressor activity.				negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			GTCACTATCATCTGTTTCTTC	0.363													7	741	---	---	---	---	PASS
AQP7	364	broad.mit.edu	37	9	33395216	33395216	+	Intron	SNP	T	G	G	rs73645286	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33395216T>G	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_5'Flank|AQP7_uc010mjt.2_5'UTR|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_Missense_Mutation_p.M1L|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		CCCGAGCCCATGGACAGAAAG	0.567													4	48	---	---	---	---	PASS
AQP7	364	broad.mit.edu	37	9	33395238	33395238	+	Intron	SNP	C	T	T	rs140061469	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33395238C>T	uc003zst.2	-						SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Intron|AQP7_uc010mjs.2_5'Flank|AQP7_uc010mjt.2_5'UTR|AQP7_uc011lnx.1_Intron|AQP7_uc011lny.1_5'UTR|AQP7_uc003zss.3_Intron|AQP7_uc011lnz.1_Intron|AQP7_uc011loa.1_Intron	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7						excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		AGACTCAAGTCTGCCTGCTGC	0.582													5	29	---	---	---	---	PASS
NAA35	60560	broad.mit.edu	37	9	88622309	88622309	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88622309A>G	uc004aoi.3	+	14	1290	c.1153A>G	c.(1153-1155)ACT>GCT	p.T385A	NAA35_uc004aoj.3_Missense_Mutation_p.T385A	NM_024635	NP_078911	Q5VZE5	NAA35_HUMAN	corneal wound healing-related protein	385					smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3						GGTCTTTGGAACTCATCTCAT	0.383													6	332	---	---	---	---	PASS
ZNF510	22869	broad.mit.edu	37	9	99522005	99522005	+	Silent	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99522005T>C	uc004awn.1	-	6	1296	c.1107A>G	c.(1105-1107)AGA>AGG	p.R369R	ZNF510_uc004awo.1_Silent_p.R369R	NM_014930	NP_055745	Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	369					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)				AAGTCTGTGTTCTGTCATTAC	0.393													6	391	---	---	---	---	PASS
TRIM14	9830	broad.mit.edu	37	9	100872183	100872183	+	Silent	SNP	G	T	T	rs151159512		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100872183G>T	uc004ayd.2	-	2	309	c.291C>A	c.(289-291)ACC>ACA	p.T97T	TRIM14_uc004ayf.1_Missense_Mutation_p.P3Q|TRIM14_uc004ayg.1_Silent_p.T97T|TRIM14_uc004ayh.1_Silent_p.T97T|TRIM14_uc004ayi.1_Silent_p.T97T|TRIM14_uc004ayj.1_Missense_Mutation_p.P3Q	NM_033220	NP_150089	Q14142	TRI14_HUMAN	tripartite motif protein TRIM14 isoform alpha	97	Potential.					cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)				TGAGCTTCTCGGTGGCATCTT	0.468													6	743	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	49239657	49239657	+	5'UTR	SNP	C	G	G	rs139696778	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49239657C>G	uc001jgd.2	-	1										RecName: Full=Arf-GAP, GTPase, ANK repeat and PH domain-containing protein 11; AltName: Full=Centaurin-gamma-like protein KIAA1975;																		TGCCTCTGCTCACAGCTTTGG	0.612													8	23	---	---	---	---	PASS
RTKN2	219790	broad.mit.edu	37	10	64022522	64022522	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64022522T>G	uc001jlw.2	-	2	216	c.119A>C	c.(118-120)AAA>ACA	p.K40T	ZNF365_uc001jly.3_Intron|RTKN2_uc001jlx.2_Missense_Mutation_p.K40T	NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2	40					signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)					AGAAAGGAGTTTCCATATTCC	0.363													6	298	---	---	---	---	PASS
ZNF365	22891	broad.mit.edu	37	10	64403642	64403642	+	5'UTR	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64403642C>T	uc001jmd.1	+	2					ZNF365_uc001jmc.2_Intron|ZNF365_uc001jme.1_RNA|ZNF365_uc001jmf.1_RNA|ZNF365_uc009xpg.1_RNA	NM_199452	NP_955524	Q70YC4	TALAN_HUMAN	zinc finger protein 365 isoform D											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					AAAGAGCATTCCATCATGACC	0.433													5	264	---	---	---	---	PASS
NODAL	4838	broad.mit.edu	37	10	72192701	72192701	+	Silent	SNP	C	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72192701C>A	uc001jrc.2	-	3	1077	c.1035G>T	c.(1033-1035)GGG>GGT	p.G345G		NM_018055	NP_060525	Q96S42	NODAL_HUMAN	nodal precursor	345					growth	extracellular space	cytokine activity|growth factor activity			large_intestine(1)|kidney(1)	2						ATCAGAGGCACCCACATTCTT	0.502													5	200	---	---	---	---	PASS
IGSF22	283284	broad.mit.edu	37	11	18729752	18729752	+	Splice_Site	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18729752A>G	uc009yht.2	-	19	3277	c.3087_splice	c.e19+1	p.S1029_splice	IGSF22_uc001mpa.2_Intron	NM_173588	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22											ovary(4)|large_intestine(2)|kidney(1)	7						GGGACAACTCACAGAGAAGGC	0.552													66	78	---	---	---	---	PASS
APIP	51074	broad.mit.edu	37	11	34904346	34904346	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34904346T>C	uc001mvs.2	-	7	755	c.647A>G	c.(646-648)TAT>TGT	p.Y216C	APIP_uc010reo.1_Missense_Mutation_p.Y233C	NM_015957	NP_057041	Q96GX9	MTNB_HUMAN	APAF1 interacting protein	216					apoptosis|L-methionine salvage	cytoplasm	identical protein binding|metal ion binding|methylthioribulose 1-phosphate dehydratase activity				0	all_epithelial(35;0.161)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.000425)			ATCAAATAAATAGTCATAACA	0.363													5	341	---	---	---	---	PASS
COMMD9	29099	broad.mit.edu	37	11	36298454	36298454	+	Intron	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36298454T>C	uc001mwn.3	-						COMMD9_uc009ykj.2_Intron|COMMD9_uc010rfb.1_3'UTR	NM_014186	NP_054905	Q9P000	COMD9_HUMAN	COMM domain containing 9 isoform 1											ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)				GCCTATATAATAATGTTTATA	0.279													23	23	---	---	---	---	PASS
AMIGO2	347902	broad.mit.edu	37	12	47471984	47471984	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47471984G>T	uc001rpm.2	-	3	1457	c.802C>A	c.(802-804)CAC>AAC	p.H268N	FAM113B_uc001rpn.2_5'Flank|AMIGO2_uc001rpk.2_Missense_Mutation_p.H268N|AMIGO2_uc001rpl.2_Missense_Mutation_p.H268N	NM_001143668	NP_001137140	Q86SJ2	AMGO2_HUMAN	adhesion molecule with Ig-like domain 2	268	Extracellular (Potential).|LRRCT.				heterophilic cell-cell adhesion|homophilic cell adhesion	integral to membrane|nucleus|plasma membrane				ovary(1)|skin(1)	2	Renal(347;0.138)|Lung SC(27;0.192)					TGACGCGAGTGCCTGGAGTCA	0.478													8	126	---	---	---	---	PASS
PTPRB	5787	broad.mit.edu	37	12	70988254	70988254	+	Silent	SNP	G	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70988254G>A	uc001swb.3	-	4	885	c.855C>T	c.(853-855)GTC>GTT	p.V285V	PTPRB_uc010sto.1_Silent_p.V285V|PTPRB_uc010stp.1_Silent_p.V285V|PTPRB_uc001swc.3_Silent_p.V503V|PTPRB_uc001swa.3_Silent_p.V503V|PTPRB_uc001swd.3_Silent_p.V502V|PTPRB_uc009zrr.1_Silent_p.V382V|PTPRB_uc001swe.2_Silent_p.V503V	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	285	Fibronectin type-III 3.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TACCTGTCCTGACTAGTTTCC	0.423													9	437	---	---	---	---	PASS
PTPRB	5787	broad.mit.edu	37	12	70988255	70988255	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70988255A>T	uc001swb.3	-	4	884	c.854T>A	c.(853-855)GTC>GAC	p.V285D	PTPRB_uc010sto.1_Missense_Mutation_p.V285D|PTPRB_uc010stp.1_Missense_Mutation_p.V285D|PTPRB_uc001swc.3_Missense_Mutation_p.V503D|PTPRB_uc001swa.3_Missense_Mutation_p.V503D|PTPRB_uc001swd.3_Missense_Mutation_p.V502D|PTPRB_uc009zrr.1_Missense_Mutation_p.V382D|PTPRB_uc001swe.2_Missense_Mutation_p.V503D	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	285	Fibronectin type-III 3.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ACCTGTCCTGACTAGTTTCCA	0.423													8	439	---	---	---	---	PASS
GLIPR1L2	144321	broad.mit.edu	37	12	75804401	75804401	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75804401A>G	uc001sxr.1	+	2	430	c.422A>G	c.(421-423)AAG>AGG	p.K141R	GLIPR1L2_uc001sxp.1_Missense_Mutation_p.K141R|GLIPR1L2_uc001sxq.1_Missense_Mutation_p.K34R	NM_152436	NP_689649	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	141						integral to membrane				ovary(1)	1						CATGCAGAGAAGAAAATGTAC	0.323													6	253	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88486458	88486458	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88486458T>C	uc001tar.2	-	29	3805	c.3461A>G	c.(3460-3462)AAA>AGA	p.K1154R	CEP290_uc001taq.2_Missense_Mutation_p.K214R	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	1154	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						ATGCACTTACTTTGACACTTC	0.333													7	532	---	---	---	---	PASS
BTBD11	121551	broad.mit.edu	37	12	108029142	108029142	+	Silent	SNP	C	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108029142C>A	uc001tmk.1	+	12	3233	c.2712C>A	c.(2710-2712)ATC>ATA	p.I904I	BTBD11_uc009zut.1_Silent_p.I785I|BTBD11_uc001tmj.2_Silent_p.I904I|BTBD11_uc001tml.1_Silent_p.I441I|BTBD11_uc001tmm.1_5'UTR	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	904						integral to membrane	DNA binding			skin(2)|ovary(1)	3						TCACAGAAATCAAACGGAAAC	0.532													5	133	---	---	---	---	PASS
NME2P1	283458	broad.mit.edu	37	12	120720384	120720384	+	RNA	SNP	T	C	C	rs3206631		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120720384T>C	uc001tyb.1	+	1		c.445T>C				NR_001577				Homo sapiens non-metastatic cells 2, protein (NM23B) expressed in, pseudogene 1 (NME2P1), non-coding RNA.												0						GTGGGGACTTTTGCATTCAGG	0.498													5	194	---	---	---	---	PASS
GOLGA3	2802	broad.mit.edu	37	12	133374959	133374959	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133374959C>G	uc001ukz.1	-	9	2464	c.1905G>C	c.(1903-1905)AAG>AAC	p.K635N	GOLGA3_uc001ula.1_Missense_Mutation_p.K635N|GOLGA3_uc001ulb.2_Missense_Mutation_p.K635N	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	635	Gln-rich.|Potential.				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)		CGATGCGCCCCTTCTCCTTCA	0.592													8	84	---	---	---	---	PASS
EBPL	84650	broad.mit.edu	37	13	50235160	50235160	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50235160G>C	uc001vdg.2	-	4	628	c.565C>G	c.(565-567)CTA>GTA	p.L189V	EBPL_uc001vdh.2_RNA|EBPL_uc001vdi.2_3'UTR	NM_032565	NP_115954	Q9BY08	EBPL_HUMAN	emopamil binding related protein, delta8-delta7	189					sterol metabolic process	endoplasmic reticulum membrane|integral to membrane	cholestenol delta-isomerase activity				0		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		TTGAGTTCTAGCCATGACTGC	0.418													6	252	---	---	---	---	PASS
CLDN10	9071	broad.mit.edu	37	13	96212458	96212458	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96212458T>C	uc001vmh.2	+	2	354	c.293T>C	c.(292-294)CTC>CCC	p.L98P	CLDN10_uc001vmg.2_Missense_Mutation_p.L96P|CLDN10_uc010tii.1_Missense_Mutation_p.L77P	NM_006984	NP_008915	P78369	CLD10_HUMAN	claudin 10 isoform b	98	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)			ATATTTGCGCTCTTTGGAATG	0.418													6	326	---	---	---	---	PASS
PRKD1	5587	broad.mit.edu	37	14	30068978	30068978	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30068978T>C	uc001wqh.2	-	14	2132	c.1951A>G	c.(1951-1953)ACG>GCG	p.T651A		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	651	Protein kinase.				cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		CTTTCAGGCGTCTCAAACATA	0.383													7	358	---	---	---	---	PASS
TRIM9	114088	broad.mit.edu	37	14	51492005	51492005	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51492005C>T	uc001wyx.3	-	2	1661	c.896G>A	c.(895-897)CGC>CAC	p.R299H	TRIM9_uc001wyy.2_Missense_Mutation_p.R299H|TRIM9_uc001wyz.3_Missense_Mutation_p.R299H	NM_015163	NP_055978	Q9C026	TRIM9_HUMAN	tripartite motif protein 9 isoform 1	299	Potential.				proteasomal ubiquitin-dependent protein catabolic process	cell junction|cytoskeleton|dendrite|synaptic vesicle	protein homodimerization activity|ubiquitin-protein ligase activity|zinc ion binding			skin(2)|lung(1)	3	all_epithelial(31;0.00418)|Breast(41;0.148)					GACCATGTTGCGCAGCTGTAC	0.552													4	153	---	---	---	---	PASS
KTN1	3895	broad.mit.edu	37	14	56084854	56084854	+	Splice_Site	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56084854T>C	uc001xcb.2	+	5	1134	c.832_splice	c.e5+2	p.E278_splice	KTN1_uc001xce.2_Splice_Site_p.E278_splice|KTN1_uc001xcc.2_Splice_Site_p.E278_splice|KTN1_uc001xcd.2_Splice_Site_p.E278_splice|KTN1_uc010trb.1_Splice_Site_p.E278_splice|KTN1_uc001xcf.1_Splice_Site_p.E278_splice	NM_182926	NP_891556	Q86UP2	KTN1_HUMAN	kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7						CTGACAAAGGTAATATATGGG	0.338			T	RET	papillary thryoid								5	350	---	---	---	---	PASS
GPHN	10243	broad.mit.edu	37	14	67147888	67147888	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67147888T>C	uc001xiy.2	+	2	1249	c.128T>C	c.(127-129)GTA>GCA	p.V43A	GPHN_uc001xiw.2_Missense_Mutation_p.V43A|GPHN_uc001xix.2_Missense_Mutation_p.V43A|GPHN_uc010tss.1_Missense_Mutation_p.V43A|GPHN_uc010tst.1_Missense_Mutation_p.V43A	NM_001024218	NP_001019389	Q9NQX3	GEPH_HUMAN	gephyrin isoform 2	43	MPT Mo-transferase.				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		AAAGATCTCGTACAAGATCCT	0.303			T	MLL	AL								5	445	---	---	---	---	PASS
C15orf57	90416	broad.mit.edu	37	15	40824402	40824402	+	3'UTR	SNP	G	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40824402G>C	uc001zly.2	-	4					uc001zlx.1_Intron|MRPL42P5_uc010bbq.1_RNA|MRPL42P5_uc001zlz.1_RNA	NM_052849	NP_443081	Q9BV29	CO057_HUMAN	coiled-coil domain containing 32 isoform a											ovary(1)	1						TCAAGGGATAGGTTTTGTGCG	0.393													4	4	---	---	---	---	PASS
RPAP1	26015	broad.mit.edu	37	15	41815547	41815547	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41815547G>T	uc001zod.2	-	18	2566	c.2442C>A	c.(2440-2442)AGC>AGA	p.S814R	RPAP1_uc001zoc.2_5'UTR	NM_015540	NP_056355	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	814						nucleus	DNA binding|DNA-directed RNA polymerase activity			large_intestine(1)	1		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CCGGGCATGAGCTTGGCTGGT	0.602													6	29	---	---	---	---	PASS
RRN3P3	100131998	broad.mit.edu	37	16	22444123	22444123	+	RNA	SNP	G	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22444123G>A	uc002dkp.2	-	4		c.1060C>T			RRN3P3_uc010vbu.1_RNA	NR_027460				Homo sapiens cDNA FLJ31180 fis, clone KIDNE2000266.												0						ATCACTATCCGCTCAAAATTC	0.333													7	46	---	---	---	---	PASS
HAS3	3038	broad.mit.edu	37	16	69149044	69149044	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69149044C>G	uc010cfh.2	+	4	1761	c.1537C>G	c.(1537-1539)CTT>GTT	p.L513V	HAS3_uc002ewk.2_Intron|HAS3_uc002ewl.2_Missense_Mutation_p.L513V	NM_005329	NP_005320	O00219	HAS3_HUMAN	hyaluronan synthase 3 isoform a	513	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	hyaluronan synthase activity				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		GCTAGCCTTCCTTGTCTCTGG	0.572													6	136	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90162272	90162272	+	3'UTR	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90162272A>G	uc002fqp.2	+	3					uc002fqq.2_3'UTR					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		ATTCAAGATAAGAACAGCAGC	0.532													6	89	---	---	---	---	PASS
FAM18B	51030	broad.mit.edu	37	17	18702143	18702143	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18702143A>G	uc002gum.2	+	5	374	c.349A>G	c.(349-351)AAA>GAA	p.K117E	FAM18B_uc002gun.2_Missense_Mutation_p.K53E	NM_016078	NP_057162	Q9NYZ1	F18B1_HUMAN	hypothetical protein LOC51030	117						integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (53;0.0872)|READ - Rectum adenocarcinoma(1115;0.0967)		TCAAGAGAATAAAACTGTGTC	0.328													6	692	---	---	---	---	PASS
LRRC37B2	147172	broad.mit.edu	37	17	28935540	28935540	+	5'UTR	SNP	G	A	A	rs144598799	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28935540G>A	uc002hfl.3	+	1					LRRC37B2_uc010csj.1_RNA|LRRC37B2_uc010wbq.1_RNA|LRRC37B2_uc010csi.2_RNA					RecName: Full=Putative LRRC37B-like protein 2;												0						CGTTGTGTTCGTCTTTTTCCA	0.313													5	82	---	---	---	---	PASS
NEUROD2	4761	broad.mit.edu	37	17	37762561	37762561	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37762561C>T	uc002hry.2	-	2	492	c.292G>A	c.(292-294)GGC>AGC	p.G98S		NM_006160	NP_006151	Q15784	NDF2_HUMAN	neurogenic differentiation 2	98					cellular response to calcium ion|cellular response to electrical stimulus|cerebellar cortex development|negative regulation of synapse maturation|positive regulation of calcium-mediated signaling|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of synapse maturation|positive regulation of synaptic plasticity|protein ubiquitination|regulation of transcription from RNA polymerase II promoter	nucleus	E-box binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Lung(15;0.00549)|LUAD - Lung adenocarcinoma(14;0.0664)			GGCCGCTCGCCCTCCGCCTCG	0.522													12	16	---	---	---	---	PASS
OSBPL1A	114876	broad.mit.edu	37	18	21751379	21751379	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21751379T>C	uc002kve.2	-	23	2459	c.2285A>G	c.(2284-2286)GAT>GGT	p.D762G	OSBPL1A_uc002kvd.2_Missense_Mutation_p.D249G|OSBPL1A_uc010xbc.1_Missense_Mutation_p.D380G	NM_080597	NP_542164	Q9BXW6	OSBL1_HUMAN	oxysterol-binding protein-like 1A isoform B	762					cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					TTACCTTTTATCTTGAATGTA	0.274													6	429	---	---	---	---	PASS
FCGRT	2217	broad.mit.edu	37	19	50017141	50017141	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50017141A>G	uc002poe.2	+	3	562	c.76A>G	c.(76-78)AGC>GGC	p.S26G	FCGRT_uc002pod.2_RNA|FCGRT_uc002pog.2_Missense_Mutation_p.S26G|FCGRT_uc002pof.1_5'UTR|FCGRT_uc010yax.1_Missense_Mutation_p.S26G|FCGRT_uc002poh.1_5'Flank	NM_001136019	NP_001129491	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	26	Extracellular (Potential).|Alpha-1.				antigen processing and presentation|female pregnancy|immune response	integral to membrane|MHC class I protein complex	IgG binding|receptor activity			ovary(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		GTCTGCAGAAAGCCACCTCTC	0.597													5	156	---	---	---	---	PASS
TTYH1	57348	broad.mit.edu	37	19	54942452	54942452	+	Intron	SNP	A	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54942452A>C	uc002qfq.2	+						TTYH1_uc010yey.1_Intron|TTYH1_uc002qfr.2_Intron|TTYH1_uc002qft.2_Intron|TTYH1_uc002qfu.1_Missense_Mutation_p.D315A	NM_020659	NP_065710	Q9H313	TTYH1_HUMAN	tweety 1 isoform 1						cell adhesion	chloride channel complex|plasma membrane	chloride channel activity|iron ion transmembrane transporter activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0767)		TTCTCCTTGGACCCCTGCCAT	0.507													6	23	---	---	---	---	PASS
BCAS1	8537	broad.mit.edu	37	20	52612686	52612686	+	Intron	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52612686T>C	uc002xws.2	-						BCAS1_uc010zza.1_5'UTR|BCAS1_uc010zzb.1_Intron|BCAS1_uc010gim.2_Intron|BCAS1_uc002xwt.2_Intron|BCAS1_uc010gil.1_Intron	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1							cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			ACCCCCTAATTCCAGCCATAC	0.453													7	43	---	---	---	---	PASS
NPEPL1	79716	broad.mit.edu	37	20	57287646	57287646	+	Intron	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57287646C>T	uc010zzs.1	+						NPEPL1_uc010zzr.1_Intron|NPEPL1_uc002xzn.2_Intron|NPEPL1_uc010gjo.1_Intron|NPEPL1_uc002xzp.2_Missense_Mutation_p.P226S	NM_024663	NP_078939	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1						proteolysis	cytoplasm	aminopeptidase activity|manganese ion binding|metalloexopeptidase activity				0	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			GTACGTCTGGCCCTCCCACTC	0.612													4	100	---	---	---	---	PASS
RTEL1	51750	broad.mit.edu	37	20	62293955	62293955	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62293955A>G	uc002yfu.1	+	5	795	c.452A>G	c.(451-453)AAG>AGG	p.K151R	RTEL1_uc011abc.1_RNA|RTEL1_uc002yft.1_Missense_Mutation_p.K151R|RTEL1_uc011abd.1_Missense_Mutation_p.K175R|RTEL1_uc002yfv.2_Missense_Mutation_p.K201R|RTEL1_uc011abe.1_5'UTR|RTEL1_uc002yfw.2_RNA	NM_016434	NP_057518	Q9NZ71	RTEL1_HUMAN	regulator of telomere elongation helicase 1	151	Helicase ATP-binding.|Nuclear localization signal (Potential).				DNA repair|regulation of double-strand break repair via homologous recombination|telomere maintenance	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding				0	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			CCTGAGGTGAAGAAACAAGAG	0.627													5	81	---	---	---	---	PASS
LOC100132288	100132288	broad.mit.edu	37	21	9907480	9907480	+	3'UTR	SNP	G	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9907480G>T	uc002zka.1	-	4					LOC100132288_uc010gqn.1_RNA	NM_001033515	NP_001028687			hypothetical protein LOC100132288												0						GTGTTGGGGGGTGTGAGCTGG	0.622													5	26	---	---	---	---	PASS
HPS4	89781	broad.mit.edu	37	22	26853885	26853885	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26853885G>T	uc003acl.2	-	13	2554	c.1895C>A	c.(1894-1896)GCC>GAC	p.A632D	HPS4_uc003aci.2_Missense_Mutation_p.A627D|HPS4_uc003acj.2_Missense_Mutation_p.A496D|HPS4_uc003ack.2_Missense_Mutation_p.A423D|HPS4_uc003acn.2_Missense_Mutation_p.A478D|HPS4_uc003ach.2_Missense_Mutation_p.A367D	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	632					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0						CAGGCTGACGGCCTGGAGGAA	0.592									Hermansky-Pudlak_syndrome				8	52	---	---	---	---	PASS
EIF4ENIF1	56478	broad.mit.edu	37	22	31846514	31846514	+	Intron	SNP	T	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31846514T>C	uc003akz.1	-						EIF4ENIF1_uc003akx.1_Intron|EIF4ENIF1_uc003aky.1_Intron|EIF4ENIF1_uc003ala.1_Intron|EIF4ENIF1_uc003alb.1_Intron|EIF4ENIF1_uc003akw.1_5'UTR	NM_019843	NP_062817	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E							nucleus	protein binding|protein transporter activity			ovary(1)	1						CACACAGGTCTCAAAGATCTG	0.433													3	15	---	---	---	---	PASS
VCX	26609	broad.mit.edu	37	X	7812130	7812130	+	3'UTR	SNP	A	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7812130A>G	uc004crz.2	+	3						NM_013452	NP_038480	Q9H320	VCX1_HUMAN	variable charge, X chromosome						chromatin organization|ribosome assembly|spermatogenesis	nucleolus	chromatin binding				0		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CAGAGATCTCACCAGCGGGGT	0.463													7	282	---	---	---	---	PASS
ZNF182	7569	broad.mit.edu	37	X	47862045	47862045	+	5'UTR	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47862045C>T	uc004dir.2	-	3					ZNF182_uc004dis.2_5'UTR|ZNF182_uc004dit.2_5'UTR|ZNF182_uc011mlu.1_5'UTR|ZNF630_uc010nhz.1_RNA|SPACA5_uc004diu.2_5'Flank	NM_006962	NP_008893	P17025	ZN182_HUMAN	zinc finger protein 21 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3						AGATGTGTGACGGCCGAGCTG	0.483													5	232	---	---	---	---	PASS
DACH2	117154	broad.mit.edu	37	X	86069820	86069820	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86069820G>T	uc004eew.2	+	10	1837	c.1667G>T	c.(1666-1668)GGC>GTC	p.G556V	DACH2_uc004eex.2_Missense_Mutation_p.G543V|DACH2_uc010nmq.2_Missense_Mutation_p.G422V|DACH2_uc011mra.1_Missense_Mutation_p.G389V|DACH2_uc010nmr.2_Missense_Mutation_p.G337V|DACH2_uc004eey.2_Missense_Mutation_p.G249V|DACH2_uc004eez.2_Missense_Mutation_p.G239V	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	556					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						AGTGACAGTGGCCTGAGGATG	0.363													12	233	---	---	---	---	PASS
MORC4	79710	broad.mit.edu	37	X	106186175	106186175	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106186175G>T	uc004emu.3	-	15	2189	c.1946C>A	c.(1945-1947)GCC>GAC	p.A649D	MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_Missense_Mutation_p.A649D|MORC4_uc004emw.3_Missense_Mutation_p.A397D	NM_024657	NP_078933	Q8TE76	MORC4_HUMAN	zinc finger, CW type with coiled-coil domain 2	649							ATP binding|zinc ion binding			ovary(1)	1						TTGGTCTTTGGCCCCTGGATA	0.463													9	271	---	---	---	---	PASS
GUCY2F	2986	broad.mit.edu	37	X	108647644	108647644	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108647644C>T	uc004eod.3	-	10	2314	c.2038G>A	c.(2038-2040)GGG>AGG	p.G680R	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	680	Protein kinase.|Cytoplasmic (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8						ACAAAACGCCCATCTACCACA	0.403													5	480	---	---	---	---	PASS
MAGEA12	4111	broad.mit.edu	37	X	151896650	151896650	+	RNA	SNP	C	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151896650C>G	uc004fgb.2	-	3		c.327G>C						P43365	MAGAC_HUMAN	Homo sapiens melanoma antigen family A, 12, mRNA (cDNA clone MGC:4914 IMAGE:3450217), complete cds.											skin(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					TCTCAACAGTCTACTCCAGTC	0.403													7	520	---	---	---	---	PASS
KIAA1751	85452	broad.mit.edu	37	1	1893558	1893559	+	Intron	INS	-	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1893558_1893559insC	uc001aim.1	-						KIAA1751_uc009vkz.1_Intron	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452											pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		CTACAAACCTGTCCACAAAGAG	0.297													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	2354609	2354612	+	IGR	DEL	TTTG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2354609_2354612delTTTG								PEX10 (10599 upstream) : PLCH2 (53142 downstream)																							atttagtttttttgtttgtttgtt	0.044													0	6	---	---	---	---	
WDR8	49856	broad.mit.edu	37	1	3549682	3549682	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3549682delA	uc001ako.2	-						WDR8_uc001akn.3_Intron|WDR8_uc010nzi.1_3'UTR	NM_017818	NP_060288	Q9P2S5	WRP73_HUMAN	WD repeat domain 8							centrosome	protein binding				0	all_cancers(77;0.0128)|all_epithelial(69;0.00526)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;4.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.16e-22)|GBM - Glioblastoma multiforme(42;1.05e-14)|Colorectal(212;1.19e-05)|BRCA - Breast invasive adenocarcinoma(365;2.67e-05)|COAD - Colon adenocarcinoma(227;5.82e-05)|Kidney(185;0.000364)|KIRC - Kidney renal clear cell carcinoma(229;0.00223)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		GAAAAACATCATTCTCGGAGC	0.468													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	4613377	4613378	+	IGR	INS	-	A	A	rs55944416		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4613377_4613378insA								LOC284661 (128633 upstream) : AJAP1 (101727 downstream)																							ATGAACCTATCATCTCTTCCTC	0.267													4	2	---	---	---	---	
CAMTA1	23261	broad.mit.edu	37	1	7200384	7200384	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7200384delT	uc001aoi.2	+							NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		ACATGGCAACTTTTTTTTCCC	0.418													4	2	---	---	---	---	
MTOR	2475	broad.mit.edu	37	1	11302680	11302681	+	Intron	INS	-	T	T	rs138032798	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11302680_11302681insT	uc001asd.2	-							NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						CACTGACCCCCTCGCCTTAGCG	0.396													4	2	---	---	---	---	
FHAD1	114827	broad.mit.edu	37	1	15669976	15669977	+	Intron	INS	-	CA	CA			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15669976_15669977insCA	uc001awb.2	+						FHAD1_uc001awa.1_Intron|uc001awc.1_Intron|FHAD1_uc001awd.1_Intron|FHAD1_uc010obl.1_5'Flank|FHAD1_uc001awe.1_5'Flank	NM_052929	NP_443161	B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding											skin(1)	1						tccttctctaccacacacacct	0.257													4	2	---	---	---	---	
ALPL	249	broad.mit.edu	37	1	21867229	21867230	+	Intron	DEL	CT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21867229_21867230delCT	uc001bet.2	+						ALPL_uc010odn.1_Intron|ALPL_uc010odo.1_Intron|ALPL_uc010odp.1_Intron	NM_000478	NP_000469	P05186	PPBT_HUMAN	tissue-nonspecific alkaline phosphatase						response to vitamin D|skeletal system development	anchored to membrane|cytoplasm|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)	TGGGAGTGTCCTCTCTCTCTCT	0.564													4	2	---	---	---	---	
KDM1A	23028	broad.mit.edu	37	1	23399534	23399534	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23399534delT	uc001bgi.2	+						KDM1A_uc001bgj.2_Intron	NM_015013	NP_055828	O60341	KDM1A_HUMAN	lysine-specific histone demethylase 1 isoform b						blood coagulation|muscle cell development|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin	androgen receptor binding|chromatin binding|enzyme binding|flavin adenine dinucleotide binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-K9 specific)|ligand-dependent nuclear receptor transcription coactivator activity|MyoD binding|oxidoreductase activity|p53 binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2						TGAAGCATTCTTTTTTTTTTT	0.239													5	4	---	---	---	---	
PIGV	55650	broad.mit.edu	37	1	27116292	27116292	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27116292delT	uc001bmz.2	+						PIGV_uc001bmy.2_Intron|PIGV_uc009vso.2_Intron|PIGV_uc010ofg.1_Intron|PIGV_uc001bna.2_Intron	NM_017837	NP_060307	Q9NUD9	PIGV_HUMAN	phosphatidylinositol glycan class V						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	glycolipid mannosyltransferase activity			ovary(1)	1		all_cancers(24;3.93e-26)|all_epithelial(13;3.96e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.26e-54)|Epithelial(14;2.85e-53)|OV - Ovarian serous cystadenocarcinoma(117;1.91e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000504)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.0222)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		TCAGTTCAAATTTTTTTTTTC	0.378													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	33706538	33706538	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33706538delA								TRIM62 (58867 upstream) : ZNF362 (15636 downstream)																							gtgacagtggaaagactttcc	0.000													4	2	---	---	---	---	
PPIH	10465	broad.mit.edu	37	1	43131362	43131362	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43131362delA	uc001chq.2	+						PPIH_uc009vwl.2_Intron	NM_006347	NP_006338	O43447	PPIH_HUMAN	peptidylprolyl isomerase H						protein complex assembly|protein folding	cytoplasm|nuclear speck|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity|protein binding|ribonucleoprotein binding				0	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)			L-Proline(DB00172)	cttaaaaaagaaaaaaaaaat	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	55986596	55986596	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55986596delT								USP24 (305834 upstream) : PPAP2B (973837 downstream)																							gcatctatcattttttttctt	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	66192316	66192316	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66192316delA								LEPR (89496 upstream) : PDE4B (65877 downstream)																							AAAAGAAAGGAAAGAAAAGGA	0.468													4	2	---	---	---	---	
SLC35D1	23169	broad.mit.edu	37	1	67496876	67496876	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67496876delT	uc001ddk.2	-						SLC35D1_uc010oph.1_Intron	NM_015139	NP_055954	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-glucuronic						chondroitin sulfate biosynthetic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	integral to endoplasmic reticulum membrane	UDP-glucuronic acid transmembrane transporter activity|UDP-N-acetylgalactosamine transmembrane transporter activity				0					Lorazepam(DB00186)	CTCATGGGACTTTTTTTTTAT	0.368													4	2	---	---	---	---	
RPF1	80135	broad.mit.edu	37	1	84948415	84948415	+	Intron	DEL	T	-	-	rs111427529		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84948415delT	uc001djv.3	+							NM_025065	NP_079341	Q9H9Y2	RPF1_HUMAN	RNA processing factor 1						rRNA processing|translation	nucleolus	aminoacyl-tRNA ligase activity|ATP binding|rRNA binding				0						GCCCAGATTGTTTAAAAAAAA	0.333													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	85234197	85234197	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85234197delA								SSX2IP (77757 upstream) : LPAR3 (44889 downstream)																							GGCCACACACAAAAAAATTGT	0.358													4	2	---	---	---	---	
DDAH1	23576	broad.mit.edu	37	1	86000655	86000657	+	Intron	DEL	AAG	-	-	rs66688926		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86000655_86000657delAAG	uc001dlc.2	-							NM_001134445	NP_001127917	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	ACCAAAGAAAAAGAAGAAAAGGA	0.389													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91296515	91296515	+	RNA	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91296515delA	uc001dnt.1	-	2		c.1575delT			uc001dnu.1_RNA					Homo sapiens cDNA FLJ12836 fis, clone NT2RP2003206.																		TCAAGAGGGGAAAAAAAGTCT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	91963237	91963240	+	IGR	DEL	ACAC	-	-	rs6143322		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91963237_91963240delACAC								HFM1 (92811 upstream) : CDC7 (3164 downstream)																							AGACAAAAAGacacacacacacac	0.324													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96042938	96042939	+	IGR	DEL	CA	-	-	rs113933941		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96042938_96042939delCA								RWDD3 (330165 upstream) : None (None downstream)																							cagatatttgcacagtttgctt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	96457909	96457910	+	IGR	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96457909_96457910delTG								RWDD3 (745136 upstream) : PTBP2 (729265 downstream)																							ttaacatttatgtgtgtgtgta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	101048250	101048250	+	IGR	DEL	C	-	-	rs35198954		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101048250delC								GPR88 (40668 upstream) : VCAM1 (137047 downstream)																							TGTAAAAAAACCCTAGACATC	0.413													2	4	---	---	---	---	
SLC30A7	148867	broad.mit.edu	37	1	101416548	101416549	+	Intron	INS	-	G	G	rs74919999	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101416548_101416549insG	uc001dtn.2	+						SLC30A7_uc001dto.2_Intron	NM_001144884	NP_001138356	Q8NEW0	ZNT7_HUMAN	zinc transporter like 2						zinc ion transport	Golgi apparatus|integral to membrane	cation transmembrane transporter activity|protein binding				0		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		ctgagtaactcggggagccagc	0.000													4	2	---	---	---	---	
TBX15	6913	broad.mit.edu	37	1	119533656	119533656	+	5'Flank	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119533656delC	uc001ehl.1	-							NM_152380	NP_689593	Q96SF7	TBX15_HUMAN	T-box 15							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		GCTGCTCCCACCCCCATTCCA	0.488													4	2	---	---	---	---	
HSD3B1	3283	broad.mit.edu	37	1	120055205	120055205	+	Intron	DEL	A	-	-	rs151061429		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120055205delA	uc001ehv.1	+						HSD3B1_uc001ehw.2_Intron	NM_000862	NP_000853	P14060	3BHS1_HUMAN	3 beta-hydroxysteroid dehydrogenase 1						androgen biosynthetic process|estrogen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process	integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	NADH(DB00157)|Trilostane(DB01108)	ACCATAAAAGAAAAAAAAAAA	0.433													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	120106536	120106536	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120106536delA								HSD3B1 (48855 upstream) : ZNF697 (55464 downstream)																							AATTTTTGCCAAAAAAAATGG	0.368													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	143540325	143540325	+	IGR	DEL	G	-	-	rs66944250		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143540325delG								None (None upstream) : LOC100286793 (107314 downstream)																							TGCTGTAGTAGTAACTGCTTC	0.368													15	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148849428	148849430	+	IGR	DEL	TCG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148849428_148849430delTCG								NBPF16 (91117 upstream) : LOC645166 (78856 downstream)																							tcttttcatctcgtcatttcatt	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148850668	148850670	+	IGR	DEL	ACA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148850668_148850670delACA								NBPF16 (92357 upstream) : LOC645166 (77616 downstream)																							tcatttcatcacatcatttcatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	148864013	148864013	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148864013delC								NBPF16 (105702 upstream) : LOC645166 (64273 downstream)																							gatttataatcccaccccagc	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	149029320	149029320	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149029320delA								LOC645166 (76266 upstream) : LOC388692 (250156 downstream)																							aaggaaggagaaaaaaagaag	0.005													4	2	---	---	---	---	
C1orf230	284485	broad.mit.edu	37	1	151700970	151700983	+	Intron	DEL	GTGGGGGGTGGGGC	-	-	rs76394333		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151700970_151700983delGTGGGGGGTGGGGC	uc010pdj.1	+						C1orf230_uc001eyu.2_Intron	NM_001144956	NP_001138428	A6NNX1	RIAD1_HUMAN	RIIa domain-containing protein						signal transduction		cAMP-dependent protein kinase regulator activity				0						ggggtggggggtggggggtggggCCAGGCACAGC	0.547													4	3	---	---	---	---	
CRTC2	200186	broad.mit.edu	37	1	153929691	153929691	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153929691delA	uc010ped.1	-						CRTC2_uc001fde.3_5'Flank|CRTC2_uc001fdf.3_5'Flank	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AAAGGACGAGAAAAAAAAAAA	0.468													4	2	---	---	---	---	
C1orf66	51093	broad.mit.edu	37	1	156704324	156704325	+	Intron	INS	-	TT	TT			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156704324_156704325insTT	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081	Q96FB5	RRNAD_HUMAN	hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGGAGAGGAGAtttcttttttt	0.332													4	2	---	---	---	---	
ETV3L	440695	broad.mit.edu	37	1	157071368	157071369	+	5'Flank	DEL	AA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157071368_157071369delAA	uc001fqq.1	-							NM_001004341	NP_001004341	Q6ZN32	ETV3L_HUMAN	ets variant 3-like							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Hepatocellular(266;0.158)	Prostate(1639;0.184)				ctTAAGACTTAAAAAAAAAAAA	0.025													4	3	---	---	---	---	
KIRREL	55243	broad.mit.edu	37	1	158002324	158002324	+	Intron	DEL	T	-	-	rs111326613		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158002324delT	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)					GAAGGCAGAATTTAAAAACTA	0.443													6	3	---	---	---	---	
SLAMF1	6504	broad.mit.edu	37	1	160595479	160595479	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160595479delA	uc001fwl.3	-						SLAMF1_uc010pjk.1_Intron|SLAMF1_uc010pjl.1_Intron|SLAMF1_uc010pjm.1_Intron	NM_003037	NP_003028	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family						interspecies interaction between organisms|lymphocyte activation|positive regulation of cell proliferation	integral to membrane	antigen binding|transmembrane receptor activity			ovary(1)|breast(1)	2	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TGCTCTGATTAAAAAAAAAAG	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	168360995	168360995	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168360995delC								MIR557 (16136 upstream) : XCL2 (149010 downstream)																							GATTTAGGATCCCAATGGAGT	0.358													4	2	---	---	---	---	
DARS2	55157	broad.mit.edu	37	1	173806411	173806411	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173806411delA	uc001gjh.1	+							NM_018122	NP_060592	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial						tRNA aminoacylation for protein translation	mitochondrial matrix|nucleus	aspartate-tRNA ligase activity|ATP binding|nucleic acid binding			central_nervous_system(2)	2					L-Aspartic Acid(DB00128)	GAGGGGATTTAAAAAAAAAAA	0.318													5	4	---	---	---	---	
PAPPA2	60676	broad.mit.edu	37	1	176638018	176638018	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176638018delG	uc001gkz.2	+						PAPPA2_uc001gky.1_Intron|PAPPA2_uc009www.2_Intron	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						ACTGTCATCTGGAAGGGTAAT	0.468													4	2	---	---	---	---	
PAPPA2	60676	broad.mit.edu	37	1	176785738	176785738	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176785738delT	uc001gkz.2	+						PAPPA2_uc009www.2_Intron	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						tcctgttgtctttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	177287767	177287768	+	IGR	INS	-	CT	CT	rs148896589	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177287767_177287768insCT								FAM5B (36210 upstream) : SEC16B (609721 downstream)																							TTTTTGTAATACTGTCTCAAGA	0.361													0	9	---	---	---	---	
FAM20B	9917	broad.mit.edu	37	1	179004366	179004366	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179004366delT	uc001gmc.2	+							NM_014864	NP_055679	O75063	XYLK_HUMAN	hypothetical protein LOC9917 precursor							Golgi membrane|integral to membrane	ATP binding|kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(3)	3						ATCAGCCAGATTTTTTTTTAA	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	193818799	193818799	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193818799delT								CDC73 (594859 upstream) : None (None downstream)																							TAAGTGTTCATTTTTTTTTCT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	195807282	195807283	+	IGR	INS	-	T	T	rs143801512	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195807282_195807283insT								None (None upstream) : KCNT2 (387630 downstream)																							ACTGCACCACATCTTTGCTTAC	0.436													3	5	---	---	---	---	
CAMSAP1L1	23271	broad.mit.edu	37	1	200801665	200801665	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200801665delA	uc001gvl.2	+						CAMSAP1L1_uc001gvk.2_Intron|CAMSAP1L1_uc001gvm.2_Intron	NM_203459	NP_982284	Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4						GAGGTAGTTCAAAAAAAAATA	0.189													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	203048914	203048914	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203048914delT								PPFIA4 (1051 upstream) : MYOG (3345 downstream)																							GTATTTATCATTTTTTTTTTC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	214866129	214866130	+	IGR	DEL	TT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214866129_214866130delTT								CENPF (28217 upstream) : KCNK2 (312755 downstream)																							tcagacttaCtttttttttttg	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	216636910	216636910	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216636910delA								USH2A (40172 upstream) : ESRRG (39678 downstream)																							AGCAGAGTTGAAAGGGCTGAA	0.408													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	222629788	222629788	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222629788delA								DUSP10 (714327 upstream) : HHIPL2 (65814 downstream)																							taacttggccaagggtgcaga	0.085													4	2	---	---	---	---	
ENAH	55740	broad.mit.edu	37	1	225758091	225758091	+	Intron	DEL	T	-	-	rs112014685		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225758091delT	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493	Q8N8S7	ENAH_HUMAN	enabled homolog isoform a						axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)		tatacatggatttttttTTTC	0.209													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	232726471	232726471	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232726471delA								SIPA1L2 (75228 upstream) : KIAA1383 (214167 downstream)																							CAAAAAAAGGAAAAAAAAAAT	0.403													3	3	---	---	---	---	
LGALS8	3964	broad.mit.edu	37	1	236701098	236701099	+	Intron	INS	-	A	A	rs145113368	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236701098_236701099insA	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)			GATTTCAGTATAAAAAATTAGA	0.208													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238727405	238727405	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238727405delT								LOC339535 (78088 upstream) : CHRM3 (822460 downstream)																							gcgactttgcttttttttgtt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	238816665	238816665	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238816665delG								LOC339535 (167348 upstream) : CHRM3 (733200 downstream)																							AATACCTACAGGGGCCAGCGA	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	240135200	240135201	+	IGR	INS	-	AAAG	AAAG	rs150304904	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240135200_240135201insAAAG								CHRM3 (62485 upstream) : FMN2 (119984 downstream)																							ggaaagaaagaaaagaaagaaa	0.000													2	4	---	---	---	---	
OR2T11	127077	broad.mit.edu	37	1	248791234	248791234	+	5'Flank	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248791234delA	uc001ier.1	-							NM_001001964	NP_001001964	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			lung(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATTAGAAGGTAAAAAAAACTA	0.323													3	9	---	---	---	---	
RNF144A	9781	broad.mit.edu	37	2	7128909	7128909	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7128909delC	uc002qys.2	+						RNF144A_uc002qyt.2_Intron	NM_014746	NP_055561	P50876	R144A_HUMAN	ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		gagttaggctccacctccttg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12139079	12139079	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12139079delG								LPIN1 (171548 upstream) : TRIB2 (717919 downstream)																							GTGCAGGCCAGGGGGATGaaa	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	13790267	13790267	+	IGR	DEL	A	-	-	rs112542456		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13790267delA								TRIB2 (907411 upstream) : FAM84A (982589 downstream)																							ttcaacagggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	19452572	19452572	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19452572delG								NT5C1B (681734 upstream) : OSR1 (98675 downstream)																							gtaggaagcagggaaagattt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	26399113	26399113	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26399113delG	uc002rgw.1	+											SubName: Full=Putative uncharacterized protein FAM59B;																		CTGTCCCTCAGGGGGGCGGTC	0.622													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	26867954	26867955	+	IGR	DEL	TC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26867954_26867955delTC								CIB4 (3743 upstream) : KCNK3 (47626 downstream)																							tctctctcagtctctctctctc	0.218													4	2	---	---	---	---	
BRE	9577	broad.mit.edu	37	2	28364934	28364935	+	Intron	INS	-	GTC	GTC			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28364934_28364935insGTC	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664	Q9NXR7	BRE_HUMAN	brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)					ACACTGTTGTTGGAGGAACGGT	0.356													4	2	---	---	---	---	
MEMO1	51072	broad.mit.edu	37	2	32157422	32157423	+	Intron	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32157422_32157423insT	uc002rnx.2	-						MEMO1_uc010ymu.1_Intron|MEMO1_uc010ezq.2_Intron|MEMO1_uc002rny.2_Intron|MEMO1_uc002rnz.2_Intron|MEMO1_uc010ymv.1_Intron	NM_015955	NP_057039	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1 isoform 1						regulation of microtubule-based process	cytosol|nucleus				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					ATACTTTGTAATTTTTTTTTGT	0.252													4	2	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47641747	47641747	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47641747delT	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ACTTTTTAACttttttttttt	0.154			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				6	4	---	---	---	---	
MSH2	4436	broad.mit.edu	37	2	47784563	47784563	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47784563delT	uc002rvz.2	+						KCNK12_uc002rwb.2_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			tgaaatcaacttttttttgtt	0.045			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				4	2	---	---	---	---	
FSHR	2492	broad.mit.edu	37	2	49269889	49269889	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49269889delG	uc002rww.2	-						FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Intron|FSHR_uc010fbo.1_Intron	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1						female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)	CTAGACTCTAGGGACAGGAGG	0.408									Gonadal_Dysgenesis_46_XX				4	2	---	---	---	---	
PSME4	23198	broad.mit.edu	37	2	54192727	54192727	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54192727delT	uc002rxp.2	-						PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|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|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CAAGGAAGTATTTTTTTTTTT	0.269													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	59273428	59273428	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59273428delC	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																		TTAAGCATTGCCACCTGTCCC	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	67060335	67060335	+	IGR	DEL	C	-	-	rs11365296		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67060335delC								MEIS1 (260445 upstream) : ETAA1 (564107 downstream)																							AGAAAGTGCTCCAGGGGCCGG	0.502													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91739761	91739765	+	IGR	DEL	ATTTC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91739761_91739765delATTTC								None (None upstream) : LOC654342 (65427 downstream)																							tcatctcatgatttcatctcatctc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91762595	91762596	+	IGR	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91762595_91762596insT								None (None upstream) : LOC654342 (42596 downstream)																							GCGGGGAGGGCTCCGGGGCATA	0.579													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91774995	91774996	+	IGR	INS	-	TGAG	TGAG	rs78472690		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91774995_91774996insTGAG								None (None upstream) : LOC654342 (30196 downstream)																							CAGATAGTGACTGTTATTTATC	0.149													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91799025	91799025	+	IGR	DEL	C	-	-	rs71380649		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91799025delC								None (None upstream) : LOC654342 (6167 downstream)																							cacaATTTTACCTGACttttt	0.025													5	3	---	---	---	---	
TMEM131	23505	broad.mit.edu	37	2	98460442	98460443	+	Intron	DEL	AG	-	-	rs144504477		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98460442_98460443delAG	uc002syh.3	-						TMEM131_uc010yvg.1_Intron	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6						TGATTTGAATAGAGATATTGAA	0.287													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	106090083	106090083	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106090083delA								FHL2 (34853 upstream) : NCK2 (271271 downstream)																							AAATGCACGCAAAAATGTTTC	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	112515307	112515307	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112515307delC								LOC541471 (262615 upstream) : ANAPC1 (11334 downstream)																							ataacgataacaccaaacact	0.080													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	118162205	118162205	+	IGR	DEL	T	-	-	rs75322796		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118162205delT								None (None upstream) : DDX18 (410050 downstream)																							TCTAAACAACTTTTTTTTGTT	0.358													6	11	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129506683	129506683	+	IGR	DEL	G	-	-	rs11307416		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129506683delG								HS6ST1 (430512 upstream) : None (None downstream)																							ATGCAGTGGAGGTTGAAGAAT	0.473													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133099945	133099946	+	IGR	INS	-	CTCT	CTCT	rs147477829	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133099945_133099946insCTCT								NCRNA00164 (84403 upstream) : GPR39 (74201 downstream)																							TTAGCCCTTCCAAGTTCTGAAA	0.238													8	4	---	---	---	---	
YSK4	80122	broad.mit.edu	37	2	135740973	135740974	+	Intron	DEL	AG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135740973_135740974delAG	uc002tue.1	-						YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Intron|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Intron|YSK4_uc002tui.3_Intron	NM_025052	NP_079328	Q56UN5	YSK4_HUMAN	Yeast Sps1/Ste20-related kinase 4 isoform 1								ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)		agccaggcaaagagagagagag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	137420412	137420413	+	IGR	INS	-	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137420412_137420413insA								CXCR4 (544687 upstream) : THSD7B (102702 downstream)																							tcatagaattgaaaaaatacgg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	137452149	137452149	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137452149delA								CXCR4 (576424 upstream) : THSD7B (70966 downstream)																							ATATATATGCAAAAAATAAAT	0.358													4	2	---	---	---	---	
LYPD6	130574	broad.mit.edu	37	2	150231911	150231913	+	Intron	DEL	ATG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150231911_150231913delATG	uc002twy.2	+						LYPD6_uc010fnt.2_Intron|LYPD6_uc002twz.2_Intron|LYPD6_uc002txa.2_Intron	NM_194317	NP_919298	Q86Y78	LYPD6_HUMAN	LY6/PLAUR domain containing 6 precursor							extracellular region					0				BRCA - Breast invasive adenocarcinoma(221;0.0667)		CTCTGAAGGAATGATGATGATGA	0.453													4	2	---	---	---	---	
CSRNP3	80034	broad.mit.edu	37	2	166349445	166349446	+	Intron	DEL	AA	-	-	rs72237093		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166349445_166349446delAA	uc002udf.2	+							NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3						apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5						CAAATTCCCTAAAAAAAAAAAA	0.272													4	2	---	---	---	---	
TTC21B	79809	broad.mit.edu	37	2	166764454	166764454	+	Intron	DEL	A	-	-	rs72187517		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166764454delA	uc002udk.2	-							NM_024753	NP_079029	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5						TGGCCAAATTAAAAAAAAAAA	0.289													9	8	---	---	---	---	
SCN9A	6335	broad.mit.edu	37	2	167133012	167133012	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167133012delC	uc010fpl.2	-						uc002udp.2_Intron	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)	attcttagctcccagggccac	0.075													4	2	---	---	---	---	
NOSTRIN	115677	broad.mit.edu	37	2	169691019	169691020	+	Intron	INS	-	CACACACACG	CACACACACG	rs62175722		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169691019_169691020insCACACACACG	uc002ueg.2	+						NOSTRIN_uc002uef.2_Intron|NOSTRIN_uc002uei.2_Intron|NOSTRIN_uc010fpu.2_Intron|NOSTRIN_uc002ueh.2_Intron|NOSTRIN_uc002uej.2_Intron	NM_001039724	NP_001034813	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficker isoform 2						endocytosis|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	protein binding				0						GCGCGCGCGcacacacacacac	0.272													4	3	---	---	---	---	
C2orf77	129881	broad.mit.edu	37	2	170531679	170531680	+	Intron	INS	-	AT	AT	rs138256548	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170531679_170531680insAT	uc002ufe.2	-							NM_001085447	NP_001078916	Q0VFZ6	CB077_HUMAN	hypothetical protein LOC129881												0						taataaataaaatGAGGCTACA	0.213													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	177869010	177869011	+	IGR	INS	-	A	A	rs143943038	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177869010_177869011insA								MIR1246 (403230 upstream) : HNRNPA3 (208411 downstream)																							CTTGATAAAAGAAAAAAACTCA	0.248													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	178042463	178042463	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178042463delC								MIR1246 (576683 upstream) : HNRNPA3 (34959 downstream)																							GGACGACATTCCCAGCGCTCT	0.413													4	2	---	---	---	---	
DUSP19	142679	broad.mit.edu	37	2	183960602	183960602	+	3'UTR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183960602delT	uc002upd.2	+	4					DUSP19_uc010frp.2_3'UTR|DUSP19_uc010zfr.1_RNA|DUSP19_uc002upe.2_3'UTR	NM_080876	NP_543152	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19 isoform 1						JNK cascade|negative regulation of JNK cascade|negative regulation of JUN kinase activity|positive regulation of JNK cascade|positive regulation of JUN kinase activity	cytoplasm	JUN kinase phosphatase activity|MAP-kinase scaffold activity|mitogen-activated protein kinase kinase kinase binding|protein kinase activator activity|protein kinase inhibitor activity|protein tyrosine phosphatase activity			ovary(4)|pancreas(1)	5						GATTAAATGCTTTTTTAAATT	0.279													4	2	---	---	---	---	
TMEFF2	23671	broad.mit.edu	37	2	193007906	193007906	+	Intron	DEL	T	-	-	rs75073343		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193007906delT	uc002utc.2	-							NM_016192	NP_057276	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two							extracellular region|integral to membrane				lung(2)|pancreas(1)|breast(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			tactccTGAATTTTTTTTTAA	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193302111	193302111	+	IGR	DEL	G	-	-	rs78846247		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193302111delG								TMEFF2 (242467 upstream) : PCGEM1 (312460 downstream)																							CTGACTTTTTGTGTTACAGGT	0.353													3	3	---	---	---	---	
HECW2	57520	broad.mit.edu	37	2	197104382	197104382	+	Intron	DEL	C	-	-	rs66836058		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197104382delC	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18						TAGAAAAATTCCCTCTAGCAG	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	213407939	213407940	+	IGR	INS	-	C	C	rs139782602	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213407939_213407940insC								ERBB4 (4587 upstream) : IKZF2 (456473 downstream)																							caattcatatactgtgcccatt	0.134													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	220526782	220526783	+	IGR	DEL	GT	-	-	rs58811439		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220526782_220526783delGT								SLC4A3 (20081 upstream) : None (None downstream)																							aagtagagaagtgtgtgtgtgt	0.084													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	222467685	222467685	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222467685delC								EPHA4 (28763 upstream) : PAX3 (596922 downstream)																							ATTACTTCTTCTTTTTTTTTT	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	228843687	228843690	+	IGR	DEL	AAAC	-	-	rs10555258		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228843687_228843690delAAAC								WDR69 (54661 upstream) : SPHKAP (980 downstream)																							taacaaaacaaaacaaacaaacaa	0.000													3	3	---	---	---	---	
DIS3L2	129563	broad.mit.edu	37	2	232895186	232895186	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232895186delA	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vsn.1_Intron|DIS3L2_uc002vso.2_Intron	NM_152383	NP_689596	Q8IYB7	DI3L2_HUMAN	DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CCTCCAGTGGAAAACCCAGGC	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	239934154	239934155	+	IGR	INS	-	T	T	rs141725160	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239934154_239934155insT								TWIST2 (101917 upstream) : HDAC4 (35710 downstream)																							CCATGGGCGCCAGGCCTCCCAC	0.639													3	10	---	---	---	---	
D2HGDH	728294	broad.mit.edu	37	2	242682821	242682821	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242682821delT	uc002wce.1	+						D2HGDH_uc010zpc.1_Intron|D2HGDH_uc010fzq.1_Intron|D2HGDH_uc002wcg.1_Intron	NM_152783	NP_689996	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase precursor						2-oxoglutarate metabolic process|cellular protein metabolic process|response to cobalt ion|response to manganese ion|response to zinc ion	mitochondrial matrix	(R)-2-hydroxyglutarate dehydrogenase activity|flavin adenine dinucleotide binding|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		ATGTTACTCATTTTTTTTTTG	0.502													5	3	---	---	---	---	
CNTN4	152330	broad.mit.edu	37	3	2563512	2563513	+	Intron	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2563512_2563513insT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		ACAGCTTTGTCTTTTTTTCTAC	0.436													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	5732348	5732349	+	IGR	INS	-	ATAA	ATAA	rs144053443	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5732348_5732349insATAA								EDEM1 (470699 upstream) : None (None downstream)																							tggccctttttataaagtttta	0.064													3	3	---	---	---	---	
SRGAP3	9901	broad.mit.edu	37	3	9127863	9127863	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9127863delT	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron|SRGAP3_uc003brk.2_Intron	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		TATTTCCCTattcctgcattt	0.020			T	RAF1	pilocytic astrocytoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	23046299	23046299	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23046299delA								ZNF385D (632176 upstream) : UBE2E2 (198354 downstream)																							TTTCTCTCCTAAAGATGCTGG	0.478													4	2	---	---	---	---	
GADL1	339896	broad.mit.edu	37	3	30806423	30806424	+	Intron	DEL	AA	-	-	rs33923959		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30806423_30806424delAA	uc003cep.2	-							NM_207359	NP_997242	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)	AACATCCTGCAAAGAGGGGGGA	0.436													4	2	---	---	---	---	
OSBPL10	114884	broad.mit.edu	37	3	32006256	32006256	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32006256delG	uc003cev.2	-						OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)		AAGTTCTCATGGCTCATCATT	0.333													4	2	---	---	---	---	
FBXL2	25827	broad.mit.edu	37	3	33407214	33407217	+	Intron	DEL	CAAA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33407214_33407217delCAAA	uc003cfp.2	+						FBXL2_uc011axm.1_Intron|FBXL2_uc011axn.1_Intron|FBXL2_uc011axo.1_Intron|FBXL2_uc011axp.1_Intron|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|FBXL2_uc011axs.1_Intron	NM_012157	NP_036289	Q9UKC9	FBXL2_HUMAN	F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1						actcTTCGACcaaacaaacaaaca	0.132													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	35364153	35364154	+	IGR	INS	-	AAG	AAG	rs143848926	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35364153_35364154insAAG								None (None upstream) : ARPP21 (316927 downstream)																							cagcacacctcaatcctgaggt	0.000													3	6	---	---	---	---	
MLH1	4292	broad.mit.edu	37	3	37063385	37063385	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37063385delC	uc003cgl.2	+						MLH1_uc011aye.1_Intron|MLH1_uc011ayb.1_Intron|MLH1_uc010hge.2_Intron|MLH1_uc003cgn.3_Intron|MLH1_uc011ayc.1_Intron|MLH1_uc011ayd.1_Intron|MLH1_uc003cgo.2_Intron|MLH1_uc010hgg.1_Intron|MLH1_uc010hgh.1_Intron|MLH1_uc010hgi.1_Intron|MLH1_uc010hgj.1_Intron|MLH1_uc010hgk.2_Intron|MLH1_uc010hgl.1_Intron	NM_000249	NP_000240	P40692	MLH1_HUMAN	MutL protein homolog 1						mismatch repair|somatic hypermutation of immunoglobulin genes	chiasma|MutLalpha complex|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|protein binding	p.0?(1)		large_intestine(40)|haematopoietic_and_lymphoid_tissue(8)|ovary(6)|pancreas(5)|stomach(3)|central_nervous_system(3)|endometrium(3)|breast(3)|prostate(3)|skin(2)|NS(1)	77						GAGAATATATCCCATGGGAGA	0.294		1	D|Mis|N|F|S		colorectal|endometrial|ovarian|CNS	colorectal|endometrial|ovarian|CNS		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				4	2	---	---	---	---	
ARIH2	10425	broad.mit.edu	37	3	48964875	48964875	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48964875delT	uc003cvb.2	+						ARIH2_uc003cvc.2_Intron|ARIH2_uc003cvf.2_5'UTR|ARIH2_uc010hkl.2_5'Flank|ARIH2_uc003cvd.1_Intron|ARIH2_uc003cve.1_Intron	NM_006321	NP_006312	O95376	ARI2_HUMAN	ariadne homolog 2						developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		GTAACACTTATTTTTTTTTTC	0.408													9	4	---	---	---	---	
CACNA2D3	55799	broad.mit.edu	37	3	54157333	54157334	+	Intron	INS	-	C	C	rs143522185	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54157333_54157334insC	uc003dhf.2	+						CACNA2D3_uc011beu.1_5'Flank|CACNA2D3_uc003dhg.1_5'Flank|CACNA2D3_uc003dhh.1_5'Flank	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		TAACTCCGCGACCCCCCTCGGG	0.525													3	6	---	---	---	---	
SLMAP	7871	broad.mit.edu	37	3	57815145	57815145	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57815145delA	uc003dje.1	+						SLMAP_uc003djc.1_Intron|SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron	NM_007159	NP_009090	Q14BN4	SLMAP_HUMAN	sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		ACATATTACTAAAAATAACCT	0.214													4	2	---	---	---	---	
PTPRG	5793	broad.mit.edu	37	3	61684913	61684913	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61684913delA	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc003dla.3_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)		tggccgtaggaaaaaaaaaat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	70397955	70397955	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70397955delT								MITF (380469 upstream) : FOXP1 (606782 downstream)																							aagaactgtgttttttttccc	0.070													4	2	---	---	---	---	
ROBO2	6092	broad.mit.edu	37	3	77666382	77666385	+	Intron	DEL	GTTT	-	-	rs71629660		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77666382_77666385delGTTT	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron|ROBO2_uc003dqa.2_Intron	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		ACATGAGTAAGTTTGTTGGGAAGT	0.319													4	3	---	---	---	---	
TRAT1	50852	broad.mit.edu	37	3	108542146	108542147	+	Intron	INS	-	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108542146_108542147insC	uc003dxi.1	+						TRAT1_uc010hpx.1_Intron	NM_016388	NP_057472	Q6PIZ9	TRAT1_HUMAN	T-cell receptor interacting molecule						cellular defense response|negative regulation of receptor recycling|negative regulation of transport|positive regulation of calcium-mediated signaling|positive regulation of T cell receptor signaling pathway|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	phosphatidylinositol-4,5-bisphosphate 3-kinase activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(1)	1						CTAATTCCTCAGAGATTAGGCA	0.312													4	2	---	---	---	---	
TRAT1	50852	broad.mit.edu	37	3	108542151	108542152	+	Intron	DEL	TT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108542151_108542152delTT	uc003dxi.1	+						TRAT1_uc010hpx.1_Intron	NM_016388	NP_057472	Q6PIZ9	TRAT1_HUMAN	T-cell receptor interacting molecule						cellular defense response|negative regulation of receptor recycling|negative regulation of transport|positive regulation of calcium-mediated signaling|positive regulation of T cell receptor signaling pathway|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	phosphatidylinositol-4,5-bisphosphate 3-kinase activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(1)	1						TCCTCAGAGATTAGGCACTATA	0.302													4	2	---	---	---	---	
TRAT1	50852	broad.mit.edu	37	3	108542160	108542160	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108542160delA	uc003dxi.1	+						TRAT1_uc010hpx.1_Intron	NM_016388	NP_057472	Q6PIZ9	TRAT1_HUMAN	T-cell receptor interacting molecule						cellular defense response|negative regulation of receptor recycling|negative regulation of transport|positive regulation of calcium-mediated signaling|positive regulation of T cell receptor signaling pathway|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	phosphatidylinositol-4,5-bisphosphate 3-kinase activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(1)	1						ATTAGGCACTATAGTATTTTC	0.318													4	2	---	---	---	---	
SLC9A10	285335	broad.mit.edu	37	3	111949987	111949988	+	Intron	INS	-	C	C	rs9288944		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111949987_111949988insC	uc003dyu.2	-						SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5						ctctctctttttctccctttct	0.129													4	6	---	---	---	---	
CD200	4345	broad.mit.edu	37	3	112066175	112066175	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112066175delA	uc003dyw.2	+						CD200_uc010hqd.1_Intron|CD200_uc003dyx.2_Intron|CD200_uc003dyy.2_Intron|CD200_uc003dyz.2_Intron	NM_001004196	NP_001004196	P41217	OX2G_HUMAN	CD200 antigen isoform b						regulation of immune response	integral to plasma membrane					0		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				CAAATTACAGAAAGGGTCTTT	0.413													4	2	---	---	---	---	
LSAMP	4045	broad.mit.edu	37	3	115564425	115564426	+	Intron	INS	-	G	G	rs139804051	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115564425_115564426insG	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		ggttctcctcttttctccatgt	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	127095951	127095951	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127095951delC	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																		GAGATAAATTCCAAAAGGAGG	0.438													4	2	---	---	---	---	
PODXL2	50512	broad.mit.edu	37	3	127352316	127352317	+	Intron	DEL	TG	-	-	rs145346367		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127352316_127352317delTG	uc003ejq.2	+							NM_015720	NP_056535	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2 precursor						leukocyte tethering or rolling	integral to plasma membrane	glycosaminoglycan binding|protein binding			ovary(1)|central_nervous_system(1)	2						ttaCAAATTTtgtgtgtgtgtg	0.050													6	4	---	---	---	---	
TMEM108	66000	broad.mit.edu	37	3	132857611	132857612	+	Intron	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132857611_132857612insT	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epj.1_Intron|TMEM108_uc003epk.2_Intron	NM_023943	NP_076432	Q6UXF1	TM108_HUMAN	transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4						ACCTCTGTTGATtttttttttt	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	134141567	134141567	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134141567delG								AMOTL2 (47308 upstream) : ANAPC13 (54980 downstream)																							GCTGGAGGGTGGGGTGGAAAT	0.328													4	2	---	---	---	---	
CLSTN2	64084	broad.mit.edu	37	3	140045017	140045017	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140045017delT	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7						GGCTTTACTCTTTTGAGCCTT	0.428										HNSCC(16;0.037)			4	2	---	---	---	---	
XRN1	54464	broad.mit.edu	37	3	142098708	142098709	+	Intron	INS	-	G	G	rs143458074	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142098708_142098709insG	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron|XRN1_uc003euv.1_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						TATGGATTAATAACGGGATTTC	0.371													8	7	---	---	---	---	
ATR	545	broad.mit.edu	37	3	142277829	142277831	+	Intron	DEL	AAG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142277829_142277831delAAG	uc003eux.3	-							NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein						cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						GCCTGTTTTAAAGAAGAATCACG	0.291								Other_conserved_DNA_damage_response_genes					7	4	---	---	---	---	
MED12L	116931	broad.mit.edu	37	3	150805679	150805680	+	Intron	INS	-	T	T	rs146672788	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150805679_150805680insT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|MED12L_uc003eym.1_Intron|MED12L_uc003eyn.2_Intron|MED12L_uc003eyo.2_Intron	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CCTTTTTTTTGTTTTTTTTTTG	0.401													2	4	---	---	---	---	
KCNAB1	7881	broad.mit.edu	37	3	156020335	156020335	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156020335delG	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)			GCTGAGTGCTGGGGATTTTCT	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	165853752	165853754	+	IGR	DEL	CAC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165853752_165853754delCAC								BCHE (298499 upstream) : None (None downstream)																							cttctgtggtcaccaccaccaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	179920654	179920654	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179920654delA								PEX5L (166137 upstream) : TTC14 (399264 downstream)																							cccaagaaccaaaaatgaggt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182260892	182260892	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182260892delT								SOX2OT (801889 upstream) : ATP11B (250399 downstream)																							CTGGTCTCCATTTTTTTTCTT	0.353													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182356502	182356502	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182356502delA								SOX2OT (897499 upstream) : ATP11B (154789 downstream)																							ggcggttgtcaaggagatggt	0.025													4	2	---	---	---	---	
ST6GAL1	6480	broad.mit.edu	37	3	186793130	186793130	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186793130delG	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron|ST6GAL1_uc003frd.2_Intron	NM_173216	NP_775323	P15907	SIAT1_HUMAN	ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		cctaggtgctggggattcaaa	0.179													4	2	---	---	---	---	
TMEM207	131920	broad.mit.edu	37	3	190147703	190147704	+	Intron	DEL	GA	-	-	rs78875004		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190147703_190147704delGA	uc003fsj.2	-							NM_207316	NP_997199	Q6UWW9	TM207_HUMAN	transmembrane protein 207 precursor							integral to membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		CCACAGGGGGGAAAAAAAAAAT	0.351													4	2	---	---	---	---	
TMEM175	84286	broad.mit.edu	37	4	946545	946546	+	Intron	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:946545_946546delTG	uc003gbq.2	+						TMEM175_uc010ibl.1_Intron|TMEM175_uc003gbp.1_Intron|TMEM175_uc003gbr.2_Intron|TMEM175_uc003gbu.2_Intron|TMEM175_uc003gbs.2_Intron|TMEM175_uc003gbt.2_Intron|TMEM175_uc003gbv.2_Intron|TMEM175_uc010ibm.2_Intron	NM_032326	NP_115702	Q9BSA9	TM175_HUMAN	transmembrane protein 175							integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCCCTGTGCtgtgtgtgtgtg	0.406													4	2	---	---	---	---	
ZFYVE28	57732	broad.mit.edu	37	4	2402164	2402165	+	Intron	INS	-	C	C	rs139818044	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2402164_2402165insC	uc003gex.1	-						ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28						negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3						CTGTCCCACCGCAATTCGACAG	0.510													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	3580679	3580680	+	Intron	INS	-	ATCC	ATCC	rs112972386		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3580679_3580680insATCC	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		tccacccatctatccatccatc	0.144													4	2	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20325971	20325973	+	Intron	DEL	TGT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20325971_20325973delTGT	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						gaggtgctgatgttgtattggtg	0.212													4	2	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20542899	20542899	+	Intron	DEL	A	-	-	rs3215199		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20542899delA	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						ATATTTTATCAAAAAAAAAAT	0.338													8	4	---	---	---	---	
STIM2	57620	broad.mit.edu	37	4	26860027	26860031	+	5'Flank	DEL	AAGGA	-	-	rs147233613		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26860027_26860031delAAGGA	uc003gsh.3	+						STIM2_uc003gsg.3_5'Flank|STIM2_uc010iex.2_5'Flank	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)				GGCGACAGGGAAGGAGAGAAAGCTT	0.517													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	53052800	53052801	+	IGR	INS	-	A	A	rs149239763	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53052800_53052801insA								SPATA18 (89343 upstream) : USP46 (404328 downstream)																							GACCTTCTCTCATGCTGCTAAA	0.332													0	7	---	---	---	---	
SEC31A	22872	broad.mit.edu	37	4	83801755	83801755	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83801755delA	uc003hnf.2	-						SEC31A_uc011ccl.1_Intron|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Intron|SEC31A_uc003hnh.2_Intron|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Intron|SEC31A_uc011ccm.1_Intron|SEC31A_uc011ccn.1_Intron|SEC31A_uc003hnk.2_Intron|SEC31A_uc003hnm.2_Intron|SEC31A_uc003hnn.1_Intron|SEC31A_uc003hno.2_Intron	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)				aaaaaaaaagaaaaaaaaaaG	0.134													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	97359007	97359007	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97359007delT								PDHA2 (596383 upstream) : None (None downstream)																							ATTAAATACCTTACTTTAGAA	0.299													4	2	---	---	---	---	
SLC39A8	64116	broad.mit.edu	37	4	103237183	103237183	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103237183delA	uc003hwb.1	-						SLC39A8_uc011ceo.1_Intron|SLC39A8_uc003hwa.1_Intron|SLC39A8_uc003hwc.2_Intron	NM_022154	NP_071437	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter),							integral to membrane|organelle membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		AGAAAAATAGAAAAAAAAAAA	0.353													3	3	---	---	---	---	
NHEDC1	150159	broad.mit.edu	37	4	103822597	103822597	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103822597delA	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912	Q4ZJI4	NHDC1_HUMAN	Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)		AGACTATTAGAAAAAAAAAGT	0.299													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	123073939	123073940	+	IGR	INS	-	T	T	rs139841890	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123073939_123073940insT								TRPC3 (201030 upstream) : KIAA1109 (17818 downstream)																							GTGGCAAAGTCTGGAAGGGCCA	0.584													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	129322254	129322254	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129322254delT								PGRMC2 (113306 upstream) : PHF17 (408525 downstream)																							atcttctgtatttttttttgt	0.000													4	2	---	---	---	---	
C4orf49	84709	broad.mit.edu	37	4	140200183	140200183	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140200183delG	uc003ihr.1	-							NM_032623	NP_116012	Q8TDB4	CD049_HUMAN	ovary-specific acidic protein							integral to membrane				central_nervous_system(1)|skin(1)	2						TCCACCCTCTGGGGTAAAATT	0.498													4	2	---	---	---	---	
ARHGAP10	79658	broad.mit.edu	37	4	148721736	148721736	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148721736delA	uc003ilf.2	+						ARHGAP10_uc003ile.1_Intron	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		atgggttgggaaatggtgggt	0.000													4	2	---	---	---	---	
KIAA0922	23240	broad.mit.edu	37	4	154504164	154504164	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154504164delA	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron|KIAA0922_uc010ipq.2_Intron|KIAA0922_uc010ips.1_5'Flank	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				ATTAAAAAAGAAAAAAAAAAA	0.299													6	5	---	---	---	---	
ACCN5	51802	broad.mit.edu	37	4	156771262	156771262	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156771262delT	uc003ipe.1	-							NM_017419	NP_059115	Q9NY37	ACCN5_HUMAN	amiloride-sensitive cation channel 5,							integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)		ctcctaaagattttTTTTTTA	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	163564123	163564123	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163564123delA								FSTL5 (478937 upstream) : NAF1 (483737 downstream)																							ttgatgcttgaaaaaaaaaag	0.000													4	2	---	---	---	---	
KLHL2	11275	broad.mit.edu	37	4	166198901	166198910	+	Intron	DEL	ACACACACAC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166198901_166198910delACACACACAC	uc003irb.2	+						KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1						intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		GATGTTAAAAacacacacacacacacacac	0.352													3	3	---	---	---	---	
KLHL2	11275	broad.mit.edu	37	4	166218560	166218560	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166218560delA	uc003irb.2	+						KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1						intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		TTGGGTAAATAAAAAAAAAAA	0.299													6	4	---	---	---	---	
DDX60	55601	broad.mit.edu	37	4	169170894	169170894	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169170894delT	uc003irp.2	-							NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		GTTATTAGCCTTTAAAAGAGA	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	177529570	177529572	+	IGR	DEL	CAG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177529570_177529572delCAG								SPCS3 (276176 upstream) : VEGFC (75119 downstream)																							cagagcaccacagcagcagcagc	0.000													4	2	---	---	---	---	
LOC285501	285501	broad.mit.edu	37	4	178882315	178882316	+	Intron	INS	-	A	A	rs143225684	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178882315_178882316insA	uc010iru.2	+							NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)		GTTATTTTGGGAAAAATATTTT	0.292													6	3	---	---	---	---	
FAM92A3	403315	broad.mit.edu	37	4	183960484	183960484	+	RNA	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183960484delA	uc003ivi.3	+	1		c.1667delA				NR_003612				Homo sapiens family with sequence similarity 92, member A3, mRNA (cDNA clone IMAGE:4822144).												0						TTCAACATCCAAAAAAAAAAA	0.308													6	4	---	---	---	---	
C4orf41	60684	broad.mit.edu	37	4	184585399	184585399	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184585399delT	uc003ivx.2	+						C4orf41_uc003ivw.2_Intron|C4orf41_uc010isc.2_Intron	NM_021942	NP_068761	Q7Z392	CD041_HUMAN	hypothetical protein LOC60684 isoform a												0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)		ATAATAGTTCTTTTTTTTTAA	0.333													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190603542	190603543	+	IGR	INS	-	C	C	rs72525864		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190603542_190603543insC								None (None upstream) : FRG1 (258431 downstream)																							GTAAAAAAAAAACATAACCCCA	0.351													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190647473	190647474	+	IGR	DEL	TC	-	-	rs146129828		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190647473_190647474delTC								None (None upstream) : FRG1 (214500 downstream)																							ACCTTTAAATTCTCTCTTTTTC	0.302													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	2255264	2255265	+	IGR	DEL	GT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2255264_2255265delGT								IRX4 (372384 upstream) : IRX2 (491016 downstream)																							gtgtgtgcacgtgtgtgtgtgt	0.361													4	3	---	---	---	---	
KIAA0947	23379	broad.mit.edu	37	5	5456072	5456072	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5456072delT	uc003jdm.3	+							NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379											ovary(1)|central_nervous_system(1)	2						aaagttcctgtttttttttta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	8438937	8438937	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8438937delC	uc003jeh.1	-											Homo sapiens cDNA clone IMAGE:5297486.																		aattgggaagcccaggggaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	14909832	14909833	+	IGR	INS	-	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14909832_14909833insG								ANKH (37945 upstream) : FBXL7 (590472 downstream)																							AGGGGAACACAGTTTAAAAAAA	0.337													4	2	---	---	---	---	
CDH12	1010	broad.mit.edu	37	5	21939240	21939240	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21939240delA	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						ATAGATATAGAAAAGAAAAAA	0.114										HNSCC(59;0.17)			4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	23560127	23560128	+	IGR	INS	-	AC	AC	rs146607095	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23560127_23560128insAC								PRDM9 (31423 upstream) : CDH10 (927082 downstream)																							GCTATTTAAATacacacacaca	0.243													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	27415179	27415180	+	IGR	INS	-	TGT	TGT	rs150334492	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27415179_27415180insTGT								CDH9 (376490 upstream) : None (None downstream)																							ggactttttgctgttgttgttg	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	49435669	49435670	+	IGR	INS	-	A	A	rs146576257	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49435669_49435670insA								None (None upstream) : EMB (256363 downstream)																							ctacatatcacaaaaaagtttc	0.000													4	2	---	---	---	---	
SLC38A9	153129	broad.mit.edu	37	5	54968743	54968743	+	Intron	DEL	T	-	-	rs5867996		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54968743delT	uc003jqf.2	-						SLC38A9_uc003jqd.2_Intron|SLC38A9_uc010ivx.2_Intron|SLC38A9_uc003jqe.2_Intron|SLC38A9_uc010ivy.2_Intron	NM_173514	NP_775785	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9						amino acid transport|sodium ion transport	integral to membrane					0		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				TTAAGCACACTTTTTTTGTAA	0.303													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	57703105	57703105	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57703105delG								ACTBL2 (924469 upstream) : PLK2 (46707 downstream)																							ACTAGGAACTGGAATGCAGAG	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	58264111	58264111	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58264111delG								RAB3C (116706 upstream) : PDE4D (755 downstream)																							TTGATTTAAAGGAAATAAAGT	0.418													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	68142815	68142816	+	IGR	INS	-	A	A	rs149666584	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68142815_68142816insA								PIK3R1 (545168 upstream) : SLC30A5 (247002 downstream)																							aaaagctttctaatgtggtgac	0.015													2	5	---	---	---	---	
IQGAP2	10788	broad.mit.edu	37	5	75922855	75922856	+	Intron	INS	-	G	G	rs147069484	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75922855_75922856insG	uc003kek.2	+						IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		ttctaactgccgggggaagcct	0.000													6	4	---	---	---	---	
AP3B1	8546	broad.mit.edu	37	5	77405792	77405793	+	Intron	INS	-	C	C	rs147437738	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77405792_77405793insC	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)		CTTCAGCAAAACCCCCCCCTTG	0.361									Hermansky-Pudlak_syndrome				3	5	---	---	---	---	
LNPEP	4012	broad.mit.edu	37	5	96358341	96358341	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96358341delT	uc003kmv.1	+						LNPEP_uc003kmw.1_Intron	NM_005575	NP_005566	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase isoform 1						cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		CAAACAAGACttttttttttt	0.184													10	5	---	---	---	---	
MCC	4163	broad.mit.edu	37	5	112438100	112438100	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112438100delA	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CCCACATGCCAACTCAGCGAT	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	133210316	133210316	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133210316delT								FSTL4 (262093 upstream) : C5orf15 (80883 downstream)																							ctctcccttctttttttttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	135754937	135754937	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135754937delA								TRPC7 (61864 upstream) : SPOCK1 (556051 downstream)																							gtctgtctccaaaaaaaaaaa	0.199													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	139104433	139104433	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139104433delT								CXXC5 (41753 upstream) : PSD2 (70973 downstream)																							accgtggtcattttacggatg	0.035													4	2	---	---	---	---	
PCDHGA1	56114	broad.mit.edu	37	5	140710038	140710038	+	5'Flank	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140710038delA	uc003lji.1	+						PCDHGA1_uc011dan.1_5'Flank	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGAGGAGGaaaaaaaaaaa	0.418													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	151658957	151658957	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151658957delG								GLRA1 (354560 upstream) : NMUR2 (112145 downstream)																							TGATTTGCTAGGGGTAAAGGA	0.448													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155926050	155926050	+	Intron	DEL	T	-	-	rs75971559		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155926050delT	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ccttttcgtcttagtgtttag	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	162736453	162736453	+	IGR	DEL	A	-	-	rs150201183		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162736453delA								None (None upstream) : CCNG1 (128124 downstream)																							accaacatccaaaaaaaaaaa	0.030													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	164317953	164317953	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164317953delG								None (None upstream) : None (None downstream)																							cactgGCCTTGGGTtatctat	0.095													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	168050737	168050738	+	IGR	INS	-	A	A	rs142506776	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168050737_168050738insA								PANK3 (44149 upstream) : SLIT3 (42334 downstream)																							ttctttctgttactgatttcta	0.005													5	3	---	---	---	---	
BNIP1	662	broad.mit.edu	37	5	172587243	172587243	+	Intron	DEL	T	-	-	rs10693152		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172587243delT	uc003mcj.3	+						BNIP1_uc003mci.3_Intron|BNIP1_uc003mck.3_Intron|BNIP1_uc003mcl.3_Intron	NM_001205	NP_001196	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kD interacting protein 1						anti-apoptosis|apoptosis|endoplasmic reticulum membrane fusion|endoplasmic reticulum organization|induction of apoptosis|vesicle-mediated transport	integral to endoplasmic reticulum membrane|nuclear envelope|SNARE complex	protein binding			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCTAtttctcttttttttttt	0.244													4	2	---	---	---	---	
C5orf25	375484	broad.mit.edu	37	5	175737945	175737945	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175737945delA	uc003mds.3	+						C5orf25_uc003mdt.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc003mdv.2_5'Flank			Q8NDZ2	CE025_HUMAN	RecName: Full=Uncharacterized protein C5orf25;												0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.119)		ggcagacgttaaaaaaaataa	0.020													4	3	---	---	---	---	
MAPK9	5601	broad.mit.edu	37	5	179676518	179676519	+	Intron	INS	-	CTCT	CTCT	rs141492717	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179676518_179676519insCTCT	uc003mls.3	-						MAPK9_uc003mlt.3_Intron|MAPK9_uc010jlc.2_Intron|MAPK9_uc003mlv.3_Intron|MAPK9_uc011dgx.1_Intron	NM_002752	NP_002743	P45984	MK09_HUMAN	mitogen-activated protein kinase 9 isoform JNK2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-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;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGTCCTCATGCTGTCAGTCCA	0.569													6	3	---	---	---	---	
GMDS	2762	broad.mit.edu	37	6	1779737	1779737	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1779737delT	uc003mtq.2	-							NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		GGAAGGAAAGTTTTTGATAGA	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	2646555	2646556	+	IGR	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2646555_2646556delTG								C6orf195 (11257 upstream) : MYLK4 (17308 downstream)																							tgtgtgtgcatgtgtgtgtgtg	0.139													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	11606780	11606780	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11606780delA								TMEM170B (23024 upstream) : C6orf105 (107110 downstream)																							CAGTGGGATGAAAAAAACTAA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	14572150	14572150	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14572150delC								CD83 (435004 upstream) : JARID2 (673584 downstream)																							gctaaaccaaccacctagtag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18636440	18636440	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18636440delT	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																		TTCCTTAAAATTTTTTTTTCT	0.398													4	2	---	---	---	---	
DCDC2	51473	broad.mit.edu	37	6	24302520	24302521	+	Intron	INS	-	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24302520_24302521insG	uc003ndx.2	-						DCDC2_uc003ndy.2_Intron	NM_016356	NP_057440	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2						cellular defense response|intracellular signal transduction|neuron migration					ovary(1)	1		Ovarian(999;0.101)				TCATGATCTGTGGAAAAAAAAA	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	33307400	33307401	+	IGR	INS	-	G	G	rs116146176	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33307400_33307401insG								DAXX (16607 upstream) : LYPLA2P1 (25114 downstream)																							TTTTTTTTTTTATGTATTTATT	0.347													4	7	---	---	---	---	
UHRF1BP1	54887	broad.mit.edu	37	6	34841704	34841704	+	3'UTR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34841704delA	uc003oju.3	+	21					UHRF1BP1_uc010jvm.1_Intron|UHRF1BP1_uc010jvn.2_RNA|UHRF1BP1_uc010jvo.2_RNA	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1											ovary(3)	3						atttgactagAAAAAAAAAAT	0.075													4	2	---	---	---	---	
DNAH8	1769	broad.mit.edu	37	6	38792142	38792143	+	Intron	INS	-	G	G	rs76360403	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38792142_38792143insG	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						CACTCAGAGGCGGGTTTATTGG	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	54156793	54156794	+	IGR	INS	-	CTTC	CTTC	rs147211419	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54156793_54156794insCTTC								C6orf142 (25719 upstream) : TINAG (16409 downstream)																							ATGGAGAGCAGCTATGACTCAA	0.401													2	4	---	---	---	---	
HCRTR2	3062	broad.mit.edu	37	6	55021371	55021372	+	Intron	DEL	AC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55021371_55021372delAC	uc010jzu.1	+									O43614	OX2R_HUMAN	Homo sapiens orexin receptor 2 variant 1A mRNA, 5' UTR and partial cds, alternatively spliced.						feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|breast(1)	6	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			tctctctGAGacacacacacac	0.040													4	2	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57468797	57468798	+	Intron	DEL	AA	-	-	rs36024117		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57468797_57468798delAA	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)		TATTTGTTGGAAACATTTACTT	0.084													4	3	---	---	---	---	
EYS	346007	broad.mit.edu	37	6	66094702	66094702	+	Intron	DEL	A	-	-	rs5876962		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66094702delA	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						AAATATGAAGAAAAAACATGA	0.294													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	77484818	77484819	+	IGR	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77484818_77484819delTG								IMPG1 (702483 upstream) : HTR1B (687129 downstream)																							cttcatatattgtgtgtgtgag	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	83234790	83234790	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83234790delT								TPBG (158176 upstream) : UBE2CBP (367396 downstream)																							aactcttttctttttttttag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	109630694	109630694	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109630694delT								C6orf182 (145581 upstream) : CD164 (57024 downstream)																							GGTTTTTTTGTTTTTTTTTAG	0.418													4	2	---	---	---	---	
NT5DC1	221294	broad.mit.edu	37	6	116427690	116427690	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116427690delT	uc003pwj.2	+						NT5DC1_uc003pwk.2_Intron	NM_152729	NP_689942	Q5TFE4	NT5D1_HUMAN	5'-nucleotidase, cytosolic II-like 1 protein								hydrolase activity|metal ion binding				0		all_cancers(87;0.00367)|all_epithelial(87;0.00449)|Colorectal(196;0.0469)		all cancers(137;0.0327)|OV - Ovarian serous cystadenocarcinoma(136;0.0445)|GBM - Glioblastoma multiforme(226;0.0719)|Epithelial(106;0.112)		TTTAAACAAGTTTAGACTTGC	0.264													4	2	---	---	---	---	
RWDD1	51389	broad.mit.edu	37	6	116892953	116892954	+	Intron	INS	-	TT	TT	rs140789860	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116892953_116892954insTT	uc003pxd.2	+						RWDD1_uc003pxb.2_Intron|RWDD1_uc003pxc.2_Intron	NM_015952	NP_057036	Q9H446	RWDD1_HUMAN	RWD domain containing 1 isoform a								protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.0312)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)|Epithelial(106;0.161)		GCCCTCCACTCCTCAAGTTCTT	0.584													4	3	---	---	---	---	
GOPC	57120	broad.mit.edu	37	6	117790755	117790755	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117790755delA	uc003pxq.1	-							NM_001017408	NP_001017408	Q9HD26	GOPC_HUMAN	golgi associated PDZ and coiled-coil motif						apical protein localization|cytoplasmic sequestering of CFTR protein|ER to Golgi vesicle-mediated transport|Golgi to plasma membrane transport|protein homooligomerization|protein transport	cell junction|dendrite|Golgi membrane|postsynaptic density|postsynaptic membrane|trans-Golgi network transport vesicle	cystic fibrosis transmembrane conductance regulator binding			ovary(1)	1		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		aaaaacagagaaaaaaaatct	0.000			O	ROS1	glioblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	139902536	139902536	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139902536delT								CITED2 (206751 upstream) : None (None downstream)																							AGACAACAGGTTTGGGAGGTG	0.383													4	2	---	---	---	---	
ZDHHC14	79683	broad.mit.edu	37	6	158032861	158032862	+	Intron	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158032861_158032862delTG	uc003qqt.2	+						ZDHHC14_uc003qqs.2_Intron|ZDHHC14_uc010kjm.1_Intron	NM_024630	NP_078906	Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14 isoform 1							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|skin(1)	2		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		CCGTCCCTTTTGTGTGTGTGTG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	158375072	158375072	+	IGR	DEL	A	-	-	rs68028724		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158375072delA								SNX9 (8963 upstream) : SYNJ2 (27847 downstream)																							CTGATAGCTTAAAAAAAACAA	0.373													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	159889918	159889919	+	IGR	INS	-	AATG	AATG	rs149792569	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159889918_159889919insAATG								FNDC1 (196779 upstream) : SOD2 (210232 downstream)																							AATACTGACCAaatgaatgaat	0.386													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166822308	166822308	+	IGR	DEL	A	-	-	rs111304849		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166822308delA								BRP44L (25822 upstream) : RPS6KA2 (546 downstream)																							TGCATCCCCCACACACACACA	0.522													3	4	---	---	---	---	
DNAH11	8701	broad.mit.edu	37	7	21742839	21742839	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21742839delA	uc003svc.2	+							NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						ATGAAACAGGAAGGGTGGGTG	0.443									Kartagener_syndrome				4	2	---	---	---	---	
RAPGEF5	9771	broad.mit.edu	37	7	22262595	22262595	+	Intron	DEL	G	-	-	rs5882837		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22262595delG	uc003svg.2	-							NM_012294	NP_036426	Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1						gagttgtcatggggggaggca	0.000													3	4	---	---	---	---	
AVL9	23080	broad.mit.edu	37	7	32762896	32762896	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32762896delA	uc011kai.1	+							NM_015060	NP_055875	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)							integral to membrane					0						TTAATTAGTCAAAAAAAAATC	0.318													4	3	---	---	---	---	
BMPER	168667	broad.mit.edu	37	7	33983459	33983459	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33983459delC	uc011kap.1	+							NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3						CTCTGGATTTCCCCTTATTAC	0.468													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36825915	36825915	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36825915delC								AOAH (61762 upstream) : ELMO1 (68046 downstream)																							GTGTGTAGTTCCCTATTCTAC	0.378													4	2	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40553743	40553743	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40553743delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						ATATGGACTGTTTTTTTTTTC	0.264													3	3	---	---	---	---	
ZNF716	441234	broad.mit.edu	37	7	57529812	57529812	+	3'UTR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57529812delA	uc011kdi.1	+	4						NM_001159279	NP_001152751			zinc finger protein 716											ovary(2)	2						TTATAAATGTAAAAAAAAAAG	0.274													5	3	---	---	---	---	
PMS2L4	5382	broad.mit.edu	37	7	66752653	66752654	+	Intron	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66752653_66752654insT	uc003tvo.2	-						PMS2L4_uc003tvq.2_RNA					Homo sapiens cDNA clone IMAGE:4081618.												0						CAGTGATCACGTGTCCTCCTGG	0.515													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68798147	68798147	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68798147delG								None (None upstream) : AUTS2 (265758 downstream)																							GGATATTGCTGGGGGGTTTAT	0.488													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	73065110	73065111	+	IGR	INS	-	GTGT	GTGT	rs151037759	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73065110_73065111insGTGT								MLXIPL (26240 upstream) : VPS37D (17063 downstream)																							ccagagtcagcgtgtgtgtgtg	0.223													2	4	---	---	---	---	
TMEM120A	83862	broad.mit.edu	37	7	75618424	75618425	+	Intron	INS	-	TGGA	TGGA			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75618424_75618425insTGGA	uc003ued.2	-						TMEM120A_uc003uee.2_Intron|TMEM120A_uc003ueb.1_5'Flank|TMEM120A_uc003uec.2_Intron	NM_031925	NP_114131	Q9BXJ8	T120A_HUMAN	transmembrane protein 120A							integral to membrane					0						ggggggaggggggtagggggct	0.158													3	4	---	---	---	---	
TMEM120A	83862	broad.mit.edu	37	7	75618427	75618428	+	Intron	INS	-	TG	TG			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75618427_75618428insTG	uc003ued.2	-						TMEM120A_uc003uee.2_Intron|TMEM120A_uc003ueb.1_5'Flank|TMEM120A_uc003uec.2_Intron	NM_031925	NP_114131	Q9BXJ8	T120A_HUMAN	transmembrane protein 120A							integral to membrane					0						gggaggggggtagggggctagg	0.168													4	4	---	---	---	---	
SRRM3	222183	broad.mit.edu	37	7	75887518	75887519	+	Intron	INS	-	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75887518_75887519insG	uc010ldi.2	+							NM_001110199	NP_001103669			serine/arginine repetitive matrix 3												0						AGAGATGAGCAGGGGGGGCCCC	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	76727993	76727993	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76727993delT								LOC100132832 (45638 upstream) : CCDC146 (23941 downstream)																							TTTTTCTTTCTTTTTTTTTTC	0.284													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81028060	81028060	+	IGR	DEL	A	-	-	rs59727848		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81028060delA								SEMA3C (476385 upstream) : HGF (303385 downstream)																							atccaggctgacacctgcttt	0.035													1	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	81511728	81511728	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81511728delA								HGF (112276 upstream) : CACNA2D1 (67690 downstream)																							AAAAACAAACAAAAAAAATCA	0.303													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	84378411	84378411	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84378411delG								SEMA3A (554194 upstream) : SEMA3D (246463 downstream)																							cccagagtcaggtcagtccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	87945456	87945456	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87945456delC								STEAP4 (9247 upstream) : ZNF804B (443297 downstream)																							GCTTTGGATTCCCACCCCATA	0.303													4	2	---	---	---	---	
ACN9	57001	broad.mit.edu	37	7	96745684	96745685	+	5'Flank	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96745684_96745685delCA	uc003uoo.3	+							NM_020186	NP_064571	Q9NRP4	ACN9_HUMAN	ACN9 homolog precursor						regulation of gluconeogenesis	mitochondrial intermembrane space					0	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)					agcgcacgtgcacacacacaca	0.000													4	2	---	---	---	---	
TECPR1	25851	broad.mit.edu	37	7	97863412	97863412	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97863412delG	uc003upg.2	-						TECPR1_uc003uph.1_Intron	NM_015395	NP_056210	Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1							integral to membrane	protein binding			pancreas(1)	1						gctgacacctgggccaccctg	0.000													4	2	---	---	---	---	
BAIAP2L1	55971	broad.mit.edu	37	7	97964627	97964629	+	Intron	DEL	ATA	-	-	rs141165128		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97964627_97964629delATA	uc003upj.2	-							NM_018842	NP_061330	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	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)		STAD - Stomach adenocarcinoma(171;0.215)			ATTACATATCATACCCTGACACT	0.463													14	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	99605867	99605868	+	IGR	DEL	TG	-	-	rs10609713		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99605867_99605868delTG								AZGP1 (32180 upstream) : ZKSCAN1 (7351 downstream)																							taaattcatctgtgtccaatgc	0.059													0	7	---	---	---	---	
PILRB	29990	broad.mit.edu	37	7	99963058	99963058	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99963058delC	uc003uuk.2	+						PILRB_uc003uul.2_Intron|PILRB_uc003uun.2_Intron	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta						activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					tctagagtagccagattccta	0.000													4	2	---	---	---	---	
CUX1	1523	broad.mit.edu	37	7	101860166	101860169	+	Intron	DEL	CACA	-	-	rs148256350		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101860166_101860169delCACA	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						cacattatctcacacacacacaca	0.118													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	106061352	106061353	+	IGR	INS	-	A	A	rs149583299	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106061352_106061353insA								NAMPT (135714 upstream) : FLJ36031 (237797 downstream)																							agaagcAGCACGGGAAAAGAGG	0.262													3	3	---	---	---	---	
DNAJB9	4189	broad.mit.edu	37	7	108213939	108213939	+	3'UTR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108213939delT	uc003vfn.2	+	3						NM_012328	NP_036460	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9						ER-associated protein catabolic process|protein folding	endoplasmic reticulum|nucleolus	heat shock protein binding|misfolded protein binding|unfolded protein binding				0						TATTTAAGGGTTTTTTTTTTT	0.264													4	2	---	---	---	---	
DOCK4	9732	broad.mit.edu	37	7	111653097	111653098	+	Intron	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111653097_111653098delCA	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)				ACCCAGCCTCCACACACACCAC	0.446													4	2	---	---	---	---	
ST7	7982	broad.mit.edu	37	7	116759990	116759990	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116759990delT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7OT2_uc003viu.2_Intron|ST7_uc011knn.1_Intron|ST7OT2_uc003viw.2_Intron|ST7_uc003vix.1_Intron	NM_021908	NP_068708	Q9NRC1	ST7_HUMAN	suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		TTTACCCTCCttttttttttt	0.199													4	4	---	---	---	---	
CADPS2	93664	broad.mit.edu	37	7	122120409	122120410	+	Intron	INS	-	TTTTAA	TTTTAA	rs139396203	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122120409_122120410insTTTTAA	uc010lkp.2	-						CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2						AATAAGCTTCTGATTTATACTT	0.252													5	3	---	---	---	---	
CNTNAP2	26047	broad.mit.edu	37	7	147621823	147621823	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147621823delC	uc003weu.1	+							NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			AAGATGTAAGCCCAGTCTTAG	0.458										HNSCC(39;0.1)			4	2	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152106896	152106898	+	Intron	DEL	TTA	-	-	rs66662919		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152106896_152106898delTTA	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)		GGGTTTTTTTTTAAATCATCATG	0.251			N		medulloblastoma								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	153506643	153506643	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153506643delC								ACTR3B (954180 upstream) : DPP6 (77776 downstream)																							ATCTATGCTTCCTACCTAGAA	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155121532	155121533	+	IGR	DEL	CT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155121532_155121533delCT								INSIG1 (19590 upstream) : EN2 (129291 downstream)																							TCATCTCTCCCTCTCCCCAAAG	0.554													4	2	---	---	---	---	
PTPRN2	5799	broad.mit.edu	37	7	157957757	157957758	+	Intron	INS	-	A	A	rs33929694		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157957757_157957758insA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCAGTGAAGACCCCTGATAGCA	0.564													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	2208114	2208115	+	IGR	DEL	AG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2208114_2208115delAG								MYOM2 (114735 upstream) : CSMD1 (584761 downstream)																							AGGAAGTGACAGAGAGAGAGAG	0.500													6	3	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	2857300	2857301	+	Intron	INS	-	A	A	rs140414939	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2857300_2857301insA	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)		GGAAGGAGATCAAAAAAGGAAA	0.396													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	5517958	5517959	+	IGR	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5517958_5517959delCA								CSMD1 (665630 upstream) : MCPH1 (746162 downstream)																							AAAACATATTCACACACACATG	0.327													4	2	---	---	---	---	
SLC39A14	23516	broad.mit.edu	37	8	22254223	22254223	+	Intron	DEL	T	-	-	rs112051827		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22254223delT	uc003xbq.3	+						SLC39A14_uc011kzg.1_Intron|SLC39A14_uc003xbp.3_Intron|SLC39A14_uc011kzh.1_Intron	NM_001128431	NP_001121903	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter),							endoplasmic reticulum|Golgi apparatus|integral to membrane|lamellipodium|plasma membrane	zinc ion transmembrane transporter activity				0				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		AGGTGCACCGTTTTTTTTTTT	0.458													4	2	---	---	---	---	
TNFRSF10D	8793	broad.mit.edu	37	8	23006338	23006339	+	Intron	INS	-	CTAT	CTAT	rs146686261	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23006338_23006339insCTAT	uc003xcz.1	-							NM_003840	NP_003831	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily,						anti-apoptosis|apoptosis	integral to membrane	TRAIL binding|transmembrane receptor activity				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		attaattttaactattttttag	0.005													2	5	---	---	---	---	
CCDC25	55246	broad.mit.edu	37	8	27610343	27610344	+	Intron	INS	-	A	A	rs140102479	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27610343_27610344insA	uc003xgc.2	-						CCDC25_uc003xgd.2_Intron|CCDC25_uc011lan.1_Intron|CCDC25_uc011lao.1_Intron|CCDC25_uc003xge.2_Intron|CCDC25_uc003xgf.1_Intron	NM_018246	NP_060716	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25												0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		aaaaaaaaagcaaaaaaaaaca	0.218													8	4	---	---	---	---	
BAG4	9530	broad.mit.edu	37	8	38065463	38065464	+	Intron	INS	-	GTACCTTAGAT	GTACCTTAGAT	rs141559186	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38065463_38065464insGTACCTTAGAT	uc003xky.1	+						BAG4_uc003xkz.1_Intron	NM_004874	NP_004865	O95429	BAG4_HUMAN	BCL2-associated athanogene 4						anti-apoptosis|apoptosis|protein folding	cytoplasm|nucleus	receptor signaling protein activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				TTTGGCTGAAGGTCATAATCAT	0.302													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	41111923	41111924	+	IGR	DEL	AC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41111923_41111924delAC								ZMAT4 (356580 upstream) : SFRP1 (7555 downstream)																							ccatacatatacacacacacCC	0.149													4	2	---	---	---	---	
PRKDC	5591	broad.mit.edu	37	8	48802691	48802693	+	Intron	DEL	ATA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48802691_48802693delATA	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				AGGATGAAATataataataataa	0.305								NHEJ					3	3	---	---	---	---	
SNTG1	54212	broad.mit.edu	37	8	51056681	51056681	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51056681delT	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				gcctagaaaatttCATCCGAT	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54437867	54437867	+	5'Flank	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54437867delA	uc003xrj.1	-											Homo sapiens full length insert cDNA clone ZC64C06.																		tgagctccccaaaaaaaaatt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	54466531	54466532	+	IGR	DEL	TC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54466531_54466532delTC								OPRK1 (302337 upstream) : ATP6V1H (161584 downstream)																							tatctttctatctctctctctt	0.000													4	2	---	---	---	---	
NSMAF	8439	broad.mit.edu	37	8	59507673	59507674	+	Intron	INS	-	TTG	TTG	rs143063886	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59507673_59507674insTTG	uc003xtt.2	-						NSMAF_uc011lee.1_Intron	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation						ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)				aagcataattatttttaaaatt	0.144													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	60216956	60216957	+	IGR	INS	-	T	T	rs150553450	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60216956_60216957insT								TOX (185189 upstream) : CA8 (884466 downstream)																							TGTCACATGAGTCATAGGGAGG	0.416													2	4	---	---	---	---	
PREX2	80243	broad.mit.edu	37	8	68930366	68930367	+	Intron	INS	-	T	T	rs111503892		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68930366_68930367insT	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						TCATAGAGTTGTTTTTTTTTTC	0.272													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	75500777	75500778	+	IGR	INS	-	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75500777_75500778insA								GDAP1 (221444 upstream) : MIR2052 (117150 downstream)																							ttggaagcattaaaaaaatgcc	0.000													4	2	---	---	---	---	
SLC26A7	115111	broad.mit.edu	37	8	92226252	92226253	+	Intron	DEL	GT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92226252_92226253delGT	uc003yex.2	+						SLC26A7_uc003yey.2_Intron|LRRC69_uc010mal.1_Intron|LRRC69_uc003yev.1_Intron|LRRC69_uc003yew.1_Intron	NM_052832	NP_439897	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform a							basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)			ATATGTGTTCGTGTGTGTGTGT	0.396													4	2	---	---	---	---	
NIPAL2	79815	broad.mit.edu	37	8	99234434	99234434	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99234434delT	uc003yil.1	-						NIPAL2_uc011lgw.1_Intron|NIPAL2_uc003yim.1_Intron	NM_024759	NP_079035	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2							integral to membrane					0						GAAGGGAATGTTTTTTTTTAC	0.358													4	2	---	---	---	---	
COLEC10	10584	broad.mit.edu	37	8	120079921	120079921	+	Intron	DEL	G	-	-	rs71569790		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120079921delG	uc003yoo.2	+							NM_006438	NP_006429	Q9Y6Z7	COL10_HUMAN	collectin sub-family member 10 precursor							collagen|cytoplasm	mannose binding			ovary(2)|skin(1)	3	all_cancers(13;4.13e-26)|Lung NSC(37;1.36e-07)|Ovarian(258;0.018)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00113)			ACCCAGGGCAGGGGGAAATTC	0.493													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	120681401	120681402	+	IGR	DEL	GT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120681401_120681402delGT								ENPP2 (30295 upstream) : TAF2 (61613 downstream)																							acagaggccagtagcatgccac	0.069													4	2	---	---	---	---	
FER1L6	654463	broad.mit.edu	37	8	124894422	124894422	+	Intron	DEL	T	-	-	rs112183007		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124894422delT	uc003yqw.2	+							NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CAAAACCACATTTTTTTTTTT	0.363													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	125400245	125400246	+	IGR	INS	-	T	T	rs143231342	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125400245_125400246insT								TMEM65 (15305 upstream) : TRMT12 (62802 downstream)																							ttcaaatggacttttttttgtg	0.173													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127210642	127210642	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127210642delA								TRIB1 (760000 upstream) : FAM84B (354045 downstream)																							atgctcattgaaaaaaaagta	0.035													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127957088	127957088	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127957088delA								FAM84B (386622 upstream) : LOC727677 (344974 downstream)																							GAATTTTTGTAGGAAGGCAAT	0.393													4	2	---	---	---	---	
TG	7038	broad.mit.edu	37	8	134007056	134007057	+	Intron	INS	-	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134007056_134007057insG	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_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)		GAAGGTGAGATGGGGAAAGAGG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	138790846	138790846	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138790846delT								None (None upstream) : FAM135B (351422 downstream)																							gaagctgctcttttttttgcc	0.139													4	3	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139817380	139817381	+	Intron	DEL	GT	-	-	rs147343259		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139817380_139817381delGT	uc003yvd.2	-							NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			gtgtgatggggtgtgtgtgcat	0.000										HNSCC(7;0.00092)			3	3	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139904014	139904014	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139904014delA	uc003yvd.2	-							NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ACAATGAGAGAAAAAAGCAAA	0.333										HNSCC(7;0.00092)			4	2	---	---	---	---	
VPS28	51160	broad.mit.edu	37	8	145652160	145652160	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145652160delG	uc003zcr.1	-						VPS28_uc003zcs.1_Intron|VPS28_uc003zct.1_Intron	NM_016208	NP_057292	Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 isoform 1						cellular membrane organization|endosome transport|negative regulation of protein ubiquitination|protein transport	cytosol|late endosome membrane|plasma membrane	protein binding				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GAACTATTTAGCCCCTGGCCA	0.597													5	6	---	---	---	---	
MGC70857	414919	broad.mit.edu	37	8	145751848	145751848	+	3'UTR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145751848delC	uc003zdp.1	-	3					LRRC24_uc003zdm.2_Intron|LRRC24_uc003zdn.2_Intron|MGC70857_uc003zdq.1_3'UTR|MGC70857_uc003zdr.1_RNA	NM_001001795	NP_001001795	Q6P1X6	CH082_HUMAN	hypothetical protein LOC414919												0	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-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;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTCACGCTGACCCCCCACTAG	0.607													4	2	---	---	---	---	
KANK1	23189	broad.mit.edu	37	9	501079	501080	+	Intron	INS	-	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:501079_501080insA	uc003zgl.1	+							NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a						negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		TGAGAAAAAAGAAAAAAAAAAC	0.366													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	1122509	1122509	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1122509delG								DMRT2 (64956 upstream) : SMARCA2 (892833 downstream)																							GATGGGATGTGGGAGCTCAGC	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	2232466	2232466	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2232466delG								SMARCA2 (38845 upstream) : FLJ35024 (190236 downstream)																							GGGAAGCAGAGGGCTTTTTGG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	7824963	7824963	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7824963delA								C9orf123 (25164 upstream) : PTPRD (489284 downstream)																							gctcataagtaaaaaatctgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	13440201	13440201	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13440201delA								MPDZ (160638 upstream) : NFIB (641647 downstream)																							CTTTGCTTGTAAAATGTGTTG	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	15372656	15372656	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15372656delA								TTC39B (65412 upstream) : SNAPC3 (50126 downstream)																							ccttttcaagaaaaaaaaagt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	16201678	16201678	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16201678delG								C9orf93 (229783 upstream) : BNC2 (207824 downstream)																							GTGCCAGGAAGTCAATGAGAC	0.418													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	25955951	25955951	+	IGR	DEL	A	-	-	rs74593513		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25955951delA								TUSC1 (277095 upstream) : C9orf82 (884733 downstream)																							ctagagttagaaaaaaaaagt	0.100													4	2	---	---	---	---	
MOBKL2B	79817	broad.mit.edu	37	9	27327549	27327550	+	3'UTR	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27327549_27327550delCA	uc003zqn.2	-	4						NM_024761	NP_079037	Q86TA1	MOL2B_HUMAN	MOB1, Mps One Binder kinase activator-like 2B								metal ion binding|protein binding			ovary(1)|pleura(1)	2		all_neural(11;9.12e-11)		Lung(218;6.54e-05)|LUSC - Lung squamous cell carcinoma(38;0.000397)		aaagacacaccacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	27721609	27721610	+	IGR	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27721609_27721610delTG								C9orf72 (147767 upstream) : LINGO2 (226918 downstream)																							GTTCTGTCTCTGTGTGTGTGTG	0.337													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	47212494	47212494	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:47212494delG								KGFLP1 (464109 upstream) : None (None downstream)																							atcttattgtggggactggcg	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66695553	66695553	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66695553delC	uc004aej.2	-											Homo sapiens cDNA clone IMAGE:4668947, partial cds.																		gttgagcaaacagggaaggaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68398095	68398095	+	IGR	DEL	C	-	-	rs74487823		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68398095delC								FAM27B (603906 upstream) : MIR1299 (604144 downstream)																							CCATGCTTAGCTTGGGTTTCT	0.353													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68427396	68427396	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68427396delC								FAM27B (633207 upstream) : MIR1299 (574843 downstream)																							CTCTGCCCAGCCCCCTAGTTC	0.438													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68457870	68457870	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68457870delA								FAM27B (663681 upstream) : MIR1299 (544369 downstream)																							TCATATTTACAGTTGAAGATG	0.328													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68481357	68481357	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68481357delA								FAM27B (687168 upstream) : MIR1299 (520882 downstream)																							aaagcaatctacacatttaat	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69034058	69034058	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69034058delG								MIR1299 (31737 upstream) : PGM5P2 (46187 downstream)																							ATACACAATAGGGTAGGAATG	0.323													2	4	---	---	---	---	
TMEM2	23670	broad.mit.edu	37	9	74339504	74339505	+	Intron	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74339504_74339505delCA	uc011lsa.1	-						TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		ATCTGGGCATCACACACATAAC	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	92137336	92137337	+	IGR	DEL	AG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92137336_92137337delAG								SEMA4D (24448 upstream) : GADD45G (82590 downstream)																							TGAAGGGGTCAGAGAGAGAGGA	0.520													4	2	---	---	---	---	
ROR2	4920	broad.mit.edu	37	9	94572474	94572474	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94572474delG	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20						GAATCAGAATGGGGTCTATGG	0.577													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	101566189	101566189	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101566189delA								ANKS6 (7395 upstream) : GALNT12 (3792 downstream)																							atatttgttgaaaaaaaaaca	0.000													6	3	---	---	---	---	
TMEFF1	8577	broad.mit.edu	37	9	103255057	103255057	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103255057delC	uc004baz.1	+						TMEFF1_uc004bay.1_Intron	NM_003692	NP_003683	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two						multicellular organismal development	integral to membrane|plasma membrane					0		Acute lymphoblastic leukemia(62;0.0452)				AAGAAAAAAGCCACTGGATCT	0.453													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	106726940	106726940	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106726940delG								CYLC2 (946170 upstream) : SMC2 (129601 downstream)																							TAGTTTATCTGGTAAAGCAGC	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107879765	107879766	+	IGR	INS	-	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107879765_107879766insG								ABCA1 (189329 upstream) : SLC44A1 (127163 downstream)																							AGCAGTGCCCTGGGCCCCTGCA	0.550													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	113126350	113126350	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113126350delA								TXNDC8 (26225 upstream) : SVEP1 (1181 downstream)																							GATGTAGGCcaaaaaggcagc	0.144													4	2	---	---	---	---	
SUSD1	64420	broad.mit.edu	37	9	114920105	114920105	+	Intron	DEL	T	-	-	rs147276607		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114920105delT	uc004bfu.2	-						SUSD1_uc010mui.2_Intron|SUSD1_uc010muj.2_Intron	NM_022486	NP_071931	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1 precursor							integral to membrane	calcium ion binding				0						tctttctttcttttttttttt	0.179													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	115431501	115431501	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115431501delT								KIAA1958 (8795 upstream) : C9orf80 (17292 downstream)																							TTGGAAGGGATTTTTTTTTGT	0.463													6	4	---	---	---	---	
ALAD	210	broad.mit.edu	37	9	116152318	116152318	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116152318delT	uc011lxf.1	-						ALAD_uc011lxe.1_Intron|ALAD_uc004bhl.3_Intron	NM_000031	NP_000022	P13716	HEM2_HUMAN	delta-aminolevulinic acid dehydratase						heme biosynthetic process|protein homooligomerization	cytosol	identical protein binding|lead ion binding|porphobilinogen synthase activity|zinc ion binding				0					Aminolevulinic acid(DB00855)	TCTGTGAttcttttttttttt	0.254													4	3	---	---	---	---	
PAPPA	5069	broad.mit.edu	37	9	119043794	119043794	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119043794delA	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						CTCTGAGGCTAAAAAGGGTGG	0.498													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	121054204	121054205	+	IGR	DEL	AT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121054204_121054205delAT								TLR4 (574440 upstream) : DBC1 (874703 downstream)																							tctaaggaacatatatataTCC	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	122204648	122204649	+	IGR	INS	-	G	G	rs138120984	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122204648_122204649insG								DBC1 (72909 upstream) : MIR147 (802608 downstream)																							ttcaaatctcacaggctgactc	0.163													5	4	---	---	---	---	
VAV2	7410	broad.mit.edu	37	9	136716922	136716923	+	Intron	INS	-	ATGG	ATGG	rs141641770	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136716922_136716923insATGG	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)		tgggtgaataaatggatggatg	0.000													4	2	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140604119	140604120	+	Intron	INS	-	CTTATA	CTTATA	rs140183634	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140604119_140604120insCTTATA	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)		TTTTGCAGCCTCTTCTTACCTG	0.550													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4045744	4045745	+	IGR	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4045744_4045745delCA								KLF6 (218271 upstream) : LOC100216001 (575699 downstream)																							CCCTTCATTGCACACACCGTCC	0.530													4	2	---	---	---	---	
ASB13	79754	broad.mit.edu	37	10	5707762	5707762	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5707762delT	uc001iig.2	-						ASB13_uc001iii.2_Intron|ASB13_uc001iih.2_Intron|ASB13_uc009xic.2_Intron	NM_024701	NP_078977	Q8WXK3	ASB13_HUMAN	ankyrin repeat and SOCS box-containing protein						intracellular signal transduction		protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(2;9.59e-09)		ATGCTTTAGATTTTTTTTTTC	0.378													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8328712	8328713	+	IGR	INS	-	T	T	rs138260727	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8328712_8328713insT								GATA3 (211550 upstream) : None (None downstream)																							TGCAAATGCTATTTTTTGACAT	0.401													2	4	---	---	---	---	
DNAJC1	64215	broad.mit.edu	37	10	22202939	22202940	+	Intron	DEL	AC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22202939_22202940delAC	uc001irc.2	-						DNAJC1_uc001ird.2_Intron	NM_022365	NP_071760	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1						negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				ATCTCTCTAAACACACACACAC	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	26031572	26031572	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26031572delA								GPR158 (140417 upstream) : MYO3A (191430 downstream)																							gaaacagcagaaaaaaaggaa	0.000													4	2	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27355175	27355175	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27355175delT	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						TTTTCTTTTCTTTTTTTTTTT	0.279													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30594022	30594023	+	IGR	INS	-	A	A	rs141415237	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30594022_30594023insA								KIAA1462 (189602 upstream) : MTPAP (4708 downstream)																							tccaggatcataaataccccta	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38817915	38817916	+	IGR	DEL	AG	-	-	rs143593432		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38817915_38817916delAG								LOC399744 (76835 upstream) : None (None downstream)																							tgaatgaaatagaatggaatgg	0.000													7	4	---	---	---	---	
CSGALNACT2	55454	broad.mit.edu	37	10	43653973	43653973	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43653973delT	uc001jan.2	+						CSGALNACT2_uc001jam.1_Intron	NM_018590	NP_061060	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate						chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process	Golgi cisterna membrane|integral to Golgi membrane	glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding			ovary(1)	1						AACAGTGAACTTTTTTTTTAA	0.284													5	3	---	---	---	---	
ZNF239	8187	broad.mit.edu	37	10	44066177	44066177	+	5'Flank	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44066177delT	uc001jaw.3	-						ZNF239_uc001jax.3_Intron|ZNF239_uc009xmj.2_Intron|ZNF239_uc009xmk.2_Intron	NM_005674	NP_005665	Q16600	ZN239_HUMAN	zinc finger protein 239						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|RNA binding|zinc ion binding				0						AAGACCCTTATTTTTTTTCTT	0.363													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	44687906	44687906	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44687906delC								HNRNPA3P1 (402041 upstream) : CXCL12 (177701 downstream)																							TCCACTGTGTCCGTCTCAGCA	0.567													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	45106253	45106253	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45106253delA								CXCL12 (225711 upstream) : TMEM72 (300511 downstream)																							tgatctaaggaaaaaaagcaa	0.000													4	2	---	---	---	---	
ANXA8	653145	broad.mit.edu	37	10	47129269	47129269	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47129269delT	uc001jed.3	-						uc001jef.2_Intron			P13928	ANXA8_HUMAN	Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3						gagtccattctttgggtttgg	0.194													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	91761899	91761900	+	IGR	DEL	GA	-	-	rs145577326		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91761899_91761900delGA								KIF20B (227199 upstream) : HTR7 (738678 downstream)																							AAAAAagagcgagagagagaga	0.312													4	2	---	---	---	---	
BTAF1	9044	broad.mit.edu	37	10	93716747	93716747	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93716747delA	uc001khr.2	+						BTAF1_uc009xua.1_Intron|BTAF1_uc001khs.1_Intron	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				tctctgtctcaaaaaaaaaaa	0.075													3	3	---	---	---	---	
EXOC6	54536	broad.mit.edu	37	10	94688406	94688407	+	Intron	DEL	AA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94688406_94688407delAA	uc001kig.2	+						EXOC6_uc010qnr.1_Intron|EXOC6_uc001kie.2_Intron|EXOC6_uc009xub.2_Intron|EXOC6_uc009xuc.2_Intron|EXOC6_uc001kih.2_Intron	NM_019053	NP_061926	Q8TAG9	EXOC6_HUMAN	SEC15-like 1 isoform a						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)				cagcgaatttaaaaaaaaaaaa	0.084													4	4	---	---	---	---	
TMEM20	159371	broad.mit.edu	37	10	95654006	95654006	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95654006delG	uc001kjg.1	+						TMEM20_uc001kji.2_Intron|TMEM20_uc001kjf.1_Intron|TMEM20_uc001kjh.2_Intron|TMEM20_uc010qnw.1_Intron|TMEM20_uc001kjj.2_Intron	NM_001134658	NP_001128130	Q2M3R5	TMM20_HUMAN	transmembrane protein 20 isoform 1							integral to membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;3.46e-05)|Renal(717;0.018)|Ovarian(717;0.0228)|all_hematologic(284;0.189)		STAD - Stomach adenocarcinoma(243;0.00345)		GGTCTCGCTCGGGGGTCCCGA	0.756													4	2	---	---	---	---	
ERLIN1	10613	broad.mit.edu	37	10	101940214	101940214	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101940214delA	uc001kqn.3	-						ERLIN1_uc001kqo.3_Intron|ERLIN1_uc010qpm.1_Intron	NM_006459	NP_006450	O75477	ERLN1_HUMAN	ER lipid raft associated 1						ER-associated protein catabolic process	endoplasmic reticulum membrane|integral to membrane	protein binding				0		Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		ACAGAAAGTGAAAAAAATAGT	0.279													4	2	---	---	---	---	
SCD	6319	broad.mit.edu	37	10	102111105	102111105	+	Intron	DEL	C	-	-	rs77607180		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102111105delC	uc001kqy.2	+							NM_005063	NP_005054	O00767	ACOD_HUMAN	stearoyl-CoA desaturase 1						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity				0		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		GAGAGCGTTGCCCGGTGAGAG	0.547													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	107322349	107322349	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107322349delG								SORCS3 (297356 upstream) : None (None downstream)																							CAAGGGAGAAGGAGTCTATTC	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	113688213	113688214	+	IGR	DEL	TC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113688213_113688214delTC								ADRA2A (847553 upstream) : GPAM (221408 downstream)																							TGTGAAGACATCTCTCTCTCTC	0.495													4	2	---	---	---	---	
ACSL5	51703	broad.mit.edu	37	10	114172646	114172647	+	Intron	INS	-	G	G	rs150228688	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114172646_114172647insG	uc001kzs.2	+						ACSL5_uc001kzt.2_Intron|ACSL5_uc001kzu.2_Intron|ACSL5_uc009xxz.2_Intron|ACSL5_uc010qrj.1_Intron	NM_203379	NP_976313	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5						fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane	ATP binding|long-chain fatty acid-CoA ligase activity			large_intestine(2)|skin(1)	3		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		TGGTGGAGTCTGGGGGACCACA	0.297													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	130262725	130262734	+	IGR	DEL	CCTCCTCCTC	-	-	rs66913631		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130262725_130262734delCCTCCTCCTC								MKI67 (338257 upstream) : None (None downstream)																							ctagacttctcctcctcctccctcctcctc	0.000													4	3	---	---	---	---	
POLR2L	5441	broad.mit.edu	37	11	840579	840579	+	Intron	DEL	C	-	-	rs34627090		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:840579delC	uc001lsc.2	-						TSPAN4_uc001lsd.1_5'Flank|TSPAN4_uc001lse.1_5'Flank|TSPAN4_uc001lsf.1_5'Flank|TSPAN4_uc001lsg.1_5'Flank|TSPAN4_uc001lsh.1_5'Flank	NM_021128	NP_066951	P62875	RPAB5_HUMAN	DNA directed RNA polymerase II polypeptide L						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|zinc ion binding				0		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;4.1e-25)|Epithelial(43;3.15e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCTGGCCTCACCCCCCCCGCC	0.607													4	5	---	---	---	---	
ARNTL	406	broad.mit.edu	37	11	13297674	13297676	+	5'Flank	DEL	TCT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13297674_13297676delTCT	uc001mkr.2	+						ARNTL_uc001mko.2_5'Flank|ARNTL_uc001mkp.2_5'Flank|ARNTL_uc001mkq.2_5'Flank|ARNTL_uc001mks.2_5'Flank|ARNTL_uc001mkt.2_5'Flank|ARNTL_uc001mku.2_5'Flank	NM_001178	NP_001169	O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear						circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0				Epithelial(150;0.0243)		CTCCCTGCAatcttcttttcggt	0.064													6	6	---	---	---	---	
SPON1	10418	broad.mit.edu	37	11	14032976	14032978	+	Intron	DEL	TAT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14032976_14032978delTAT	uc001mle.2	+							NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)		attttgcttgtatttcagggatt	0.227													4	6	---	---	---	---	
PDE3B	5140	broad.mit.edu	37	11	14694951	14694951	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14694951delA	uc001mln.2	+						PDE3B_uc001mlm.2_Intron|PDE3B_uc010rcr.1_Intron	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B						cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0						CTTTGAAATTAAAAAAAAAAA	0.318													5	3	---	---	---	---	
ZDHHC13	54503	broad.mit.edu	37	11	19191686	19191686	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19191686delT	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						TGAATGCTGATTTTAGTAAAG	0.328													2	5	---	---	---	---	
ANO5	203859	broad.mit.edu	37	11	22250957	22250958	+	Intron	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22250957_22250958insT	uc001mqi.2	+						ANO5_uc001mqj.2_Intron	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a							chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4						AATGTTCTTCCTTTTTTTTTAA	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	22448230	22448230	+	IGR	DEL	G	-	-	rs67638947		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22448230delG								SLC17A6 (47186 upstream) : FANCF (195849 downstream)																							TTGGGGCTCAGGGGGTTAGAC	0.358													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	27310261	27310261	+	IGR	DEL	T	-	-	rs78511808		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27310261delT								BBOX1 (160907 upstream) : CCDC34 (49800 downstream)																							CTTTTGTTCATTTTTTTTTTC	0.398													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	33492765	33492765	+	IGR	DEL	T	-	-	rs113201118		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33492765delT								HIPK3 (116826 upstream) : C11orf41 (71112 downstream)																							TCTCAGAACCTTTTTTTTTTT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	34573383	34573384	+	IGR	INS	-	T	T	rs143918802	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34573383_34573384insT								ELF5 (38053 upstream) : EHF (69284 downstream)																							ggtgctgttgattttttttcat	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	36809150	36809151	+	IGR	DEL	AC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36809150_36809151delAC								C11orf74 (112760 upstream) : None (None downstream)																							TGCTTAGACTACATCGAGATGC	0.342													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	36974912	36974913	+	IGR	INS	-	T	T	rs144461046	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36974912_36974913insT								C11orf74 (278522 upstream) : None (None downstream)																							TCCTTCCTTAATTTTTTTCCTC	0.218													1	5	---	---	---	---	
ACCSL	390110	broad.mit.edu	37	11	44072390	44072391	+	Intron	INS	-	T	T	rs66464203		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44072390_44072391insT	uc001mxw.1	+						ACCSL_uc009ykr.2_Intron	NM_001031854	NP_001027025	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase								1-aminocyclopropane-1-carboxylate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(5)	5						GGCCTGAGttcttttttttttt	0.193													3	3	---	---	---	---	
PRDM11	56981	broad.mit.edu	37	11	45169292	45169292	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45169292delG	uc001myo.2	+							NM_020229	NP_064614	Q9NQV5	PRD11_HUMAN	PR domain containing 11											upper_aerodigestive_tract(1)	1						GTTGGGAGATGGGGGCTTAGA	0.537													4	2	---	---	---	---	
AMBRA1	55626	broad.mit.edu	37	11	46567012	46567012	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46567012delA	uc010rgu.1	-						AMBRA1_uc010rgt.1_5'Flank|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		accctgtctcaaaaaaaaaaT	0.219													4	3	---	---	---	---	
LRP4	4038	broad.mit.edu	37	11	46912172	46912172	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46912172delT	uc001ndn.3	-							NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein						endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)		ACAGAATGAAtttttttttta	0.229													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	48341217	48341218	+	IGR	INS	-	A	A	rs139166096	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48341217_48341218insA								OR4S1 (12514 upstream) : OR4C3 (5275 downstream)																							TTGCATATATGATAAGTATTAA	0.134													2	5	---	---	---	---	
LOC440040	440040	broad.mit.edu	37	11	49829403	49829403	+	Intron	DEL	A	-	-	rs144435832	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49829403delA	uc010rhy.1	+						LOC440040_uc009ymb.2_Intron	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0						aaaaataaataaataaatagt	0.274													5	3	---	---	---	---	
UBE2L6	9246	broad.mit.edu	37	11	57328097	57328097	+	Intron	DEL	T	-	-	rs67576121		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57328097delT	uc001nkn.1	-						UBE2L6_uc001nko.1_Intron	NM_004223	NP_004214	O14933	UB2L6_HUMAN	ubiquitin-conjugating enzyme E2L 6 isoform 1						negative regulation of type I interferon production	cytosol	protein binding|ubiquitin-protein ligase activity			ovary(1)	1						ttcttttttcttttttttttt	0.095													4	2	---	---	---	---	
ZFP91	80829	broad.mit.edu	37	11	58355255	58355255	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58355255delT	uc001nmx.3	+						ZFP91_uc001nmy.3_Intron|ZFP91-CNTF_uc010rkm.1_Intron	NM_053023	NP_444251	Q96JP5	ZFP91_HUMAN	zinc finger protein 91						activation of NF-kappaB-inducing kinase activity|protein K63-linked ubiquitination	nucleus	nucleic acid binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TGAAGCCTAATTTTTTTTTCT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	61264636	61264639	+	IGR	DEL	TGTG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61264636_61264639delTGTG								C11orf66 (6237 upstream) : LRRC10B (11633 downstream)																							tgtgtgtatttgtgtgtatgtatc	0.010													4	2	---	---	---	---	
INTS5	80789	broad.mit.edu	37	11	62414351	62414351	+	3'UTR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62414351delA	uc001nud.2	-	2					GANAB_uc001nua.2_5'Flank|GANAB_uc001nub.2_5'Flank|GANAB_uc001nuc.2_5'Flank|GANAB_uc010rma.1_5'Flank|GANAB_uc010rmb.1_5'Flank	NM_030628	NP_085131	Q6P9B9	INT5_HUMAN	integrator complex subunit 5						snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2						TTTTATTTAGAAAAAAAAAAG	0.493													4	2	---	---	---	---	
NAA40	79829	broad.mit.edu	37	11	63707477	63707477	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63707477delA	uc009yoz.2	+						NAA40_uc010rmw.1_Intron|NAA40_uc010rmx.1_Intron	NM_024771	NP_079047	Q86UY6	NAA40_HUMAN	N-acetyltransferase 11								N-acetyltransferase activity				0						TCACCCTCCTAAAAAGATAAC	0.274													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	73492707	73492707	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73492707delT								RAB6A (20506 upstream) : MRPL48 (6210 downstream)																							GCCTCCCTACTTTTTTTTTTC	0.398													4	2	---	---	---	---	
SLCO2B1	11309	broad.mit.edu	37	11	74868599	74868599	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74868599delC	uc001owb.2	+						SLCO2B1_uc010rrp.1_Intron|SLCO2B1_uc010rrq.1_Intron|SLCO2B1_uc010rrr.1_Intron|SLCO2B1_uc010rrs.1_Intron|SLCO2B1_uc001owc.2_Intron|SLCO2B1_uc001owd.2_5'Flank	NM_007256	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)	TGGAGGAAGACCAGGTGTGTA	0.522													4	2	---	---	---	---	
ODZ4	26011	broad.mit.edu	37	11	78385715	78385716	+	Intron	INS	-	A	A	rs141668438	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78385715_78385716insA	uc001ozl.3	-						ODZ4_uc001ozk.3_Intron|ODZ4_uc009yvb.1_Intron	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4						AATTCAGACGGGGGAGCTCAGT	0.441													6	3	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83585243	83585246	+	Intron	DEL	AGAA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83585243_83585246delAGAA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				caaaagaaagagaaagaaagacag	0.123													8	6	---	---	---	---	
DLG2	1740	broad.mit.edu	37	11	83737046	83737047	+	Intron	INS	-	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83737046_83737047insA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TTCTGAAACTTAAAAAAAATTA	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	89356959	89356960	+	IGR	INS	-	TG	TG	rs149413636	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89356959_89356960insTG								NOX4 (34180 upstream) : FOLH1B (35505 downstream)																							AAAATTATGAAtgtgtgtgtgt	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	93963956	93963957	+	IGR	INS	-	A	A	rs59526725	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93963956_93963957insA								PANX1 (48821 upstream) : FOLR4 (74846 downstream)																							acagagactgcaaggtttagca	0.069													4	2	---	---	---	---	
TMEM123	114908	broad.mit.edu	37	11	102269328	102269328	+	3'UTR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102269328delA	uc001pha.2	-	5					TMEM123_uc009yxc.2_3'UTR	NM_052932	NP_443164	Q8N131	PORIM_HUMAN	transmembrane protein 123 precursor						oncosis	external side of plasma membrane|integral to membrane	receptor activity			breast(2)	2	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		CACCCCAGCCAAAAAAAAAAA	0.388													4	3	---	---	---	---	
TMEM123	114908	broad.mit.edu	37	11	102277073	102277073	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102277073delG	uc001pha.2	-						TMEM123_uc009yxc.2_Intron	NM_052932	NP_443164	Q8N131	PORIM_HUMAN	transmembrane protein 123 precursor						oncosis	external side of plasma membrane|integral to membrane	receptor activity			breast(2)	2	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		AAGGCTTCTAGGGCACTACCT	0.517													4	2	---	---	---	---	
DLAT	1737	broad.mit.edu	37	11	111922293	111922295	+	Intron	DEL	TTG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111922293_111922295delTTG	uc001pmo.2	+						DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Intron	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)	gtttttgtttttgttgttgttgt	0.123													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112527870	112527871	+	IGR	DEL	CT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112527870_112527871delCT								PTS (387193 upstream) : NCAM1 (304124 downstream)																							CTCCCCTCTCCTCTCTCTCTCT	0.525													5	3	---	---	---	---	
TECTA	7007	broad.mit.edu	37	11	120978998	120978999	+	Intron	DEL	AC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120978998_120978999delAC	uc010rzo.1	+							NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor						cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GTacacacatacacacacacac	0.223													3	3	---	---	---	---	
SORL1	6653	broad.mit.edu	37	11	121348571	121348574	+	Intron	DEL	TGCT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121348571_121348574delTGCT	uc001pxx.2	+							NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		accctgtctctgctaaaaatacaa	0.000													3	4	---	---	---	---	
ZNF202	7753	broad.mit.edu	37	11	123600684	123600686	+	Intron	DEL	AGG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123600684_123600686delAGG	uc001pzd.1	-						ZNF202_uc001pzc.1_Intron|ZNF202_uc001pze.1_Intron|ZNF202_uc001pzf.1_Intron	NM_003455	NP_003446	O95125	ZN202_HUMAN	zinc finger protein 202						lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		GGAGCAGGCAAGGAGGAGCTGAA	0.581													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	127480905	127480906	+	IGR	INS	-	TTTTA	TTTTA	rs140633318	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127480905_127480906insTTTTA								KIRREL3 (607550 upstream) : ETS1 (847750 downstream)																							AAAGGTGGGAGTAGCTGTGTTT	0.411													3	3	---	---	---	---	
PARP11	57097	broad.mit.edu	37	12	3943957	3943959	+	Intron	DEL	GAG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3943957_3943959delGAG	uc001qml.2	-						PARP11_uc009zef.2_Intron|PARP11_uc001qmm.2_Intron|PARP11_uc001qmn.2_Intron	NM_020367	NP_065100	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11								NAD+ ADP-ribosyltransferase activity			ovary(1)|central_nervous_system(1)	2			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)			ttagatcagaGAGGAGTCAGAAA	0.241													4	3	---	---	---	---	
CCND2	894	broad.mit.edu	37	12	4409271	4409271	+	3'UTR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4409271delA	uc001qmo.2	+	5						NM_001759	NP_001750	P30279	CCND2_HUMAN	cyclin D2						cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding			haematopoietic_and_lymphoid_tissue(1)|breast(1)|kidney(1)	3			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)			GGTGAAACTTAAAAAAAAAAT	0.388			T	IGL@	NHL,CLL								9	4	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6159099	6159099	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6159099delC	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	tctgaacattcccccaagttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	8968028	8968029	+	IGR	INS	-	GGTG	GGTG	rs146218175		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8968028_8968029insGGTG								RIMKLB (32343 upstream) : A2ML1 (7121 downstream)																							TATTAAACCCTGGACATTTCCT	0.426													4	2	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	13939610	13939610	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13939610delA	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	GGCTGAGGGGAAAAAAAAAAG	0.458													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	15138540	15138541	+	IGR	INS	-	CA	CA	rs149295724	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15138540_15138541insCA								PDE6H (3743 upstream) : RERG (122177 downstream)																							GTAGCCTGTGTCACTCCCTGGC	0.569													3	4	---	---	---	---	
EPS8	2059	broad.mit.edu	37	12	15871763	15871763	+	Intron	DEL	T	-	-	rs34389536		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15871763delT	uc001rdb.2	-						EPS8_uc009zig.2_Intron	NM_004447	NP_004438	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway						cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		CTACTTCAGCTTATTAAAATC	0.353													4	3	---	---	---	---	
SLCO1B1	10599	broad.mit.edu	37	12	21350373	21350373	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21350373delT	uc001req.3	+							NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)	CAAACATCCATTTTTTATGAG	0.244													4	2	---	---	---	---	
SOX5	6660	broad.mit.edu	37	12	23910467	23910468	+	Intron	DEL	AA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23910467_23910468delAA	uc001rfw.2	-						SOX5_uc001rfx.2_Intron|SOX5_uc001rfy.2_Intron|SOX5_uc010siv.1_Intron|SOX5_uc010siw.1_Intron|SOX5_uc001rfz.1_Intron	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						ATTATTTCTTAAACCTTATCAG	0.361													4	2	---	---	---	---	
KIF21A	55605	broad.mit.edu	37	12	39700070	39700070	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39700070delA	uc001rly.2	-						KIF21A_uc001rlv.2_Intron|KIF21A_uc001rlw.2_Intron|KIF21A_uc001rlx.2_Intron|KIF21A_uc001rlz.2_Intron|KIF21A_uc010skl.1_Intron|KIF21A_uc001rlt.2_Intron|KIF21A_uc001rlu.2_Intron	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)				TCAGCAAATTAAAAAGTGCAA	0.333													4	2	---	---	---	---	
CNTN1	1272	broad.mit.edu	37	12	41463526	41463527	+	Intron	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41463526_41463527insT	uc001rmm.1	+						CNTN1_uc001rmn.1_Intron	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TTGTGATCATATTATTTTAAAT	0.307													3	5	---	---	---	---	
LASS5	91012	broad.mit.edu	37	12	50528687	50528687	+	Intron	DEL	A	-	-	rs3830643		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50528687delA	uc001rwd.3	-						LASS5_uc001rwc.2_Intron|LASS5_uc001rwe.3_Intron|LASS5_uc001rwf.3_Intron|LASS5_uc010smq.1_Intron	NM_147190	NP_671723	Q8N5B7	CERS5_HUMAN	LAG1 homolog, ceramide synthase 5						ceramide biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity				0						ACAGAGAAAGATATATAAATC	0.388													2	8	---	---	---	---	
ATF1	466	broad.mit.edu	37	12	51190003	51190003	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51190003delC	uc001rww.3	+						ATF1_uc010smu.1_Intron	NM_005171	NP_005162	P18846	ATF1_HUMAN	activating transcription factor 1						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|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				EWSR1/ATF1(323)|FUS/ATF1(4)	soft_tissue(321)|ovary(2)|NS(2)|bone(2)|skin(2)	329						catggcaagaccctgtctctt	0.010			T	EWSR1|FUS	malignant melanoma of soft parts |angiomatoid fibrous histiocytoma 								4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	55618292	55618294	+	IGR	DEL	GCG	-	-	rs144604313		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55618292_55618294delGCG								OR10A7 (2534 upstream) : OR6C74 (22778 downstream)																							gagaggagcagcgtggaacagat	0.000													4	4	---	---	---	---	
STAT6	6778	broad.mit.edu	37	12	57521004	57521004	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57521004delG	uc009zpg.2	-						LRP1_uc010sre.1_5'Flank|LRP1_uc001snb.2_5'Flank|LRP1_uc001snc.1_5'Flank|LRP1_uc001snd.2_5'Flank	NM_003153	NP_003144	P42226	STAT6_HUMAN	signal transducer and activator of transcription						regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4						AGACTGGAGTGGGGACTTTTC	0.542											OREG0021935	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	60529811	60529813	+	IGR	DEL	TGC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60529811_60529813delTGC								SLC16A7 (354404 upstream) : None (None downstream)																							tatttatagttgctgcaaatgag	0.000													4	2	---	---	---	---	
GRIP1	23426	broad.mit.edu	37	12	67129399	67129399	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67129399delA	uc010sta.1	-							NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GCAGGAGGGGAAAAAAAGAAA	0.428													4	2	---	---	---	---	
MDM1	56890	broad.mit.edu	37	12	68714492	68714492	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68714492delA	uc001stz.2	-						MDM1_uc010stc.1_Intron|MDM1_uc009zqv.1_Intron	NM_017440	NP_059136	Q8TC05	MDM1_HUMAN	mouse Mdm1 nuclear protein homolog isoform 1							nucleus				ovary(3)|skin(2)	5			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		CAGAAAAGGCAAAAAAAAGTC	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70119179	70119179	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70119179delA	uc001svj.1	-						uc001svk.2_Intron					Homo sapiens cDNA clone IMAGE:4829132.																		TCTGCAAAAGAAAAAAAAAAT	0.224													4	2	---	---	---	---	
MGAT4C	25834	broad.mit.edu	37	12	87231419	87231419	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87231419delA	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3						TTTAACACAGAAAAACAGCAA	0.333													4	2	---	---	---	---	
C12orf50	160419	broad.mit.edu	37	12	88388162	88388163	+	Intron	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88388162_88388163delCA	uc001tam.1	-						C12orf50_uc001tan.2_Intron	NM_152589	NP_689802	Q8NA57	CL050_HUMAN	hypothetical protein LOC160419											skin(2)|ovary(1)	3						cacatacatgcacacacacaca	0.267													4	2	---	---	---	---	
CRADD	8738	broad.mit.edu	37	12	94236297	94236297	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94236297delG	uc001tda.2	+						CRADD_uc010sur.1_Intron|CRADD_uc010sus.1_Intron	NM_003805	NP_003796	P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1						AAGGGCTAAAGACTGAGGGGA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	96221338	96221338	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96221338delT								NTN4 (36408 upstream) : SNRPF (31371 downstream)																							TGCTGAAAGCTTTACCTACAA	0.313													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	102774615	102774615	+	IGR	DEL	T	-	-	rs5800506		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102774615delT								PMCH (183001 upstream) : IGF1 (15030 downstream)																							TGTATACATATTTGTTCTTAG	0.408													4	4	---	---	---	---	
C12orf42	374470	broad.mit.edu	37	12	103666341	103666341	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103666341delG	uc001tjs.2	-									Q96LP6	CL042_HUMAN	Homo sapiens cDNA FLJ25323 fis, clone TST00323.											ovary(1)|central_nervous_system(1)	2						ACGTTTTCAAGAAAGAACACC	0.378													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	106356758	106356758	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106356758delA								C12orf75 (591463 upstream) : NUAK1 (100367 downstream)																							AGTGATTGGGACACAGAGGAG	0.493													4	2	---	---	---	---	
RPH3A	22895	broad.mit.edu	37	12	113292826	113292827	+	Intron	INS	-	CT	CT	rs141084697	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113292826_113292827insCT	uc010syl.1	+						RPH3A_uc001ttz.2_Intron|RPH3A_uc001tty.2_Intron|RPH3A_uc009zwe.1_Intron|RPH3A_uc010sym.1_Intron	NM_001143854	NP_001137326	Q9Y2J0	RP3A_HUMAN	rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)		CCCCTTCAGGCCTCAGCACCAC	0.416													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	113991487	113991487	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113991487delT								LHX5 (81610 upstream) : RBM19 (263056 downstream)																							CTTCTGAGGATTTTTTTTTTA	0.358													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	115036699	115036699	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115036699delG								TBX5 (190452 upstream) : TBX3 (71360 downstream)																							AGATGCTCTAGGACATCAGAT	0.448													4	2	---	---	---	---	
SRRM4	84530	broad.mit.edu	37	12	119560098	119560101	+	Intron	DEL	AGGA	-	-	rs146974381	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119560098_119560101delAGGA	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						gcaggaaggcaggaaggaaggaag	0.191													11	5	---	---	---	---	
GCN1L1	10985	broad.mit.edu	37	12	120600800	120600800	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120600800delG	uc001txo.2	-							NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGCTCTTTGAGGCCTTCTGCC	0.577													76	51	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	125711733	125711733	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125711733delC								AACS (83861 upstream) : TMEM132B (99429 downstream)																							gtgTTCTGTGCCACAGCACTG	0.219													4	2	---	---	---	---	
LOC100128554	100128554	broad.mit.edu	37	12	126927245	126927245	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126927245delA	uc010tbf.1	+						LOC100128554_uc009zyj.1_Intron|LOC100128554_uc010tbg.1_Intron|LOC100128554_uc001uhj.2_Intron					Homo sapiens hypothetical protein LOC144678, mRNA (cDNA clone IMAGE:4837867).												0						AGGGTCCCCCAAAAAGACTTA	0.463													4	2	---	---	---	---	
TMEM132D	121256	broad.mit.edu	37	12	130386416	130386416	+	Intron	DEL	C	-	-	rs34571915		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130386416delC	uc009zyl.1	-							NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		ACCCCCCCCGCCCCAAAAAAA	0.403													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	132285629	132285630	+	IGR	INS	-	G	G	rs140487873		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132285629_132285630insG								SFRS8 (1347 upstream) : MMP17 (27311 downstream)																							tgtttcaaaatgcgtttccatt	0.005													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22471385	22471385	+	IGR	DEL	T	-	-	rs5802138		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22471385delT								FGF9 (192745 upstream) : None (None downstream)																							CTGTTGACTCTTTTTTTTTTA	0.463													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22554948	22554948	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22554948delG								FGF9 (276308 upstream) : None (None downstream)																							TGTACCTTCTGCAGCTGTGTG	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	22945224	22945224	+	IGR	DEL	A	-	-	rs35775191		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22945224delA								FGF9 (666584 upstream) : SGCG (809836 downstream)																							GAAACAGGGTAAAAAAAACGT	0.328													4	2	---	---	---	---	
SLC7A1	6541	broad.mit.edu	37	13	30120534	30120534	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30120534delT	uc001uso.2	-							NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid						cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity				0		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GGCACTTTAATTTTCTGAGCC	0.323													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30994430	30994430	+	IGR	DEL	C	-	-	rs71192654		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30994430delC								LOC100188949 (46394 upstream) : HMGB1 (38451 downstream)																							CAAAAAAAAACATCCTTAGTG	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	37303822	37303822	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37303822delA								C13orf36 (31849 upstream) : RFXAP (89517 downstream)																							GGGTTAGATCAAAAAAAGAAC	0.393													4	2	---	---	---	---	
FOXO1	2308	broad.mit.edu	37	13	41222712	41222712	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41222712delT	uc001uxl.3	-							NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1						anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		TAATACTTTCTTAGTGCATTC	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	47858049	47858049	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47858049delT								HTR2A (386999 upstream) : SUCLA2 (658743 downstream)																							tcatttgcaatttttgatctc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	49494679	49494679	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49494679delG								CYSLTR2 (211181 upstream) : FNDC3A (55369 downstream)																							gaaggactgagaaagggcagg	0.109													4	2	---	---	---	---	
GUCY1B2	2974	broad.mit.edu	37	13	51609954	51609954	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51609954delG	uc001vfd.3	-						GUCY1B2_uc010tgo.1_Intron|GUCY1B2_uc001vfc.3_Intron					SubName: Full=Guanylate cyclase 1, soluble, beta 2;												0						AGCTTGGGATGGTAGAGAAGC	0.438													4	2	---	---	---	---	
TPTE2P3	220115	broad.mit.edu	37	13	53151275	53151275	+	RNA	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53151275delC	uc001vgw.2	+	20		c.2040delC				NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0						AAGAAAAACACTGTTTATAAA	0.368													36	22	---	---	---	---	
DIAPH3	81624	broad.mit.edu	37	13	60312392	60312392	+	Intron	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60312392delG	uc001vht.2	-						DIAPH3_uc001vhs.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)		ACAACGGCCTGGGGTCATCTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	66252082	66252082	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66252082delG								None (None upstream) : PCDH9 (624885 downstream)																							tgcagagggaggagcactaag	0.109													4	2	---	---	---	---	
KLF5	688	broad.mit.edu	37	13	73650108	73650109	+	3'UTR	INS	-	A	A	rs148760123	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73650108_73650109insA	uc001vje.2	+	4					KLF5_uc001vjd.2_3'UTR	NM_001730	NP_001721	Q13887	KLF5_HUMAN	Kruppel-like factor 5						transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		ACAACAAAAACAAACAAAAGCA	0.396													8	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	80675129	80675129	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80675129delA								NDFIP2 (544924 upstream) : SPRY2 (234985 downstream)																							GGAGAAGGACAAAAAAAAACA	0.403													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	89760801	89760801	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89760801delT								None (None upstream) : None (None downstream)																							AAGCAACTAGTTTTTTTTTCT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90619605	90619605	+	IGR	DEL	A	-	-	rs5805602		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90619605delA								None (None upstream) : MIR622 (263831 downstream)																							AGGAGCACAGAAAAAAAAAAT	0.358													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	90976227	90976227	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90976227delT								MIR622 (92696 upstream) : LOC144776 (566981 downstream)																							TGTTTTGATCTTTTTTTACTC	0.323													4	2	---	---	---	---	
HS6ST3	266722	broad.mit.edu	37	13	97251327	97251327	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97251327delT	uc001vmw.2	+							NM_153456	NP_703157	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					tttgctagtatttttttgagg	0.000													4	2	---	---	---	---	
ITGBL1	9358	broad.mit.edu	37	13	102322351	102322351	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102322351delT	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					tcctactgcctttttttcccc	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	106553844	106553844	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106553844delA								DAOA (410462 upstream) : EFNB2 (588254 downstream)																							AAATTTTGGCAAATCCTTCAA	0.398													4	2	---	---	---	---	
TFDP1	7027	broad.mit.edu	37	13	114268036	114268037	+	Intron	INS	-	GTGT	GTGT			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114268036_114268037insGTGT	uc001vtw.2	+						TFDP1_uc010tkd.1_Intron|TFDP1_uc010tke.1_Intron|TFDP1_uc001vty.3_Intron|TFDP1_uc010agx.2_Intron	NM_007111	NP_009042	Q14186	TFDP1_HUMAN	transcription factor Dp-1						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding			lung(4)|ovary(2)|skin(1)	7	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			gtatgtgaggagtgtgtgcatg	0.109										TSP Lung(29;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	26863257	26863257	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26863257delG								None (None upstream) : NOVA1 (51833 downstream)																							GGTGTAAGGTGGGGGGAGTTT	0.433													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	33312438	33312439	+	IGR	INS	-	C	C	rs72526375	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33312438_33312439insC								AKAP6 (10171 upstream) : NPAS3 (96020 downstream)																							aaattcattgtttctggctgat	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	48251010	48251011	+	Intron	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48251010_48251011delTG	uc001wwk.1	-											Homo sapiens cDNA FLJ31650 fis, clone NT2RI2004079.																		TTCATTGTTCTGTGTGTGTGAG	0.297													4	2	---	---	---	---	
SOS2	6655	broad.mit.edu	37	14	50689615	50689615	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50689615delA	uc001wxs.3	-						SOS2_uc010tql.1_Intron	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)					gtttggggagaaaaagaaact	0.000													4	2	---	---	---	---	
CDKL1	8814	broad.mit.edu	37	14	50816285	50816285	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50816285delC	uc010anu.1	-						CDKL1_uc001wxz.2_Intron	NM_004196	NP_004187	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1							cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)|stomach(1)	2	all_epithelial(31;0.000746)|Breast(41;0.0102)					gaCAGTGTGACCCAAGAGCCA	0.229													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	60979040	60979041	+	IGR	INS	-	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60979040_60979041insA								SIX6 (517 upstream) : SIX1 (132377 downstream)																							CCTTCAAGGCCCCCTCCAATAC	0.401													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	65071679	65071679	+	IGR	DEL	A	-	-	rs143745162		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65071679delA								C14orf50 (15583 upstream) : PLEKHG3 (99514 downstream)																							TGAGAATGTTAAAAAAAAAAA	0.388													4	2	---	---	---	---	
GSTZ1	2954	broad.mit.edu	37	14	77793494	77793494	+	Intron	DEL	G	-	-	rs10716979		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77793494delG	uc001xtj.2	+						GSTZ1_uc001xtk.2_Intron|GSTZ1_uc010ass.2_Intron|GSTZ1_uc001xtm.2_Intron	NM_145870	NP_665877	O43708	MAAI_HUMAN	glutathione transferase zeta 1 isoform 1						glutathione metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol|mitochondrion	glutathione peroxidase activity|glutathione transferase activity|maleylacetoacetate isomerase activity|protein homodimerization activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	GACCCTGGGAGGGTGGGTGGC	0.642													4	3	---	---	---	---	
ALKBH1	8846	broad.mit.edu	37	14	78149924	78149924	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78149924delT	uc001xuc.1	-						ALKBH1_uc001xud.1_Intron	NM_006020	NP_006011	Q13686	ALKB1_HUMAN	alkylated DNA repair protein alkB homolog						DNA dealkylation involved in DNA repair|DNA demethylation|oxidative demethylation|RNA repair	mitochondrion	DNA-(apurinic or apyrimidinic site) lyase activity|ferrous iron binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(1)|skin(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		ATCATCCTCCtttttttttga	0.219													4	3	---	---	---	---	
EML5	161436	broad.mit.edu	37	14	89134779	89134779	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89134779delA	uc001xxg.2	-						EML5_uc001xxf.2_5'Flank|EML5_uc001xxh.1_Intron	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3						agtatttcagaaaaaaaaaag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	92691303	92691303	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92691303delA								CPSF2 (60760 upstream) : SLC24A4 (97622 downstream)																							CAGTTTACCTAAACTTCAGGT	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98137050	98137050	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98137050delT	uc001yfv.1	-											human full-length cDNA clone CS0DI087YB20 of Placenta of Homo sapiens (human).																		GGCGAACGTATTTTTTTTTAT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	99582080	99582080	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99582080delT								C14orf177 (397983 upstream) : BCL11B (53547 downstream)																							GGTTCCTGTCTTTTCCAAATA	0.383													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106015709	106015709	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106015709delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ccaccagaagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	107060159	107060160	+	Intron	INS	-	T	T	rs146826802	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107060159_107060160insT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						TTAAAAGTGTCTTCACTTTCCC	0.441													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20393612	20393614	+	IGR	DEL	CCT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20393612_20393614delCCT								None (None upstream) : GOLGA6L6 (343480 downstream)																							GTAACTGATCCCTCCTCATATCA	0.207													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	20514044	20514045	+	IGR	INS	-	GGG	GGG	rs57819183		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20514044_20514045insGGG								None (None upstream) : GOLGA6L6 (223049 downstream)																							aaatgagatgagatgatataat	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21930021	21930023	+	IGR	DEL	AAC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21930021_21930023delAAC								NF1P1 (795396 upstream) : LOC646214 (2491 downstream)																							CATATTCATTAACAACGAGACCC	0.251													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	21931004	21931004	+	IGR	DEL	A	-	-	rs113406709		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21931004delA								NF1P1 (796379 upstream) : LOC646214 (1510 downstream)																							tctaggcatgaattttcatga	0.174													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23040922	23040922	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23040922delT								NIPA2 (6512 upstream) : NIPA1 (2359 downstream)																							TACCTAGATCttttttttttt	0.249													4	2	---	---	---	---	
APBA2	321	broad.mit.edu	37	15	29234644	29234645	+	Intron	INS	-	TGTC	TGTC	rs145378063	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29234644_29234645insTGTC	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron|APBA2_uc010uas.1_Intron	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		TGGGAATAGTTTGATGATTCCA	0.475													5	4	---	---	---	---	
FAM189A1	23359	broad.mit.edu	37	15	29808296	29808297	+	Intron	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29808296_29808297insT	uc010azk.1	-							NM_015307	NP_056122	O60320	F1891_HUMAN	hypothetical protein LOC23359							integral to membrane					0						tcctggagagatttttttttaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	37790341	37790342	+	IGR	INS	-	A	A	rs142467493	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37790341_37790342insA								MEIS2 (396841 upstream) : TMCO5A (436485 downstream)																							TAAATATCACTGCAATACCATC	0.337													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	38132092	38132092	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38132092delA								MEIS2 (738592 upstream) : TMCO5A (94735 downstream)																							cttaataaggaaaaaaaaaga	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	39813045	39813045	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39813045delT								C15orf54 (265997 upstream) : THBS1 (60235 downstream)																							GTTTACTATGttttttttttt	0.219													4	5	---	---	---	---	
EIF2AK4	440275	broad.mit.edu	37	15	40235231	40235231	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40235231delT	uc001zkm.1	+						EIF2AK4_uc001zkl.2_Intron	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha						translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		ACTGGAATGATTTTTTTTTTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	42953150	42953150	+	Intron	DEL	T	-	-	rs147143825		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42953150delT	uc001zqg.2	+						uc001zqh.2_Intron					Homo sapiens cDNA FLJ16106 fis, clone THYMU1000496, moderately similar to KINESIN-LIKE PROTEIN KIF1C.																		TTTTGTTTTGTTTTTTTTTTT	0.353													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	45613110	45613110	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45613110delT								SLC28A2 (44978 upstream) : GATM (40214 downstream)																							gcttccaagctttcagggaga	0.000													4	2	---	---	---	---	
MYO5A	4644	broad.mit.edu	37	15	52697286	52697287	+	Intron	INS	-	C	C	rs67471357		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52697286_52697287insC	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		acacacacacaATCACTATGCA	0.277													4	3	---	---	---	---	
TRIP4	9325	broad.mit.edu	37	15	64692689	64692689	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64692689delC	uc002anm.2	+							NM_016213	NP_057297	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4						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						TTTTTTTTTTCTAAACCATTA	0.169													4	2	---	---	---	---	
RPL4	6124	broad.mit.edu	37	15	66796912	66796912	+	Intron	DEL	C	-	-	rs139436991	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66796912delC	uc002apv.2	-						RPL4_uc010bhr.2_Intron|RPL4_uc002apw.2_Intron|RPL4_uc002apx.2_Intron|RPL4_uc010ujq.1_Intron|SNORD18B_uc002apy.1_5'Flank|SNORD16_uc010bht.2_5'Flank|SNORD18A_uc002apz.1_5'Flank|ZWILCH_uc010bhu.1_5'Flank|ZWILCH_uc002aqb.2_5'Flank|ZWILCH_uc002aqa.2_5'Flank|ZWILCH_uc010bhv.2_5'Flank	NM_000968	NP_000959	P36578	RL4_HUMAN	ribosomal protein L4						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0						TCCACTACTGCTTCCCGGCGC	0.532													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	68142757	68142757	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68142757delA								LBXCOR1 (16583 upstream) : PIAS1 (203815 downstream)																							ggaagttaccaaaaaTAAGAA	0.114													4	2	---	---	---	---	
MYO9A	4649	broad.mit.edu	37	15	72408676	72408676	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72408676delT	uc002atl.3	-						MYO9A_uc010biq.2_Intron|MYO9A_uc002ato.2_Intron|SENP8_uc002atp.2_5'Flank	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3						ATATTTCATCTTTATACCAAT	0.279													4	2	---	---	---	---	
NEO1	4756	broad.mit.edu	37	15	73532546	73532546	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73532546delT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_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						TTGAGACTTATTTTTTTTTAA	0.343													4	2	---	---	---	---	
TBC1D2B	23102	broad.mit.edu	37	15	78343371	78343371	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78343371delC	uc002bcy.3	-						TBC1D2B_uc010bla.2_Intron	NM_144572	NP_653173	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B isoform a							intracellular	protein binding|Rab GTPase activator activity			ovary(1)|large_intestine(1)|breast(1)	3						GATGTAAGTGCCACCCCCAGG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	81698506	81698508	+	IGR	DEL	AGG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81698506_81698508delAGG								TMC3 (32088 upstream) : MEX3B (635620 downstream)																							aaaAAGAAAAAGGAGGAGGAGGA	0.074													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84858138	84858139	+	IGR	INS	-	T	T	rs71453232		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84858138_84858139insT								ADAMTSL3 (149547 upstream) : LOC388152 (9461 downstream)																							TGGGGAGCTGGTGCAGAGGCCT	0.599													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	85070267	85070267	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85070267delA								GOLGA6L5 (10189 upstream) : UBE2Q2P1 (160 downstream)																							AGAATCTCACAAAAAAAAAAC	0.368													6	4	---	---	---	---	
KLHL25	64410	broad.mit.edu	37	15	86331753	86331753	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86331753delA	uc002bly.2	-							NM_022480	NP_071925	Q9H0H3	ENC2_HUMAN	BTB/POZ KELCH domain protein							cytoplasm				ovary(2)	2						cAGATGGGGGAAAAAAATTCC	0.124													4	2	---	---	---	---	
AGBL1	123624	broad.mit.edu	37	15	86823386	86823386	+	Intron	DEL	C	-	-	rs5814234		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86823386delC	uc002blz.1	+						AGBL1_uc002bma.1_Intron|AGBL1_uc002bmb.1_Intron	NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						AGATGCAAATCTGAAGAAAAT	0.418													2	5	---	---	---	---	
FAM174B	400451	broad.mit.edu	37	15	93277451	93277454	+	5'Flank	DEL	CCTC	-	-	rs56380044		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93277451_93277454delCCTC	uc002bsl.3	-									Q3ZCQ3	F174B_HUMAN	Homo sapiens cDNA PSEC0264 fis, clone NT2RP3002337.							integral to membrane					0						tccgcctccgcctccgccccgccg	0.245													5	3	---	---	---	---	
FAM174B	400451	broad.mit.edu	37	15	93277457	93277458	+	5'Flank	DEL	CC	-	-	rs12442756	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93277457_93277458delCC	uc002bsl.3	-									Q3ZCQ3	F174B_HUMAN	Homo sapiens cDNA PSEC0264 fis, clone NT2RP3002337.							integral to membrane					0						tccgcctccgccccgccgcgcg	0.233													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	94235855	94235855	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94235855delA								RGMA (603422 upstream) : MCTP2 (538946 downstream)																							TTTATTTTTTAAAAGCACATT	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	99090599	99090599	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99090599delT								FAM169B (32988 upstream) : IGF1R (102162 downstream)																							ACTTCATTTGTTTTTCTTTTA	0.418													4	2	---	---	---	---	
ADAMTS17	170691	broad.mit.edu	37	15	100882625	100882626	+	5'Flank	DEL	AA	-	-	rs72119230		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100882625_100882626delAA	uc002bvv.1	-							NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		TTGTGGCCGCAAAGACTCCCAG	0.416													1	5	---	---	---	---	
CLUAP1	23059	broad.mit.edu	37	16	3558722	3558723	+	Intron	DEL	GT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3558722_3558723delGT	uc002cvk.1	+						CLUAP1_uc002cvj.1_Intron|CLUAP1_uc002cvl.1_Intron|CLUAP1_uc002cvm.1_5'Flank	NM_015041	NP_055856	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1 isoform 1							nucleus	protein binding			ovary(1)|breast(1)|pancreas(1)	3						gacaaaaatcgtgtgtttattc	0.015													2	6	---	---	---	---	
A2BP1	54715	broad.mit.edu	37	16	7133770	7133771	+	Intron	INS	-	G	G			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7133770_7133771insG	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		cagaaggcaccgtgcatgggtc	0.000													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16926321	16926321	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16926321delC								LOC339047 (481884 upstream) : XYLT1 (269862 downstream)																							attatggcatccaacaaactc	0.000													4	2	---	---	---	---	
TMC5	79838	broad.mit.edu	37	16	19439183	19439184	+	Intron	DEL	TC	-	-	rs141091340		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19439183_19439184delTC	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1						CCACTCTCTTTCTTAAATAGAA	0.287													1	5	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	21082370	21082370	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21082370delT	uc010vbe.1	-							NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		catgcctggattttttttttt	0.000													5	3	---	---	---	---	
UQCRC2	7385	broad.mit.edu	37	16	21985756	21985756	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21985756delA	uc002djx.2	+						UQCRC2_uc002djy.2_Intron|UQCRC2_uc010bxa.2_Intron|UQCRC2_uc002djz.1_Intron	NM_003366	NP_003357	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II						aerobic respiration|oxidative phosphorylation|proteolysis|respiratory electron transport chain|transport		metalloendopeptidase activity|zinc ion binding			large_intestine(2)	2				GBM - Glioblastoma multiforme(48;0.0264)		AGAAAAAGAGAAGCTGATATA	0.363													4	2	---	---	---	---	
LOC653786	653786	broad.mit.edu	37	16	22580309	22580309	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22580309delT	uc002dlh.3	+							NR_003676				RecName: Full=Otoancorin; Flags: Precursor;												0						GTGACCCACATTTTTTTTTTC	0.418													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32558547	32558547	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32558547delT								HERC2P4 (394673 upstream) : TP53TG3B (126294 downstream)																							agagttaaacttttttttgat	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32641120	32641121	+	IGR	INS	-	T	T	rs143610959	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32641120_32641121insT								HERC2P4 (477246 upstream) : TP53TG3B (43720 downstream)																							GTAAAATTGTGttttttatttc	0.238													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32783854	32783857	+	IGR	DEL	TGTT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32783854_32783857delTGTT								TP53TG3B (94976 upstream) : SLC6A10P (104940 downstream)																							attgtgtgtgtgttagtgattgcg	0.152													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32847223	32847224	+	IGR	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32847223_32847224insT								TP53TG3B (158345 upstream) : SLC6A10P (41573 downstream)																							gttctcttctactacacattcc	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33042909	33042909	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33042909delA								SLC6A10P (146446 upstream) : MIR1826 (922599 downstream)																							CTGTTGTGGGAAAACAGGCTT	0.398													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33522266	33522266	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33522266delG								SLC6A10P (625803 upstream) : MIR1826 (443242 downstream)																							ataatctcatgggaccacttt	0.045													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	33540997	33541000	+	IGR	DEL	AAAC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33540997_33541000delAAAC								SLC6A10P (644534 upstream) : MIR1826 (424508 downstream)																							TCCTCCAGTTAAACAAACAAAAAG	0.382													5	9	---	---	---	---	
SIAH1	6477	broad.mit.edu	37	16	48440582	48440582	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48440582delC	uc002efl.2	-									Q8IUQ4	SIAH1_HUMAN	Homo sapiens SIAH1 mRNA for seven in absentia homolog 1 isoform a, complete cds, clone: FLJ08065AAAN.						axon guidance|cell cycle|neuron apoptosis|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	beta-catenin destruction complex|cytosol|nucleus	protein C-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)				ccatggtcagccccactgcac	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	50275269	50275269	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50275269delG								PAPD5 (6052 upstream) : ADCY7 (25193 downstream)																							tttaagagctggggggaagct	0.000													4	2	---	---	---	---	
CBFB	865	broad.mit.edu	37	16	67064203	67064203	+	Intron	DEL	G	-	-	rs113002822		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67064203delG	uc002era.2	+						CBFB_uc002erb.2_Intron|CBFB_uc010vja.1_Intron	NM_001755	NP_001746	Q13951	PEBB_HUMAN	core-binding factor, beta subunit isoform 2						transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		AGAGAGGGGAGGGGGGGGAAA	0.443			T	MYH11	AML								3	4	---	---	---	---	
HYDIN	54768	broad.mit.edu	37	16	70884149	70884150	+	Intron	INS	-	C	C	rs138239619	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70884149_70884150insC	uc002ezr.2	-						HYDIN_uc010cfy.2_Intron	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)				CCATCTCTCCACCCCCCCCTGA	0.416													4	2	---	---	---	---	
ZFHX3	463	broad.mit.edu	37	16	72818152	72818152	+	3'UTR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72818152delA	uc002fck.2	-	10					uc002fcj.1_Intron|ZFHX3_uc002fcl.2_3'UTR	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A						muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				TAGCTCCATGaaaaaaaaaaa	0.413													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	73437843	73437843	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73437843delT	uc002fco.1	+											Homo sapiens cDNA clone IMAGE:5272469.																		GATCTTGGGATTTTTTTTTTC	0.458													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	74343003	74343004	+	IGR	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74343003_74343004delTG								PSMD7 (2819 upstream) : LOC283922 (23300 downstream)																							CAAAAAAAAATGAAAAAGAAAA	0.307													4	2	---	---	---	---	
SYCE1L	100130958	broad.mit.edu	37	16	77241867	77241870	+	Intron	DEL	ACTT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77241867_77241870delACTT	uc010vnh.1	+							NM_001129979	NP_001123451	A8MT33	SYC1L_HUMAN	hypothetical protein LOC100130958						meiosis						0						actttgcctcactttatttctctt	0.000													7	5	---	---	---	---	
NUDT7	283927	broad.mit.edu	37	16	77761240	77761240	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77761240delA	uc010chd.2	+						NUDT7_uc010vnj.1_Intron	NM_001105663	NP_001099133	P0C024	NUDT7_HUMAN	nudix motif 7						nucleoside diphosphate metabolic process	peroxisome	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides|magnesium ion binding|manganese ion binding			ovary(1)|kidney(1)	2						TATTTTGTTTAAAAAAAAAAT	0.338													4	2	---	---	---	---	
CDH13	1012	broad.mit.edu	37	16	83150961	83150963	+	Intron	DEL	CCT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83150961_83150963delCCT	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		gctggcagtgcctcctcctcctg	0.000													4	2	---	---	---	---	
MLYCD	23417	broad.mit.edu	37	16	83940346	83940347	+	Intron	INS	-	A	A	rs147664302	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83940346_83940347insA	uc002fgz.2	+							NM_012213	NP_036345	O95822	DCMC_HUMAN	malonyl-CoA decarboxylase precursor						acyl-CoA metabolic process|fatty acid biosynthetic process	mitochondrion|peroxisome	malonyl-CoA decarboxylase activity|methylmalonyl-CoA decarboxylase activity				0						GAATTGTTTCCTTCAGAGGTCT	0.342													4	3	---	---	---	---	
LRRC50	123872	broad.mit.edu	37	16	84184222	84184222	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84184222delT	uc002fhl.3	+						LRRC50_uc010chi.1_Intron	NM_178452	NP_848547	Q8NEP3	DAAF1_HUMAN	leucine rich repeat containing 50						axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding				0						cttttctttcttttttttttt	0.159									Kartagener_syndrome				6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	84233700	84233701	+	IGR	INS	-	CTCCGTC	CTCCGTC	rs147791434	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84233700_84233701insCTCCGTC								ADAD2 (2928 upstream) : KCNG4 (22124 downstream)																							CCATCCCGTCACTTCCTCCTGC	0.530													5	3	---	---	---	---	
RPH3AL	9501	broad.mit.edu	37	17	115644	115645	+	Intron	INS	-	G	G	rs140935609	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:115644_115645insG	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		TCTTCTCTCCTTGTGAGTGTTC	0.559													2	4	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2894871	2894872	+	Intron	DEL	AG	-	-	rs34542136		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2894871_2894872delAG	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						GGAGTGATCCAGTGTGGCAGAT	0.530													6	3	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2894874	2894874	+	Intron	DEL	G	-	-	rs5818885		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2894874delG	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						GTGATCCAGTGTGGCAGATTC	0.527													5	3	---	---	---	---	
DHRS7C	201140	broad.mit.edu	37	17	9680853	9680854	+	Intron	INS	-	T	T	rs71363788		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9680853_9680854insT	uc010vvb.1	-						DHRS7C_uc010cof.2_Intron	NM_001105571	NP_001099041	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C							extracellular region	binding|oxidoreductase activity				0						ACACTGATTTCTTTTTTTTTTT	0.233													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	10670871	10670871	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10670871delG								TMEM220 (37225 upstream) : PIRT (54922 downstream)																							GCTGCTGGGTGGGCCACCAAT	0.522													4	2	---	---	---	---	
DNAH9	1770	broad.mit.edu	37	17	11825282	11825283	+	Intron	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11825282_11825283delCA	uc002gne.2	+						DNAH9_uc010coo.2_Intron|DNAH9_uc002gnf.2_Intron|DNAH9_uc010vvh.1_Intron	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GCAGAAATGTCACAGAAGACAT	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13349063	13349063	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13349063delA								ELAC2 (427704 upstream) : HS3ST3A1 (49943 downstream)																							CATATACTACAAAAATGTATG	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	14613995	14613995	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14613995delA								HS3ST3B1 (364503 upstream) : PMP22 (519102 downstream)																							TATTTTCATGATTGTTTGGTG	0.254													4	2	---	---	---	---	
TOM1L2	146691	broad.mit.edu	37	17	17761164	17761164	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17761164delA	uc002grz.3	-						TOM1L2_uc002gry.3_Intron|TOM1L2_uc010vwy.1_Frame_Shift_Del_p.F375fs|TOM1L2_uc010cpr.2_Intron|TOM1L2_uc010vwz.1_Frame_Shift_Del_p.F280fs|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc002grv.3_Intron	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3						intracellular protein transport	intracellular					0	all_neural(463;0.228)					CCGAGGACAGAAAAGTCTCAG	0.488													4	2	---	---	---	---	
CCDC144NL	339184	broad.mit.edu	37	17	20772154	20772155	+	Intron	INS	-	A	A	rs140129415		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20772154_20772155insA	uc002gyf.2	-						uc002gyg.1_Intron|uc002gyh.1_Intron	NM_001004306	NP_001004306	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family,												0						gatggaggtgtaaaaacagggt	0.000													2	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21233713	21233714	+	IGR	INS	-	C	C	rs148233399		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21233713_21233714insC								MAP2K3 (15164 upstream) : KCNJ12 (45985 downstream)																							gggaaatctcacccagataggg	0.000													3	4	---	---	---	---	
C17orf63	55731	broad.mit.edu	37	17	27085150	27085150	+	3'UTR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27085150delC	uc002hct.1	-	3					C17orf63_uc010wax.1_3'UTR|C17orf63_uc010way.1_3'UTR|C17orf63_uc002hcw.2_3'UTR	NM_018182	NP_060652	Q8WU58	CQ063_HUMAN	hypothetical protein LOC55731											ovary(1)	1	all_epithelial(6;5.06e-20)|Lung NSC(42;0.01)		Epithelial(11;3.38e-06)|all cancers(11;2.46e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.104)			CCACTTAGATCCCACCAAATT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	33704121	33704121	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33704121delA								SLFN11 (3401 upstream) : SLFN12 (33962 downstream)																							AATTGTTCTCAAAAAAAAAAT	0.318													3	4	---	---	---	---	
TBC1D3	729873	broad.mit.edu	37	17	36366881	36366881	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36366881delA	uc010wdn.1	-						uc002hpx.2_Intron			Q8IZP1	TBC3A_HUMAN	Homo sapiens TBC1D3 mRNA for TBC1 domain family, member 3, complete cds.							intracellular	Rab GTPase activator activity				0	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCATTCTGAGAAAAAAACAAC	0.289													4	2	---	---	---	---	
CASC3	22794	broad.mit.edu	37	17	38322783	38322783	+	Intron	DEL	A	-	-	rs71701084		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38322783delA	uc010cwt.1	+						CASC3_uc010cws.1_Intron|CASC3_uc002hue.2_Intron	NM_007359	NP_031385	O15234	CASC3_HUMAN	metastatic lymph node 51						mRNA processing|mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|response to stress|RNA splicing	exon-exon junction complex|nuclear speck|perinuclear region of cytoplasm	identical protein binding|RNA binding|ubiquitin protein ligase binding			ovary(1)	1						ATTTGATAGGAAAAAATTTGA	0.323													4	5	---	---	---	---	
RAPGEFL1	51195	broad.mit.edu	37	17	38341030	38341031	+	Intron	INS	-	TTGT	TTGT			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38341030_38341031insTTGT	uc010cwu.1	+							NM_016339	NP_057423	Q9UHV5	RPGFL_HUMAN	Rap guanine nucleotide exchange factor						G-protein coupled receptor protein signaling pathway|nervous system development|small GTPase mediated signal transduction	intracellular|membrane fraction	guanyl-nucleotide exchange factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3						TATGGAtttgcttgtttgtttg	0.292													6	9	---	---	---	---	
TOP2A	7153	broad.mit.edu	37	17	38555583	38555584	+	Intron	INS	-	TATGAGGC	TATGAGGC	rs143313613	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38555583_38555584insTATGAGGC	uc002huq.2	-							NM_001067	NP_001058	P11388	TOP2A_HUMAN	DNA topoisomerase II, alpha isozyme						apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GTCAAATCATATATGATCAAAT	0.218													11	5	---	---	---	---	
BECN1	8678	broad.mit.edu	37	17	40971839	40971839	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40971839delT	uc002ibo.3	-						BECN1_uc010whb.1_Intron|BECN1_uc010whc.1_Intron|BECN1_uc002ibn.2_Intron	NM_003766	NP_003757	Q14457	BECN1_HUMAN	beclin 1						anti-apoptosis|cell cycle|cellular defense response|cytokinesis|response to virus	membrane	protein binding			ovary(1)	1		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		TCCCATTTGATTTTTTTTTTG	0.383											OREG0024429	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	4	---	---	---	---	
NME1-NME2	654364	broad.mit.edu	37	17	49240858	49240858	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49240858delT	uc002itk.2	+						NME1-NME2_uc002itj.2_Intron|NME2_uc002itl.2_5'Flank|NME2_uc002itm.2_5'Flank	NM_002512	NP_002503	P22392	NDKB_HUMAN	nucleoside diphosphate kinase B						cell adhesion|CTP biosynthetic process|GTP biosynthetic process|negative regulation of apoptosis|nucleobase, nucleoside and nucleotide interconversion|positive regulation of epithelial cell proliferation|positive regulation of keratinocyte differentiation|UTP biosynthetic process	cytosol|lamellipodium|nucleus|ruffle	ATP binding|DNA binding|metal ion binding|nucleoside diphosphate kinase activity|protein binding|protein histidine kinase activity|sequence-specific DNA binding transcription factor activity				0			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)			gaaattagaattttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	49669515	49669515	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49669515delA								UTP18 (294225 upstream) : CA10 (38160 downstream)																							tgtctgtactagggaaaaggg	0.000													4	2	---	---	---	---	
KCNH6	81033	broad.mit.edu	37	17	61602965	61602966	+	Intron	DEL	GA	-	-	rs7212529	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61602965_61602966delGA	uc002jay.2	+						KCNH6_uc002jax.1_Intron|KCNH6_uc010wpl.1_Intron|KCNH6_uc010wpm.1_Intron|KCNH6_uc002jaz.1_Intron	NM_030779	NP_110406	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent|signal transduction					skin(1)	1					Ibutilide(DB00308)	ctctgtgtgtgagtgtgtgctt	0.361													4	2	---	---	---	---	
FTSJ3	117246	broad.mit.edu	37	17	61898063	61898064	+	Intron	INS	-	GCTTGAACCTGGAAGACGG	GCTTGAACCTGGAAGACGG	rs142835534	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61898063_61898064insGCTTGAACCTGGAAGACGG	uc002jbz.2	-						FTSJ3_uc002jca.2_Intron	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3						RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1						caaggagaatcaggctgcagtg	0.059													7	4	---	---	---	---	
PITPNC1	26207	broad.mit.edu	37	17	65447697	65447697	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65447697delA	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			tgtcttttctagtaatttcgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	66235940	66235941	+	IGR	INS	-	C	C	rs151033304	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66235940_66235941insC								LOC440461 (39504 upstream) : AMZ2 (8204 downstream)																							tgcacacagaaccccccaccag	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	69662648	69662649	+	IGR	INS	-	T	T	rs75715710		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69662648_69662649insT								None (None upstream) : SOX9 (454512 downstream)																							tggatcagagattttttttttc	0.059													4	2	---	---	---	---	
C17orf99	100141515	broad.mit.edu	37	17	76154382	76154383	+	Intron	DEL	TT	-	-	rs6501181	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76154382_76154383delTT	uc002jus.3	+						C17orf99_uc010wts.1_5'Flank	NM_001163075	NP_001156547	Q6UX52	CQ099_HUMAN	hypothetical protein LOC100141515 precursor							extracellular region					0						CTCCTACACAtttttttttttt	0.332													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	4888610	4888611	+	IGR	INS	-	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4888610_4888611insA								DLGAP1 (433344 upstream) : LOC642597 (255061 downstream)																							AGTCTTCATTTAAAAAAAAAGC	0.386													4	2	---	---	---	---	
ARHGAP28	79822	broad.mit.edu	37	18	6887429	6887430	+	Intron	INS	-	TT	TT	rs10651246		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6887429_6887430insTT	uc010wzi.1	+						ARHGAP28_uc002knc.2_Intron|ARHGAP28_uc002knd.2_Intron|ARHGAP28_uc002kne.2_Intron|ARHGAP28_uc002knf.2_Intron			B4DXL2	B4DXL2_HUMAN	SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)				TTGGTATCTTGttttttttttt	0.262													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11883224	11883225	+	IGR	INS	-	T	T	rs111393316		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11883224_11883225insT								GNAL (80 upstream) : MPPE1 (249 downstream)																							CTTACTGCCTCCCCATCCACTG	0.366													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	13208468	13208468	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13208468delT	uc002krz.2	-											Homo sapiens cDNA clone IMAGE:5270453.																		TGATTTGAGATTTTACCTAGA	0.443													4	2	---	---	---	---	
C18orf1	753	broad.mit.edu	37	18	13648631	13648631	+	3'UTR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13648631delT	uc002ksa.2	+	7					C18orf1_uc002ksb.2_3'UTR|C18orf1_uc002kse.2_3'UTR|C18orf1_uc002ksf.2_3'UTR|C18orf1_uc002ksg.1_3'UTR|C18orf1_uc002ksh.1_3'UTR|C18orf1_uc002ksi.1_3'UTR	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)		TCAAGAACCCTTTTTTTAGCT	0.413													4	2	---	---	---	---	
POTEC	388468	broad.mit.edu	37	18	14535288	14535288	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14535288delT	uc010dln.2	-						POTEC_uc010xaj.1_Intron	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2											skin(3)	3						Ttttggatgattttttttttc	0.184													9	4	---	---	---	---	
C18orf45	85019	broad.mit.edu	37	18	20976829	20976829	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20976829delA	uc002kuf.2	-						C18orf45_uc010xaq.1_Intron|C18orf45_uc010xar.1_Intron|C18orf45_uc002kug.2_Intron|C18orf45_uc002kuh.2_Intron	NM_032933	NP_116322	Q24JQ0	CR045_HUMAN	hypothetical protein LOC85019							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)					aatgtcttgcaaaaaaaaaaa	0.020													7	4	---	---	---	---	
LAMA3	3909	broad.mit.edu	37	18	21516993	21516993	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21516993delC	uc002kuq.2	+						LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_Intron	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1						cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGTTCTAGAGCCAAGGAGTCA	0.348													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	22161475	22161476	+	IGR	DEL	TC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22161475_22161476delTC								HRH4 (101555 upstream) : ZNF521 (480412 downstream)																							GTCCACTATTTCTCTCTCTCTC	0.351													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	29665798	29665805	+	IGR	DEL	AGTTTATA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29665798_29665805delAGTTTATA								RNF125 (12644 upstream) : RNF138 (6032 downstream)																							actgggaaacagtttataagagtcagct	0.005													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	32992658	32992658	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32992658delT								ZNF396 (35357 upstream) : INO80C (40632 downstream)																							AGGAAGCAAGTTTTTTTTTTT	0.478													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	35421089	35421089	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35421089delT								CELF4 (275089 upstream) : None (None downstream)																							atgtcttcagtttAGGACTTG	0.264													4	2	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	36798788	36798788	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36798788delT	uc002lak.1	-						LOC647946_uc010xcj.1_Intron|LOC647946_uc002lal.1_Intron					Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						TGGATGAAGATTTGATTGCTG	0.403													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	47261436	47261436	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47261436delT								LIPG (142160 upstream) : ACAA2 (48439 downstream)																							gaggcagccctcgtggtaact	0.174													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	53509625	53509626	+	IGR	INS	-	ATTT	ATTT			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53509625_53509626insATTT								TCF4 (206440 upstream) : TXNL1 (760429 downstream)																							actgcaacccaatttatagtga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	54220375	54220384	+	IGR	DEL	TTCAAATATC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54220375_54220384delTTCAAATATC								TCF4 (917190 upstream) : TXNL1 (49671 downstream)																							GCTCCAGCCATTCAAATATCTCTCTTTCAC	0.357													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57507462	57507462	+	IGR	DEL	A	-	-	rs112607358		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57507462delA								CCBE1 (142818 upstream) : PMAIP1 (59730 downstream)																							tttatgtaataaaaaaatcac	0.080													3	3	---	---	---	---	
SERPINB3	6317	broad.mit.edu	37	18	61326073	61326073	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61326073delA	uc002lji.2	-						SERPINB4_uc002ljg.2_Intron|SERPINB3_uc010dqa.2_Intron|SERPINB3_uc010dqb.2_3'UTR	NM_006919	NP_008850	P29508	SPB3_HUMAN	serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3						ACCGAAGGTCAATATCATCTG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	68059592	68059592	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68059592delT								SOCS6 (62158 upstream) : None (None downstream)																							GAATTTTTCATTTTTGTTTGT	0.259													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	76071452	76071453	+	IGR	INS	-	T	T	rs148437070	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76071452_76071453insT								None (None upstream) : SALL3 (668822 downstream)																							TGGTTAAAATGTTAATAAATGG	0.460													3	6	---	---	---	---	
MKNK2	2872	broad.mit.edu	37	19	2039435	2039435	+	3'UTR	DEL	A	-	-	rs71337110		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2039435delA	uc002lus.2	-	14					MKNK2_uc002luq.1_Intron|MKNK2_uc010xgu.1_3'UTR|MKNK2_uc010xgv.1_3'UTR|MKNK2_uc002lur.2_Intron|MKNK2_uc002lut.1_3'UTR	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2						cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGAAACAGGAAAAAAAAAAC	0.537													9	4	---	---	---	---	
LINGO3	645191	broad.mit.edu	37	19	2301259	2301259	+	Intron	DEL	T	-	-	rs79783822		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2301259delT	uc010dsx.1	-						SPPL2B_uc010dsw.1_Intron	NM_001101391	NP_001094861	P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3							integral to membrane					0						AGATTTAGTGttttttttttt	0.303													4	2	---	---	---	---	
TBXA2R	6915	broad.mit.edu	37	19	3606095	3606097	+	Intron	DEL	ACC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3606095_3606097delACC	uc002lyg.1	-							NM_001060	NP_001051	P21731	TA2R_HUMAN	thromboxane A2 receptor isoform alpha						platelet activation	integral to plasma membrane	guanyl-nucleotide exchange factor activity|protein binding|thromboxane A2 receptor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)	cacacacaaaaccaccacacacg	0.202													4	2	---	---	---	---	
ANKRD24	170961	broad.mit.edu	37	19	4216161	4216162	+	Intron	INS	-	T	T	rs138190701	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4216161_4216162insT	uc010dtt.1	+						ANKRD24_uc002lzs.2_Intron|ANKRD24_uc002lzt.2_Intron	NM_133475	NP_597732	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24												0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		GTACTCATCCGTTTTTTAAATT	0.639													5	4	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7128634	7128635	+	Intron	INS	-	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7128634_7128635insA	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)	aaggtttgggcaaaaaaaaaaa	0.000													6	3	---	---	---	---	
ZNF317	57693	broad.mit.edu	37	19	9260465	9260465	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9260465delT	uc002mku.2	+						ZNF317_uc010xkm.1_Intron|ZNF317_uc002mkv.2_Intron|ZNF317_uc002mkw.2_Intron	NM_020933	NP_065984	Q96PQ6	ZN317_HUMAN	zinc finger protein 317						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						gtgatcttcattttacccata	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	11192318	11192318	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11192318delT								SMARCA4 (19359 upstream) : LDLR (7739 downstream)																							CAGAACATTCTTTTTTTTTTC	0.443													4	4	---	---	---	---	
CNN1	1264	broad.mit.edu	37	19	11654730	11654730	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11654730delA	uc002msc.1	+						CNN1_uc010xmb.1_Intron|CNN1_uc010xmc.1_Intron	NM_001299	NP_001290	P51911	CNN1_HUMAN	calponin 1, basic, smooth muscle						actomyosin structure organization|regulation of smooth muscle contraction	cytoskeleton	actin binding|calmodulin binding				0						aaagtataagaaaaaaaaaaa	0.095													3	5	---	---	---	---	
CD97	976	broad.mit.edu	37	19	14518616	14518623	+	Intron	DEL	AAACACAA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14518616_14518623delAAACACAA	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						aaaaaaagacaaacacaaaaaCACCAAG	0.312													10	9	---	---	---	---	
EMR3	84658	broad.mit.edu	37	19	14773131	14773132	+	Intron	INS	-	TATAAG	TATAAG	rs150464360	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14773131_14773132insTATAAG	uc002mzi.3	-						EMR3_uc010dzp.2_Intron|EMR3_uc010xnv.1_Intron	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor						neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						tgagacgagaatataagtactt	0.104													7	5	---	---	---	---	
ZNF626	199777	broad.mit.edu	37	19	20806607	20806607	+	3'UTR	DEL	A	-	-	rs138949164		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20806607delA	uc002npb.1	-	4					ZNF626_uc002npc.1_3'UTR	NM_001076675	NP_001070143	Q68DY1	ZN626_HUMAN	zinc finger protein 626 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1						actccatctcaaaaaaaaaaa	0.149													4	2	---	---	---	---	
ZNF43	7594	broad.mit.edu	37	19	22009807	22009807	+	Intron	DEL	A	-	-	rs78773989	byFrequency	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22009807delA	uc002nqj.2	-						ZNF43_uc010ecv.2_Intron|ZNF43_uc002nql.2_Intron|ZNF43_uc002nqm.2_Intron|ZNF43_uc002nqk.2_Intron	NM_003423	NP_003414	P17038	ZNF43_HUMAN	zinc finger protein 43						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		CTGTATTGAGAAAAAAAAAAA	0.348													5	3	---	---	---	---	
ZNF507	22847	broad.mit.edu	37	19	32847175	32847175	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32847175delT	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)					ACTGATTGGATTTTTTTTTGT	0.413													4	3	---	---	---	---	
CD22	933	broad.mit.edu	37	19	35822750	35822750	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35822750delA	uc010edt.2	+						CD22_uc010xst.1_Intron|CD22_uc010edu.2_Intron|CD22_uc010edv.2_Intron|CD22_uc002nzb.3_5'Flank	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule precursor						cell adhesion		protein binding|sugar binding			ovary(5)|lung(3)|breast(1)	9	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)	actctgtctcaaaaaaaaaga	0.259													4	4	---	---	---	---	
PLEKHG2	64857	broad.mit.edu	37	19	39915952	39915952	+	3'UTR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39915952delC	uc010xuz.1	+	19					PLEKHG2_uc010xuy.1_Frame_Shift_Del_p.S1216fs|PLEKHG2_uc002olj.2_3'UTR|PLEKHG2_uc010xva.1_3'UTR	NM_022835	NP_073746	Q9H7P9	PKHG2_HUMAN	common-site lymphoma/leukemia guanine nucleotide						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)|breast(1)	4	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CATGAGGCTTCCCTGAAGCAA	0.577													4	2	---	---	---	---	
LIG1	3978	broad.mit.edu	37	19	48668516	48668516	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48668516delA	uc002pia.1	-						LIG1_uc002phz.1_Intron|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron|LIG1_uc010xzh.1_Intron	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I						anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	actccaactcaaaaaaaaaaa	0.000								NER					6	5	---	---	---	---	
STK35	140901	broad.mit.edu	37	20	2107698	2107698	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2107698delT	uc002wfw.3	+						STK35_uc010zpu.1_Intron	NM_080836	NP_543026	Q8TDR2	STK35_HUMAN	serine/threonine kinase 35							cytoplasm|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1						GTCACCTTTATTTTTTTTTCC	0.433													5	3	---	---	---	---	
C20orf194	25943	broad.mit.edu	37	20	3356496	3356497	+	Intron	INS	-	A	A			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3356496_3356497insA	uc002wii.2	-						C20orf194_uc002wik.2_5'Flank|C20orf194_uc010gay.1_Intron	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943												0						ctccgtcccagaaaaaaaaaaa	0.203													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	4463050	4463050	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4463050delG								ADRA1D (233391 upstream) : PRNP (203747 downstream)																							ATACACCCCAGGTCTGTGGGG	0.527													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	7677109	7677109	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7677109delA								BMP2 (916199 upstream) : HAO1 (186522 downstream)																							AGAAATCAGGAAGAATAGCAT	0.443													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	12554347	12554347	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12554347delC								BTBD3 (647105 upstream) : SPTLC3 (435280 downstream)																							CAAGCTCAGACCCCAGGCATT	0.448													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	26147215	26147215	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26147215delT								C20orf191 (52538 upstream) : MIR663 (41607 downstream)																							AATTTTAATCTGTTTAGATTT	0.318													2	5	---	---	---	---	
CTNNBL1	56259	broad.mit.edu	37	20	36493233	36493234	+	Intron	INS	-	TTTG	TTTG	rs142991606	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36493233_36493234insTTTG	uc010zvw.1	+						CTNNBL1_uc002xhh.2_Intron|CTNNBL1_uc002xhi.2_Intron|CTNNBL1_uc002xhj.2_Intron	NM_030877	NP_110517	Q8WYA6	CTBL1_HUMAN	beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)				CTGTAGGCTTCTTCTATTCCAG	0.351													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42452760	42452760	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42452760delA								GTSF1L (97118 upstream) : TOX2 (90732 downstream)																							ttattgttagaaagctccact	0.194													4	2	---	---	---	---	
ACOT8	10005	broad.mit.edu	37	20	44472491	44472492	+	Intron	DEL	GT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44472491_44472492delGT	uc002xqa.1	-						ACOT8_uc010zxe.1_3'UTR|ACOT8_uc002xqc.1_3'UTR|ACOT8_uc010zxf.1_Intron	NM_005469	NP_005460	O14734	ACOT8_HUMAN	peroxisomal acyl-CoA thioesterase 1 isoform a						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|interspecies interaction between organisms|peroxisome organization	peroxisomal matrix	acetyl-CoA hydrolase activity|acyl-CoA thioesterase activity|carboxylesterase activity|choloyl-CoA hydrolase activity|protein binding			skin(1)	1		Myeloproliferative disorder(115;0.0122)				TTGGCCTACAGTGTGTGTGTGT	0.584													4	2	---	---	---	---	
TFAP2C	7022	broad.mit.edu	37	20	55206242	55206242	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55206242delT	uc002xya.2	+						TFAP2C_uc010zzi.1_Intron	NM_003222	NP_003213	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma						cell-cell signaling|male gonad development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Colorectal(105;0.229)			GGGTCTCCTGTTTTTTTTTTT	0.692													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9451851	9451854	+	IGR	DEL	TTTG	-	-	rs67090075		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9451851_9451854delTTTG								None (None upstream) : None (None downstream)																							AATGAACGTATTTGTTTGGGTATT	0.368													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10410518	10410519	+	IGR	INS	-	C	C	rs78155981	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10410518_10410519insC								None (None upstream) : TPTE (496224 downstream)																							AAACAAACAAAAAAAAACaaaa	0.163													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10567215	10567218	+	Intron	DEL	CTGG	-	-	rs71270918		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10567215_10567218delCTGG	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																		AACCACAAAACTGGCTTTTTACTC	0.338													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	10711367	10711367	+	IGR	DEL	T	-	-	rs112070792		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10711367delT								None (None upstream) : TPTE (195376 downstream)																							aaaatatccctttgcagactc	0.000													6	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11088890	11088891	+	Intron	INS	-	A	A	rs148198939		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11088890_11088891insA	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)		GAAAAATATACAAAAAAAGTTT	0.292													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11149030	11149032	+	IGR	DEL	GAA	-	-	rs143833307		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11149030_11149032delGAA								BAGE (50093 upstream) : None (None downstream)																							catctaaagggaagaagacaaat	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11155113	11155113	+	IGR	DEL	A	-	-	rs149249762		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11155113delA								BAGE (56176 upstream) : None (None downstream)																							TGTAGATCTGAAAAAAAATGA	0.264													3	6	---	---	---	---	
GRIK1	2897	broad.mit.edu	37	21	31260043	31260043	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31260043delT	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)	tgtgttggcattttttttcct	0.095													4	2	---	---	---	---	
UBASH3A	53347	broad.mit.edu	37	21	43830888	43830889	+	Intron	DEL	CA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43830888_43830889delCA	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						GAGGTGCAAGcacacacacaca	0.342													4	3	---	---	---	---	
PCBP3	54039	broad.mit.edu	37	21	47126610	47126610	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47126610delC	uc010gqb.2	+							NM_020528	NP_065389	P57721	PCBP3_HUMAN	poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		GGTTGAGAAGCCCTAGCCAGG	0.493													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17236829	17236829	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17236829delT								psiTPTE22 (57308 upstream) : XKR3 (27484 downstream)																							ttttgttttgttttgttttga	0.109													4	3	---	---	---	---	
PI4KA	5297	broad.mit.edu	37	22	21063975	21063976	+	Intron	INS	-	AT	AT	rs67808752		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21063975_21063976insAT	uc002zsz.3	-						PI4KA_uc010gsp.2_Intron|PI4KA_uc002zsy.3_Intron	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CCTTGACATAAAGAGGCCCCTG	0.609													6	3	---	---	---	---	
SUSD2	56241	broad.mit.edu	37	22	24577515	24577517	+	In_Frame_Del	DEL	CTG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24577515_24577517delCTG	uc002zzn.1	+	1	72_74	c.28_30delCTG	c.(28-30)CTGdel	p.L13del		NM_019601	NP_062547	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2 precursor	13					immune response	integral to membrane	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						GCCCTGGGCCCTGCTGCTGCTGG	0.685													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25340200	25340201	+	IGR	DEL	GA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25340200_25340201delGA								TMEM211 (4886 upstream) : KIAA1671 (83740 downstream)																							actctggagggagagagagaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	27282808	27282808	+	IGR	DEL	T	-	-	rs77242810		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27282808delT								MIAT (167859 upstream) : MN1 (861458 downstream)																							AGTCCCGTTCTTTTTTTTTTG	0.408													6	4	---	---	---	---	
DEPDC5	9681	broad.mit.edu	37	22	32233339	32233339	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32233339delT	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alu.2_Intron|DEPDC5_uc003alv.2_Intron|DEPDC5_uc011alw.1_Intron|DEPDC5_uc003alw.2_Intron|DEPDC5_uc011alx.1_Intron	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						ttttttttccttttttttttt	0.020													5	3	---	---	---	---	
LARGE	9215	broad.mit.edu	37	22	34110880	34110880	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34110880delT	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				CCGCTTCAGATTGTCCTCTGA	0.463													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35203122	35203123	+	IGR	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35203122_35203123insT								LARGE (884538 upstream) : ISX (259006 downstream)																							AAATAAAATAgtttcttcccaa	0.193													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	35268546	35268547	+	IGR	DEL	TC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35268546_35268547delTC								LARGE (949962 upstream) : ISX (193582 downstream)																							agagctgcaatctctctctctg	0.089													3	3	---	---	---	---	
CACNG2	10369	broad.mit.edu	37	22	37097400	37097401	+	Intron	INS	-	T	T	rs138609632	by1000genomes	TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37097400_37097401insT	uc003aps.1	-						uc003apt.1_5'Flank	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						ACCCACAGGAGTTTTTTTTTCT	0.485													4	2	---	---	---	---	
POLR2F	5435	broad.mit.edu	37	22	38382745	38382746	+	Intron	DEL	TG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38382745_38382746delTG	uc003aum.2	+						SOX10_uc003aun.1_5'Flank|SOX10_uc003auo.1_Intron|SOX10_uc010gxj.2_5'Flank|uc003aup.2_Frame_Shift_Del_p.C93fs			P61218	RPAB2_HUMAN	Synthetic construct DNA, clone: pF1KB9548, Homo sapiens POLR2F gene for polymerase (RNA) II (DNA directed) polypeptide F, without stop codon, in Flexi system.						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex|nucleolus	DNA binding|DNA-directed RNA polymerase activity			breast(1)	1	Melanoma(58;0.045)					TGACCAGTGCTGTGTGTGTGTG	0.644													4	2	---	---	---	---	
FAM109B	150368	broad.mit.edu	37	22	42470795	42470795	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42470795delC	uc003bbz.2	+							NM_001002034	NP_001002034	Q6ICB4	SESQ2_HUMAN	hypothetical protein LOC150368						endosome organization|receptor recycling|retrograde transport, endosome to Golgi	clathrin-coated vesicle|early endosome|recycling endosome|trans-Golgi network	protein homodimerization activity				0						CCTTCCTGGGCCccccctact	0.348													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	45015824	45015825	+	IGR	DEL	GT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45015824_45015825delGT								NCRNA00207 (47495 upstream) : PRR5 (48768 downstream)																							tgtggagtgcgtgtgtgtgtgg	0.000													4	2	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1536657	1536659	+	Intron	DEL	TGT	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1536657_1536659delTGT	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				acatgctccatgtcacaggtatg	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6515078	6515078	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6515078delA								VCX3A (61919 upstream) : HDHD1A (451883 downstream)																							AATAAATGGCAAAAAAAAATC	0.333													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	15233304	15233304	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15233304delT								MOSPD2 (293849 upstream) : ASB9 (28807 downstream)																							AACTTAACCCTTTCTCTGCTC	0.438													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	21010903	21010903	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21010903delA								RPS6KA3 (725380 upstream) : CNKSR2 (382077 downstream)																							agtgacaagcaaagggggaaa	0.000													4	2	---	---	---	---	
IL1RAPL1	11141	broad.mit.edu	37	X	29323580	29323580	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29323580delT	uc004dby.2	+							NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5						gagaaggaaatccataaacca	0.055													17	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	38747660	38747661	+	IGR	DEL	AC	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38747660_38747661delAC								MID1IP1 (81879 upstream) : None (None downstream)																							TTAAGAAACAACACACACACAC	0.406													4	2	---	---	---	---	
WDR45	11152	broad.mit.edu	37	X	48936294	48936294	+	Intron	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48936294delC	uc004dmk.1	-						PRAF2_uc011mmt.1_Intron|WDR45_uc004dmj.1_5'Flank|WDR45_uc004dml.1_Intron|WDR45_uc004dmm.1_Intron|WDR45_uc010nim.1_Intron|WDR45_uc004dmn.1_Intron|WDR45_uc004dmo.1_Intron|WDR45_uc004dmp.1_Intron|WDR45_uc011mmu.1_Intron	NM_001029896	NP_001025067	Q9Y484	WIPI4_HUMAN	WD repeat domain 45 isoform 2						autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1						AAGCTCCAGGCCCACACTGAC	0.537													4	2	---	---	---	---	
HUWE1	10075	broad.mit.edu	37	X	53616284	53616284	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53616284delA	uc004dsp.2	-						HUWE1_uc004dsn.2_Intron	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1						base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						ATTTTAAGAGAAAAGTAGAAA	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	56716614	56716615	+	IGR	DEL	AG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56716614_56716615delAG								UBQLN2 (123245 upstream) : LOC550643 (39103 downstream)																							agagacagacagagagagagag	0.262													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	58330361	58330361	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:58330361delT								ZXDA (393294 upstream) : None (None downstream)																							ggaaacactctttttgtagac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	81988510	81988510	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:81988510delT								None (None upstream) : POU3F4 (774759 downstream)																							GCTGACTCAGTTTTTTGTTAC	0.413													4	2	---	---	---	---	
KLHL4	56062	broad.mit.edu	37	X	86784068	86784068	+	Intron	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86784068delA	uc004efb.2	+						KLHL4_uc004efa.2_Intron	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1							cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						tgataaaaggaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	89712782	89712783	+	IGR	DEL	AG	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89712782_89712783delAG								TGIF2LX (534902 upstream) : PABPC5 (976814 downstream)																							aggcagcataagagagagagaa	0.000													4	2	---	---	---	---	
IL1RAPL2	26280	broad.mit.edu	37	X	103867182	103867182	+	Intron	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103867182delT	uc004elz.1	+							NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2						central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3						AAACTTGTGCTTTTTTTTTTT	0.363													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	124352942	124352942	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124352942delT								ODZ1 (255276 upstream) : DCAF12L2 (945572 downstream)																							GTGTGTAAGGTTTGAGAAAGT	0.368													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	134358966	134358967	+	IGR	DEL	AA	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134358966_134358967delAA								CXorf48 (53215 upstream) : ZNF75D (23922 downstream)																							TCCAGAGAATAAacacacacac	0.332													4	2	---	---	---	---	
ATP11C	286410	broad.mit.edu	37	X	138887026	138887027	+	Intron	INS	-	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138887026_138887027insC	uc004faz.2	-						ATP11C_uc004fba.2_Intron	NM_173694	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C isoform a						ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)					GTTTGCTCTCTGATATTTCTTG	0.351													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	141509780	141509780	+	IGR	DEL	A	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141509780delA								MAGEC2 (216704 upstream) : SPANXN4 (603924 downstream)																							tgtctgtcccaagtaaaaact	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9941658	9941659	+	IGR	INS	-	C	C			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9941658_9941659insC								TTTY22 (290804 upstream) : None (None downstream)																							TTATTTTAGATTTTTACCTCTT	0.307													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9952020	9952020	+	IGR	DEL	T	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9952020delT								TTTY22 (301166 upstream) : None (None downstream)																							aaaaagttgattttttgaaaa	0.000													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13445900	13445900	+	IGR	DEL	C	-	-	rs149511831		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13445900delC								None (None upstream) : None (None downstream)																							AAAGTCCCAACAAACTTCTCA	0.244													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	58993772	58993773	+	IGR	INS	-	A	A	rs76109375		TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58993772_58993773insA								None (None upstream) : None (None downstream)																							cattttgacatactctgccctg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59008746	59008747	+	IGR	INS	-	T	T			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59008746_59008747insT								None (None upstream) : None (None downstream)																							tgccaacagactttaaagcata	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59009972	59009972	+	IGR	DEL	C	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59009972delC								None (None upstream) : None (None downstream)																							attattttctctgatgacaga	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	59009974	59009974	+	IGR	DEL	G	-	-			TCGA-B8-5546-01A-01D-1534-10	TCGA-B8-5546-10A-01D-1535-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59009974delG								None (None upstream) : None (None downstream)																							tattttctctgatgacagaat	0.005													4	2	---	---	---	---	
